Job Listings

Note: Job listings are free. To post a job listing, please submit it to the SMB Digest. The listings here are typically pulled from each Digest. Please contact the webmaster for further details.

Listings shown below were posted in the following Digests:

Studentships

(Click on job title for additional information.)
  • PhD Position: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
    • SMB Digest Vol 15, Issue 28 - July 15, 2015

      We invite applications for a PhD fellowship in the School of Mathematical and Geospatial Sciences, RMIT University, Melbourne, Australia, The applicants will have the opportunity to work on subjects that cross the interface of mathematical biology, theoretical epidemiology and ecology, network theory, and BigData. The Department has a vibrant group of active researchers in these areas, and intends to build this group further. Please contact Prof. Lewi Stone, in the first instance by emailing: lewistone2@gmail.com.

  • PhD Position: Gastrointestinal Electrophysiology..., U Auckland
    • SMB Digest Vol 15, Issue 26 - July 1, 2015

      PhD Positions: Gastrointestinal Electrophysiology/Motility, U Auckland, New Zealand

      The Gastrointestinal Motility group based at the Auckland Bioengineering Institute, University of Auckland, New Zealand is recruiting PhD students.

      The research group seeks to apply mathematical and engineering techniques to improve the understanding of both normal and abnormal gut function. In particular, we target a number of functional motility disorders and seek to translate our techniques to improving human health. The group is well established with a strong track record with high-impact publications and international awards. The group maintain close links with surgeons/clinicians in Auckland and also have close collaborations and joint grants with universities in USA, Australia, Germany and Belgium.

      Ideal candidates are excellent, motivated students who are interested in translational research projects with an undergraduate degree in engineering, applied maths, physics, medicine or equivalent. Background knowledge of gastrointestinal physiology is not a pre-requisite, but some experiences with signal/image processing, mathematical modelling or instrumentation would be preferred.

      The Auckland Bioengineering Institute (ABI) is a cross-faculty research institute funded primarily from national and international research grants. It hosts approximately 100 PhD and ME students. ABI staff are devoted to research and supervision of post-graduate projects.

      We have a variety of interesting projects including:
      -Image-based analysis and modelling of the pacemaker cells in the stomach and small intestine
      -Analysis of the repolarisation phase of gastric slow wave activity via novel signal processing techniques
      -Development of novel high-resolution electrode platforms for measuring electrical activity from the stomach/small intestine.

      More information is available at: http://www.abi.auckland.ac.nz/en/about/our-research/gi-system.html
      Please send expressions of interest via email to , stating the project/research area you are interested in. Please attach your CV, grades, and list of skills and research interests as a single pdf file.

  • PhD Position: Pharmacometrics & Comp. Disease Modelling, Berlin
    • SMB Digest Vol 15, Issue 26 - July 1, 2015

      The Graduate Research Training Program PharMetrX: Pharmacometrics & Computational Disease Modelling is an interdisciplinary PhD program bridging pharmacy and mathematics. PharMetrX provides its graduate students a unique opportunity to experience research in drug development and optimising drug therapy.

      PharMetrX offers:
      -a transdisciplinary research environment
      -a competitive three-year research fellowship
      -a structured research training curriculum of basic and advanced academic and industry modules
      -a joint supervision of the scientific progress by both program chairs
      -an individual research and development plan
      -an individual mentorship from one of the industry partners

      We are currently inviting applications to start the PharMetrX PhD program in March 2016. PharMetrX is open to candidates with a university degree in natural/life sciences or medicine. Deadline for applications: September 15th, 2015. For details see https://www.PharMetrX.de.

      PharMetrX is a joint program of the Freie Universität Berlin and the Universitat Potsdam, supported by several global research-driven pharmaceutical companies.

  • PhD Position: Biological Physics, Leiden U
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Leiden University is currently looking for a student for a joint PhD project between the groups of Daniela Kraft and Luca Giomi at the Casimir Research School at Leiden University. The project will investigate the interplay between curvature and the organisation of lipid domains in membranes supported by colloidal and micro-fabricated scaffolds. The student will use a combined experimental and computational approach to develop a fundamental framework and unravel the biologically relevant correlation between local geometry and membrane composition.

      The four year position is available immediately, with latest starting date in June 2016. Candidates should hold an MSc degree in physics, physical chemistry or material science, and should have affinity for experimental and computational work in soft matter.

      Applications consisting of a resume, a motivation letter, and two references should be sent to: giomi@lorentz.leidenuniv.nl and kraft@physics.leidenuniv.nl.

  • PhD Position: Deciphering Regulatory Interactions..., Utrecht U
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      PhD: Deciphering regulatory interactions underlying repetitive lateral root formation (1,0 fte)

      Job description
      The root system of a plant is crucial for its survival and yield, as it ensures anchorage to the substrate as well as access to water and nutrients. Lateral root patterning, the positioning of lateral roots along the main root of a plant, is a major determinant of overall root system architecture. Due to the complexity of this developmental process, involving factors such as root growth mechanics, gene regulation and hormonal signalling that act at different spatial and temporal scales and interact in complex manners, lateral root patterning has thus far remained poorly understood.

      In the current project we aim to develop state-of-the art multi-scale models of plant root development to increase our understanding of lateral root patterning. For this we will intensively collaborate with experimental groups. The project is funded by a Vidi-grant awarded to Dr. K. ten Tusscher.

      The candidate will develop sophisticated multi-scale models incorporating root growth dynamics, genetic regulation and hormonal signalling. Goal is to unravel how these processes together give rise to the oscillation-type dynamics that underly the regular formation of lateral roots along the main root. In addition, the candidate will investigate the role of spatial, long range interactions between lateral roots at different positions along the main root in this patterning process.

      Qualifications
      For the above described project we are looking for a PhD candidate with a proven experience in multi-scale modeling and either a biological background or a keen interest in biology.

      Offer
      The candidate is offered a full-time PhD position for four years.

      The salary is supplemented with a holiday bonus of 8% and an end-of-year bonus of 8,3% per year. In addition we offer: a pension scheme, a partially paid parental leave, flexible employment conditions. Conditions are based on the Collective Labour Agreement Dutch Universities. The research group will provide the candidate with necessary support on all aspects of the project.

      The gross salary is in the range between 2.125 euros,- and maximum 2.717 euros,- per month.

      About the organisation
      Utrecht University has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Dynamics of Youth, Institutions, Life Sciences and Sustainability. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues.

      The Faculty of Science consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Chemistry and Mathematics. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The Faculty's academic programmes reflect developments in today's society.

      The candidate will be working in the Theoretical Biology Group at the Biology Department of Utrecht University, The Netherlands. The work will take place in the Computational Developmental and Evolutionary Biology subgroup of Dr. Kirsten ten Tusscher.

      About the Group
      The researchers of the Theoretical Biology Group use mathematical modeling and computer simulations to perform fundamental biological research in a variety of biological disciplines ranging from developmental biology and immunology to evolution.

      The Theoretical Biology group is part of the Institute of Biodynamics and Biocomplexity (IBB), which focuses on the interaction between experiments, theory and modeling to obtain a systems level understanding of complex dynamic biological processes and their evolution. The IBB is embedded in one of the largest Biology departments in the Netherlands (>200 new students per year), and collaborates with other departments of the Faculty of Science, the Faculty of Medicine, and the Hubrecht Institute in Utrecht.

      The Theoretical Biology Group teaches Systemsbiology to biology students at the bachelor and master level. PhD students in the group have diverse backgrounds ranging from biology, mathematics, physics to computer science, and typically half of them are from abroad.

      Additional information
      Additional information about the vacancy can be obtained from: Dr. Kirsten ten Tusscher, email: k.h.w.j.tentusscher@uu.nl.

      As part of the selection procedure, candidates are expected to give an oral presentation of their prior research.

      Apply
      To apply please attach a letter of motivation, curriculum vitae and (email) addresses of two referees. The application deadline is 31/08/2015.

  • Student/Post-doc Positions: Computation. Immunology, Bar-Ilan U
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Student and postdoc positions in Computational Immunology

      The Computational Immunology Lab of Prof. Ramit Mehr in Bar-Ilan University, Israel (http://immsilico2.lnx.biu.ac.il) is recruiting research Students at all levels (undergrad projects, MSc or PhD) and Post-Doctoral Trainees.

      Prof. Ramit Mehr is a leader in computational immunology. The work performed in her group has led to several discoveries, which have significantly advanced the field beyond the state of the art. The group applies modeling and simulation, bioinformatics and statistical analysis to immunological questions. Our main focus is the development, population dynamics and function of B, T and NK cell repertoires, in health, aging, autoimmune diseases and cancer.

      Prof. Mehr devotes much time to career training and has a good track record in terms of the careers of lab alumni. Over 50% of PhD alumni published several papers before submitting their theses, and most MSc students have published at least one. All of them presented their work in national (PhDs also in international) scientific meetings. As a result, over 50% of PhD alumni have gone on to post-doctoral training, and all PhD and most MSC alumni work in bioinformatics and related fields.

      We have several fascinating projects, including:
      -Lineage tree - based studies of mutations in antibody genes
      -Analysis of lymphocyte repertoires
      -Simulations of antibody gene rearrangement
      -Math modeling of lymphocyte population dynamics
      -Math modeling of immune cell recovery from stem cell transplantation
      -Analysis of stem cell transplantation patient data
      -Analysis of cell marker data from HIV patients

      More info: http://immsilico2.lnx.biu.ac.il/Open-Positions.html

      Candidates - please send email to ramit.mehr@biu.ac.il , stating the position you're interested in. Please attach your CV, grades and publications so far, and the names and contact information of two people who can recommend you.

  • PhD Position: Projecting Effects of Vaccination..., Dutch...
    • SMB Digest Vol 15, Issue 24 - June 17, 2015

      Project description
      In order to prevent serious illness and disease outbreaks, the Dutch government offers free vaccination against specific infectious diseases to all children through the National Immunization Programme. The most recent additions to this Programme are the vaccines against pneumococcus, associated amongst others with meningitis, and against papillomavirus, associated with various forms of cancer. Both pneumococcus and papillomavirus are characterized by the existence of various strains. The vaccines protect against a selected set of all strains that can cause disease, being so-called polyvalent vaccines. An anticipated effect of polyvalent vaccination is the elimination of vaccine-specific strains from the population. A possible unwanted effect is the take-over by other strains against which the vaccine is not protective, such that the health benefit partly disappears. This phenomenon is known as type-replacement and is caused by competition between pathogenic strains. This project aims to deliver a better assessment of type-replacement and its long-term consequences for the effectiveness of polyvalent vaccination. Partners in this project are the University Medical Centres of Utrecht (Paediatrics) and of Leiden (Medical Statistics).

      Your challenge
      Quantification of interactions between pathogenic strains requires diverse statistical techniques (graphical models, multi-state modelling, survival analysis) for a diversity of data structures. The question is which techniques and which data are informative for inferring competitive interactions, and which are sensitive for the occurrence of type-replacement. To this end, you will develop dynamic transmission models for multi-strain pathogens that can incorporate a variety of interactions between strains. You will use these models to simulate data for the joint occurrence of multiple strains in epidemiological studies. You will develop statistical techniques based on simulated data and apply these to available data on pneumococcus and papillomavirus. You will investigate indications for type-replacement and answer the question how type-replacement may alter the expected health benefit of vaccination. In the end, your research provides a consistent methodology for multi-strain modelling that can be used to describe the effectiveness of pneumococcal vaccination in an adequate way. You will publish your findings in scientific journals and present your findings on international conferences. After four years, your research is intended to result in an academic dissertation. An abroad stay as part of your PhD research belongs to the possibilities.

      Your profile
      We seek a highly motivated, enthusiastic researcher with an MSc or comparable degree in (applied) mathematics, physics, biostatistics, theoretical biology or bioinformatics. Excellent verbal and written command of English is required, programming experience in C/C++ and R are welcome. We expect affinity with the promotion of public health through prevention of infectious diseases.

      Terms of employment
      You will be stationed at the Dutch National Institute of Public Health and the Environment (RIVM). Appointment takes place based on 36 working hours a week for the initial term of one year. Your contract will be prolonged in case of good performance. Salary is in conformity with that of a PhD student (OIO) at a Dutch university. The closing date for applications is June 30th 2015.

      More information
      Dr. J.A. Bogaards, Project leader (hans.bogaards@rivm.nl, tel +3130-2744765)
      Dr. J. Wallinga, Head Dept. Infectious Disease Modelling (jacco.wallinga@rivm.nl, tel. +3130-2742553)

      Proclaimer RIVM http://www.rivm.nl/Proclaimer

  • PhD Positions: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
    • SMB Digest Vol 15, Issue 24 - June 17, 2015

      We invite applications for two PhD studentships in the School of Mathematical and Geospatial Sciences, RMIT University, Melbourne, Australia, The applicants will have the opportunity to work on subjects that cross the interface of mathematical biology, theoretical epidemiology and ecology, and network theory. The Department has a vibrant group of active researchers in these areas, and intends to build this group further. Please contact Prof. Lewi Stone, in the first instance by emailing: lewistone2@gmail.com

  • PhD Positions: Mathematics & Statistics, Barcelona Grad School
    • SMB Digest Vol 15, Issue 23 - June 10, 2015

      Below please find the call for 4 PhD scholarships within the BGSMath/Maria de Maeztu programme in different areas of Mathematics, including Mathematics and Statistics for Life and Social Sciences. Interested candidates within this area are encouraged to contact either of the researchers involved:
      -Tomas Alarcon, talarcon@crm.cat.
      Area of expertise: multi-scale modelling of tumour growth.
      -Angel Calsina, acalsina@mat.uab.es.
      Area of expertise: structured population dynamics, selection-mutation equations
      -Marta Casanellas, marta.casanellas@upc.edu.
      Area of expertise: algebraic and geometric tools in phylogenetics
      -Guadalupe Gomez, lupe.gomez@upc.edu.
      Area of expertise: survival analysis, statistical methods for omics data integration, statistical genetics, functional data analysis, bioinformatics
      -Pere Puig, ppuig@mat.uab.cat.
      Area of expertise: characterisation of distributions, count data modelling, count data time series, extreme value theory
      -Alex Roxin, aroxin@crm.cat.
      Area of expertise: computational neuroscience

      The program BGSMath/Maria de Maeztu will very soon call for applications for 4 PhD scholarships in mathematics in the areas
      -Algebra, Geometry and Topology
      -Analysis, PDEs and Probability
      -Mathematics and Statistics for Life and Social Sciences
      -Dynamical Systems

      The duration of the scholarships is four years and the gross salary is about 16.500 euros/year.

      These will be the first PhD contracts offered by the Barcelona Graduate School in Mathematics (http://www.bgsmath.cat), through the recently obtained grant "Maria de Maeztu". BGSMath students can choose to work with any of the research groups in mathematics in the Barcelona area, as well as participating in the activities offered by the three member universities and the CRM. For this particular call, the chosen research groups should be in the areas above, understood in a broad sense.

      The official call will appear about June 15th and the deadline will probably be June 30th, so time is short.
      These contracts come directly from the Ministry of Science, hence the regulation is the official one for these type of calls: The applicants will need to have their official transcripts translated to Spanish (English and French could be ok too) and must have been accepted in (or at least need to have sent an application to) a PhD program at one of the member universities (UB, UAB or UPC). As soon as the call is launched a link will be available at the bgsmath website http://www.bgsmath.cat

      Please let us know if you have a strong candidate and we will be glad to help her/him through the application process.

  • PhD Position: Projecting the..., Dutch National Institute of...
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      PhD student: Projecting the effects of vaccination against multi-strain pathogens, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Dept. Infectious Disease Modelling

      Project description: In order to prevent serious illness and disease outbreaks, the Dutch government offers free vaccination against specific infectious diseases to all children through the National Immunization Programme. The most recent additions to this Programme are the vaccines against pneumococcus, associated amongst others with meningitis, and against papillomavirus, associated with various forms of cancer. Both pneumococcus and papillomavirus are characterized by the existence of various strains. The vaccines protect against a selected set of all strains that can cause disease, being so-called polyvalent vaccines. An anticipated effect of polyvalent vaccination is the elimination of vaccine-specific strains from the population. A possible unwanted effect is the take-over by other strains against which the vaccine is not protective, such that the health benefit partly disappears. This phenomenon is known as type-replacement and is caused by competition between pathogenic strains. This project aims to deliver a better assessment of type-replacement and its long-term consequences for the effectiveness of polyvalent vaccination. Partners in this project are the University Medical Centres of Utrecht (Paediatrics) and of Leiden (Medical Statistics).

      Your challenge: 1. Quantification of interactions between pathogenic strains requires diverse statistical techniques (graphical models, multi-state modelling, survival analysis) for a diversity of data structures. The question is which techniques and which data are informative for inferring competitive interactions, and which are sensitive for the occurrence of type-replacement. To this end, you will develop dynamic transmission models for multi-strain pathogens that can incorporate a variety of interactions between strains. You will use these models to simulate data for the joint occurrence of multiple strains in epidemiological studies.
      2. You will develop statistical techniques based on simulated data and apply these to available data on pneumococcus and papillomavirus. You will investigate indications for type-replacement and answer the question how type-replacement may alter the expected health benefit of vaccination. In the end, your research provides a consistent methodology for multi-strain modelling that can be used to describe the effectiveness of pneumococcal vaccination in an adequate way.
      3. You will publish your findings in scientific journals and present your findings on international conferences. After four years, your research is intended to result in an academic dissertation. An abroad stay as part of your PhD research belongs to the possibilities.

      Your profile: We seek a highly motivated, enthusiastic researcher with an MSc or comparable degree in (applied) mathematics, physics, biostatistics, theoretical biology or bioinformatics. Excellent verbal and written command of English is required, programming experience in C/C++ and R are welcome. We expect affinity with the promotion of public health through prevention of infectious diseases.

      Terms of employment: You will be stationed at the Dutch National Institute of Public Health and the Environment (RIVM). Appointment takes place based on 36 working hours a week for the initial term of one year. Your contract will be prolonged in case of good performance. Salary is in conformity with that of a PhD student (OIO) at a Dutch university.

      More information: Dr. J.A. Bogaards, Project leader (hans.bogaards@rivm.nl, tel 030-2744765), Dr. J. Wallinga, Head Dept. Infectious Disease Modelling (jacco.wallinga@rivm.nl, tel. 030-2742553)

  • PhD Position: Computational Biology & Medicine, U Oslo
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      PhD fellowships available through the SUURPh international training programme

      The Simula Research Laboratory and University of Oslo (UiO) welcome applications for doctoral fellowships in computational biology and medicine funded through the SUURPh programme. SUURPh fellows will be enrolled through the faculty of Mathematics and Natural Sciences at UiO, and conduct their work with advisors located primarily at Simula or UiO. An important feature of these collaborative fellowships is that students will also be supported (and required) to complete a portion of their work at the University of California San Diego (USA). Typically this period will last from 6 months to 1 year depending on the project. We will accept applications from students of all backgrounds but recommend that applicants possess a strong foundation in computational and quantitative sciences. To be eligible, students must also have completed a Masters in an appropriate field by the end of summer of 2015.

      For more information and to submit your application, please visit the SUURPh home page: www.simula.no/education/suurph-collaboration

  • PhD Position: Monitoring of Invasive Pest..., U Leicester
    • SMB Digest Vol 15, Issue 21 - May 27, 2015

      A fully-funded PhD position is available in the Department of Mathematics, University of Leicester, UK, under supervision of Prof. Sergei Petrovskii.

      Project title: 'Monitoring of Invasive Pest Species Under the Climate Change: Mathematical Modelling Approach'

      For a description of the project, please visit http://www2.le.ac.uk/departments/mathematics/postgraduate-study/phd/epsrc-dtp-projects-2015-16-climate-change

      The position is available from October 1, 2015 or as soon as possible thereafter. To apply, please visit
      http://www2.le.ac.uk/study/research/how-to-apply
      and follow the instructions there.

      Please note that only EU/UK citizens are eligible to apply.

      For inquiries and more details, please contact Prof. Sergei Petrovskii at sp237@le.ac.uk

  • PhD Position: Math Bio, Hemholtz Centre for Infection Research
    • SMB Digest Vol 15, Issue 20 - May 20, 2015

      The Helmholtz Centre for Infection Research (HZI) and the Braunschweig Integrated Centre of Systems Biology (BRICS) offers a position as PhD student in Mathematical Biology at the Department of Systems Immunology. This position is offered in the context of a Human Frontier Science Program (HFSP) research project on multiscale mathematical modelling of the dynamics of antibody optimisation in germinal centres and of the immunological synapse.

      You will be embedded in a strong team of modellers headed by Michael Meyer-Hermann with expertise in a wide range of quantitative modelling methods, including spatio-temporal techniques and application to a large range of biological problems. You will benefit from an environment with long-standing experience in germinal centre modelling. You are expected to actively shape the research with new ideas and will be supported by strong team of experimental collaborators including Michael Dustin (Oxford UK), Gabriel Victora (Cambridge MA USA), and Carola Vinuesa (Canberra Australia). This team will generate quantitative data on the immunological synapse, cell dynamics in germinal centres and inter-germinal centre information processing.

      The successful candidate will be educated in one of the following disciplines: Theoretical Biology, Mathematical Biology, Computational Biology, Physics, Mathematics, or other quantitative sciences. Severely disabled applicants will be favoured if equally qualified.

      Please submit your application until June 30, 2015 in our online application tool at https://hzi.opencampus.net/ (after registration choose "Application HZI Jobs" and select job no. 20/2015).

      The HZI is a research centre under the roof of the Helmholtz Society, which is a world leading and powerful institution funding basic and applied research in natural sciences. HZI is narrowly connected to the Technical University of Braunschweig and the University of Hannover and is, thus, embedded in a dense environment of fundamental research in Biology and Immunology. The HZI has proven in the past to provide excellent support for the appointed scientists in order to promote their career.

      For further information please refer to www.systems-immunology.de or contact Prof. Dr. Michael Meyer-Hermann by phone +49(0)531/6181-5400 or by e-mail michael.meyer-hermann@helmholtz-hzi.de.

  • PhD Position: Mechanics of Living Tissue During..., U Grenoble
    • SMB Digest Vol 15, Issue 20 - May 20, 2015

      PhD position: Mechanics of living tissue during embryo development: understanding biological observations with a mechanical model Based in the Laboratoire Interdisciplinaire de Physique, Universite Grenoble Alpes, in collaboration with the Dept. of Physiology, Development and Neuroscience, University of Cambridge. Advisors: Dr Jocelyn Etienne (Grenoble) & Dr Guy Blanchard (Cambridge)

      During the development of living organisms, large-scale movements of tissues occur to sculpt the adult form from a single fertilized egg. The mechanics of these deformations is poorly understood, although their driving forces are known to originate in the subcellular dynamics of filaments of actin proteins, which are contracted by the action of myosin, a motor-molecule. Understanding the self-organizing capacity of networks of actin and myosin and how this is controlled during development to generate appropriate form is one of the great current challenges at the interface between physics and biology. The objective of this PhD project is to work on physical models of the subcellular dynamics of these filaments, and of the resulting tissue-scale dynamics of cells, in order to understand how the molecular processes give rise to the correct morphogenetic movements.

      Full advert and details:
      http://www-liphy.ujf-grenoble.fr/pagesperso/etienne/droso_en/
      Deadline: 24th May 2015

  • PhD Position: Spatio-temporal Dynamic Model of the..., France
    • SMB Digest Vol 15, Issue 20 - May 20, 2015

      PhD topic
      Spatio-temporal dynamic model of the translation repressor 4E-BP regulation network

      In this project, we aim to study three levels of the dynamics of the translation repressor 4E-BP.
      1. We will study the impact of numerous and hierarchical phosphorylation sites found in 4E-BP on the ultra-sensitivity of conformation modifications and association with eIF4E. The proteins that are activated only through the phosphorylation of several sites may have a ultra-sensitive response and lead to a sigmoid-type functional response (Ferrell & Ha, 2014a; Ferrell & Ha, 2014b). First, we want to integrate in the existing model the different conformations that the proteins may have (no folding, partial or full folding), and thus the different reaction rates that they may have, and the different degradation rates. One can think that the model would need to be either compartmented into a finite (small) number of possible conformations or structured through a (continuous) phosphorylation variable (similar to a methylation variable). This question needs to be addressed during the course of the PhD studies.
      Keywords : compartmented vs structured models, conformational structuration
      2. We will also extend the current ordinary differential equations model and take into account the aforementioned delay happening between fertilization and activation of protein synthesis. This will be done through a partial differential equations model involving active and passive transport (diffusion). Appropriate interaction with the biologists in the lab will allow to weigh the relative importance of these phenomena.
      Keywords : spatial structuration, (active) transport, diffusion
      3. We then want to analyze the spatio-temporal dynamics of the TORC1 pathway and its impact on the protein synthesis. The model will be made as realistic as possible by taking into account the form on the cell in vivo. The quasi-spherical shape and the constant volume of the sea urchin egg offer a simple model to begin with. The spatial repartition of the organelles (such as the vesicles) can be acutely determined through interaction with the biologists in the lab and then be included in the model (Elias & Clairambault, 2014).
      Keywords : 3D models, spatial heterogeneity

      The PhD project comes with a standard 3-year-contract called 'contrat doctoral'. The selected candidate will work in the Roscoff marine station under the supervision of Patrick Cormier (biologist) and Benoît Sarels (mathematician). The candidate will be encouraged to actively collaborate with the mathematicians in the LJLL in Paris.

      The candidate should have obtained or be about to complete a master's degree in applied mathematics. Other profiles may be considered if the candidate demonstrates a strong ability either in applied mathematics or modeling. Prior knowledge of transport-reaction-diffusion PDE would be a plus. The candidate must master a numerical computing software or programming language, and be able to use and further develop numerical schemes. The candidate will have to demonstrate a strong interest for system biology approaches that aim at modeling, analyzing and simulating complex biological systems. It is critical for the candidate to be willing to work in a strongly multidisciplinary environment. An outstanding candidate would have the opportunity to take part in the creation of an emerging team of mathematical modeling in the Roscoff marine station. No knowledge of French is required as both supervisors are fluent in English. Please note however that the work language in the lab is French.

      Applications should be sent by email with the string "MoDyST" in the subject to patrick.cormier@sb-roscoff.fr and benoit.sarels@ljll.math.upmc.fr. Please send in a CV, a student certificate, a transcript with the grades obtained during the current and the last years and a cover letter. Applications will be reviewed as soon as they are received. We expect to interview candidates in Roscoff in June 2015. The PhD contract will start between September 1st and December 1st. The candidate will have the opportunity to teach classes over the course of the PhD studies. The teaching load is then of 64 hours per year with an additional salary of approximately 300 euros per month. The teaching would consist of supervisions sessions in the "double major biology - mathematics" UPMC bachelor program in Roscoff.

  • PhD Positions: Bioengineering & Robotics, Italian Inst of Tech
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Three PhD positions are offered at the Italian Institute of Technology (IIT), Robotics, Brain and Cognitive Science Department (RBCS). http://www.iit.it/rbcs

      Theme 5. Neural and motor bases of social interaction
      Tutors: Prof. Thierry Pozzo, Dr. Alberto Inuggi, Dr. Alessandro D'Ausilio

      Description: While progress has been made in the field of social neuroscience, the neural mechanisms underlying social interactions represent the 'dark matter' of cognition. We need to study real-time social encounters in a truly interactive manner, with the assumption that cognition is fundamentally different when we interact with others rather than merely observe them passively (Schilbach et al., 2013). In the classic motor control frame of reference, individuals can be conceived as proactively building models of their action and of their sensory consequence. During interaction, these sensorimotor models can be extended to the social space whereby the control signal becomes the negotiated behavior of other people (Wolpert et al., 2003). Here, we intend to map the brain activities responsible for the emergence of such a shared behavior. Recent research has employed the hyper-scanning technique consisting in the recording of brain activities from multiple participants engaged in artificial interactive tasks (Hasson et al., 2012).
      The current projects will go beyond current approaches by recording multimodal data of real face-to-face interaction between two subjects/agents recorded simultaneously. Recording will include Electroencephalographic (EEG), Electromyographic (EMG) and body motion kinematics (MoCap) data. The neural metrics of group collaboration will be extrapolated by calculating cortical connectivity indexes (Directed Transfer Function, Partial Directed Coherence), coherence factors among EEG, EMG and MoCap data and whole body movement features (Berret et al. 2009). This approach will allow the study of the neural and motor bases of social non-verbal interaction within a group of participants engaged in a collaborative realistic task.

      Requirements: The successful candidate will have a background in computer science or engineering, programming skills as well as a strong interest in cognitive neuroscience. Electroencephalographic and kinematic data analyses skills are a plus.

      References:
      1. D.M. Wolpert, K. Doya, M. Kawato, A unifying computational framework for motor control and social interaction, Phil Trans Roy al Soc Lond Series B: Biol Sci 358, pp. 593?602, 2013
      2. U. Hasson, A.A. Ghazanfar, B. Galantucci, S. Garrod, C. Keysers C., Brain-to-brain coupling: a mechanism for creating and sharing a social world. Trends Cognitive Sciences 16(2), pp. 114-121, 2012
      3. L. Schilbach, B. Timmermans, V. Reddy, A. Costall, G. Bente, T. Schlicht, K. Vogeley Toward a second-person neuroscience, Behav Brain Sci 36, pp. 393-414, 2013
      4. B. Berret, F. Bonnetblanc, C. Papaxanthis, T. Pozzo, Modular control of pointing beyond arm's length, Journal of Neuroscience, 29, pp. 191-205, 2009

      Contacts: thierry.pozzo@iit.it; alberto.inuggi@iit.it; alessandro.dausilio@iit.it

      Theme 7. Augmented sensorimotor interaction
      Tutors: Dr. Alessandro D'Ausilio, Dr. Leonardo Badino, Prof. Luciano Fadiga Department: RBCS

      Description: The project starts from the assumption that human cultural and moral evolution can only be based on the development of efficient cooperation, and coherence among people. In fact, human perception, action and cognition are geared to enable successful coordination with others. The MNIlab devises computational methods to quantify the information flow between human body movements in small group of participants (Badino et al. 2014). In fact, body movement is the key channel for non-verbal communication (D'Ausilio et al., 2015). The successful candidate will work on the extension and consolidation of this methodology to different scenarios (i.e. small group behavior during meetings or sport activities) and the development of the analytical tools to extract in real-time the quantitative flow of sensorimotor communication (Granger Causality, Transfer Entropy, Cross-Recurrence Quantification Analysis). The research program will be complemented by basic motor neurophysiological research on behavioral coordination (D'Ausilio et al., 2015). All these aspects will be critical to implement the next generation of biologically inspired automatic sensorimotor communication recognition systems. These automatic systems will be essential to augment natural human-human coordination and promote the future of efficient human-robot interaction.

      Requirements: The successful candidate will have a background in computer science, engineering, computational neuroscience or experimental psychology. Programming skills as well as a strong motivation in bridging the gap between technology and neuroscience are necessary. Kinematic data analyses skills are a plus.

      References:
      1. L. Badino, A. D'Ausilio, D. Glowinski, A. Camurri, L. Fadiga, Sensorimotor communication in professional quartets, Neuropsychologia, 55(1), pp. 98-104, 2014
      2. A. D'Ausilio, G. Novembre, L. Fadiga, P.E. Keller, What can music tell us about social interaction?, Trends Cognitive Sciences, 19(3), pp. 111-114, 2015
      3. A. D'Ausilio, E. Bartoli, L. Maffongelli L., Grasping Synergies: A motor-control approach to the mirror neuron mechanism, Phys Life Rev. 12, pp. 91-103, 2015

      Contacts: alessandro.dausilio@iit.it; leonardo.badino@iit.it; luciano.fadiga@iit.it

      Theme 9. Speaking in Concert
      Tutors: Prof. Luciano Fadiga, Dr. Leonardo Badino, Dr. Alessandro D'Ausilio Department: RBCS

      Description: While it is now undisputed that speakers engaged in a conversational interaction are perceived by external listeners as converging towards each other in how they speak, we do not know yet what exactly in their speech makes them sound more similar to each other. Both perceptual tests and detailed acoustic analyses have shown their limits, the former because they have failed to reveal along which acoustic/phonetic parameters convergence may occur between speakers, and the latter because we may not have looked at the right acoustic/phonetic parameters yet. In addition, little is known about the cerebral underpinnings of phonetic convergence in speech. The goal of this project is to better understand what makes speakers sound more like each other in a conversational interaction. We will achieve this by means of a set of simultaneous recordings at the neural, articulatory and acoustic levels, in order to identify the neural features that may control and modulate the articulatory movements that in turn are at the origin of convergence in speech. Another major issue will be to determine whether convergence is symmetrical or asymmetrical, i.e. whether one partner converges to a greater extent towards the other partner than the reverse. To address this issue, we will conduct a series of analyses based on methods such as Granger Causality and Transfer Entropy, which have already been successfully employed in studies on sensorimotor convergence (D'Ausilio et al., 2012).

      Requirements: A degree in Computer Science, Engineering or equivalent, with interests in Neuroscience. A background in speech processing, statistical analysis and machine learning will be appreciated.

      Reference:
      A. D'Ausilio, L. Badino, L. Yi, S. Tokay, L. Craighero, R. Canto, Y. Aloimonos, L. Fadiga, Leadership in Orchestra Emerges from the Causal Relationships of Movement Kinematics. PLoS ONE 7(5)

      Contacts: leonardo.badino@iit.it, alessandro.dausilio@iit.it, luciano.fadiga@iit.it

      How to apply

      Please note that the positions are available through the PhD course of BIOENGINEERING AND ROBOTICS, Curriculum Cognitive robotics, interaction and rehabilitation technologies, offered jointly by IIT and the University of Genoa. The official call and application forms are available on the website of the University of Genoa.

      The official calls are available here:
      [ENG] http://www.iit.it/en/openings/phd-calls.html
      [ENG] http://www.iit.it/images/phd-xxxi/RES.THEMES.COGNIROB.INTER.pdf
      [ITA] http://www.studenti.unige.it/postlaurea/dottorati/XXXI/IT

      Applications must be submitted online, instructions for applicants are available here:
      [ENG] http://phd.dibris.unige.it/biorob/index.php/how-to-apply

      Applications are considered for the subsequent selection ONLY if received ELECTRONICALLY through the UNIVERSITY of GENOA's website by the deadline.

      Application deadline: 10 June 2015, 12pm Italian time

      Applicants are strongly encouraged to get in touch the contact person(s) for the individual themes.

  • PhD/Post-doc Positions: Genomic-Metabolic..., Imperial College
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Postdoctoral and PhD positions in Systems & Synthetic Biology of genetic-metabolic networks, Department of Mathematics, Imperial College London

      We have two openings as part of a new project funded by the Human Frontier Science Program:

      1) Postdoctoral position in Systems and Synthetic Biology of metabolic adaptations

      2) PhD position in stochastic fluctuations of enzymatic reactions

      The successful candidate will join Dr Diego Oyarzun, (Biomathematical Sciences, Imperial College London) in exciting projects at the interface between Mathematics, Control Theory, and Systems/Synthetic Biology. Their general aims are to develop mathematical methods to analyze and predict metabolic responses from complex gene regulatory networks, and to showcase how new metabolic responses can be engineered in living cells.

      For additional information please contact Dr Diego Oyarzun (d.oyarzun@imperial.ac.uk). Details about both posts can be found in http://www.imperial.ac.uk/people/d.oyarzun. To apply for the postdoctoral position, please follow this link, application deadline: 05 June 2015. The start date for both posts is 01 September 2015.

  • PhD/Post-doc Positions: Math & Population Genetics, McGill U
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Graduate and postgraduate positions in mathematical and population genetics

      Graduate student and postdoc positions in mathematical and population genetics are available in Simon Gravel's group at McGill University in Montreal, Canada. The project aims at creating mathematical models of historical human migrations, family histories, and high-throughput genomic data. Students will be involved in conceptual methods development, implementation, and applications to exciting datasets. This is a unique opportunity to be involved in work that is relevant and interesting from a mathematical, medical, and historical perspectives.

      We welcome applications from qualified candidates from diverse backgrounds, including biology, anthropology, mathematics, physics, and computer science. Programming experience and a demonstrated interest in mathematics, statistics, or related fields is required.

      The position offers an exceptional opportunity to develop theoretical and computational ideas and apply them to cutting-edge data in a supportive and thriving research environment.

      Applications and queries should be sent to gravellab@gmail.com. Please include a statement of interest (1 page) and a CV with a list of publications, contact information for three references, and a low-resolution scan of official transcripts.

  • PhD Position: Theoretical and Applied Mechanics ..., U of Adelaide
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      PhD opportunities in the Theoretical and Applied Mechanics Group, School of Mathematical Sciences, University of Adelaide

      The School of Mathematical Sciences at the University of Adelaide has a long tradition of research excellence in Applied Mathematics, with particular strengths in mathematical biology, fluid mechanics, and dynamical systems. Potential PhD projects currently available in the group include:
      * Intercellular calcium signalling in the mammalian cumulus-oocyte complex (A. Prof Yvonne Stokes)
      * Modelling and quantification of filamentous yeast growth (Dr Ben Binder)
      * Mechanics of the spinal disc (Dr Sarthok Sircar and Dr Edward Green)
      * Modelling of the manufacturing process for Microstructured Optical Fibres (used in biosensors and other applications) (A. Prof Yvonne Stokes)
      * Models for the role of mechanics in morphogenesis and tissue development (Dr Edward Green)

      Applicants should have a Masters degree (or, in the case of Australian applicants, a good Honours degree) in mathematics, physics, engineering or a related subject, and must satisfy the entry requirements of the Adelaide Graduate Centre, which include proficiency requirements in written and spoken English. Visit http://www.adelaide.edu.au/graduatecentre/admission/how-to-apply/ for details.

      University scholarships are available for well-qualified students, which are awarded on a competitive basis. Additional scholarship schemes are open to citizens of certain countries. More information can be found at: http://www.adelaide.edu.au/graduatecentre/scholarships/

      Potential applicants should contact prospective supervisors or the Postgraduate Coordinator for more information (see http://www.maths.adelaide.edu.au for contact details).

      The University of Adelaide is one of Australia's leading universities and a member of the prestigious Group of Eight. The city of Adelaide is consistently ranked in The Economist's Top Ten Most Liveable Cities in the World, and has an international reputation for its premium food and wine, and cultural events, such as the annual Festival of the Arts and Fringe Festival. For more information about Adelaide and the University, visit http://www.adelaide.edu.au

  • PhD Position: Mathematical Modelling ..., Swiss ... Institute
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      The Swiss Tropical and Public Health Institute is a public institution with the mandate to contribute to the improvement of the health of populations internationally and nationally through excellence in research, services, and teaching and training.

      The Department of Epidemiology and Public Health (EPH), within the Swiss Tropical and Public Health Institute, develops and applies epidemiological, statistical and mathematical methods to advance innovation, validation, and application in the field of public health. In partnership with the Department of Chemistry of the University of Basel (Prof. Anatole O. Lilienfeld) and our partners in Chad, the Institut de Recherches en Elevage pour le Developpement (IRED) and the Centre de Support en Sante Internationale (CSSI), we are seeking an interested candidate for the following position:

      PhD Mathematical Modelling of Dog Rabies Elimination

      This PhD studentship is available in the area of meta-population and contact network modelling approaches applied to dog rabies elimination.

      Required qualifications:
      (1) Master's degree in Mathematics, Statistics, Epidemiology or other relevant field;
      (2) strong quantitative, analytical and programming skills (preferably in at least one of MATLAB, R, C++, Fortran or Python);
      (3) background and/or interest in epidemiology and infectious disease dynamics;
      (4) ability to communicate effectively in spoken and written English (ability to communicate in French is an advantage).

      The successful applicant will be registered for a PhD degree at the University of Basel, Switzerland. The studentship provides support for 3 years and covers tuition fees and a doctoral salary at Swiss National Science Foundation scale.

      Chadian candidates are especially encouraged to apply.

      If you are interested, please submit your application online via the link provided below, in English with CV, and the names of 3 references: https://recruitingapp-2698.umantis.com/Vacancies/360/Description/2

      Kindly note that we can only consider applications from our online tool (no email). The closing date for applications is 31 May 2015. The positions are available immediately but a later starting date is possible by negotiation.

      For further information about the position please contact Prof. Dr. Jakob Zinsstag at jakob.zinsstag@unibas.ch or Dr. Nakul Chitnis at nakul.chitnis@unibas.ch.

Postdoctoral positions

(Click on job title for additional information.)
  • Postdoc: Information Processing within Wound Healing Signaling Networks
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      Applications are invited for a postdoctoral position in the Wollman Lab (http://wollmanlab.ucsd.edu). The Wollman lab is part of the San Diego Center for Systems Biology, the qBio program, and the Departments of Cell and Developmental Biology and Chemistry and Biochemistry, University of California San Diego. The lab is highly interdisciplinary and combines quantitative microscopy, computational image analysis and mathematical modeling to investigate information processing within mammalian signaling networks.

      The project aims at understanding how initial wound response signal transduction networks function in the presence of biological "noise". The following paper is an example of the project:

      Accurate information transmission through dynamic biochemical signaling networks. Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R. Science. 2014

      The successful applicant should: 1. Believe that science is fun and exciting. 2. Be fascinated by the ability of signal transduction networks to allow cells to respond to a changing environment. 3. Have a recent PhD degree in cell biology, bioengineering, computational biology, biophysics, or a related field. And 4. Demonstrate expertize in at least a subset of the following: mammalian cell culture, mathematical modeling, microscopy, and computational image analysis.

      Self-motivated individuals are encouraged to send their CV, a brief (1-2 paragraphs) statement of interest and contact information of two references to Roy Wollman, rwollman@ucsd.edu.

  • Postdoc Position: Theoretical Ecology/laboratory microcosms, UC Davis
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      Post-doctoral position in Theoretical Ecology/laboratory microcosms (species interactions in a dynamic spatial context)

      A three-year post-doctoral position (3 years of support from an NSF grant with possible extension from other funds) is available with Alan Hastings at UC Davis in the Department of Environmental as part of a collaborative project with Brett Melbourne at the University of Colorado. The post-doc will work with an experimental laboratory system using Tribolium species and on associated theoretical aspects to look at species interactions across space and time in highly replicated laboratory systems.

      Familiarity with Tribolium would be useful, but not required. Strong background in theoretical ecology, mathematical approaches to spatial models, statistical approaches and experimental design, and programming experience important.

      The post-doc will be expected to help design and co-ordinate experiments in consultation with the PIs, direct a team of undergraduate assistants, develop mathematical and statistical approaches for understanding stochastic and deterministic approaches to species interactions in space, and write up results for publication in a timely fashion.

      UC Davis houses a world class program in Ecology; post-doc can participate in seminars, and will receive professional mentoring on job applications, interview strategies, CV preparation, and additional professional development.

      Start date is flexible, between October 1 2015 and July 1, 2016. Salary commensurate with experience, starting at approximately $42,840 with generous benefits. All requirements for the PhD must be completed before starting.

      Interested candidates should submit a cover letter, CV, a short (1-2 page) description of research accomplishments, copies of publications, and email addresses and phone numbers of three references to Alan Hastings at amhastings@ucdavis.edu

      Review of applicants will begin upon receipt.

      The University of California at Davis is an affirmative action/ equal opportunity employer with a strong institutional commitment to the achievement of diversity among its faculty and staff. UC Davis is a smoke and tobacco free campus effective January 1, 2014.

  • Post-doc: Quant. Biol. of Virus-Host interactions, U Wisconsin
    • SMB Digest Vol 15, Issue 29 - July 12, 2015

      Post-doctoral Opening
      Quantitative Biology of Virus-Host Interactions

      A position is available immediately for a highly motivated individual to develop methods that advance our mechanistic and systems-level understanding of virus and host processes during virus infections. Our approach combines single-cell measures of viral and cellular processes, within-cell readouts of viral and anti-viral intermediates, use of established and novel culture systems, mathematical modeling, and quantitative imaging of infection spread. Our studies focus on RNA viruses relevant to human health and technology development, including human rhinovirus and vesicular stomatitis virus. This NIH-supported work involves close collaboration among biological and physical scientists, including molecular biologists, engineers and clinicians. Applicants with a strong background in data-driven mathematical modeling, computer simulation, microscopy, quantitative imaging, microbiology, immunology, are especially encouraged to apply.

      We pursue our research at the Wisconsin Institutes for Discovery, a major public- and private-sponsored initiative, housed in an award-winning facility, that promotes cross-disciplinary training and research, as well as public outreach, for societal benefit (see discovery.wisc.edu). Madison is an attractive and affordable city surrounded by beautiful lakes. Among U.S. cities, Madison routinely ranks among "best places to live," and residents thrive on its diversity of educational, cultural and outdoor opportunities.

      Interested candidates should submit by email a single PDF that includes a letter of interest, curriculum vitae, and contact information for at least three references to:
      Professor John Yin
      Systems Biology Theme, Wisconsin Institute for Discovery Chemical and Biological Engineering Department University of Wisconsin-Madison
      Madison, WI 53715, USA

      Email with a subject line that states "Postdoc Application" to: john.yin@wisc.edu

  • Post-doc: Comp. Structured Population Models, UL Lafayette
    • SMB Digest Vol 15, Issue 29 - July 12, 2015

      Position: Post-Doctoral Research Associate
      Affiliated Dept: Ray P. Authement College of Sciences
      Effective Date: August 19, 2015, or as soon as selected candidate is available.

      Qualifications: Ph.D. degree required. Applicants must possess a Ph.D. degree in Mathematics or Applied Mathematics with substantial knowledge of statistics and experience in developing and analyzing discrete and continuous structured population models and in developing and implementing numerical methods for solving such models. Also, experience in writing and publishing papers is required and a history of presentations at professional meetings is desired.

      Duties: The selected candidate will be a member of the consortium "Littoral Acoustic Demonstration Center - Gulf Ecological Monitoring and Modeling (LADC-GEMM)" working closely with Dr. Ackleh and his graduate students and the rest of the UL Lafayette LADC-GEMM Team. Current research projects focus on modeling and monitoring marine mammals in the Gulf of Mexico. For more details go to the following site: http://www.ladcgemm.org/ and click on "Research".

      Applications: We will review applications as they are received and continue until the position is filled. Send letters of application with vitae and a list of three (3) references to: graceb@louisiana.edu

  • Post-docs: Biophysics & Computational Biology, U Notre Dame
    • SMB Digest Vol 15, Issue 29 - July 12, 2015

      Postdoctoral Fellow Positions: Interdisciplinary Projects between University of Notre Dame, University of Pennsylvania and Argonne National Laboratory

      Applications are invited for two NIH and NSF funded postdoctoral research positions to participate in two interdisciplinary projects in Prof. Mark Alber's group at the University of Notre Dame. This work will be carried out in close collaboration with computational modelers and experimentalists from the University of Pennsylvania and Argonne National Laboratory. The group's work spans fields ranging from biophysics and computational biology to high-performance computing and image processing.

      We are seeking highly motivated, driven and curious applicants with a strong background in computational methods and modeling, strong communication skills, and an ability to work independently and collaborate effectively. Experience with computational implementation of numerical algorithms for solving partial differential equations or Monte Carlo models, programming with C or C++, and parallelizing simulation code using MPI or GPUs is desirable.

      The goal of the first project is to develop multi-scale computational models to study blood clot formation and mechanical properties of fibrin networks that will be calibrated using specific experiments. The second project will combine computer simulations with new biophysical methods, live imaging, and advanced organ culture techniques to investigate intercellular signaling in intact epithelial organs within a controlled microenvironment. Success in this project will lead to a better understanding of how exogenous factors impact the endogenous regulation of organ growth and differentiation.

      We are offering a highly interactive and exciting interdisciplinary research environment with strong mentoring and career development support. Positions will involve regular visits to the University of Pennsylvania and Argonne National Laboratory. We will also provide support for participation in conferences. The University of Notre Dame is located 1.5 hours from downtown Chicago and Argonne National Laboratory.

      Recent selected publications:
      Anyan et al. Proc. Natl. Acad. Sci. USA vol. 111, no. 50, 18013-18018(2014),
      Kim et al., Biomaterials 35, 6739-6749 (2014),
      Wu et al., Philosophical Transactions of the Royal Society A 372: 20130380 (2014),
      Gupta et al., Proc. Natl. Acad. Sci. USA, 2013 Dec 17;110(51): 20449-54(2013),
      Kim et al., Computational Biology 9 (6), e1003095 (2013).

      Positions are for 1 year with possible extension for up to two more years. To apply, please send CV and cover letter explaining your interest in the position to malber@nd.edu. Also, arrange for at least three letters of recommendation to be sent to the same email address. The evaluation of candidates will begin immediately and continue until the positions are filled.

  • Post-docs: Systems Biology of Human Microbiome, Korea
    • SMB Digest Vol 15, Issue 29 - July 12, 2015

      Postdoctoral Positions in Systems Biology of Human Microbiome (Asia Pacific Center for Theoretical Physics)

      The Junior Research Group (JRG), "Emergent Dynamics of Complex Living Systems" led by Dr. Pan-Jun Kim at the Asia Pacific Center for Theoretical Physics (APCTP, http://apctp.org) in Korea, invites applications for postdoctoral positions in the area of computational and systems biology. JRGs at the APCTP are supported by the Korean government and POSTECH.

      The research will focus on the computational study of biological networks of microbial communities inside the human gut. The ideal candidates are expected to have experience/interest in the areas of systems biology, bioinformatics, data analysis, and/or complex networks. Previous experience with nonlinear dynamics, and/or computer simulation would be a plus.

      Screening of applications begins immediately and will continue until the position is filled. Salary will be commensurate with qualifications and experience. To apply, please e-mail curriculum vitae along with a brief statement of your research interests to Pan-Jun Kim at pjkim@apctp.org and arrange to have three letters of recommendation e-mailed to the same address.

  • Post-doc: Computational Systems Biology, U Lille, France
    • SMB Digest Vol 15, Issue 28 - July 15, 2015

      A Postdoctoral Position in Computational Systems Biology at the University of Lille, France

      Topic: Computational modeling of stress response in normal and cancer cells

      Our team combines experimental and computational modeling techniques to study the response of mammalian cells to various stresses such as oxidative, thermal and metabolic stresses. The goal of this project is to characterize the main differences between non-cancerous and cancerous cells in their sensitivity (survival/death rates) to stress signals, with the long-term objective to develop novel anti-cancer therapeutic strategies. The fact that cancer cells typically show aberrant metabolism and proliferation and our experimental ability to induce various types, intensities and durations of stresses motivate the study of several related issues: What are the relevant timescales involved in stress responses? Are there non-trivial effects in combining stress signals? How do cells coordinate stress response, metabolism and cell cycle?

      The postdoctoral position is dedicated to working on the computational modeling aspect of this stress response project. Models will be useful to provide both quantitative and qualitative insights into the dynamics of stress-response factors and of cell fate decisions under various stress conditions. Modeling work will mainly consist in (i) identifying the known cellular pathways involved in stress-specific responses, (ii) translating these signaling, regulatory and metabolic networks into ordinary differential equation models, (iii) simulating and analyzing the model behavior under various settings, and (iv) comparing with experimental data.

      CANDIDATE PROFILE
      The candidate should have: (i) a strong background in applied mathematics or physics, especially computational and theoretical skills in working with systems of differential equations; (ii) basic notions of cell biology and biophysics gained from previous research experience; (iii) ability to work within a team environment.

      POSITION AND APPLICATION DETAILS
      The position is for one year renewable, and would start between October 2015 and January 2016. Net annual salary is about 28000 euros and includes a benefits package (health insurance, retirement and unemployment benefits). The laboratory (http://www.phlam.univ-lille1.fr/) is located on the Villeneuve d'Ascq campus of the University of Lille. Lille is a lively city connected by highspeed train to Brussel (30mn), Paris (1h) and London (1h30). Applicants should send a letter of motivation, a CV including a complete list of publication and at least 2 letters of recommendation to: quentin.thommen@univ-lille1.fr and Benjamin.pfeuty@univ-lille1.fr

      For more informations: http://www.phlam.univ-lille1.fr/spip.php?article1066

  • Post-doc: Antibody Formulations, Pfizer, St. Louis
    • SMB Digest Vol 15, Issue 28 - July 15, 2015

      Job Title: Postdoctoral Fellow, Antibody Formulations
      Job Id: 1014595
      Target Openings: 1
      Locations: United States-Missouri-Saint Louis

      Responsibilities
      A postdoctoral researcher is sought to conduct fundamental computational research towards understanding solution behavior of highly concentrated antibody formulations. The research shall involve an inter-disciplinary mix of multi-scale molecular modeling and dynamics simulations, and high performance computing to advance our understanding of inter-molecular interactions (protein:protein and protein: cosolutes) in highly concentrated biologic drug solutions. The researcher will be expected to discover/design novel viscosity reducing excipients, and contribute toward development of novel approaches focused at early detection of develop-ability challenged therapeutic candidates.
      Other duties as assigned time to time by research supervisor.
      The successful candidate shall be highly motivated, hardworking, and intellectually productive team player. He/she shall be expected to publish in high impact scientific journals and contribute towards Pfizer's expertise on biopharmaceutical drug development. Fluency in oral and written English is required. Good inter-personal and communication skills are required.

      Qualifications
      EDUCATIONAL BACKGROUND: Ph.D. in Computational Molecular Biophysics, Chemical Engineering or related fields
      DESIRABLE: One or two years of postdoctoral research experience. Record of first class scientific research productivity as demonstrated by publications in high impact journals
      WORK EXPERIENCE/SKILLS: Advanced understanding of antibody structure-function, Protein: Protein interactions, and viscosity issues in highly concentrated antibody solutions is essential. Expertise in computer programming, molecular modeling, coarse-grained and all atom MD simulations of large macromolecules is required. Expertise with MOE, Discovery Studio, Schrodinger, VMD, MATLAB and modern programming languages is required.

      Equal Employment Opportunity
      Pfizer is committed to equal opportunity in the terms and conditions of employment for all employees and job applicants without regard to race, color, religion, sex, sexual orientation, age, gender identity or gender expression, national origin, disability or veteran status. Pfizer also complies with all applicable national, state and local laws governing nondiscrimination in employment as well as work authorization and employment eligibility verification requirements of the Immigration and Nationality Act and IRCA. Pfizer is an E-Verify employer.

  • Post-doc: Systems Pharmacology, Bridgewater, NJ, USA
    • SMB Digest Vol 15, Issue 28 - July 15, 2015

      Job Description:
      This is a postdoctoral position in the area of systems pharmacology. The individual will be based in the Department of Clinical and Exploratory Pharmacology in Bridgewater NJ, and will be a member of the Interdisciplinary Program in Pharmacometrics which links pharmacometric experts across the Scientific Core Platforms. The individual will primarily be involved with the development of systems pharmacology models, working as part of a modeling team. The models will aim to quantitatively integrate pathway biology, physiology and clinical pharmacology, i.e. systems pharmacology.
      -Major Duties & Responsibilities: Develop computational systems models working with internal and external collaborators, Communicate with clarity the results of modeling in presentations to key stakeholders.

      Qualifications
      -Formal Education And Experience Required: PhD with a track record of productivity in the areas of systems pharmacology, computational biology or related field, as manifested in publications and presentations.
      -Basic experience in Pharmacometrics or Clinical Pharmacology. Knowledge And Skills: Extensive knowledge of biological pathways relevant to disease. Superb skill in communicating both highly technical material as well as the distilled take-home messages. Knowledge And Skills Desirable: Expert knowledge in at least one area (e.g. rare diseases, cardiovascular) highly desirable.
      -Modeling and computational experience, Excellent scientific computing and programming skills in a variety of computational tools such as MATLAB, Monolix, NONMEM, Mathematica, R and excellent working knowledge of Linux and Windows environments

      Please email karim.azer@sanofi.com to inquire about the position.

  • Evolutionary Dynamics in Cancer..., Moffitt, Tampa
    • SMB Digest Vol 15, Issue 27 - July 8, 2015

      Our group is part of the Integrated Mathematical Oncology department at the H. Lee Moffitt Cancer Center & Research institute in Tampa, FL. We are looking for candidates for a postdoctoral position modeling the evolutionary dynamics in cancer metastasis. The successful candidate will have a doctorate in mathematics, physics, computer science or a related discipline. University of Pittsburgh, USA to develop new methods to combine multimodal neuroimaging data to understand brain networks.

      The aim of the project is to understand how the interactions between metastatic tumor cells and normal bone cells shape the selection in bone cancer. Given the nature of the work, we are looking for a candidate able to work at the intersection between biology and mathematics. Interpersonal skills and willingness to work closely with our experimental partners will be key.

      The successful candidate will attend lab meetings with our experimental collaborator, the lab run by Dr. Conner Lynch, as well as meetings with other mathematical modelers at IMO, they will present work at cancer research and mathematical meetings and publish in cancer and computational biology journals.

      To apply, please complete send curriculum vitae and three (3) letters of reference to: david [at] cancerEvo [dot] org

  • Post-doc: Neuroimaging Data/Brain Networks, CMU/U Pittsburgh
    • SMB Digest Vol 15, Issue 26 - July 1, 2015

      Applications are invited for a postdoctoral position to support a collaboration between researchers at Carnegie Mellon University and the University of Pittsburgh, USA to develop new methods to combine multimodal neuroimaging data to understand brain networks.

      The research will focus on the development of new tools to combine high dimensional MEG (magnetoencephalography), fMRI, and structural MRI data to discover brain network structure. This will include developing algorithms to understand similarities between data types (neurovascular relationships, structure-function relationships, etc.) as well as discovering what unique information each modality provides. These tools will be developed with the purpose of uncovering how brain networks are disturbed in existing multimodal data from individuals with autism spectrum disorder and schizophrenia. Furthermore, these tools will be developed with aim of applying it to large pubic neuroimaging datasets, such as those being released as part of the Human Connectome Project.

      Applicants should hold a Ph.D. in Neuroscience, Computer Science, Mathematics, Statistics, Engineering or a related field. Advanced skills in multivariate statistics, missing data problems, graph theory, dimensionality reduction, network analysis, machine learning and/or computational neuroscience are required. Experience with analysis of human neuroimaging data is desirable. Applicants should have a strong track record of publication.

      The position is fully funded. The initial period is 1 year with additional years depending on fit and progress. Interested applicants should send a letter of interest, a CV, and the names and contact information for 3 researchers who can provide a recommendation. For further information or to submit an application, please contact Avniel Ghuman, Ph.D. at ghumana@upmc.edu or Aarti Singh at aarti@cs.cmu.edu .

      The position is available immediately and applications will be considered until the position is filled.

  • Student/Post-doc Positions: Computation. Immunology, Bar-Ilan U
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Student and postdoc positions in Computational Immunology

      The Computational Immunology Lab of Prof. Ramit Mehr in Bar-Ilan University, Israel (http://immsilico2.lnx.biu.ac.il) is recruiting research Students at all levels (undergrad projects, MSc or PhD) and Post-Doctoral Trainees.

      Prof. Ramit Mehr is a leader in computational immunology. The work performed in her group has led to several discoveries, which have significantly advanced the field beyond the state of the art. The group applies modeling and simulation, bioinformatics and statistical analysis to immunological questions. Our main focus is the development, population dynamics and function of B, T and NK cell repertoires, in health, aging, autoimmune diseases and cancer.

      Prof. Mehr devotes much time to career training and has a good track record in terms of the careers of lab alumni. Over 50% of PhD alumni published several papers before submitting their theses, and most MSc students have published at least one. All of them presented their work in national (PhDs also in international) scientific meetings. As a result, over 50% of PhD alumni have gone on to post-doctoral training, and all PhD and most MSC alumni work in bioinformatics and related fields.

      We have several fascinating projects, including:
      -Lineage tree - based studies of mutations in antibody genes
      -Analysis of lymphocyte repertoires
      -Simulations of antibody gene rearrangement
      -Math modeling of lymphocyte population dynamics
      -Math modeling of immune cell recovery from stem cell transplantation
      -Analysis of stem cell transplantation patient data
      -Analysis of cell marker data from HIV patients

      More info: http://immsilico2.lnx.biu.ac.il/Open-Positions.html

      Candidates - please send email to ramit.mehr@biu.ac.il , stating the position you're interested in. Please attach your CV, grades and publications so far, and the names and contact information of two people who can recommend you.

  • Post-doc: Cell Cycle Modeling, Virginia Tech
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Postdoc: Cell Cycle Modeling, Virginia Tech

      Seeking a postdoctoral associate with experience in mathematical modeling to join a team exploring the molecular basis of cell cycle checkpoints in budding yeast. The research will be supervised Drs. John Tyson, Jean Peccoud and Neil Adames on the campus of Virginia Tech in Blacksburg, VA.

      Responsibilities and Expertise: construct, analyze, simulate and optimize stochastic models of the spindle assembly checkpoint and the DNA damage checkpoint in Saccharomyces cerevisiae. cell cycle checkpoints. Will require close attention to experimental data from our lab and the literature, expertise in building realistic models using chemical rate equations, familiarity with nonlinear dynamical systems theory and stochastic simulations (Gillespie's stochastic simulation algorithm), and facility using software tools for bifurcation analysis and parameter estimation.

      Expectations: participate in lab meetings, interact productively with graduate and undergraduate students, make presentations at professional meetings, publish results in peer-reviewed scientific journals, and participate in grant proposal preparation.

      Qualifications: a Ph.D. degree in applied mathematics, biophysical chemistry, biomedical engineering or other relevant discipline; a strong background in mathematical modeling; good team-working and communication skills. A genuine interest in computational cell biology is necessary.

      To Apply: submit a curriculum vitae and statement of interest online at: www.jobs.vt.edu (Posting #SR0150080). Three letters of recommendation should be sent via email to Dr. John Tyson, Department of Biological Sciences, MC 0406, Virginia Tech, Blacksburg VA 24061 USA or as a pdf attachment to: tyson@vt.edu. Review of applications will begin July 15, 2015.

      Virginia Tech is an Equal Opportunity/Affirmative Action Institution.

  • Post-doc: Computational Epigenomics, NIH, Baltimore
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Postdoctoral fellowship opportunity in Computational Epigenomics at National Institutes of Health, USA

      A postdoctoral fellowship is available, pending administrative approval, at the National Institute on Aging, NIH, for developing computational methods to analyze high-throughput sequencing-based chromatin assays. The successful applicant will work in the laboratory of Dr. Myong-Hee Sung at the Bayview campus, Baltimore, Maryland, beginning in September, 2015. We are seeking highly motivated recent Ph.D. scientists who are interested in investigating outstanding questions in epigenomics using statistical and computational tools. Relevant publications for future projects include Sung et al. Mol Cell 2014 (PMID: 25242143); Kwon et al. Cell 2013 (PMID: 24360274); Hakim et al. Genome Res 2013 (PMID: 23212947); Sung and Hager, Nat Gen 2011 (PMID: 22030604). An ideal candidate will have a Ph.D. degree in mathematics, physics, engineering, or a related quantitative discipline, and has some knowledge in molecular biology or genomics methods. Interested individuals must send a cover letter, CV, and contact information for 3 references to: sungm@mail.nih.gov

      About training at NIH: Postdoctoral training in the NIH Intramural Research Program (IRP) provides the opportunity for recent doctoral degree recipients to enhance their research skills in the resource-rich National Institutes of Health (NIH) environment, which consists of more than 1200 laboratories/research projects located on the main campus in Bethesda, MD and the surrounding area as well as in Baltimore and Frederick, MD; Research Triangle Park, NC; Hamilton, MT; Framingham, MA; and Detroit, MI. Trainees pursue basic, translational, and clinical research free from the demands of obtaining grants and teaching, although opportunities to do both are available. At the NIH, postdocs work in a highly collaborative research environment with leading scientists and clinicians. The postdoctoral community at the NIH is large (approximately 4,000 strong) and vibrant. Trainees come from across the U.S. and around the world. Support for international postdocs is provided by the NIH Division of International Services.

      Eligibility: To be eligible for postdoctoral training in the NIH IRP, individuals must hold a doctoral degree (PhD, MD, DDS, or the equivalent) and have no more than five years of relevant research experience since receipt of their most recent doctoral degree. U.S. citizens and permanent residents are appointed to Postdoctoral Intramural Research Training Awards (IRTAs); citizens of other nations are appointed as Visiting Fellows.

      Stipend and Benefits: The stipends for postdoctoral trainees at the NIH are adjusted yearly; with supplements for prior experience, multiple degrees, and expertise in areas of current interest to the NIH such as mathematics, engineering, chemistry, and bioinformatics. Note that stipends for Postdoc IRTAs and Visiting Fellows are identical. Benefits include health insurance for the trainee and his/her family, and support for coursework related to the trainee's research and travel to meetings is often available. In addition, the NIH Fellows Committee (FelCom) and the NIH Office of Intramural Training & Education (OITE) sponsor a wide range of career development and social activities. The OITE includes an Office of Postdoctoral Services, a Career Services Center and Career Library.

      The NIH is dedicated to building a diverse community in its training and employment programs.

  • Post-doc: Pharmacometrics, U Cape Town
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      The Division of Clinical Pharmacology at the University of Cape Town (South Africa) is looking for highly a motivated science/engineering PhD graduate to join the pharmacometrics group as a post-doctoral fellow.

      Pharmacometrics is an emerging discipline that applies mathematical modelling and simulation to pharmacology, aiding the interpretation of data from clinical trials, helping decision making, and improving study design. This fellowship is a great opportunity for a scientist in quantitative sciences to apply their expertise within the framework of biomedical research, and pharmacometrics is a highly-sought set of professional skills both in academia and in the pharmaceutical industry.

      Our division has established clinical and pharmacokinetic/ pharmacodynamic expertise in the area of tuberculosis, HIV, and malaria. The pharmacometrics group within the division is active internationally and supported by on-going collaborations with some of the most renowned modelling groups worldwide.

      What you need:
      A PhD in engineering, physics, mathematics or (bio-)statistics obtained within the past 5 years. OR a PhD in biological sciences AND evidence of keen interest and proficiency towards the quantitative side of the subject. Experience with computer programming (e.g. R, Matlab, C++) and data analysis. Previous experience in pharmacometrics (e.g. NONMEM, Monolix) would be advantageous, but not essential. A good command of English, passion about scientific research, and the ability to work within a team.

      What we offer:
      Mentorship and guidance to learn pharmacometrics (although the candidate is expected to be able to learn independently). A range of research projects, mainly in the area of PK/PD of TB/HIV, and malaria. A generous scholarship renewable for up to 3 years.

      For more details (please take notice of all the conditions of the award): http://www.clinpharm.uct.ac.za/wp-content/uploads/2015/06/Postdoc-Announcement-2015-UCT-pharmacometrics-website.pdf

      To apply, please email paolo.denti@uct.ac.za with your CV and a letter of motivation.

  • Post-doc: Mechanics of Plant Root Growth & Bending, Utrecht U
    • SMB Digest Vol 15, Issue 25 - June 24, 2015

      Postdoc: mechanics of plant root growth and bending (1,0 fte)

      Job description
      The root system of a plant is crucial for its survival and yield, as it ensures anchorage to the substrate as well as access to water and nutrients. Lateral root patterning, the positioning of lateral roots along the main root of a plant, is a major determinant of overall root system architecture. Due to the complexity of this developmental process, involving factors such as root growth mechanics, gene regulation and hormonal signalling that act at different spatial and temporal scales and interact in complex manners, lateral root patterning has thus far remained poorly understood.

      In the current project we aim to develop state-of-the art multi-scale models of plant root development to increase our understanding of lateral root patterning. For this we will intensively collaborate with experimental groups. The project is funded by a Vidi-grant awarded to Dr. K. ten Tusscher.

      The candidate will be developing a model for the mechanics of root growth, incorporating processes such as cell growth, division and expansion, asymmetric growth leading to root bending and root waving, as well as emergence of lateral roots from the main plant root. His/her challenge will be to develop a model that is biologically realistic, yet computationally efficient.

      Qualifications
      For the above described project we are looking for a postdoctoral researcher with a firm knowledge and established experience in the computational modelling of mechanical processes and a genuine interest in (plant) biology.

      Offer
      The candidate is offered a full-time position for two years.

      The salary is supplemented with a holiday bonus of 8% and an end-of-year bonus of 8,3% per year. In addition we offer: a pension scheme, a partially paid parental leave, flexible employment conditions. Conditions are based on the Collective Labour Agreement Dutch Universities. The research group will provide the candidate with necessary support on all aspects of the project.

      The gross salary is in the range between 2.977 euros,- and maximum 3.908 euros,- per month.

      About the organisation
      Utrecht University has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Dynamics of Youth, Institutions, Life Sciences and Sustainability. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues.

      The Faculty of Science consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Chemistry and Mathematics. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The Faculty's academic programmes reflect developments in today's society.

      The candidate will be working in the Theoretical Biology Group at the Biology Department of Utrecht University, The Netherlands. The work will take place in the Computational Developmental and Evolutionary Biology subgroup of Dr. Kirsten ten Tusscher.

      About the Group
      The researchers of the Theoretical Biology Group use mathematical modeling and computer simulations to perform fundamental biological research in a variety of biological disciplines ranging from developmental biology and immunology to evolution.

      The Theoretical Biology group is part of the Institute of Biodynamics and Biocomplexity (IBB), which focuses on the interaction between experiments, theory and modeling to obtain a systems level understanding of complex dynamic biological processes and their evolution. The IBB is embedded in one of the largest Biology departments in the Netherlands (>200 new students per year), and collaborates with other departments of the Faculty of Science, the Faculty of Medicine, and the Hubrecht Institute in Utrecht.

      The Theoretical Biology Group teaches Systemsbiology to biology students at the bachelor and master level. PhD students in the group have diverse backgrounds ranging from biology, mathematics, physics to computer science, and typically half of them are from abroad.

      Additional information
      Additional information about the vacancy can be obtained from: Dr. Kirsten ten Tusscher, email: k.h.w.j.tentusscher@uu.nl. As part of the selection procedure, candidates are expected to give an oral presentation of their prior research.

      Apply
      To apply please attach a letter of motivation, curriculum vitae and (email) addresses of two referees. The application deadline is 31/08/2015.

  • Post-doc: Math/Biostats/Epidemiology, Norwegian U Life Sciences
    • SMB Digest Vol 15, Issue 24 - June 17, 2015

      For information about the post-doctoral position, see http://www.jobbnorge.no/ledige-stillinger/stilling/114975/post-doctoral-research-fellow-in-mathematics-biostatistics-epidemiology-refnr-15-02198

  • Post-doc: Model Schistosomiasis..., Case Western Reserve U
    • SMB Digest Vol 15, Issue 23 - June 10, 2015

      Postdoctoral opportunity: Modeling ecology, transmission, control of schistosomiasis in complex environments.

      Applications are being accepted for a 2-4 year postdoctoral position to join a multi-institutional team (CWRU, Yale University, Erasmus MC, Netherlands).

      The overarching goal of this project is to model schistosomiasis transmission in complex environments and realistic host demographics, and apply such systems for prediction and control analysis. The models will range in scope from individual-based in-host biology, to population-based distributed human-snail systems. Different intervention strategies will be explored combining drug therapies with snail control.

      New methodologies and computers tools will be developed for such systems, and applied to multiple data sets collected in several countries. Sub-projects include: developing new epidemiological approaches to human infection, snail population biology, case studies, statistical methods and algorithms, and software codes and tools.

      Qualified applicants will have a PhD in applied mathematics, quantitative ecology, epidemiology, biostatistics, physical sciences, computational statistics or related quantitative discipline. Computer skills and experience with data analysis are important, in particular familiarity with Wolfram Mathematica.

      Successful applicants will be based at the Case Western Reserve University (Drs D. Gurarie, C. King), but they will collaborate with Yale group (Dr. A. Galvani), and Erasmus MC (Dr. S. DeVlas). To apply, send CV and covering letter to dxg5@case.edu. The letter should include a description of research interests, contact information for three references, and any preferences for location of employment. Also describe any relevant skills and prior research experience.

      Review of applications will begin on 1 June 2015 and continue until position is filled.

  • Post-doc: Data Analyst: Environment & Human Health, Harvard U
    • SMB Digest Vol 15, Issue 23 - June 10, 2015

      Job Advertisement: Data Analyst: Environment and Human Health

      Search: We are looking to hire a post-doctoral researcher with a strong quantitative, (bio)statistical, and/or epidemiological background to integrate several databases for complex systems analysis.

      Project Description: We have recently received a 2-3 year research grant to study the intersection of global fisheries declines and the destabilization of local to global food security, leading to drastic changes in human nutrition. Our research will answer the following four questions: 1) what is the current role of seafood in maintaining macro and micro-nutrient nutrition for populations around the world; 2) how will projected changes in global fish stocks affect human nutrition; 3) which populations have the greatest nutritional vulnerability to changes in the status of fisheries; and 4) which marine conservation and fisheries management strategies would pay the largest health dividends at a variety of scales from local to global? One of the centerpiece products of this effort will be an analytic framework and architecture that will allow decision-makers to calculate the health implications of different marine management strategies at a variety of scales from local to global. To perform this work, we have assembled a group of specialists whose expertise ranges across several disciplines from climate modeling and fisheries ecology to resource/development economics and nutritional epidemiology. By modeling shifts in diets based on changes in access to fisheries, we can estimate per capita changes in fish consumption and calculate changes in the prevalence of risk for a variety of micronutrient deficiencies (i.e. iron, zinc, vitamin B12, omega-3 fatty acids). Using this modeling approach, we can estimate shifts in burdens of disease for particular populations associated with either increased or decreased access to seafood in the diet. Such estimates will allow decision makers to calculate, for the first time, the public health implications of their management decisions, creating policy tools that have the potential to revolutionize how we think about fisheries management, how we internalize health costs into marine management, and how we improve food insecurity in the Global South.

      The post-doctoral researcher will be based at the Harvard School of Public Health and/or the Harvard University Center for the Environment and work closely with Dr. Chris Golden (PI) and Dr. Sam Myers (co-PI). The post-doc will lead the health modeling of this working group and will liaise with experts from UBC, UCSB, and UW (and their post-doc) who will do the environmental and economic modeling. This research fellowship will last for 1 year and be renewable for a second year. Salary will be $74K per year of which $18K is designated for benefits (take-home salary roughly $56K). At Harvard, we have a rich community of researchers investigating the interrelationship of ecosystem transformation and human health and we believe the post-doc will find the community of scholars an inspiring one.

      Skills/Background Experience:
      -Strong statistical and quantitative analysis background required. Preference for working in Stata or R
      -Preference for training in epidemiology, biostatistics, complex systems analysis, quantitative methods, or related fields
      -Preference for experience working with large datasets and integrating multiple kinds of data in an analytic framework.

      To apply: Please submit a CV and brief cover letter detailing relevant experience and reason for interest in the project to Dr. Chris Golden (golden@hsph.harvard.edu). Please also send the names of three references. Interviewing and hiring will take place prior to July 30th. Position will start around September 1, 2015.

  • Post-doc: Yeast Systems Biology, U North Carolina
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      Postdoctoral position in yeast systems biology - University of North Carolina

      We are seeking one or more postdoctoral fellows to develop computational models and/or conduct live cell imaging analysis. The goal of the project is to study the role of noise in cellular signal transduction pathways (via G protein coupled receptors and MAPKs) and cell fate transitions. This NIH-funded project is a collaborative effort between the labs of Drs. Timothy Elston, Henrik Dohlman and Beverly Errede. The successful candidate will have a PhD in computational biology, biophysics, physics, applied mathematics, biochemistry, cell biology, or a related field, a proven track record of research productivity, and enjoy participating in interdisciplinary team science.

      Project details: All intracellular processes are subject to large amounts of molecular-level fluctuations. In certain contexts, this "noise" may serve as a bet-hedging mechanism to diversify the response of a population of otherwise identical cells, whereas in other contexts noise suppression may be required to properly coordinate response pathways when cells are faced with multiple competing stimuli. The yeast Saccharomyces cerevisiae is the premier model system for studying mechanisms of noise regulation. Planned investigations will combine microfluidic devices and fluorescent imaging to follow single cells in well controlled environments, quantitative image analysis to characterize fluctuations in signaling and gene expression, and stochastic modeling to suggest and test noise regulation mechanisms.

      Lab websites:
      http://www.med.unc.edu/~hdohlman/research.html
      http://www.med.unc.edu/pharm/elstonlab/index.html
      http://www.med.unc.edu/biochem/errede

      Please email letter of interest, CV, and the names of three references to Prof. Tim Elston at telston@med.unc.edu.

  • Post-doc: Cell Metabolism of Cancer Cells, U Southern Cal.
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      The Computational Systems Biology Laboratory (CSBL) is seeking a Postdoctoral Research Fellow interested in understanding the cellular metabolism of cancer cells. The fellow will work to develop an experiment-based, validated computational model of metabolism in pancreatic cancer and apply the model to identify therapies that inhibit tumor metabolism. Ultimately, the goal of this work is to impact the development of therapeutics for treating pancreatic cancer by providing a more in-depth understanding of the dynamics of altered metabolism and how the metabolic pathways can be exploited to impede cancer progression. The fellow will interact with experimental collaborators and clinical consultants.

      Required Knowledge, Skills, and Abilities: Research experience in computational modeling of biochemical or metabolic reactions as evidenced by publication record; Proficient knowledge of MATLAB; Desire to identify and tackle new problems in cancer metabolism; Desire to work in a multi-disciplinary research environment; Interpersonal skills to communicate effectively with faculty, students, and staff; Experience with any of the following techniques is particularly desirable: kinetic modeling of metabolic pathways, parameter fitting, and stochastic simulations.

      Minimum Education: Doctorate degree in Biomedical Engineering, Bioengineering, Chemical Engineering, or related field, from an accredited institution.

      Work Environment: The CSBL is located on the University Park campus of the University of Southern California (USC). The position will involve interactions with faculty, postdocs, and students both within and outside of USC.

      Salary: Commensurate with experience

      Interested individuals should contact Professor Stacey Finley via email (sfinley@usc.edu) and provide a cover letter, CV, and contact information for three references that can affirm the applicant's qualifications for this position.

  • Post-doc: Computational Neuroscience, Louisiana State U
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      Postdoctoral Researcher
      Louisiana State University Health Sciences Center

      A two (2) year Postdoctoral Researcher position is available in the lab of Carmen Canavier in the School of Medicine, Department of Cell Biology and Anatomy at LSU Health Sciences Center in New Orleans. The focus of the lab is computational neuroscience. The main project is to model bursting and tonic firing in midbrain dopamine neurons, in close collaboration with experimentalists. Additional projects focus on oscillations and synchrony in cortical and basal ganglia networks. The primary duties will involve linear and non-linear analyses, writing code, calibrating single neuron models, and generating predictions that lead to additional experiments.

      Candidates must have a Ph.D. in Engineering, Mathematics, Neuroscience, Physics, Computer Science or a related field of study. Familiarity with nonlinear dynamics, writing code, running the simulation package NEURON, and modeling single neurons is preferred.

      Qualified candidates may submit resume along with cover letter and contact information for three references electronically to: SOM-recruits@lsuhsc.edu; reference 00049561. This appointment is a two (2) year assigned only. Applications should be received before July 1 to ensure consideration for the position. LSUHSC is an Equal Opportunity Employer for females, minorities, individuals with disabilities and protected veterans.

  • Post-doc: Modelling in Synthetic Biology, U Nottingham
    • SMB Digest Vol 15, Issue 21 - May 27, 2015

      Vacancy Mathematical/Computational Modelling in Synthetic Biology at the University of Nottingham.

      See:
      Research Associate/Fellow - Mathematical/Computational Modelling in Synthetic Biology
      http://www.nottingham.ac.uk/jobs/currentvacancies/ref/MED284314X2

      Closing date 18 June 2015. Informal enquiries to john.king@nottingham.ac.uk

  • Post-doc: Infectious Disease Modeling, St. Jude Children's...
    • SMB Digest Vol 15, Issue 21 - May 27, 2015

      Postdoctoral Research Associate in Infectious Disease Modeling

      Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN

      Job Description:
      The Department of Infectious Diseases is recruiting a postdoctoral fellow interested in mathematical/computational modeling of viral infections, bacterial infections, and host immune responses in the laboratory of Amber Smith. The candidate will develop and analyze dynamical models and use parameter estimation to investigate experimental kinetic data, help develop new experiments, and generate new hypotheses about the biology of influenza infections and coinfections. The individual will pursue interdisciplinary research at the boundary of mathematics and biology, with activities that include directly working with experimentalists within the laboratory and the department, publishing results in peer-reviewed journals, and presenting results at conferences.

      Job Qualifications:
      Candidates should have a PhD in applied mathematics, mathematical biology, computer or computational science, physics (or other related field) with some knowledge of biology and experience in modeling and analyzing biological data. Candidates should have strong mathematical and statistical skills, and an interest in viral dynamics, bacterial dynamics, and/or immunology. Preference will be given to candidates with previous research experience in these areas, good programming skills (e.g. MatLab, R, Python) and excellent written and oral English.

      Salary & Benefits:
      Salary and benefits will be commensurate with experience and offered according to St. Jude and NIH guidelines. St. Jude offers an above-average benefits package to postdoctoral fellows including health and dental insurance; group life insurance; liability insurance; workers compensation; accidental death and dismemberment eligibility; short term/long term disability eligibility; a professional development account; paid holidays; paid vacation plus two personal days per year; and paid sick leave.

      Applications:
      The position is available immediately (start date negotiable) and applications will be accepted until the position is filled. Applications should be submitted directly to Amber Smith at amber.smith@stjude.org

      For more information, contact Amber Smith (email: amber.smith@stjude.org) or visit www.stjude.org/academic-programs

  • Post-docs: Mathematical Biology, NIMBioS, U Tennessee
    • SMB Digest Vol 15, Issue 21 - May 27, 2015

      Call for Postdoctoral Fellowship Applications at NIMBioS
      Next Deadline: September 1, 2015

      The National Institute for Mathematical and Biological Synthesis (NIMBioS), located at the Univ. of Tennessee, Knoxville, is currently accepting applications for postdoctoral scholarship at the interface between mathematics and biology. Highest priority will be given to those with explicit plans to develop their ability to effectively carry on research across these fields. We are particularly interested in requests to support research that integrates diverse fields, requires synthesis at multiple scales, and/or makes use of or requires development of new mathematical/computational approaches. NIMBioS Postdoctoral Fellows are chosen based upon indications that the applicant's research plans are consistent with the mission of NIMBioS, the applicant has the demonstrated ability to carry out the proposed research, and the opportunities provided through NIMBioS will enhance the capacity for the research to be completed in an efficient and timely manner. Support: annual stipend of $51,000, full University of Tennessee employee fringe benefits, and an annual travel allowance of $3,000.

      How to apply: Complete the online application and submit a brief project description, references, and CV following the guidelines available at http://www.nimbios.org/postdocs/

      Deadline: NIMBioS postdoctoral requests for support are reviewed two times per year, and the selected researchers are offered positions at NIMBioS where they conduct research that is mostly self-directed. The deadline for activities beginning in summer/fall 2016 is September 1, 2015 but applications for positions starting later in 2016 are also accepted at this time. All letters of recommendation must be submitted before the request deadline.

      The National Institute for Mathematical and Biological Synthesis (NIMBioS) (http://www.nimbios.org) brings together researchers from around the world to collaborate across disciplinary boundaries to investigate solutions to basic and applied problems in the life sciences. NIMBioS is sponsored by the National Science Foundation, with additional support from The University of Tennessee, Knoxville.

  • PhD/Post-doc Positions: Genomic-Metabolic..., Imperial College
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Postdoctoral and PhD positions in Systems & Synthetic Biology of genetic-metabolic networks, Department of Mathematics, Imperial College London

      We have two openings as part of a new project funded by the Human Frontier Science Program:

      1) Postdoctoral position in Systems and Synthetic Biology of metabolic adaptations

      2) PhD position in stochastic fluctuations of enzymatic reactions

      The successful candidate will join Dr Diego Oyarzun, (Biomathematical Sciences, Imperial College London) in exciting projects at the interface between Mathematics, Control Theory, and Systems/Synthetic Biology. Their general aims are to develop mathematical methods to analyze and predict metabolic responses from complex gene regulatory networks, and to showcase how new metabolic responses can be engineered in living cells.

      For additional information please contact Dr Diego Oyarzun (d.oyarzun@imperial.ac.uk). Details about both posts can be found in http://www.imperial.ac.uk/people/d.oyarzun. To apply for the postdoctoral position, please follow this link, application deadline: 05 June 2015. The start date for both posts is 01 September 2015.

  • PhD/Post-doc Positions: Math & Population Genetics, McGill U
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Graduate and postgraduate positions in mathematical and population genetics

      Graduate student and postdoc positions in mathematical and population genetics are available in Simon Gravel's group at McGill University in Montreal, Canada. The project aims at creating mathematical models of historical human migrations, family histories, and high-throughput genomic data. Students will be involved in conceptual methods development, implementation, and applications to exciting datasets. This is a unique opportunity to be involved in work that is relevant and interesting from a mathematical, medical, and historical perspectives.

      We welcome applications from qualified candidates from diverse backgrounds, including biology, anthropology, mathematics, physics, and computer science. Programming experience and a demonstrated interest in mathematics, statistics, or related fields is required.

      The position offers an exceptional opportunity to develop theoretical and computational ideas and apply them to cutting-edge data in a supportive and thriving research environment.

      Applications and queries should be sent to gravellab@gmail.com. Please include a statement of interest (1 page) and a CV with a list of publications, contact information for three references, and a low-resolution scan of official transcripts.

  • Post-doc: Infectious Disease/Epidemiol. Modeling, Case Western
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      POSTDOCTORAL RESEARCH POSITION IN INFECTIOUS DISEASE EPIDEMIOLOGY AND MODELING

      We are seeking applications for an exciting position beginning in the summer of 2015, involving infectious disease modeling for the study of HIV prevention, antiretroviral drug resistance and public health policy. This is a full-time position that may be renewed annually subject to satisfactory performance and the availability of funds.
      Qualifications:
      -A Ph.D. degree in mathematical epidemiology, applied mathematics, theoretical physics, engineering, computer science, or related field.
      -Strong research experience in mathematical and computational modeling including formulation and analysis of deterministic and individual-based models.
      -Experience in analytical and quantitative methods, including deterministic and stochastic differential equations, integral equations, nonlinear dynamics, probability theory, and stochastic processes.
      -Proficiency in scientific computing involving programming, numerical analysis, symbolic and logical analysis, Monte Carlo simulations, and computer graphics.
      -Outstanding skills in programming (C++) and experience in using software packages such as Matlab, Mathematica and Microsoft Office.
      -Experience with statistical data analysis and related packages, such as Stata and R.
      -Excellent skills in communication, review of scientific literature and scientific writing.
      -Working knowledge of the biology and epidemiology of infectious diseases, especially HIV, though preferred, is not necessary.

      Please submit your curriculum vitae, a statement of research interests and goals and contact information for three references via email to:
      Ume L. Abbas, MD.
      Email: abbasu@ccf.org
      Cleveland Clinic / Case Western Reserve University
      Cleveland, OH United States

  • Post-doc: Infectious Disease Modeling, North Carolina State U
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      One postdoctoral associate position on infectious disease modeling is available in Cristina Lanzas' group (Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University). Applicants with a background in mathematical modeling of infectious diseases and/or network and agent-based modeling are highly encouraged to apply.

      Our group focus is the epidemiology and ecology of enteric and antimicrobial resistant pathogens in animal and human populations. We combine data, epidemiological analysis and mathematical models to study transmission mechanisms, sources of transmission heterogeneity, and to identify and design control measures to reduce the public health burden associated with infectious diseases. Our research is currently supported by NIH and USDA.

      The post-doc will work will use animal movement data collected through real time location systems to develop contact networks and will integrate the networks on agent-based models for the transmission of pathogens in cattle populations. Mean-field/compartmental models will be also developed. The models will be used to assess transmission of directly and indirectly transmitted pathogens, and evaluate sources of transmission heterogeneity.

      Necessary Education, Experience Skills, Training and Education: The postdoctoral associates shall have a Ph.D. degree in a relevant quantitative discipline (ecology, epidemiology, engineering, applied mathematics, physics, statistics and related fields) and have a deep interest in interdisciplinary collaboration, strong quantitative and programming skills and good oral and writing skills are expected. Experience developing and implementing agent-based models and/or network models is desirable.

      The initial appointment will be for one year, with renewal for two or more years subject to satisfactory progress and mutual agreement. The salary will be commensurate with the qualifications and experience of the individuals. Review of applications will begin May 15th 2015 and will continue until suitable candidates are identified.

      To apply for the position please follow the link: https://jobs.ncsu.edu/postings/52006

      Applicant material includes a cover letter, CV and contact information for three references.

      If you have questions specific to the positions please contact me at clanzas@ncsu.edu

  • Postdoc Position: Ecological/Environmental Modeling, Germany
    • SMB Digest Vol 15, Issue 18 - May 6, 2015

      The Institute of Environmental Systems Research at the School of Mathematics/Computer Science of Osnabruck University (Germany) has an opening for a Scientific Research Associate in environmental/ecological modeling (salary scale E 13, 100%) for the duration of three years, starting on 1 October 2015.

      The successful candidate will perform research in mathematical or computer-based modeling of ecological and environmental systems. In addition, the position comes with a teaching duty amounting to 4 contact hours(180 minutes) per week during the teaching period (29 weeks per year).

      Required Qualifications:
      Qualifications required are a doctoral degree in (Applied or Bio-) Mathematics, Physics, Theoretical or Quantitative Biology, Geoecology, Computer Science, or an interdisciplinary program such as Applied Systems Science or Environmental Modeling.

      Ideally, the successful candidate has research experience in one of the following fields:
      - Riverine modeling
      - Modeling integrated pest management
      - Spatio-temporal population dynamics
      - Modeling of wildlife diseases

      Salary and conditions:
      Salary is according to German salary scale TV-L E 13, 100% (gross salary of approx. EUR 42,000-49,000 depending on experience).

      Applications:
      To apply, please email Prof. Frank M. Hilker(frank.hilker@uni-osnabrueck.de) with a statement of interest, CV, transcripts, and the names and contact addresses of at least two academic references (in one pdf file) by May 29, 2015. For further information and inquiries, please contact Frank M. Hilker (frank.hilker@uni-osnabrueck.de, phone +49 541 969 3441).

  • Postdoc Position: Mathematical Models of Kidney Physiology, Duke U
    • SMB Digest Vol 15, Issue 18 - May 6, 2015

      Applications are sought for a two-year postdoctoral position for the Layton Lab in the Department of Mathematics at Duke University. Research will focus on the development and analysis of mathematical models of kidney physiology. The position also involves teaching up to 2 classes a year.

      Desirable qualities of candidates include (1) a PhD in mathematics or applied mathematics, engineering, computer science, or another relevant field, (2) strong programming and numerical skills, and (3) background and/or interest in physiology.

      Salary will be competitive and commensurate with skills and experience. Benefits will be provided. Support is available for travel to conferences as appropriate.

      For further information, please email Prof. Anita Layton (alayton@math.duke.edu) with a statement of interest, a CV, and the names and contract information for three references. The position is open immediatley and applications will be considered until the position is filled.

      Lab website: http://www.math.duke.edu/~alayton/

  • Postdoc Position: Pharmacometrics and Systems ..., U of Florida
    • SMB Digest Vol 15, Issue 18 - May 6, 2015

      Postdoctoral Research Associate in Pharmacometrics and Systems Pharmacology Center for Pharmacometrics and System Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando (Lake Nona), Florida.

      Job Function: Postdoctoral Research Associate Positions in Pharmacometrics, PBPK modeling, Systems Biology/Pharmacology
      Entry Level: N/A
      Setting: College/University/Medical City Campus
      Location: Orlando (Lake Nona), Florida, United States
      Job Type: Full-Time
      Minimum Education: Ph.D. or equivalent degree in quantitative sciences including Engineering, Statistics, Mathematics and Systems Biology/ Pharmacology

      Fellowship Description
      The mission of the Center for Pharmacometrics and System Pharmacology (CPSP) at the University of Florida (UF) is to develop new quantitative tools and mechanistic approaches to evaluate and predict the efficacy and safety of medicines. The CPSP has several two year fellowships available for scientists who intend to further their training for a career in drug development, academia or regulatory science.

      The successful applicants will have access to clinical trial data in order to learn how to apply and become proficient in using population-based PK/PD modeling, Systems Biology/Pharmacology and computer simulation approaches to solve drug development and regulatory problems such as optimal dosing and biomarker qualification. Depending on the availability of projects and interests of the applicant, he or she will also learn how to effectively use disease progression models and physiologically based PK/PD models to design clinical trials, understand the pharmacological mechanisms of drug action, explore covariate effects on PK and PD and determine the influence of genetic factors on drug dosing. The fellow will have the opportunity to participate in systems pharmacology research under the direction of a CPSP faculty to identify the mechanistic basis of drug adverse drug events arising out of drug development programs, FDA safety alerts or clinical practice.

      Postdoctoral research associates will engage in a combination of duties that will include research projects, graduate student mentoring, grant writing and classroom teaching experiences. Fellows will also gain experience outside the University of Florida through industry or FDA internships or off-site participation in research with our Orlando partners including the Sanford Burnham Medical Research Institute (SBMRI), Nemours Children Hospital, and SBMRI-Florida Hospital Translational Research Institute. It is expected that fellows attend and present at professional meetings, participate in workshops and seminars and prepare at least 3-4 peer- reviewed publications to build a foundation for personal career achievements. In addition to the scientific and clinical duties, fellows are given the opportunity to grow their "soft skills", such as oral communication, presentation skills and working on multi-disciplinary teams.

      Job Qualifications

      Preferred qualifications for the position are a doctoral (Ph.D. or equivalent) degree in quantitative sciences including Engineering, Statistics, Mathematics and Systems Biology as well as knowledge of, or experience in, therapeutics in one or more disease areas with an interest in pursuing a career in Pharmacometrics and/or Systems Pharmacology. The ideal candidate should possess strong programming skills, excellent written and verbal communication, good organizational abilities, and team work. A background and understanding of basic pharmacology, pharmacometrics and/or systems biology/pharmacology is preferred as is hands-on knowledge in using software platforms such as NONMEM, MATLAB, R, SAS, PK-Sim, GastroPlus, SimCYP or other software/scripting languages is required. The candidate must be self-directed and self-motivated.

      To Apply
      Please send curriculum vitae and contact information for three references to Dr. Lawrence J. Lesko, llesko@cop.ufl.edu, 6550 Sanger Road Orlando, FL 32827.

  • 3 Postdoc Positions: Biomedical Informatics, Harvard Medical School
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      Position 1: Areas of Interest: Epigenetic Regulation, Cancer, Genomic Analysis, Computational Biology.

      Job Description: A laboratory at the Center for Biomedical Informatics at the Harvard Medical School (HMS) is looking for a postdoctoral Research Associate interested in computational analysis of epigenetic mechanisms disrupted in cancer and other disease tissues. The Research Associate will be responsible for developing and applying statistical and computational methods for integrative analysis of genome-wide epigenetic, transcriptional and proteomic data, aiming to identify specific factors and molecular mechanisms underlying misregulation of the epigenetic states. The projects are being conducted in close cooperation with several experimental laboratories, providing an excellent opportunity for collaborative research.

      Requirements:
      - Hands-on experience with DNA or RNA sequencing assays
      - Good understanding of the basic statistical techniques
      - A strong interest in conducting collaborative research on the topics outlined above
      - Track record of publications in peer-reviewed journals
      - PhD degree in Molecular Biology, Computational Biology, or a related discipline.

      How to apply: Please send cover letter, curriculum vitae and contact information for at least two references to Dr. Peter Kharchenko at peter_kharchenko@hms.harvard.edu. Applications will be considered until the position is filled.

      Position 2: Postdoctoral Research Associate Position (Statistical Modeling of the Scientific Workforce)

      Summary:
      The Weber Lab in the Center for Biomedical Informatics (CBMI) at Harvard Medical School is seeking a Postdoctoral Research Associate to help model the scientific workforce. The scientific workforce is increasingly relying on teams to solve the most critical intellectual and social problems that confront us today. Team collaborations, a growing trend across all disciplines, yield publications with higher intellectual impact than single researchers; and, the careers of young scientists are influenced by relationships with others in the community. We are developing a systems- based approach to studying scientific workforce dynamics that models the mechanisms of how new collaborations form and how these influence both the effectiveness of teams and the career trajectories of individual scientists.

      Requirements:
      Candidates must have a PhD or other advance degree in statistics, computer science, biomedical informatics, or a related field. A strong background in statistical modeling is required. Some experience programming or working with databases is needed due to the size of the data, though database programmers within the Weber Lab will be available for help and training. Candidates should be highly motivated, creative, and interested in learning new skills. They must enjoy solving complex and challenging problems and being part of a multidisciplinary research team. Excellent written and verbal communication skills are essential.

      Preferences:
      Experience with R statistical software and/or Microsoft SQL Server is desirable. Experience with social network analysis, natural language processing, or data visualization would also be helpful for the project.

      Terms:
      The position is available immediately and can be renewed annually.

      How to apply:
      Email applications including curriculum vitae, summary statement of personal objective and research interests, PDFs of the best two papers, and the names and email addresses of three references to: Griffin M Weber, MD, PhD, weber@hms.harvard.edu

      Position 3: Postdoctoral Research Associate Position (Probabilistic Algorithms and Software for Biomedical Big Data)

      Summary:
      The Weber Lab in the Center for Biomedical Informatics (CBMI) at Harvard Medical School is seeking a Postdoctoral Research Associate to help develop probabilistic algorithms and software for biomedical "Big Data". Despite all the recent attention to Big Data in both the scientific literature and popular press, it has yet to have the same impact on medicine as it has in other areas, such as finance, retail business, political campaigns, and national security. We believe the key for clinical applications of Big Data is the ability to create a holistic view of a patient's health history by linking disparate data sources, such as electronic health records, administrative claims, genomic data, and data outside the healthcare system, including social media and information about the environment. Because there are legal and ethical concerns about sharing health data, coupled with the fact that there is no universal patient identifier, our approach is to use probabilistic algorithms that can protect patient privacy and scale efficiently while searching for information about patients across datasets with billions of records.

      Requirements:
      Candidates must have a PhD or other advanced degree in computer science, biomedical informatics, computational biology, artificial intelligence, biostatics, or a related field. A strong background in collaborative software development, and in particular probabilistic algorithms and/or statistical modeling is required. Experience with large relational databases and/or other Big Data tools such as Hadoop is also important. Software components in the distributed query tool, including the patient linkage module, will be hosted in AWS and communicate using RESTful APIs. Candidates should be highly motivated, creative, and interested in learning new skills. They must enjoy solving complex and challenging problems and being part of a multidisciplinary research team. Excellent written and verbal communication skills are essential.

      Preferences:
      Experience with version control software and project management tools like JIRA are desirable. We primarily use Microsoft SQL Server and write software in C# for .NET; though, this is not a requirement, and other development groups that are part of this project use different programming languages including Java, Python, Perl, and R.

      Terms:
      The position is available immediately and can be renewed annually.

      How to apply:
      Email applications including curriculum vitae, summary statement of personal objective and research interests, PDFs of the best two papers, and the names and email addresses of three references to: Griffin M Weber, MD, PhD, weber@hms.harvard.edu

  • Postdoc Position: Health Policy Simulation Modeling, Stanford U
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      Postdoctoral Fellowship in Health Policy Simulation Modeling, Stanford University, Stanford, CA

      Postdoctoral Fellowship in Health Policy Simulation Modeling is available in Dr. Sylvia Plevritis' Lab located in the James H. Clark Center at Stanford University. The fellowship will involve the development and application of computer simulation modeling to study the impact of alternative cancer screening and treatment strategies on cancer incidence and mortality rates in the US population and inform health policy. The ideal candidate should have a Ph.D. in a field related to simulation modeling (i.e. operations research, applied mathematics) or a field that involves training in statistical analysis of clinical data (i.e. biostatistics, health-outcomes research, epidemiology). Experience in stochastic simulation modeling, Monte Carlo methods, parameter estimation, survival analysis and computer programming (C/C++, R) is critical. Knowledge of cancer epidemiology, cancer screening and treatment trials and analysis of cancer registry data is needed. Excellent verbal and written communication skills are necessary. Applicants should submit a cover letter, CV and 3 references to Ramzi Totah via email: rtotah@stanford.edu, with subject line "Postdoctoral Fellow in Health Policy Simulation Modeling."

  • Postdoc Position: Bioinformatics and computational modeling, NIH
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      Postdoctoral Position at the NIH
      Position Title: Bioinformatics and computational modeling
      Position Description:
      * Theoretical systems biology with a particular emphasis on elucidating mechanisms in disease processes, integrating physiological and genome-scale datasets
      * The Computational Medicine Section is part of the Laboratory of Biological Modeling, a laboratory with a broad range of projects in applying quantitative analysis to biomedical problems, ranging from genome scale inference to diabetes and obesity.
      * Strong mathematical and computational skills, some knowledge of machine learning, and a broad knowledge of biology
      * Please email a curriculum vitae, names and contact information of at least three individuals familiar with your academic work, and a statement of research interests and future goals to Vipul Periwal, vipulp@niddk.nih.gov, with subject heading: Computational Medicine Search.

      Employer Name: National Institute of Diabetes and Digestive and Kidney Diseases
      Position Location: Bethesda, MD
      Application Deadline Date: 5/30/2015

  • 6 Postdoc Positions: Modeling Complex Interactions, U of Idaho
    • SMB Digest Vol 15, Issue 17 - April 29, 2015

      The NIH-funded Center for Modeling Complex Interactions (CMCI) at the University of Idaho will create the intellectual, cultural, and physical environment to foster convergence in interdisciplinary biomedical research. The Center will address complex biomedical problems across all levels of biological organization, from biophysical to ecological, beginning with the study of viral co-infection. Co-infection is a common but understudied area of infectious disease. The focal point of CMCI is the Collaboratorium, a space and a culture for collaborative modeling. It will bring together faculty from both the empirical and modeling realms with postdoctoral scientists who reside in the Collaboratorium and devote full-time effort to collaborative modeling.

      We currently have openings for four postdocs in the Collaboratorium and two in experimental laboratories:

      1) epidemiological and biostatistical modeling (SP000473P)
      2) transcriptomic and proteomic analysis and modeling (SP000470P)
      3) deterministic and agent-based modeling (SP000472P)
      4) molecular modeling of proteins (SP000471P)
      5) pathogenesis of viral coinfection in mice(SP000474P)
      6) molecular biology of viral coinfection in flies (SP000475P)

      To apply, go to http://apptrkr.com/608858 and search by the posting number following each positon. Review of applications will begin May 18, 2015. Applications will be accepted until all positions are filled.

      Contact Center for Modeling Complex Interactions: cmci@uidaho.edu or http://www.cmciuidaho.org/

Faculty and other positions

(Click on job title for additional information.)
  • Faculty Position in Systems Genomics, University of Melbourne
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      Lecturer in Systems Genomics (tenure-track) faculty position available at the University of Melbourne, Australia

      The School of BioSciences at the University of Melbourne is seeking to recruit an excellent researcher with a commitment to research and teaching in the area of systems genomics. Systems genomics is defined broadly to include any area of computational, mathematical or statistics-based research on aspects of the processes which lead from genotype to phenotype.

      The successful applicant will have the opportunity to be a member of the University's new Centre for Systems Genomics http://sysgenmelb.org/

      Closing date Aug 12, 2015

      Further details are available from http://jobs.unimelb.edu.au/caw/en/job/886164/lecturer-in-systems-genomics

      For more information contact Professor David Balding (School of BioSciences, University of Melbourne) dbalding@unimelb.edu.au

  • Positions in Applied Mathematics, Northwestern University
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      The Department of Engineering Sciences and Applied Mathematics is recruiting for two positions for the upcoming year. For further information please see

      http://www.mccormick.northwestern.edu/applied-math/job-opportunities.html

  • Research Scientist: Metabolic Network Modeling (209456)
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      The Henry M. Jackson Foundation (HJF) is looking for junior and senior scientists to join the U.S. Army Medical Research and Materiel Command's Biotechnology High Performance Computing Software Applications Institute (BHSAI) [www.BHSAI.org]. HJF provides scientific, technical, and programmatic support services to the BHSAI.

      This opening is for a dynamic scientist with interest in working in an interdisciplinary environment with a focus on the development and application of computational solutions to biomedical problems, including toxicology, drug resistance, and infectious disease.

      Responsibilities:

      1. Use computational modeling to integrate transcriptomic and metabolomic data with metabolic networks to understand malaria host/pathogen responses to different physiological stressors, including drug treatment.
      2. Perform both basic and applied research in close collaboration with experimental laboratories.
      3. Simultaneously work on multiple projects, involving a diverse and interdisciplinary team of scientists across multiple laboratories.

      The candidate should have a Ph.D. in a related discipline and a strong publication record. Experience in high-performance computing, biostatistics or population genomics, mathematical modeling, and biological network analysis is a plus. Expertise in at least one of C, C++, Java, Python or Perl is a must. PLEASE ONLY APPLY IF YOU HAVE PROVEN COMPUTATIONAL BIOLOGY EXPERIENCE.

      Foreign nationals are welcome to apply. U.S. citizenship or permanent resident status is not required. This position is located in Frederick, Maryland.

      Please apply on-line at careers.hjf.org click "Advanced Search" and enter job number 209456 in the Job Opening ID box.

      The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status or other status protected by law.

  • Research Scientist: Computational Bioinformatics/Systems Biology (209457)
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      The Henry M. Jackson Foundation (HJF) is looking for junior and senior scientists to join the U.S. Army Medical Research and Materiel Command's Biotechnology High Performance Computing Software Applications Institute (BHSAI) [www.BHSAI.org]. HJF provides scientific, technical, and programmatic support services to the BHSAI.

      This opening is for dynamic scientists interested in working in an interdisciplinary environment.

      Responsibilities:

      1. Develop and apply computational solutions to biomedical problems involving computational bioinformatics and systems biology approaches.
      2. Analyze and model protein networks relevant to infectious diseases and human disorders, cell signaling, and gene regulatory networks using, among others, ordinary/partial differential equations and stochastic simulation algorithms.
      3. Work simultaneously on multiple projects, involving a diverse and interdisciplinary team of scientists across multiple laboratories.

      The candidate should have a Ph.D. in a related discipline, extensive computational experience, and a strong publication record. PLEASE ONLY APPLY IF YOU HAVE PROVEN COMPUTATIONAL BIOLOGY EXPERIENCE.

      Foreign nationals are welcome to apply. U.S. citizenship or permanent resident status is not required. This position is located in Frederick, Maryland.

      Please apply on-line at careers.hjf.org click "Advanced Search" and enter job number 209457 in the Job Opening ID box.

      The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status or other status protected by law.

  • Chair and Professor: Department of Mathematics and Statistics, TTU
    • SMB Digest Vol 15, Issue 30 - July 29, 2015

      Texas Tech University
      Department of Mathematics and Statistics
      Chair and Professor


      The Department of Mathematics and Statistics at Texas Tech University invites applications for the position of Department Chair and Professor beginning fall 2016. The salary will be competitive and commensurate with qualifications and experience.

      Candidates must have demonstrated outstanding vision, leadership, and scholarship, possess strong commitments to interdisciplinary research and educational activities, and be a collegial motivator and advocate for faculty. A Ph.D. in mathematics or statistics is required. The successful candidate is expected to work with the faculty to develop the department under a strategic vision, foster excellence in research and teaching, and provide appropriate service to the college, university, and profession.

      The department currently has 45 full-time faculty members with active research groups in pure and applied mathematics and statistics. Six degrees are offered: B.A., B.S., M.A., M.S., and Ph.D. in Mathematics and M.S. in Statistics, as well as several interdisciplinary and combined undergraduate and graduate degrees. For further information regarding the Department of Mathematics and Statistics, please refer to the department.s website: http://www.math.ttu.edu. Texas Tech University, located in west Texas in the city of Lubbock, was founded in 1923. The student population is 35,000 and is anticipated to grow to 40,000. Texas Tech is a state- designated national research university. Its strategic plan charts a course for becoming a great public research university by 2020. The university has the characteristics of a Carnegie-classified doctoral granting university with very high research productivity.

      Applicants should apply at http://www.texastech.edu/careers/ using Requisition 4369BR. Applicants should submit a detailed letter of application along with a current resumé including externally-funded research, teaching, administrative experience, publications. and four letters of professional reference. Questions about the position and/or the application process can be directed to mathchairsearch@ttu.edu

      Review of applications will begin immediately. Applications will be accepted until the position is filled, with those received prior to October 1, 2015, assured full consideration.

      As an Equal Employment Opportunity/Affirmative Action employer, Texas Tech University is dedicated to the goal of building a culturally diverse faculty committed to teaching and working in a multicultural environment. We actively encourage applications from all those who can contribute, through their research, teaching, and/or service, to the diversity and excellence of the academic community at Texas Tech University. The university welcomes applications from minorities, women, veterans, persons with disabilities, and dual-career couples.

  • Tenure-Tracks: ...Lab. of Experimental Mathematics, Hokkaido U
    • SMB Digest Vol 15, Issue 29 - July 22, 2015

      Hokkaido University invites applications for Six Tenure-Track positions at the Assistant Professor level, beginning in January, 2016. We seek accomplished young individuals who can enhance the research capabilities of the university and display extraordinary leadership as new generation of leaders.The tenure-track selection process evaluates not only research skills, but also comprehensive abilities as leaders (administration, motivation, planning skills, analytical skills and internationality).

      One of six positions is in Research Center of Mathematics for Social Creativity/Laboratory of Experimental Mathematics. Please see the details NO. 27-1 in the following web site: http://tenure-track.cris.hokudai.ac.jp/en/opencall/fy2015-international-open-call-for-tenure-track-positions/

  • Faculty Positions: Applied Mathematics, U Bath
    • SMB Digest Vol 15, Issue 29 - July 22, 2015

      Department of Mathematical Sciences, University of Bath, UK

      Faculty Positions in Applied Mathematics

      The Department wishes to make two appointments in Applied Mathematics. Applications are welcome in any area of Applied Mathematics which complements and enhances existing activity at Bath, which includes Mathematical Biology.

      Appointments may be made at Lecturer, Senior Lecturer or Reader level, equivalent to Assistant or Associate Professor.

      Further information is available from https://www.bath.ac.uk/jobs/Vacancy.aspx?ref=FY3282

  • NIH: Selected Intramural Research & Other Openings, July 2015
    • SMB Digest Vol 15, Issue 27 - July 8, 2015

      Tenure-Track/Tenure-Eligible Investigator
      Epidemiology and Biostatistics Program, NCI-DCEG
      (Review of Applications Begins: July 1)

      The National Cancer Institute (NCI), a major component of the NIH and the Department of Health and Human Services, is recruiting a descriptive epidemiologist for a tenure-track or tenure-eligible position available in the Epidemiology and Biostatistics Program of the Division of Cancer Epidemiology and Genetics (DCEG). Descriptive epidemiology is used in its broad definition, including but not restricted to cancer surveillance research, population-based cancer incidence and mortality registry studies to test existing or generate new etiologic and survival hypotheses, and leveraging data on molecular heterogeneity, gender, ethnicity, age, secular trends and geography (including cancer mapping and other geospatial studies). These would include studies within relatively small geographic areas, countries, and internationally, and would utilize the opportunities afforded by new technologies including record-linkage studies that supplement aggregate-level data with individual-level information. The scope could also encompass development of novel biostatistical methods to supplement standard descriptive techniques, particularly in the emerging opportunities in tumor heterogeneity and application of new technologies. A candidate for this position need not have experience in all aspects of descriptive epidemiology, but should be familiar with them and be experienced in several.

      The mission of DCEG is to conduct broad-based, high quality, high impact research to uncover the causes of cancer and the means of its prevention. DCEG maintains a national and international perspective, giving priority to emergent issues identified through epidemiologic, clinical, and laboratory observations, as well as to public health concerns identified by the NCI, Congress, regulatory agencies, and other appropriate bodies. The Division develops research resources and strategic partnerships in epidemiology and related disciplines across NCI, NIH, and the global research community. The Division holds as its top priority the training and development of the next generation of scientists in cancer epidemiology and related fields.

      Applicants must have a doctorate in epidemiology, medicine, biostatistics or equivalent doctoral level qualifications, relevant experience after the doctorate in chronic disease epidemiology including significant experience in descriptive epidemiology, and excellent computational skills. A strong record of high quality publications demonstrating an ability to collaborate effectively and to lead independent research is required. The candidates will be evaluated on evidence of specific accomplishments; creativity and novelty of scientific vision; sound analytic knowledge and skills; collaborative teamwork, especially across disciplines; ability to work on multiple projects simultaneously and complete projects in a timely fashion; productivity; evidence of effective and efficient leadership of new projects; and skill at effective oral and written scientific communication. Applicants at the tenure-eligible level will be leading experts in descriptive epidemiology. Experience working in studies with molecular and genetic components would be advantageous.

      Salary is commensurate with research experience and accomplishments, and a full Civil Service package of benefits (including retirement, health insurance, life insurance, and a Thrift Savings Plan) is available. Interested individuals should send a complete application to Tricia C. Wilkerson at wilkersont@mail.nih.gov. The application should include: cover letter; curriculum vitae; summary of experience and research accomplishments; statement of research interests; copies of up to five publications or reprints; and three letters of reference, including at least one reference from a collaborator in epidemiology. Reference letters must be sent directly from the referee to the email address listed above. Any questions can also be directed to the e-mail address above. Review of applications will begin on or about July 1, 2015, but applications will be accepted until the position is filled. More information about this job announcement and about research programs in the Division of Cancer Epidemiology and Genetics are available at http://dceg.cancer.gov/.

      The NIH Intramural Research Program
      http://irp.nih.gov/
      http://irp.nih.gov/careers/tenured-and-tenure-track-scientific-careers

      Link to Fellowships and Positions of Interest to fellows
      https://www.training.nih.gov/
      https://www.training.nih.gov/career_services/jobs

  • Tenure-Track: Life Sciences, Centrum Wiskunde &..., Netherlands
    • SMB Digest Vol 15, Issue 24 - June 17, 2015

      Centrum Wiskunde & Informatica (CWI) invites excellent postdoctoral researchers to apply for a tenure-track position in Life Sciences.

      The young and lively Life Sciences group at CWI performs fundamental research on algorithms, theory, models and simulations on topics from the Life Sciences. The core themes of the group are biomodeling and biosystems analysis, combinatorial algorithms for computational biology, computational genomics, medical informatics, neuroinformatics and scientific computing for systems biology.

      As a researcher at CWI Amsterdam you are expected to perform fundamental and application-oriented research, to supervise Ph.D. students, to participate in or lead research projects together with other academic institutes or industry, and to acquire external funding. You are able to work as an independent researcher who can set his/her own research agenda, as demonstrated by previous post-doctoral work experience. You can connect to current research at CWI while at the same time bringing in substantial new expertise.

      Requirements:
      We are looking for a candidate who is demonstrably an expert in the field of mathematics/computer science/computational science for the Life Sciences. The candidate is willing to cooperate within the Life Sciences group and CWI and to build up interdisciplinary collaborations with researchers in the Life Sciences, e.g., with experimental biologists. A preference will be given to candidates who convincingly show how they strengthen existing core themes of the group or build bridges between them.

      The candidate has the ambition and potential to acquire personal research grants such as VENI/VIDI/VICI (NWO) or ERC grants (EU), as well as to acquire external funding for applied research (e.g. from NWO, STW, EU or industry). Moreover, she/he should have post-doctoral experience, and excellent communication skills.

      For more information, see http://www.cwi.nl/jobs/tenure-track-position-in-life-sciences.

  • Lecturer: Applied Mathematics, U Liverpool
    • SMB Digest Vol 15, Issue 23 - June 10, 2015

      Lecturer (equivalent to Assistant Professor) in Applied Mathematics.

      University of Liverpool, UK

      The Department of Mathematical Sciences at the University of Liverpool is seeking to appoint a Lecturer in the area of Applied Mathematics. Individuals with a record of success in interdisciplinary modelling projects in areas such as mathematical biology, mathematical imaging, homogenisation and multi-scale modelling are particularly encouraged to apply. Further details can be found here: https://www.liv.ac.uk/working/jobvacancies/currentvacancies/academic/a-588061/

      Closing date: 3rd July 2015

  • NIH: Selected NIH Intramural Research & Other Openings
    • SMB Digest Vol 15, Issue 23 - June 10, 2015

      Tenure-Track/Tenure-Eligible Investigator
      Epidemiology and Biostatistics Program, NCI-DCEG
      (deadline: July 1)

      The National Cancer Institute (NCI), a major component of the NIH and the Department of Health and Human Services, is recruiting a descriptive epidemiologist for a tenure-track or tenure-eligible position available in the Epidemiology and Biostatistics Program of the Division of Cancer Epidemiology and Genetics (DCEG). Descriptive epidemiology is used in its broad definition, including but not restricted to cancer surveillance research, population-based cancer incidence and mortality registry studies to test existing or generate new etiologic and survival hypotheses, and leveraging data on molecular heterogeneity, gender, ethnicity, age, secular trends and geography (including cancer mapping and other geospatial studies). These would include studies within relatively small geographic areas, countries, and internationally, and would utilize the opportunities afforded by new technologies including record-linkage studies that supplement aggregate-level data with individual-level information. The scope could also encompass development of novel biostatistical methods to supplement standard descriptive techniques, particularly in the emerging opportunities in tumor heterogeneity and application of new technologies. A candidate for this position need not have experience in all aspects of descriptive epidemiology, but should be familiar with them and be experienced in several.

      The mission of DCEG is to conduct broad-based, high quality, high impact research to uncover the causes of cancer and the means of its prevention. DCEG maintains a national and international perspective, giving priority to emergent issues identified through epidemiologic, clinical, and laboratory observations, as well as to public health concerns identified by the NCI, Congress, regulatory agencies, and other appropriate bodies. The Division develops research resources and strategic partnerships in epidemiology and related disciplines across NCI, NIH, and the global research community. The Division holds as its top priority the training and development of the next generation of scientists in cancer epidemiology and related fields.

      Applicants must have a doctorate in epidemiology, medicine, biostatistics or equivalent doctoral level qualifications, relevant experience after the doctorate in chronic disease epidemiology including significant experience in descriptive epidemiology, and excellent computational skills. A strong record of high quality publications demonstrating an ability to collaborate effectively and to lead independent research is required. The candidates will be evaluated on evidence of specific accomplishments; creativity and novelty of scientific vision; sound analytic knowledge and skills; collaborative teamwork, especially across disciplines; ability to work on multiple projects simultaneously and complete projects in a timely fashion; productivity; evidence of effective and efficient leadership of new projects; and skill at effective oral and written scientific communication. Applicants at the tenure-eligible level will be leading experts in descriptive epidemiology. Experience working in studies with molecular and genetic components would be advantageous.

      Salary is commensurate with research experience and accomplishments, and a full Civil Service package of benefits (including retirement, health insurance, life insurance, and a Thrift Savings Plan) is available. Interested individuals should send a complete application to Tricia C. Wilkerson at wilkersont@mail.nih.gov. The application should include: cover letter; curriculum vitae; summary of experience and research accomplishments; statement of research interests; copies of up to five publications or reprints; and three letters of reference, including at least one reference from a collaborator in epidemiology. Reference letters must be sent directly from the referee to the email address listed above. Any questions can also be directed to the e-mail address above. Review of applications will begin on or about July 1, 2015, but applications will be accepted until the position is filled. More information about this job announcement and about research programs in the Division of Cancer Epidemiology and Genetics are available at http://dceg.cancer.gov/.

      The NIH Intramural Research Program
      http://irp.nih.gov/
      http://irp.nih.gov/careers/tenured-and-tenure-track-scientific-careers

      Link to Fellowships and Positions of Interest to fellows
      https://www.training.nih.gov/
      https://www.training.nih.gov/career_services/jobs

      Link to NIH Jobs
      http://www.jobs.nih.gov/

  • Lecturer: Applied Mathematics, U Manchester, UK
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      Lecturer in Applied Mathematics
      University of Manchester, UK

      The School of Mathematics at the University of Manchester seeks a new Lecturer in Applied Mathematics. Applications are welcome from researchers whose interests complement and extend existing activity within the School. Researchers with interests addressing data-driven or interdisciplinary applications (for example in industry, medicine, biology or geophysics) are particularly encouraged to apply. For further details, see https://www.jobs.manchester.ac.uk/universityofmanchesterinternal/displayjob.aspx?jobid=9845

      Closing date: 31/07/2015

  • Position: Computational Biologist, ARA, Arlington, VA, US
    • SMB Digest Vol 15, Issue 22 - June 3, 2015

      Applied Research Associates, Inc. (ARA) is seeking a scientist to help develop mathematical models of the biological and physiological effects of hazardous materials and the environments due to chemical, biological, radiological and nuclear (CBRN) weapons.

      The candidate should have a background in computational biology or other life science, and well-developed skills in mathematical modeling and computer programming. The candidate should have an understanding of the physiological effects associated with acute injuries (burns and trauma) and exposure to radiation, hazardous materials and infectious organisms. The individual must have good research, analysis, and model development skills. The successful candidate will help develop and implement physiologically-based mathematical models of human response to hazardous exposures in support of consequence assessment and medical planning for emergency response. The candidate will work in a team environment and will assist in cultivating marketing opportunities.

      Required Skills: The candidate must have a B.S. in computational biology or a related science discipline, be proficient with mathematical or statistical modeling, and have an understanding of human response from the level of molecular biology to clinical presentation. The candidate must have well-developed oral and written communication skills and be able to work with little supervision, including setting and achieving interim milestones that support higher task objectives. The candidate must be able to obtain a U.S. government security clearance, which includes U.S. citizenship.

      Required Experience: Position requires two to four years of experience in a relevant scientific discipline.

      Desired Qualifications: A candidate with an advanced degree (Masters or PhD) is preferred. Proficiency in programming languages such as Python or MATLAB is highly desired; experience with Java or C++ is considered a plus. Candidate should have strong research and analytical skills.

      Application Instructions: Please apply at www.careers.ara.com for the Computational Biologist, (AD-2015-03) position. ARA is an EEO/AA employer.

  • Position: Senior Health Econ./Modeller, Public Health England
  • Lectureship: Mathematical Biology, St Andrews U
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      The University of St Andrews seeks to appoint an outstanding candidate to a lectureship position in Mathematical Biology within the School of Mathematics & Statistics.

      Following the appointment of Professor M. Chaplain to the Gregory Chair of Applied Mathematics, the School is investing in a new research group in mathematical biology. The successful candidate will join the School at an exciting time and be part of shaping the future development, strategy and growth of the new research group. A further lectureship appointment will be made in early 2016. There is an expected commitment to interact with colleagues in the Schools of Biology and Medicine and the James Hutton Institute (http://www.hutton.ac.uk), and develop interdisciplinary collaborative research projects in the areas of mathematical/computational biology, medicine and theoretical ecology. It is also intended that the lecturer will be involved in the development and running of the new MSc degree programme in Mathematical Biology, which will commence in September 2016.

      The successful candidate should therefore have a PhD in Mathematics (or cognate discipline), and have either an outstanding research record in Mathematical Biology, or display a clear potential to work at the highest level within the field. They must also demonstrate enthusiasm for genuinely inter-disciplinary research.

      Informal approaches concerning this appointment may be made to: Prof Nik Ruskuc, Head of School, mathshead@mcs.st-andrews.ac.uk

      Salary: 38,511 - 47,328 GBP per annum

      Full details:
      http://www.jobs.ac.uk/job/ATV305/lecturers-in-mathematics-and-mathematical-biology-kc1856/
      https://www.vacancies.st-andrews.ac.uk

  • Position: Biomathematician, Inst Genomics & Multiscale..., NY
    • SMB Digest Vol 15, Issue 19 - May 13, 2015

      Position: Bioinformatician
      Description: The Icahn School of Medicine at Mount Sinai in NY is seeking a talented, self-motivated individual to participate in cutting edge research as a member of the Asthma and Allergy group at the Institute for Genomics and Multiscale Biology (http://icahn.mssm.edu/departments-and-institutes/genomics). The successful applicant will join a team that applies computational analysis and bioinformatics to interpret multi-scale data generated from subjects with asthma and allergic diseases. Members of the team work closely with Dr. Supinda Bunyavanich and Dr. Eric Schadt.

      Responsibilities:
      -Analyze next generation sequencing data, including whole genome, RNA-Seq, 16S rRNA, metagenome, and methylation data.
      -Develop and implement statistical methods and software to analyze next generation sequencing data for genetic risk, disease mechanism, and drug response. Projects will include network construction and mining.
      -Integrate and translate genetic, genomic, eQTL, structural, and clinical data into novel diagnostics, therapeutics and disease mechanisms.
      -Maintain complex next generation sequence and array datasets linked to clinical data.
      -Communicate progress with PI regularly and contribute to the success of the research team.
      -Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
      -Publish and present novel research findings in academic journals and conferences.
      -Some supervision of trainees and technical staff may also be required.

      Requirements:
      -Outstanding programming skills in R, Perl, Python, Java, C++, and Unix shell scripting.
      -Excellent track record of analyzing next generation sequencing data. Experience in network analysis a plus.
      -Demonstrated knowledge of statistics, statistical genetics, bioinformatics concepts, methods and tools. Familiarity with genomic data tools, repositories, and databases.
      -Strong attention to detail and solid analytical skills.
      -Ability to work hard and independently while contributing to the team effort and adhering to deadlines.
      -Excellent oral and written communication skills with track record of productive collaborations.
      -Demonstrated ability to work concurrently on several projects, and good understanding of analytic complexities to do independent research as well as assist other researchers.

      Education:
      MS or PhD in bioinformatics, computer science, computational biology, genomics, or a related field.

      If interested, please submit a letter of interest and CV to Dr. Supinda Bunyavanich at supinda.bunyavanich@mssm.edu

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