---------------------------------------------------- Subject: SMB Digest v08i25 SMB Digest June 27, 2008 Volume 08 Issue 25 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 on Biomathematics and Ecology Education and Research DIMACS Workshop on Nanotechnology and Biology, October 22 - 23 TOC: MBE Volume 5, Issue 3 Increased Impact Factor: Nonlinearity, IOP Impact Factor Rises 41%: Inverse Problems, IOP Postdoc Positions: University of Alberta Postdoc: CERES-ERTI, Ecology & Evolution Lab UMR 7625, ENS Paris Post-doctoral Fellow: Computational Biologist, Hamilton, Ontario SMBnet Reminders ---------------------------------------------------- From: bmasmith@ncsu.edu Date: Sat, 21 Jun 2008 02:12:50 -0400 (EDT) Subject: Symposium on Biomathematics and Ecology Education and Research You are invited to join us for the Symposium on Biomathematics and Ecology Education and Research (BEER-2008), which will take place at Illinois State University, Normal, IL during September 6-7, 2008. The scientific theme and the program of BEER-2008 will include sessions with invited talks and a workshop from a broad range of topics of Biomathematics and Ecology research as well as education. Please see the attached flyer for details. Special emphasis will be given to interdisciplinary research and the interaction between mathematics, biology and ecology. The meeting is planned around the theme of linking mathematical and statistical modeling to biology and ecology to stimulate cross-fertilization of theoretical, methodological and computational research issues of high-dimensional data by focusing attention to the arena of applied problems in these cross-disciplinary areas . A primary goal of the conference is to present important venues for young researchers, international researchers, and graduate students an opportunity to interact with world class senior researchers, to share, and to disseminate their research and expertise. Additionally a workshop focusing on educational aspects of biomathematics will be conducted by Dr. Tim Comar of Benedictine University. Participants intending to present a talk are invited to submit an abstract by e-mail or online from the symposium website. The deadline for the abstract submission is July 28, 2008. All the relevant information for attending the Conference and for submitting an abstract will soon be available on the conference web site: http://www.biomath.ilstu.edu/beer ---------------------------------------------------- From: Linda Casals Date: Tue, 24 Jun 2008 11:53:51 -0400 (EDT) Subject: DIMACS Workshop on Nanotechnology and Biology, October 22 - 23 DIMACS Workshop on Nanotechnology and Biology October 22 - 23, 2008 DIMACS Center, CoRE Building, Rutgers University Organizers: Stan Dunn, Rutgers University, smd at occlusal.rutgers.edu Yannis Androulakis, Rutgers University, yannis at rci.rutgers.edu Charlie Roth, Rutgers University, cmroth at rci.rutgers.edu Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology. Workshop Announcement: Recent years have witnessed the development of fabrication and characterization technologies to manipulate and analyze matter at the nanoscale. These technologies have applications in myriad areas, including in biology, where nature has evolved its own nanotechnologies that inspire many contemporary engineered nanodevices. As first generation nanotechnologies have provided proofs of principle for many exciting applications, the need for better understanding of biology and physics at the nanoscale through modeling and computation has become apparent. This workshop will explore the foundations of nanoscale assembly in natural and engineered systems. Natural systems may include viruses, organelles, or multi-molecular machines as they self-assemble and take shape in processes that might include, for example, development, adaptation, or cancer. Engineered systems under development include smart drug delivery systems, DNA-based fabrication, layer-by-layer assembly and electrospun nanofibers. The ability to model and understand the natural systems will accelerate the development of engineered nanosystems. While efforts to attain better understanding through modeling and computation are of primary interest, the integration of modeling and experiments is quite relevant and necessary to advance our understanding of self-assembly at the nanoscale. Because this field is so interdisciplinary, we envision an audience that includes biologists, chemists, physicists, computer scientists and engineers. Call for Participation: While several speakers will be invited, there will be room for both podium and poster presentations from unsolicited abstracts. We welcome submissions from biologists, chemists, physicists, computer scientists and engineers working in areas related to modeling of biological systems at the nanoscale. Those interested should submit an abstract (not longer than 2 pages) to cmroth at rci.rutgers.edu by September 1, 2008. Registration: Pre-registration deadline: October 15, 2008 Please see website for additional registration information. Information on participation, registration, accommodations, and travel can be found at: http://dimacs.rutgers.edu/Workshops/Nanotechnology/ ---------------------------------------------------- From: kuang Date: Fri, 20 Jun 2008 13:20:29 -0700 Subject: TOC: MBE Volume 5, Issue 3 Mathematical Biosciences and Engineering Volume 5, Number 3, July, 2008 http://www.mbejournal.org/StaticLinks/Vol-5-No-3.htm Akinori Awazu, Input-dependent wave propagations in asymmetric cellular automata: possible behaviors of feed-forward loop in biological reaction network, pp. 419 - 427. Luis F. Gordillo, Stephen A. Marion and Priscilla E. Greenwood, The effect of patterns of infectiousness on epidemic size, pp. 429 - 435. Abba B. Gumel and Baojun Song, Existence of multiple-stable equilibria for a multi-drug-resistant model of mycobacterium tuberculosis, pp. 437 - 455. Shingo Iwami, Shinji Nakaoka and Yasuhiro Takeuchi, Mathematical analysis of a HIV model with frequency dependence and viral diversity, pp. 457 - 476. Guichen Lu and Zhengyi Lu, Permanence for two-species Lotka-Volterra cooperative systems with delays, pp. 477 - 484. Gesham Magombedze, Winston Garira and Eddie Mwenje, Modelling the immunopathogenesis of HIV-1 infection and the effect of multidrug therapy: The role of fusion inhibitors in HAART, pp. 485 - 504. Fabio Augusto Milner and Ruijun Zhao, A deterministic model of schistosomiasis with spatial structure, pp. 505 - 522. Arni S. R. Srinivasa Rao, Modeling the rapid spread of avian influenza (H5N1) in India, pp. 523 - 537. Alain Rapaport and Jerome Harmand, Biological control of the chemostat with nonmonotonic response and different removal rates, pp. 539 - 547. Ivo Siekmann, Horst Malchow and Ezio Venturino, An extension of the Beretta-Kuang model of viral diseases, pp. 549 - 565. G. A. K. van Voorn, D. Stiefs, T. Gross, B. W. Kooi, U. Feudel and S. A. L. M. Kooijman, Stabilization due to predator interference: Comparison of different analysis approaches, pp. 567 - 583. Christine K. Yang and Fred Brauer, Calculation of R0 for age-of-infection models, pp. 585 - 599. ---------------------------------------------------- From: Zoe Crossman Date: Fri, 27 Jun 2008 12:10:58 +0100 Subject: Increased Impact Factor: Nonlinearity, IOP We are pleased to report that, on the release of ISI's 2007 Journal Citation Reports, Nonlinearity's impact factor has increased to 1.339. For further reasons to publish with us, please visit our author benefits page at: http://herald.iop.org/NONIF2008SMB/m128/cid//link/1743 Best wishes Kate Watt Publisher Nonlinearity ---------------------------------------------------- From: Zoe Crossman Date: Fri, 27 Jun 2008 12:19:28 +0100 Subject: Impact Factor Rises 41%: Inverse Problems, IOP We are pleased to report that, on the release of ISI's 2007 Journal Citation Reports, Inverse Problems' impact factor has increased to 1.854. For further reasons to publish with us, please visit our author benefits page at: http://herald.iop.org/IPIF2008SMB/m128/cid//link/1744 Best wishes Kate Watt Publisher Inverse Problems ---------------------------------------------------- From: Cecilia Hutchinson Date: Thu, 26 Jun 2008 16:15:08 -0600 Subject: Postdoc Positions: University of Alberta New postdoctoral positions at the University of Alberta Postdoctoral position modelling spatial ecology of streams. Postdoctoral position modelling mountain pine beetle. Full details of the positions are available at the home page of Mark Lewis (www.math.ualberta.ca/~mlewis). ---------------------------------------------------- From: David Claessen Date: Mon, 23 Jun 2008 10:44:41 +0200 Subject: Postdoc: CERES-ERTI, Ecology & Evolution Lab UMR 7625, ENS Paris Post-doc in theoretical ecology at ENS Paris (CERES-ERTI, Ecology & Evolution Lab UMR 7625) Physiologically structured population models for viability analysis Second call with new submission deadline: 1 September 2008 Applications are invited for a one-year postdoctoral position funded by R2DS (http://www.r2ds.centre-cired.fr/) to investigate the dynamics of small populations with plastic life histories, using physiologically structured population models. Project description: Population persistence is notably conditioned by the degree of individual variation in reproductive success, which depends on variation in any part of the life cycle. Yet, the majority of studies that examined population extinction have tended to ignore life history variation and plasticity. Here, we wish to use life history models to inform the dynamics of small populations and ask how plasticity in life history traits influences extinction dynamics. Many aspects of life history can interact with population dynamics and the project concentrates on three of them, namely growth, maturation and survival. The post-doc will explore this issue by developing models that account for variation in life history traits using the theory of physiologically structured populations (PSP). This theory takes into account that physiological development (e.g. growth, maturation) depends on the current state of the environment (e.g., temperature, food and predator densities). In turn, the influence of the population on the environment closes a feedback loop between environment, population and life history. The theory of PSP models is thus particularly well-suited to study the interaction between population dynamics and plastic life history. Small populations are subject to stochastic fluctuation in abundance. The project aims to study the feedback of this variability on life history and the consequences for extinction dynamics. The models will be parameterized with estimates from field and experimental studies undertaken with the common lizard, a species with strong thermal and food plasticity in life history traits. The post-doc will be based at the Ecology & Evolution Lab (CNRS, UMR 7625) at the Ecole Normale Supérieure (CERES-ERTI) in Paris, where the applicant will work with David Claessen and Jean-François Le Galliard. This post-doc project is part of a research network on the dynamics of small populations funded by ANR from 2008 to 2012 and will therefore interact with a larger group of researchers. The post can start on October 1st or November 1st 2008 and will run for one year with a possible one year extension by applying to extended funding from the R2DS network in spring 2009. Gross salary will be 2500 EUR per month. The starting date can be postponed in exceptional circumstances. Candidate profile: There are no nationality restrictions and the successful candidate will: (1) Possess a doctoral degree in ecology and/or mathematics, dating no more than 2 years before 1 October 2008, though the last condition may be negotiated in exceptional circumstances. (2) Not have worked in the hosting lab, nor have prepared his thesis within the hosting lab, except for a return after a period of absence of at least one year. (3) Have strong competence in modeling, with an interest in population dynamics, viability analyses and conservation biology and knowledge of C programming or closely related languages. (4) Personal qualities needed for group work and inter-disciplinary study. Contact: Application: Chantal Cuisinier, tel.: +33 1 44 27 36 89, email: Chantal.Cuisinier@snv.jussieu.fr, postal address: CNRS UMR 7625, Université Paris 6, 7 Quai St Bernard, 75005 Paris Research project: David Claessen, tel.: +33 1 44 32 27 21, email: david.claessen@ens.fr How to apply: 1. Applicants have until September 1 2008 to send a completed application form available below to the Application contact point. 2. The lab director and a local jury will select one candidate from the application forms and contact the candidates from September 31 2008. 3. The regional office of the CNRS will be responsible for drawing up the contract. Download a pdf version of the Application form from http://www.environnement.ens.fr/postdoc.html ---------------------------------------------------- From: Jonathan Dushoff Date: Tue, 24 Jun 2008 16:33:02 -0400 Subject: Post-doctoral Fellow: Computational Biologist, Hamilton, Ontario We are seeking a computational biologist to work on theoretical methods for analyzing metagenomic data, and exploring the 'space' in which genomes evolve. The successful candidate will pursue collaborative research with Dr. Jonathan Dushoff, and collaborators at Georgia Tech, Princeton University, and UC Davis, and will be expected to take an active role in shaping the direction of this research. We are looking for a candidate with a solid grounding in biology, as well as computational and mathematical skills. The candidate will be expected to help develop, and to apply, novel statistical and mathematical methods to understanding genomic data. The position will be based in the Disease Modeling lab at the Department of Biology, where we are currently developing a state-of-the-art computer platform for collaborative multi-scale modeling. Our lab also has access to the high-performance Sharcnet computer cluster. Hamilton, Ontario is a pleasant place to live and work, less than an hour from both the Niagara gorge and from Toronto (and convenient to the latter by public transportation). The McMaster campus is large and green; conveniently accessible by city buses; within walking distance of pleasant residential neighborhoods; and adjacent to the Cootes Paradise section of the Royal Botanical Gardens. The position is expected to last for two years. Review of applications will begin on 1 July 2008. Anticipated starting date is 1 Oct 2008, and is negotiable. To apply, please send (by email, in PDF format, to the address below): (1) a CV; (2) a list of three scientists who can be contacted for letters of reference; (3) a one-page statement of research interests; and (4) a half-page summary of skills and experience relevant to the pursuit of computational biology. ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------