---------------------------------------------------- Subject: SMB Digest v08i17 SMB Digest April 30, 2008 Volume 08 Issue 17 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: TOC: Computational and Mathematical Methods in Medicine CfP: HAIS 2008, 24 - 27 September, Burgos PhD Studentship: Evolutionary Biology, University of Zurich Postdoctoral Fellow: Evolutionary Ecology, Umeå University Postdoctoral Position: DNA Barcoding, INRA - Jouy-en-Josas Postdoctoral Position: Systems Biology (Modeling), U Zurich Postdoctoral / More Senior Position: Cell Modeling SMBnet Reminders ---------------------------------------------------- From: "Sternberg, Zoe" Date: Mon, 28 Apr 2008 16:41:02 +0100 Subject: TOC: Computational and Mathematical Methods in Medicine Computational and Mathematical Methods in Medicine: An Interdisciplinary Journal of Mathematical, Theoretical and Clinical Aspects of Medicine Volume 9 Issue 2 is now available online at informaworldTM. http://www.informaworld.com/smpp/title~db=all~content=t713653639 This new issue contains the following articles: Numerical simulation of the coagulation dynamics of blood p. 83 Authors: T. Bodnár; A. Sequeira A simple mathematical standardized measurement of acetabulum anteversion after total hip arthroplasty p. 105 Authors: Chen-Kun Liaw; Rong-Sen Yang; Sheng-Mou Hou; Tai-Yin Wu; Chiou-Shann Fuh Stability analysis of a model of atherogenesis: An energy estimate approach p. 121 Authors: A. I. Ibragimov; C. J. McNeal; L. R. Ritter; J. R. Walton Modelling immune response and drug therapy in human malaria infection p. 143 Authors: C. Chiyaka; W. Garira; S. Dube ---------------------------------------------------- From: Dacheng Tao Date: Mon, 28 Apr 2008 21:42:24 +0800 Subject: CfP: HAIS 2008, 24 - 27 September, Burgos 5TH CFP HAIS 2008.- SOCIAL EVENTS!!! 3rd International Workshop on Hybrid Artificial Intelligence Systems HAIS´08) 24th-27th September, 2008.- Burgos, Spain http://www2.ubu.es/hais2008/home.shtml Dear Colleague, It's our pleasure to inform you that we have organized several SOCIAL EVENTS under the frame of HAIS 2008 in order to make your staying in BURGOS more enjoyable. The social events are shown at the following web page: http://www2.ubu.es/hais2008/main/socialevents.shtml Best regards, HAIS 2008.-Organising Committee Chairs ---------------------------------------------------- From: Christiane Gujan Date: Wed, 30 Apr 2008 17:40:26 +0200 Subject: PhD Studentship: Evolutionary Biology, University of Zurich PhD thesis in computational evolutionary genomics A three-year Ph.D. studentship in evolutionary biology is available in the laboratory of Andreas Wagner at the University of Zurich. The Wagner lab at the University of Zurich studies biological evolution on all levels of organization, from genes, genomes, and genetic networks to whole organisms. Ongoing projects range from laboratory evolution experiments in yeast to human population genomics. A sample of our research can be found at http://www.bioc.uzh.ch/wagner/. Lab members are a group with very diverse backgrounds and research projects, unified by their interests in evolution and /or fundamental organizational principles of life. The successful candidate will have a strong background in bioinformatics and computational biology. Fluency in a major scripting language such as perl, and experience in software development is a must. Also necessary is a strong background in biology. Applications without a demonstrated interest and research history in evolutionary biology will not be considered further We are looking for an individual with a Masters Degree or equivalent, who is highly self-motivated and can work independently. The working language in the laboratory is English. German skills, although helpful, are not essential. Zurich is a highly attractive city in beautiful surroundings, with a multinational population, and many educational and recreational opportunities. To be considered, please send a single (!) PDF file merged from the following parts to jobs_aw@bioc.uzh.ch : CV including publication list (if available), a scanned academic transcript (list of grades in university courses), a statement of research interests not exceeding two pages, and three references. Please include the word "COMP" in the subject line. Applications will be considered until the position has been filled. ---------------------------------------------------- From: Åke Brännström Date: Wed, 23 Apr 2008 11:54:29 +0200 Subject: Postdoctoral Fellow: Evolutionary Ecology, Umeå University Postdoctoral fellow, Umeå University, Sweden Numerical methods and computational tools for evolutionary ecology vegetation models based on integro-partial differential equations We are looking for a postdoctoral fellow to take on the numerical and computational challenges arising in an international research collaboration that aims to develop an evolutionary ecology vegetation model capable of predicting vegetation structures favored under different environmental conditions. The model is physiologically structured and represented mathematically by an integro-partial differential equation, i.e., by a PDE in which coefficients depend on properties of the solution such as the light availability at a given height above ground. A major objective of your work will be the development of a fast solver for integro-partial differential equations and the development of related computational tools required for simulations. There is also scope for developing algorithms and methods for studying phenotypic evolution in physiologically structured population models. Ume University hosts a center for high-performance computing, HPC2N, and we expect that you can make use of these computing resources if needed. Depending on the direction in which you take your work, the position may lead to publications in computational mathematics, mathematical/theoretical ecology, or both. In addition, there is a good opportunity that your contributions will become incorporated in the next generation of world vegetation models. The position is available for one year with a possible prolongation for another period of one year. The postdoc will be based at the Department of Mathematics and Mathematical Statistics and will work in close collaboration with our international partners, including the International Institute for Applied Systems Analysis (IIASA) in Laxenburg, Austria, and Macquarie University, Sydney, Australia. The position is expected to entail visits and secondments to one or both of these institutions, possibly for durations of up to several months. To qualify for this position, you need a PhD degree in computational mathematics or a quantitative science related to the project, preferably not older than five years. Experience of programming in C++, parallel computing, or mathematical ecology will be an advantage, but is not required. Proficiency in written and spoken English is essential. Umeå university in northern Sweden is a dynamic university with ca 3 900 employees and more than 29 000 students, of which 1 300 are in PhD programs. The department of Mathematics and Mathematical Statistics has about 65 employees including 25 PhD students. The department of Ecology and Environmental Science has about 170 members including 65 PhD students. For further information, please contact assistant professor Åke Brännström, +46-90-786 78 62, ake.brannstrom@math.umu.se, professor Mats Larson, +46-90-7865502, mats.larson@math.umu.se or Head of department Anders Fällström anders.fallstrom@math.umu.se. For a general presentation of the department, see www.math.umu.se . The International Office, http://www.umu.se>/international_office provides a general presentation of Umeå and the University. The application should contain a curriculum vitae, copies of degree certificates, names and contact details of at least two references, and short accounts of scientific and teaching activities. Reprints of your most relevant publications and other documents that you wish to refer to should be attached. Union information is available from SACO, +46-(0)90-786 53 65, SEKO civil, +46-(0)90-786 52 96 and ST, +46-(0)90-786 54 31. Your complete application, marked with reference number 315-1620-08, should be sent to jobb@umu.se or to the Registrar, Umeå University, SE-901 87 Umeå, Sweden to arrive June 2, 2008 at the latest. We look forward to receiving your application! ---------------------------------------------------- From: Olivier.David@jouy.inra.fr Date: Tue, 29 Apr 2008 12:28:29 +0200 (CEST) Subject: Postdoctoral Position: DNA Barcoding, INRA - Jouy-en-Josas Postdoctoral fellowship on Classification methods for DNA barcoding. DNA Barcoding consists in assigning an individual to a given species according to the sequence of this individual at a given locus (for the animals, often a fraction of the COI mitochondrial DNA gene). The technique consists first in sequencing a sample of reference individuals for which the taxonomic status is unambiguous. This reference sample is then used as a training data set for a classification algorithm, which aims at assigning newly sampled individuals to a given species on the basis of their DNA sequence only. The postdoctoral fellow will work in particular in the development and comparison of the efficiency of various classification algorithms in this context. These algorithms include classical phylogenetic methods (e.g. neighbour joining, maximum likelihood?), statistical classification methods (e.g. CART, Random Forest, neural networks, kernel and SVM methods?) and coalescent-based methods. Methods that take advantage of recent advances in statistical learning and inference and in population genetics will be favoured in particular. The comparisons will be carried out on simulated data sets and also on well-characterized experimental data sets. In particular, the impact on the efficiency of the different methods of events like gene flow between species or population expansions will be investigated. The contribution of additional information at nuclear loci will also be considered. Finally the question of the detection of new species might also be addressed. The position is opened for 20 months. It should start around May 2008. The salary will be around 1800 euros/month. The postdoctoral fellow will be mainly located at the Unite Mathematiques et Informatique Appliquees of the INRA - Jouy-en-Josas, near Paris, in strong interactions with two other laboratories (see below). A strong background in mathematics, statistics and computer science is requested for this position. An experience in interacting with biologists, especially population geneticists, will be a plus. Interested candidates are invited to submit by email to C. Laredo and F. Austerlitz (see addresses below) the following elements. a CV with a list of publications two or three relevant publications an application letter the names and e-mail addresses of three referees. Supervisors: Catherine Laredo, INRA, Unite Mathematiques et Informatique Appliquees, Centre de Recherche de Jouy-en-Josas, F-78352 JOUY-EN-JOSAS, France. Tel : +33 1 34 65 22 26, FAX : +33 1 34 65 22 17, Email: Catherine.Laredo@jouy.inra.fr http://w3.jouy.inra.fr/unites/miaj/index.php3 and Laboratoire Probabilites et modèles Aleatoires, UMR 7599, Universites Paris VI et VII, 75013 Paris, France Frederic Austerlitz, Laboratoire Ecologie, Systematique et Evolution, U.M.R. C.N.R.S./U.P.S./E.N.G.R.E.F. 8079, Universite Paris-Sud XI, Bâtiment 360, F-91405 Orsay cedex, France. tel: + 33 1 69 15 77 20, fax: + 33 1 69 15 46 97, email: Frederic.Austerlitz@u-psud.fr http://www.ese.u-psud.fr/bases/upresa/pages/austerlitz/index_eng.html Collaborators: Olivier David (INRA, Unite Mathematiques et Informatique Appliquees) Brigitte Schaeffer (INRA, Unite Mathematiques et Informatique Appliquees) Michel Veuille (Departement Systematique et Evolution, Museum National d'Histoire Naturelle, Paris) Raphaël Leblois (Departement Systematique et Evolution, Museum National d'Histoire Naturelle, Paris) ---------------------------------------------------- From: Christiane Gujan Date: Wed, 30 Apr 2008 15:23:09 +0200 Subject: Postdoctoral Position: Systems Biology (Modeling), U Zurich Postdoctoral fellowship in Systems Biology (Modeling) A postdoctoral fellowship in Systems Biology is available in the laboratory of Andreas Wagner at the University of Zurich. The project goal is to improve our understanding of the signaling, regulatory, and metabolic networks involved in the yeast response to the nutrients nitrogen and glucose. The successful candidate will develop and improve mathematical models of yeast nutrient signaling. He or she will use multiple criteria, such as robustness of network variants to noise and mutations, and the evolvability of network topologies, to establish models for further experimental testing. The position is funded through an interdisciplinary grant by the Swiss Systems Biology Initiative, to a consortium of experimental and computational laboratories. Pertinent consortium publications include Ciliberti et al. PNAS 104, 13591-6, 2007 and Kuepfer et al. Nat. Biotech 25, 1001-6, 2007. The successful candidate will be embedded in an interdisciplinary group of experimentalists and theorists from several universities. The Wagner lab at the University of Zurich studies biological systems on all levels of organization, from genes, genomes, and genetic networks to whole organisms. Ongoing projects range from laboratory evolution experiments in yeast to human population genomics. A sample of our research can be found at http://www.bioc.uzh.ch/wagner/. Lab members are a group with very diverse backgrounds and research projects, unified by their interests in evolution and /or fundamental organizational principles of life. We are looking for an individual who has received his or her PhD within the last five years, who is highly self-motivated and can work independently. The successful candidate will have a strong background in mathematical and computational biology. He or she will have a publication record in the mathematical modeling of cellular systems. An interest in evolutionary questions, and experience with bioinformatic data analysis will be a plus. The working language in the laboratory is English. German skills, although helpful, are not essential. Zurich is a highly attractive city in beautiful surroundings, with a multinational population, and many educational and recreational opportunities. To be considered, please send a single (!) PDF file merged from the following parts to jobs_aw@bioc.uzh.ch : CV including publication list, a statement of research interests not exceeding three pages, as well as three academic references. Please include the word "YEAST" in the subject line. Applications will be considered until the position has been filled. The position is available as of August 1, 2008. It is available for one year initially, renewable up to three years. ---------------------------------------------------- From: "Maly, Ivan Viktorovich" Date: Wed, 23 Apr 2008 10:44:17 -0400 Subject: Postdoctoral / More Senior Position: Cell Modeling A postdoctoral or more senior position will be available to work on spatial-kinetic modeling of cellular morphogenesis, specifically on the interactions between signaling, transport, and cytoskeleton during self-organization of cell-cell (adherens) junctions. The position is part of a collaborative project with experimentalists from Cambridge, Rotterdam, and Brisbane. The modeling part of the project will be based in the Department of Computational Biology at the University of Pittsburgh School of Medicine, a center of the vibrant computational biology community in the city. Examples of the types of spatial-kinetic models can be found through the web page www.ccbb.pitt.edu/maly, and of the biological subject of this project, on jcs.biologists.org/cgi/content/full/119/9/1801. To inquire or apply, send an email to the head of the computational part of the project, Ivan Maly (ivanmaly@pitt.edu). Devote a paragraph to describing your experience in mathematical modeling in biology, and another paragraph to your experience in scientific computing. Attach CV with a list of publications. Provide contact information and relation to you of two references who agreed to be contacted. The target starting date is October 1, 2008, however an earlier or later appointment may be possible. This project is one of the long-term funded projects in the lab. Its funds are available for 3 years. All appointments are renewed yearly based on performance, but a mutual commitment to work together for 3 years should be implied. Incumbent must be available to travel and work overseas on the schedule dictated by the project. PhD is required by the time of appointment. Candidates with significant postdoctoral experience in a relevant field may be appointed with a non-postdoctoral title if so desired. Salary will be commensurate with experience and HIGHLY COMPETITIVE. ---------------------------------------------------- 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. 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