---------------------------------------------------- Subject: SMB Digest v09i15 SMB Digest April 13, 2009 Volume 09 Issue 15 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: Symposium: Systems Biology, June 11-14, Travel Grants Available TOC: Bulletin of Mathematical Biology, Volume 71 Number 4 New Book Series Postdoc Positions: Evolutionary Biology, Umea University Postdoc & PhD Positions: Systems Biology, IFOM, Milan Positions: Biological Modeling and Simulation, NCSB, Amsterdam Postdoc: Modeling Immune System, New York University Med School Postdoc: Modeling Infectious Diseases, UGA Lectureship & Postdoc Positions: University of Dundee SMBnet Reminders ---------------------------------------------------- From: Symposium Office Date: Thu, 09 Apr 2009 12:06:43 -0500 Subject: Symposium: Systems Biology, June 11-14, Travel Grants Available The Symposium on Systems Biology: Integrative, Comparative, and Multi-Scale Modeling has received additional funding that will provide for substantial travel grants for students and post-docs. Therefore, we are extending both the travel grant deadline and the abstract deadline until April 27. Please share this information with any students or post-docs that would be interested in attending this exciting meeting! To register and apply for a travel grant, see our website at http://www.bb.iastate.edu/~gfst/phomepg.html [See also http://www.smb.org/publications/SMBnet/digest/v09i06 .] ---------------------------------------------------- From: Springer Date: Fri, 10 Apr 2009 16:22:01 -0700 (PDT) Subject: TOC: Bulletin of Mathematical Biology, Volume 71 Number 4 Volume 71 Number 4 of "Bulletin of Mathematical Biology" is now available on the SpringerLink web site at http://www.springerlink.com/content/j50033726u04/?p=81b7443ad4b94e2395b00681 3a7480b3&pi=0 The Applicability of Ordinary Least Squares to Consistently Short Distances between Taxa in Phylogenetic Tree Construction and the Normal Distribution Test Consequences Author(s): C. Z. Roux Page: 771 - 780 Distinguishing between Directed and Undirected Cell Motility within an Invading Cell Population Author(s): Matthew J. Simpson, Kerry A. Landman, Barry D. Hughes Page: 781 - 799 Evolutionary Entropy: A Predictor of Body Size, Metabolic Rate and Maximal Life Span Author(s): Lloyd Demetrius, Stéphane Legendre, Peter Harremöes Page: 800 - 818 Evolutionary Consequences of Predation for Pathogens in Prey Author(s): Maia Martcheva Page: 819 - 844 Dynamics of Indirectly Transmitted Infectious Diseases with Immunological Threshold Author(s): Richard I. Joh, Hao Wang, Howard Weiss, Joshua S. Weitz Page: 845 - 862 Excitable Population Dynamics, Biological Control Failure, and Spatiotemporal Pattern Formation in a Model Ecosystem Author(s): Andrew Morozov, Sergei Petrovskii Page: 863 - 887 A Contact-Network-Based Formulation of a Preferential Mixing Model Author(s): Istvan Z. Kiss, Péter L. Simon, Rowland R. Kao Page: 888 - 905 A Mathematical Model of Liver Cell Aggregation In Vitro Author(s): J. E. F. Green, S. L. Waters, K. M. Shakesheff, H. M. Byrne Page: 906 - 930 Dynamical Adaptation of Parental Care Author(s): Yasuhiro Takeuchi, Wendi Wang, Shinji Nakaoka, Shingo Iwami Page: 931 - 951 Modeling the Evolution of Insect Phenology Author(s): Brian P. Yurk, James A. Powell Page: 952 - 979 Analyses of Mechanisms for Force Generation During Cell Septation in Escherichia coli Author(s): Donald A. Drew, Gretchen A. Koch, Heather Vellante, Ronak Talati, Oswaldo Sanchez Page: 980-1005 Hybrid Modeling of Noise Reduction by a Negatively Autoregulated System Author(s): Stefan Zeiser, Uwe Franz, Johannes Müller, Volkmar Liebscher Page: 1006 - 1024 ---------------------------------------------------- From: carlos.martin@urv.cat Date: Sat, 11 Apr 2009 21:02:54 +0200 Subject: New Book Series A new book series is going to be announced in a few weeks by a major publisher under the (tentative) title of Mathematics, Computing, Language, and the Life: Frontiers in Mathematical Linguistics and Language Theory SERIES DESCRIPTION: Language theory, as originated from Chomsky's seminal work in the fifties last century and in parallel to Turing-inspired automata theory, was first applied to natural language syntax within the context of the first unsuccessful attempts to achieve reliable machine translation prototypes. After this, the theory proved to be very valuable in the study of programming languages and the theory of computing. In the last 15-20 years, language and automata theory has experienced quick theoretical developments as a consequence of the emergence of new interdisciplinary domains and also as the result of demands for application to a number of disciplines, most notably: natural language processing, computational biology, natural computing, programming, and artificial intelligence. The series will collect recent research on either foundational or applied issues, and is addressed to graduate students as well as to post-docs and academics. TOPIC CATEGORIES: A. Theory: language and automata theory, combinatorics on words, descriptional and computational complexity, semigroups, graphs and graph transformation, trees, computability B. Natural language processing: mathematics of natural language processing, finite-state technology, languages and logics, parsing, transducers, text algorithms, web text retrieval C. Artificial intelligence, cognitive science, and programming: patterns, pattern matching and pattern recognition, models of concurrent systems, Petri nets, models of pictures, fuzzy languages, grammatical inference and algorithmic learning, language-based cryptography, data and image compression, automata for system analysis and program verification D. Bio-inspired computing and natural computing: cellular automata, symbolic neural networks, evolutionary algorithms, genetic algorithms, DNA computing, molecular computing, biomolecular nanotechnology, circuit theory, quantum computing, chemical and optical computing, models of artificial life E. Bioinformatics: mathematical biology, string and combinatorial issues in computational biology and bioinformatics, mathematical evolutionary genomics, language processing of biological sequences, digital libraries The connections of this broad interdisciplinary field with other areas include: computational linguistics, knowledge engineering, theoretical computer science, software science, molecular biology, etc. The first volumes will be miscellaneous and will globally define the scope of the future series. INVITATION TO CONTRIBUTE: Contributions are requested for the first five volumes. In principle, there will be no limit in length. All contributions will be submitted to strict peer-review. Collections of papers are also welcome. Potential contributors should express their interest in being considered for the volumes by April 25, 2009 to carlos.martinvide@gmail.com They should specify: - the tentative title of the contribution, - the authors and affiliations, - a 5-10 line abstract, - the most appropriate topic category (A to E above). A selection will be done immediately after, with invited authors submitting their contribution for peer-review by July 25, 2009. The volumes are expected to appear in the first months of 2010. ---------------------------------------------------- From: Roland Jansson Date: Mon, 06 Apr 2009 10:48:55 +0200 Subject: Postdoc Positions: Evolutionary Biology, Umea University Two post-doc positions (2 years) in evolutionary biology Umea University, Department of Ecology and Environmental Science, Sweden The role of climate change for the evolution of biodiversity The aim of the project is to understand how climate change affects evolution and the global distribution of species. The earth is subject to recurrent and rapid climate shifts at various time-scales, but the consequences of this has not been incorporated into models of evolution. In the project, models of past climate change are combined with phylogenetic data to address how diversification of species and spatial patterns in genetic divergence within species are affected by climate variability. Position 1 investigates the role of climate variability for the diversification of species. Data on past climate change from climate models are used together with phylogenies from a range of taxa to test for an association between climate variability and species diversification. Position 2 tests how climatic variability affects the degree of genetic divergence among populations. Data on levels of genetic divergence among populations are combined with data on past climate change from climate models to test for a correlation between genetic divergence and climatic stability, both within species (in cases where climatic stability varies across its geographic range) and between species inhabiting regions differing in climatic stability. For further information and guide on how to apply, see http://www8.umu.se/umu/aktuellt/arkiv/lediga_tjanster/315-301-09.html , or contact Roland Jansson (roland.jansson@emg.umu.se , www.emg.umu.se/roland) Last day for application is May 31, 2009. ---------------------------------------------------- From: Andrea Ciliberto Date: Tue, 07 Apr 2009 11:04:01 +0200 Subject: Postdoc & PhD Positions: Systems Biology, IFOM, Milan Fellowship in Systems Biology Fellowships for both PostDocs and PhD positions are available to work in the computational cell biology lab of Andrea Ciliberto in IFOM, Milan (http://www.ifom-ieo-campus.it/research/ciliberto.php). The lab is interested to study molecular regulatory networks with a combination of mathematical tools and molecular biology techniques. The project concerns the mechanisms of regulation of the cell division cycle with particular emphasis on the control of chromosome segregation (see Simonetta et al, The influence of dimerization in Mad2 activation dynamics, PLoS Biology 7(1): e1000010, 2009). Candidates are expected to do wet lab work (single cell live imaging, development of stable transgenic cell lines) and computational studies (with systems of ordinary differential equations). Candidates with a background in systems biology physics, chemistry, chemical engineering, are particularly encouraged to apply. Knowledge of differential equations, image analysis, molecular biology techniques is a plus. PhD candidates will have to apply to the selections of the European School of Molecular Medicine (www.semm.it) to be held next fall in Milan. If interested, please contact Andrea Ciliberto (andrea.ciliberto@ifom-ieo-campus.it). ---------------------------------------------------- From: Roeland Merks Date: Wed, 8 Apr 2009 18:09:05 +0200 Subject: Positions: Biological Modeling and Simulation, NCSB, Amsterdam Positions in biological modeling and simulation in Amsterdam, The Netherlands Within the Netherlands Consortium for Systems Biology (NCSB), biologists, computer scientists, physicists and mathematicians of Dutch universities and research institutes have joint forces to develop innovative systems biology approaches for tackling challenging, multi-factorial biological problems related to human health, plant sciences, and white biotechnology. Computer modeling and simulation are central to this highly multidisciplinary effort. NCSB's core modeling group Biomodeling and Biosystems Analysis at CWI, the Dutch national research institute for mathematics and computer science, develops innovative simulation approaches and coordinates modeling projects at the participating institutes. The Biomodeling and Biosystems Analysis group invites applications for the following positions: Postdoctoral researcher Modeling dynamics and evolution of hierarchically regulated, eukaryotic gene networks See: http://www.cwi.nl/en/node/1044 PhD student Cell-based modeling of blood vessel formation See http://www.cwi.nl/en/node/1045 Scientific programmer / PhD student Bringing modeling and simulation to the biologist's lab bench See http://www.cwi.nl/en/node/1043 Requirements for all positions: - A scientific background in simulation and modeling: a degree in theoretical biology or computational physics, computational science, or equivalent experience - Able to communicate with scientists in biology and mathematics - Good programming skills in C++ or equivalent - Minimum academic degree: for postdoc, PhD; for PhD, M.Sc.; for programmer, B.Sc. Information For full description of these positions, see http://www.cwi.nl/en/jobs. For more information about CWI, NISB, NCSB and the Biomodeling and Biosystems Analysis group, visit http://www.cwi.nl, http://www.sysbio.nl, and http://www.cwi.nl/~merks. Contact: Roeland Merks, CWI, Roeland.Merks@sysbio.nl, Tel. +31-20-5624117 Application deadline is May 1st, 2009. ---------------------------------------------------- From: Yiming Cheng Date: Tue, 07 Apr 2009 16:27:56 -0400 Subject: Postdoc: Modeling Immune System, New York University Med School Research position in mathematical modeling and computer simulation of the immune system. New York University School of Medicine is seeking a highly qualified Postdoc research fellow/research scientist with an interest in applying mathematical modeling and computer simulation to study the immune system. Ideal candidates should have a Ph.D in applied mathematics, computer science or computational biology. Advanced graduate students in New York City area may also be considered. Experience in computer programming (C/C++, PERL, Matlab/R) is required. Knowledge of immunology is desirable. Additional research about the group can be found from the website: http://immsimteam.med.nyu.edu. Interested candidates are encouraged to apply as soon as possible. Send your cover letter and curriculum vitae to fc15@nyumc.org or chengy04@nyu.edu with the subject "Researcher Position in IMMSIM". Two references will be requested." ---------------------------------------------------- From: Andrew Park Date: Wed, 8 Apr 2009 13:52:20 -0400 Subject: Postdoc: Modeling Infectious Diseases, UGA University of Georgia - Post-Doctoral Associate - Modeling infectious diseases We are seeking candidates with skills and interests in mathematical modeling of biological systems to become involved in one or more ongoing infectious disease projects with Dr Andrew Park at the Odum School of Ecology, including: * short-term pathogen evolution * the emergence of immune escape pathogen strains * vaccination and herd immunity strategies * the role of host heterogeneity in maintaining pathogen diversity * characterizing disease evolution trajectories Funding (plus health and retirement benefits) is available for 18 months, with the possibility of extension. Applicants should email a statement of interest, CV, and arrange to have 3 letters of recommendation sent to Dr Park (awpark@uga.edu). Applications received before 10 May 2009 will be reviewed and the position can be taken up from July 2009, or later. The University of Georgia is an equal opportunity, affirmative action employer ---------------------------------------------------- From: Mark Chaplain Date: Wed, 8 Apr 2009 01:16:36 +0100 Subject: Lectureship & Postdoc Positions: University of Dundee Lectureship and Post-doctoral Research Assistant Positions at the University of Dundee UNIVERSITY OF DUNDEE 5-year Tenure Track Lectureship in Mathematical Biology Following the recent award of a European Research Council Advanced Investigator Grant to Professor Mark Chaplain, FRSE (?From Mutations to Metastases: Multiscale Mathematical Modelling of Cancer Growth and Spread?), and a recent appointment to a Chair in Mathematical Biology in the Division, the University seeks to appoint a suitably qualified outstanding candidate to a 5 year tenure-track lectureship in Mathematical Biology. Subject to suitable performance, the position will be made permanent after the initial 5-year period. The Division has a long-standing history of research excellence in Mathematical Biology which it seeks to maintain and develop through this appointment, specifically in the area of cancer modelling. The successful candidate should therefore have an established research reputation in Mathematical Biology (preferably in cancer modelling) and show an enthusiasm for inter-disciplinary research, especially at the Life and Medical Sciences Interface. Start date: 1st September 2009 The position will shortly be advertised formally (jobs.ac.uk) UNIVERSITY OF DUNDEE Three 5-year Post-doctoral Research Assistants in Mathematical Biology Following the recent award of a European Research Council Advanced Investigator Grant to Professor Mark Chaplain, FRSE (?From Mutations to Metastases: Multiscale Mathematical Modelling of Cancer Growth and Spread?), the University seeks to appoint three suitably qualified candidates to three 5-year Post-doctoral Research Assistant positions in Mathematical Biology. Each position will involve inter-disciplinary research on an aspect of cancer modelling. The Division has a long-standing history of research excellence in Mathematical Biology which it seeks to maintain and develop through these appointments. The successful candidates will join a current cancer modelling group of one post-doctoral research assistant and four PhD students. An additional three PhD students will join the group in September 2009, with a further three post-doctoral research assistants joining in 2010, following substantial investment in a new Chair in Mathematical Biology. The successful candidates should have a PhD in Applied Mathematics or cognate discipline (e.g. theoretical physics) and preferably have already undertaken research in some area of Mathematical Biology (ideally cancer modelling) and show an enthusiasm for inter-disciplinary research, especially at the Life and Medical Sciences Interface. Start date: 1st September 2009 The positions will shortly be advertised formally (jobs.ac.uk) Informal approaches concerning these positions may be made to: Prof. Mark Chaplain, FRSE Head of Division Division of Mathematics University of Dundee Dundee DD1 4HN Scotland email: chaplain@maths.dundee.ac.uk tel: 01382 385369 fax: 01382 385516 ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------