---------------------------------------------------- Subject: SMB Digest v09i29 SMB Digest July 28, 2009 Volume 09 Issue 29 ISSN 1086-6566 Editor: Ray Mejía ray(at)smb(dot)org Note: Information about the Society for Mathematical Biology, including an application for membership, may be found in the SMB Home Page, http://www.smb.org/ . Access the Bulletin of Mathematical Biology, the official journal of SMB, at http://www.springer.com/11538 . Inquiries about membership or BMB fulfillment should be sent to membership(at)smb(dot)org . Issue's Topics: NIMBioS: Undergraduate Research Conference, October 23-24, UTK Conference: Mathematical Modeling & Analysis of Populations ... Interdisciplinary PhD Position: Exp. & Comput. Molecular Biology PhD Positions: Theoretical Immunology, Utrecht University PhD/Postdoc/Research Scientist: Modeling the Evolution of Aging Postdoc: Evolutionary & Ecological Theory, U Pennsylvania Postdoc: BCI signal processing, Rudolf Magnus Institute, Utrecht Postdoctoral Researchers: Systems Biology Ireland, UCD SMBnet Reminders ---------------------------------------------------- From: Sarah Duncan Date: Wed, 22 Jul 2009 09:47:58 -0400 Subject: NIMBioS: Undergraduate Research Conference, October 23-24, UTK The National Institute for Mathematical and Biological Synthesis is hosting an Undergraduate Research Conference at the Interface of Biology and Mathematics in Knoxville, TN October 23-24, 2009. This annual conference will provide an opportunity for undergraduates to present their work in talks or posters. The conference will also have a panel discussion on career opportunities for students and host the National Science Foundation UBM PI meeting. Plenary and featured speakers include Dr. Lisa Fauci, Tulane University and Paul Super, Great Smoky Mountains National Park. Faculty, students, and Tennessee teachers (grades 6-12) are invited to attend. To register please visit www.nimbios.org To apply for support please register by September 9, 2009. If no support is needed you may register by September 29, 2009. ---------------------------------------------------- From: "Elaydi, Saber" Date: Mon, 27 Jul 2009 13:10:32 -0500 Subject: Conference: Mathematical Modeling & Analysis of Populations ... The Second International Conference on Mathematical Modeling and Analysis of Populations in Biological Systems October 5-7, 2009 Huntsville, Alabama * Contact Us li@math.uah.edu subject=Math%20Biology%20Conference * About the Conference http://www.math.uah.edu/biology/Introduction.html * Conference Organizers http://www.math.uah.edu/biology/Listing.html * Conference Schedule http://www.math.uah.edu/biology/Schedule.html * Conference Speakers, Titles and Abstracts, and Participants http://www.math.uah.edu/biology/Participants.html * Conference Location http://www.math.uah.edu/biology/Location.html * Hotels http://www.math.uah.edu/biology/Hotels.html * Transportation http://www.math.uah.edu/biology/Transportation.html * About Huntsville http://www.huntsville.org/ http://www.math.uah.edu/biology/index.html ---------------------------------------------------- From: Beerenwinkel Niko Date: Wed, 22 Jul 2009 22:06:03 +0200 Subject: Interdisciplinary PhD Position: Exp. & Comput. Molecular Biology Interdisciplinary PhD Position in Experimental and Computational Molecular Biology An interdisciplinary PhD position is available in the groups of Dr. Gunter Merdes (Molecular Biology) and Prof. Niko Beerenwinkel (Computational Biology) at the Department of Biosystems Science and Engineering of ETH Zurich in Basel. Our research is at the interface of mathematics, statistics, and computer science with biology and medicine. We are particularly interested in disease-associated cellular networks and their evolutionary dynamics. The PhD project is concerned with the prediction of functional redundancy in protein networks, and the student will be involved in an alternating cycle between experiment and computational method development. The successful candidate will be a member of both research groups and receive intense interdisciplinary training. Applicants should have a strong background in molecular biology and a solid background in mathematics and statistics. Experience in the area of computational biology is a plus but not a necessity. We seek highly motivated and enthusiastic students with the willingness to cross scientific borders. Good knowledge of English both in writing and speaking is expected. The salary is according to the guidelines of the Swiss National Science Foundation. The position is funded by a SystemsX.ch interdisciplinary PhD fellowship for an initial three years with a possible extension to four years. The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hot-spot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines. Please send the usual application material, including at least two references, as a single PDF file to niko.beerenwinkel@bsse.ethz.ch and gunter.merdes@bsse.ethz.ch. For further information, please visit our web sites: Department of Biosystems Science and Engineering, http://www.bsse.ethz.ch/ Niko Beerenwinkel, http://www.cbg.ethz.ch Gunter Merdes, http://www.bsse.ethz.ch/people/gmerdes/ ---------------------------------------------------- From: Rob J De Boer Date: Fri, 24 Jul 2009 14:50:56 +0200 Subject: PhD Positions: Theoretical Immunology, Utrecht University Three PhD positions in Theoretical Immunology The Faculty of Science of Utrecht University 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. Within the Department of Biology the research in the Theoretical Biology and Bioinformatics group (see http://theory.bio.uu.nl) is concerned with the complex dynamic information processes taking place in biological systems on many space and time scales. Research topics comprise Theoretical Immunology, Multilevel evolution, Systems biology of the heart, Evolutionary Genomics and Integrative Bioinformatics, Immunological Bioinformatics, and Development. The Department is looking to appoint 3 PhD researchers Theoretical Immunology (Doctoral candidate) Job descriptions 1. Spatial models of killing by immune cells. This project, funded by an NWO/ALW Open Program grant, concerns the development and analysis of models of the killing of virus-infected and tumor cells by specialized killer cells of the immune system. These killer cells need to find and interact with suitable targets, and the target cells are killed after some time. Until now it is unclear how many target cells a killer cell kills per day, and how many killer cells are required to clear a viral infection or tumor. A spectacular development in immunology uses two-photon or confocal microscopy to "film" movements of individual cells and their interactions with other cells in living mice. This renders the most direct observations possible of how cells find each other in vivo, and how long they are attached. Using the so-called Cellular Potts Model we have developed three-dimensional simulations that give a detailed description of such videos and the dynamical behaviour of cells (see publications at http://theory.bio.uu.nl/positions.html). The PhD researcher will extend these models with the killing of targets by killer cells. In combination with detailed analysis of experimental data this will lead to a good, quantitative estimate of how many targets a killer cell can clear per day, and how this process depends on for instance local densities of killer and target cells. 2. The co-evolution of the receptor signaling network of natural killer cells with its ligands. This project, funded by an NWO computational life sciences grant, concerns the mechanisms by which natural killer cells defend their hosts to co-evolving pathogens. The activity of NK cells is tightly regulated by an array of activating and inhibitory receptors, recognizing major histocompatibility (MHC) molecules, and other partly unidentified ligands. The network of signals delivered by these receptors is tuned per individual NK cell to match the genotype (MHC molecules) of the host on a time scale of hours to days, and is co-evolving at the population level with pathogens that evolve evasion mechanisms on a time scale of decades to centuries. This is a multidisciplinary project awarded to Can Kesmir (UU), Ronald Bontrop (BPRC) and Rob de Boer (UU), and together we aim to understand the co-evolution of the NK network of activating and inhibitory receptors with its ligands by a combination of bioinformatic, biomathematic and immunogenetic approaches. For the modeling part of the project we are searching for a PhD student to develop agent-based models for host-pathogen co-evolution. These models will describe two polymorphic systems (NK receptors and MHC) that have to be matched with each other in every host. The PhD student will extend existing models and collaborate intensively with the other members of the project. 3. Acute immune responses to chronic viruses The project concerns modeling the dynamics of the cellular immune response to rapidly replicating viruses, which ultimately results in steady state where viral replication is controlled by the host immune response. For several viruses we aim to quantify the population dynamics of the various immune response and estimate the rates at which immune effector cells kill the virus infected cells. This project involves the development of simple mathematical models and the non-linear fitting of the model to experimental data. One major question is to explain the failure of vaccines that are designed to boost the cellular immune response to HIV, and there are recent papers suggesting that this failure can be indeed be understood from the population dynamics of (1) a rapidly replicating virus, (2) a more slowly growing immune response, and (3) the cell-to-cell contacts required for the killing of virus infected cells (see publications at http://theory.bio.uu.nl/positions.html). The PhD student will develop novel mathematical models and work with immunologists and virologists to fit the experimental data. Qualifications We are looking for highly motivated individuals with experience, or an interest in immunology and a training in mathematical modeling and computer simulation. He/she communicates easily in English, both verbally and in writing. Terms of employment The candidates are offered a full-time position for four years. The gross salary is in the range between 2042 Euro per month in the first year and 2612 Euro per month in year four. 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 in which you may trade salary for vacation days or vice versa. Conditions are based on the Collective Employment Agreement of the Dutch Universities. The research group will provide the candidate with necessary support on all aspects of the project. Further details Additional information about the vacancies can be obtained from: Professor Rob J. de Boer, R.J.DeBoer@uu.nl. How to apply Please send your application (including a letter of motivation, curriculum vitae and contact details of at least two references) before 31 August 2009 to e-mail: R.J.DeBoer@uu.nl. ---------------------------------------------------- From: "Baudisch, Annette" Date: Thu, 23 Jul 2009 12:24:34 +0200 Subject: PhD/Postdoc/Research Scientist: Modeling the Evolution of Aging The newly established Independent Research Group Modeling the Evolution of Aging at the MPIDR in Rostock, Germany, is seeking to make appointments at the PhD, Post-Doc, and Research Scientist levels. Starting date as soon as feasible but preferably not later than 01.04.2010 The patterns of life are stunningly diverse, and so are the patterns of aging. Our group on "Modeling the Evolution of Aging" aims to discover the unifying principles and patterns underlying this diversity. We will ask why evolution favored a certain path of aging in a certain species. In particular, we will ask why some species age fast while others age slowly or even seem to escape aging all together. Can we understand aging across animals, plants, fungi and bacteria to a degree that allows us to identify the factors responsible for whether aging is fast, slow, or even reversed? We will develop generic models that capture aging for certain groups of species such as mammals, reptiles, or trees. Our plan will be the following: 1. Conceptualize/define "aging" as well as "fast aging", "slow aging", "no-aging" in a comparative framework across animals, plants, fungi and bacteria. 2. Discover what species follow what aging patterns. To get a broad view on patterns across species, we will rely on good life table data and textbook knowledge on the phylogeny, physiology and ecology of the various species. To get an in-depth view we will collaborate with experts around the world who can provide us with empirical evidence and expert knowledge on particular species. 3. Running our creative minds, juggling available data and knowledge on the various species thinking outside of conventional boxes we then identify key variables that seem to give us a reasonable species grouping. 4. Based on these key variables, we will develop generic models for these groups. If a model becomes too clumsy with all the key variables included, we will develop several simple models to shed light on different aspects of aging in a single group. 5. What is the evolutionary successful strategy of aging in the various models? Can we develop a general algorithm that solves the various models? Our team will consist of people with a burning interest in theoretical modeling, a strong preference for revealing and understanding general mechanisms and unifying principles, and a strong interest in studying population dynamics in an interdisciplinary group. Our collective expertise should ideally cover skills and knowledge in theoretical modeling, evolutionary biology, life history biology, comparative biology (with a main focus on basic physiological, phylogenetic and ecological characteristics across the tree of life), demography, ecology, mathematics, dynamic optimization, programming, statistics, non-linear dynamics, complex adaptive systems and principles of self-organization. Our project is likely to cut across all the life sciences. The group will be established by Dr. Annette Baudisch. The group will be part of the MPIDR in Rostock, a bike-ride away from the Baltic Sea. The institute is very international, with a warm and colleagial working atmosphere hosting a diverse range of labs with interdisciplinary topics. The working language of all groups including ours is English. Applications should include a CV with relevant experience, educational degrees, a list of any publications and the contact details of 3 references. A description of your research interest and why you would enjoy becoming a member of our team would be very helpful. All material should be e-mailed to: appl-irgmea@demogr.mpg.de, preferably in a single pdf file. Applications will be considered and positions will be filled on a rolling basis. PhD and Post-Doc appointments are made on doctoral and postdoctoral stipends, respectively. Research scientists will be employed up to salary level 14 on the basis of the German TVöD system according to the qualification of the candidate and in accordance with the rules of federal employees in Germany. The Max Planck Society wishes to increase the share of women in areas where they are underrepresented, and strongly encourages women to apply. The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply. ---------------------------------------------------- From: Joshua B. Plotkin Date: Thu, 23 Jul 2009 11:04:20 -0400 Subject: Postdoc: Evolutionary & Ecological Theory, U Pennsylvania POSTDOCTORAL FELLOWSHIP, U. Penn A postdoctoral fellowship (2 years) is available in the mathematical biology group of Dr. Joshua B. Plotkin at the University of Pennsylvania (http://mathbio.sas.upenn.edu/). The specific research project is flexible and can be tailored to the interests of the individual, but it will fall under the broad purview of evolutionary and ecological theory. Areas of interest in the Plotkin lab include theoretical population genetics, the evolutionary ecology of viral populations, the evolution of robustness and adaptability, and the evolution of language and social norms. Requirements for the position include: a proven record of self-motivated research; a PhD in mathematics, statistics, physics, biology or related area; excellent communication skills. The ideal candidate should also be familiar with scientific programming. The postdoctoral fellowship provides a competitive annual stipend (minimum $38,000) plus benefits and health insurance. Start date and term are negotiable. Applications are welcome from candidates of any nationality, and will be reviewed starting August 15, 2009. The Penn Genome Frontiers Institute offers an outstanding intellectual environmental. Research at the Institute addresses basic questions in biology through genomic, computational, and modeling approaches. Collaborations among research groups and across the broader Penn community are common. The Institute is housed in the newly constructed Lynch research building. Applicants are encouraged to email a statement of research interests, CV, and contact details for three references to jplotkin (at) sas.upenn.edu. Informal inquiries are also welcomed. ---------------------------------------------------- From: "Steensel, M.J. van" Date: Fri, 24 Jul 2009 15:25:16 +0200 Subject: Postdoc: BCI signal processing, Rudolf Magnus Institute, Utrecht Postdoc in BCI signal processing The Rudolf Magnus Institute in Utrecht, The Netherlands is looking for a highly motivated postdoc interested in neural signal processing for Brain Computer Interfacing. The Utrecht BCI group, led by Prof. dr. Nick Ramsey, is part of the Department of Neurology and Neurosurgery at the University Medical Center Utrecht and participates in the nationwide BrainGain Consortium, which is devoted to application of Brain Computer Interfaces for patients and healthy individuals. The main focus of the group is conducting neuroscience research towards an invasive BCI application for paralyzed patients. We perform experiments with both healthy subjects and patients (~10 patients with electrode implants available for research each year). Available techniques: 128-channel EEG systems for extracranial and intracranial (ECoG) recordings, fMRI (1.5, 3 and 7 T human Philips systems), TMS and 64-channel intraoperative recordings in awake neurosurgery. Our highly interdisciplinary group consists of 4 postdocs, 10 PhD students and 6 master students, who have a background in neuroscience, psychology, biology or physics and their own expertise in the research field. The postdoc is expected to investigate new ECoG signal processing techniques for BCI purposes, as well as for cognitive neuroscience research. He/she will work in close collaboration with neuroscientists and needs to have excellent communication skills. The candidate is likely to have a PhD in biomedical engineering, computational neuroscience, electrical engineering or physics, with a record of publications. Solid experience in signal processing of any kind and excellent programming skills in Matlab are required. Experience in neuroscience is not a prerequisite, but we expect the candidate to acquire knowledge of underlying psychological and biological processes. Earliest starting date of the two-year position is July 1st, 2009. Application deadline is September 1st, 2009. Applications and information requests can be sent to Prof. dr. Nick Ramsey, Rudolf Magnus Institute of Neuroscience, Dept. of Neurology and Neurosurgery, Division of Neuroscience, University Medical Center Utrecht, Room G.03.122, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands, n.f.ramsey@umcutrecht.nl. ---------------------------------------------------- From: Paul Fitzgerald Date: Fri, 24 Jul 2009 15:31:33 +0100 Subject: Postdoctoral Researchers: Systems Biology Ireland, UCD Postdoctoral Researchers UCD Conway Institute Systems Biology Ireland Closing Date: 28th August 2009 Ref: 003858 Post Duration: Temporary, 4 years Applications are invited from outstanding candidates to work on computational modelling of signalling and gene networks in mammalian cells at Systems Biology Ireland, University College Dublin. Ongoing projects include the temporal and spatial dynamics of receptor tyrosine kinase signalling and transcriptional networks that govern cell proliferation, differentiation and motility (supported by a multi-PI grant to Professors Boris Kholodenko, Walter Kolch and Zoltan Neufeld). The successful applicant will work closely with experimentalists at the interface between mathematics, engineering and biology in a multi disciplinary research community at Systems Biology Ireland. This presents a unique opportunity for creative individuals who want to work at the cutting-edge of systems biology. Individuals with an interest in Systems Biology are encouraged to apply. Salary: Euro 46,300 per annum NOTE: Applications must be submitted by the closing date and time specified. UCD are unable to accept late applications / agency applications. Such applications will be returned. Closing date: 23.30hrs on Friday 28th August 2009 Please note: All current recruitment which is taking place within UCD is dependent on non-Exchequer, external and self-funding sources of finance. For further details, or to make an application, please visit our website www.ucd.ie/hr/jobvacancies UCD is an equal opportunities employer ---------------------------------------------------- Subject: SMBnet Reminders To subscribe to the SMB Digest please point your browser at http://list.auckland.ac.nz/mailman/listinfo/math-smbnet and complete the subscription information. Alternatively, if you prefer to simply receive notice when the next issue is available, send mail to LISTSERV@listserv.biu.ac.il with "subscribe SMBnet Your Name" in the body of the mail (omit the quotes and include your name). After you subscribe, you will receive a greeting with additional information. Submissions to appear in the SMB Digest may be sent to SMBnet(at)smb(dot)org . Items of interest to the mathematical biology community may be submitted for inclusion in the SMBnet archive. See instructions at: http://smb.org/publications/SMBnet/pubs/fyi . The SMB Digest is also available on the SMB Home Page at http://smb.org/publications/SMBnet/digest/ The contents of this publication may be reproduced in whole or in part with attribution. End of SMB Digest **************************************************** ----------------------------------------------------