---------------------------------------------------- Subject: SMB Digest v12i02 SMB Digest January 11, 2012 Volume 12 Issue 02 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: Workshop: Frontiers in Mathematical Biology: Young Investigator Conf Okinawa Computational Neuroscience Course 2012: Applications Open New Book: Nonlinear PDEs: Mathematical Models in Biology, ... ToC: Mathematical Biosciences and Engineering, vol. 9, no. 1 Support Available for Activities at NIMBioS Bioinformatics Programmer: Computational Immunology), Yale U PhD Studentships: Neurobiology in Strasbourg, Freiburg i. Br., ... Postdoc: Multi-scale Modeling in Immunology, University of Michigan Postdoctoral Fellowship Applications, NIMBioS Postdoc: Algorithmics for NextGen Sequencing Data, Inria Rennes Postdoc: Biomathematics/Game Theory, Math & Stat, U Guelph Postdoc: Bioeng/Applied Maths, Auckland Research Fellow, Infectious Disease Modelling, LSHTM (London) Assistant Director: Mathematical and Physical Sciences, NSF SMBnet Reminders ---------------------------------------------------- From: Doron Levy Date: Wed, Jan 4, 2012 at 11:08 AM Subject: Workshop: Frontiers in Mathematical Biology: Young Investigator Conf Dear Colleagues, The workshop 'Frontiers in Mathematical Biology: Young Investigator Conference' will be held at the Center for Scientific Computation and Mathematical Modeling (CSCAMM) at the University of Maryland, College Park, February 29 - March 2, 2012. A detailed announcement along with other relevant information on the workshop will be continuously updated at http://www2.cscamm.umd.edu/programs/fmb12/. This workshop primarily targets advanced graduate students, postdocs, and researchers at an early stage of their career. It is a follow-up meeting to the 'Frontiers in Mathematical Biology: NSF-NIH PIs Meeting 2010'. Researchers that are interested in attending the meeting must apply online no later than the deadline of *** January 20, 2012 *** through the workshop website. Please encourage your students, postdocs, and junior colleagues to apply as soon as possible as space is limited. In particular, we would like to encourage women and scientists from underrepresented minorities to apply. Partial financial support will be provided to confirmed participants. We look forward to seeing you in CSCAMM. Sincerely, Pierre-Emmanuel Jabin & Doron Levy ---------------------------------------------------- From: Erik De Schutter Date: Mon, Jan 9, 2012 at 10:41 PM Subject: Okinawa Computational Neuroscience Course 2012: Applications Open OKINAWA COMPUTATIONAL NEUROSCIENCE COURSE 2012 Methods, Neurons, Networks and Behaviors June 11 - June 29, 2012. Okinawa, Japan http://www.irp.oist.jp/ocnc/2012 The aim of the Okinawa Computational Neuroscience Course is to provide opportunities for young researchers with theoretical backgrounds to learn the latest advances in neuroscience, and for those with experimental backgrounds to have hands-on experience in computational modeling. We invite graduate students and postgraduate researchers to participate in the course, held from June 11th through June 29th, 2012 at an oceanfront seminar house of the Okinawa Institute of Science and Technology. Applications are through the course web page only; they will open January 9th and close February 12th, 2012. Applicants are required to propose a project at the time of application. Applicants will receive confirmation of acceptance in March. Like in preceding years, OCNC will be a comprehensive three-week course covering single neurons, networks, and behaviors with ample time for student projects. The first week will focus exclusively on methods with hands-on tutorials during the afternoons, while the second and third weeks will have lectures by international experts. Students receive individualized tutoring for their projects. We invite those who are interested in integrating experimental and computational approaches at each level, as well as in bridging different levels of complexity. The sponsor will provide lodging and meals during the course and support travel for those without funding. We hope that this course will be a good opportunity for theoretical and experimental neuroscientists to meet each other and to explore the attractive nature and culture of Okinawa, the southernmost island prefecture of Japan. Invited faculty: . Abbott, Larry . Arbuthnott, Gordon . Bialek, William . Buzsaki, Gyorgy . Canavier, Carmen . De Schutter, Erik . Diesmann, Markus . Doya, Kenji . Häusser, Michael . Ishii, Shin . Izhikevich, Eugene . Kuhn, Bernd . Lee, Daeyeol . Marder, Eve . Stephens, Greg ---------------------------------------------------- From: Vicentiu Radulescu Date: Wed, Jan 4, 2012 at 10:37 AM Subject: New Book: Nonlinear PDEs: Mathematical Models in Biology, ... New Springer Book: Marius Ghergu, Vicentiu D. Radulescu, Nonlinear PDEs: Mathematical Models in Biology, Chemistry and Population Genetics, Springer Monographs in Mathematics, Springer Verlag, Heidelberg, xviii+392 pp., 2011. http://www.springer.com/mathematics/dynamical+systems/book/978-3-642-22663-2?changeHeader ---------------------------------------------------- From: Liwei Ning Date: Wed, Jan 4, 2012 at 2:49 PM Subject: ToC: Mathematical Biosciences and Engineering, vol. 9, no. 1 Mathematical Biosciences and Engineering (MBE) Volume: 9, Number: 1 January 2012 http://www.aimsciences.org/journals/contentsListnew.jsp?pubID=487 1. Nonlinear stochastic Markov processes and modeling uncertainty in populations; Pages : 1 - 25 H.Thomas Banks and Shuhua Hu 2. The implications of model formulation when transitioning from spatial to landscape ecology; Pages : 27 - 60 Robert Stephen Cantrell, Chris Cosner and William F. Fagan 3. An evaluation of dynamic outlet boundary conditions in a 1D fluid dynamics model; Pages : 61 - 74 Rachel Clipp and Brooke Steele 4. Nonlinear functional response parameter estimation in a stochastic predator-prey model; Pages : 75 - 96 Gianni Gilioli, Sara Pasquali and Fabrizio Ruggeri 5. Impact of discontinuous treatments on disease dynamics in an SIR epidemic model; Pages : 97 - 110 Zhenyuan Guo, Lihong Huang and Xingfu Zou 6. Threshold dynamics for a Tuberculosis model with seasonality; Pages : 111 - 122 Xinli Hu 7. A statistical approach to the use of control entropy identifies differences in constraints of gait in highly trained versus untrained runners; Pages : 123 - 145 Rana D. Parshad, Stephen J. McGregor, Michael A. Busa, Joseph D. Skufca and Erik Bollt 8. Assessing the effect of non-pharmaceutical interventions on containing an emerging disease; Pages : 147 - 164 Zi Sang, Zhipeng Qiu, Xiefei Yan and Yun Zou 9. Global analysis of a delayed vector-bias model for malaria transmission with incubation period in mosquitoes Pages : 165 - 174 Cruz Vargas-De-León 10. A quasi-lumped model for the peripheral distortion of the arterial pulse; Pages : 175 - 198 Panagiotes A. Voltairas, Antonios Charalambopoulos, Dimitrios I. Fotiadis and Lambros K. Michalis 11. Effect of branchings on blood flow in the system of human coronary arteries; Pages : 199 - 214 Benchawan Wiwatanapataphee, Yong Hong Wu, Thanongchai Siriapisith and Buraskorn Nuntadilok ---------------------------------------------------- From: Catherine Crawley Date: Fri, Jan 6, 2012 at 10:08 AM Subject: Support Available for Activities at NIMBioS Support Available for Activities at the National Institute for Mathematical and Biological Synthesis March 1, 2012 is the deadline for requests for NIMBioS support for Working Groups, Investigative Workshops, Postdoctoral Fellows, Sabbaticals, and Short-term Visitors for activities beginning summer/fall 2012. All areas of research at the interface of biology and mathematics will be considered, but we are especially interested in activities expanding beyond the areas of research supported to date. Potential organizers of activities in areas of molecular biology, cell biology, network biology, immunology and systems biology are particularly encouraged to submit requests for support of Working Groups or Investigative Workshops. NIMBioS, located at the University of Tennessee-Knoxville, is an NSF-sponsored initiative to foster interdisciplinary research at the interface between mathematical and biological sciences. The institute's mission is to cultivate cross-disciplinary approaches in mathematical biology and to develop a cadre of researchers who address fundamental and applied biological problems in creative ways. Other NIMBIoS sponsors include DHS and USDA, with additional support from the University of Tennessee-Knoxville. More details are posted at http://www.nimbios.org Related Links: NIMBioS Working Groups http://www.nimbios.org/workinggroups/ NIMBioS Investigative Workshops http://www.nimbios.org/workshops/ Postdoctoral Fellowships http://www.nimbios.org/postdocs/ Sabbaticals http://www.nimbios.org/visitors/sabbatical Short-term Visits http://www.nimbios.org/visitors/ ---------------------------------------------------- From: Kleinstein, Steven Date: Mon, Jan 9, 2012 at 11:16 PM Subject: Bioinformatics Programmer: Computational Immunology), Yale U Bioinformatics Programmer (computational immunology) Department of Pathology Yale University School of Medicine Yale University School of Medicine, Department of Pathology is seeking a highly motivated bioinformatics programmer to support collaborative projects in the general area of computational immunology. The successful candidate will work in a highly dynamic team environment to apply bioinformatics methods in support of a diverse array of studies in collaboration with computational, laboratory and clinical investigators. The ideal candidate will have strong quantitative and programming abilities, along with a demonstrated interest in applying these skills to problems in biology. MS/Ph.D. Degree preferred. New Ph.D. graduates are encouraged. Expertise is desired in several of the following areas: gene expression analysis (microarray and RNA-Seq), promoter/cis-regulatory analysis, pathway analysis, DNA-Seq (cancer mutation detection), unsupervised and supervised learning; working knowledge of Windows/ Linux and bioinformatics languages (e.g. R/Bioconductor); web and database development; and knowledge of programming/scripting languages such as JavaScript, SQL, PHP, Java, C/C++. Novel bioinformatics algorithm development is a plus, but not required. Applicants should submit a letter of interest describing their background and curriculum vitae and the names, addresses, telephone numbers and e-mail addresses of three references to: e-mail: steven.kleinstein@yale.edu or Steven Kleinstein, Ph.D Assistant Professor of Pathology Department of Pathology Yale University School of Medicine 300 George Street, Suite 505 New Haven, CT 06511 Review of applications will begin on November 1, 2011. Yale University is an equal opportunity affirmative action employer. Minority and female applicants are encouraged to apply. ---------------------------------------------------- From: Janina Kirsch Date: Mon, 9 Jan 2012 12:49:39 +0100 Subject: PhD Studentships: Neurobiology in Strasbourg, Freiburg i. Br., ... The Erasmus Mundus Joint Doctoral Program "NeuroTime - Neural Processing on Time" is inviting applications for fully funded 4-year joint PhD studentships between 6 Universities (Strasbourg, Freiburg i. Br., Amsterdam, Basel, Bangalore and Jerusalem) and 2 Associated Partners (IHD and Neurex), coordinated by the University of Strasbourg. in the field of Neurobiology. The objective of NeuroTime is to provide PhD students with a top quality international training program in multidisplinary neuroscience that will contribute through the creation of a 'European Higher Education Area' in investigating a process lying at the heart of brain function & dysfunction: processing of time. The training provided by our program integrates developmental, molecular, cellular & behavioral neuroscience, chronobiology, computational neuroscience & neurotechnology. The projects are collaborative and typically involve two of the six above institutes and will require some travel. Students should have a solid background in biology, especially neuroscience (on a master level or equivalent). An excellent academic record, documented interest in research and fluency in English are required. If you are interested, go to http://www.neurotime-erasmus.org Deadline for applications: January 15, 2012. If you have questions regarding the program and applications, you can contact us at ntadmin@unistra.fr ---------------------------------------------------- From: Denise Kirschner Date: Wed, Jan 4, 2012 at 12:03 PM Subject: Postdoc: Multi-scale Modeling in Immunology, University of Michigan Multi-scale Modeling in Immunology A postdoctoral position is available jointly in the laboratories of Jennifer Linderman in the Departments of Chemical Engineering and Biomedical Engineering and Denise Kirschner in the Department of Microbiology and Immunology, both at the University of Michigan. The project is part of grants to use systems biology approaches to build multi-scale and multi-organ approaches to understand the immune response to tuberculosis and involves integrating data derived by our collaborators together with in silico models developed in our groups. An estimated one-third of the human population is infected with the pathogen Mycobacterium tuberculosis, making it a global health problem. The post-doctoral fellow will concentrate on projects that require skills in computational modeling in biology. Thus the ideal applicant will have extensive experience in modeling and some programming needed for working with our existing agent-based models, and, in addition, will have an ability to read scientific literature in immunology, microbiology and systems biology. Good communication skills - both written and oral - are essential. Pay is determined by the standard NIH post-doc pay scale, which is commensurate with education and experience. Applicants should send a CV, names and email addresses of 3 references, and a letter describing research interests and summarizing PhD work to Denise Kirschner kirschne@umich.edu and Jennifer Linderman linderma@umich.edu. Copies of accepted or published papers are welcome. http://malthus.micro.med.umich.edu/lab ---------------------------------------------------- From: Catherine Crawley Date: Fri, Jan 6, 2012 at 2:02 PM Subject: Postdoctoral Fellowship Applications, NIMBioS Call for Postdoctoral Fellowship Applications at NIMBioS -- Next Deadline: March 1, 2012 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 $2,000. 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 three 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 2012 is March 1, 2012. 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, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture with additional support from The University of Tennessee, Knoxville. ---------------------------------------------------- From: Claire Lemaitre Date: Mon, 09 Jan 2012 11:46:41 +0100 Subject: Postdoc: Algorithmics for NextGen Sequencing Data, Inria Rennes Inria project team SYMBIOSE is seeking highly qualified and motivated candidates for a 12 months postdoctoral position. Research Program : Next Generation Sequencing technologies generate data of a new type in huge volumes and crucial computational developments are needed to take full advantage of these data. The successful candidate will develop new algorithms to identify complex genomic variants in such data from multiple samples without the use of a reference genome. Our approach relies on a formal model based on the De-Bruijn graph structure to handle huge amounts of data and extract biologically relevant information. For further details visit our website http://www.irisa.fr/symbiose/ and the project description http://www.irisa.fr/symbiose/index.php?option=com_docman&task=doc_download&gid=29 Profile : - PhD in computational biology or algorithmics with a strong interest for biology - good programming skills (C, C++, python, java, ...) - background in sequence and graph algorithmics - a prior experience with high throughput sequencing data will be appreciated - to apply, the candidate must have spent less than 6 months in France during the period April 2010 - April 2011 Working environment : The position is located in France, in the city of Rennes at the INRIA Rennes - Bretagne Atlantique center. SYMBIOSE is a dynamic and multi-disciplinary research team working in computational biology and bioinformatics. The contract is for 12 months, starting as soon as January 2012. Salary is 2620 euros monthly before taxes deduction. Application : Please send a cover letter, a CV with publications and two references contacts to claire.lemaitre@inria.fr. ---------------------------------------------------- From: Chris Bauch Date: Mon, Jan 9, 2012 at 9:56 AM Subject: Postdoc: Biomathematics/Game Theory, Math & Stat, U Guelph Postdoctoral Research Position in Biomathematics/Game Theory Department of Mathematics and Statistics, University of Guelph Outstanding, highly motivated candidates are invited to apply for a postdoctoral research position in biomathematics. Potential topics include sustainability science, applications of game theory and related approaches, common pool resource problems, emergence of social norms and cooperative behaviour, and health (broadly defined, including ecosystem health and social/cultural health). Research will emphasize projects that integrate game theoretical/behavioural modeling perspectives with biomathematical approaches. The successful applicant will have a strong quantitative background including a Ph.D. in mathematics, physics, theoretical biology, engineering, computer science or a related field. The position also requires strong expertise in computer programming or modelling software; previous experience with biomathematics research; excellent written and oral communication skills; ability to work in on interdisciplinary research topics; and ability to work collaboratively. The applicant will be based in the laboratory of Professor Chris Bauch (www.uoguelph.ca/~cbauch ) in the Department of Mathematics and Statistics and will collaborate with Bauch and colleagues. The applicant will have access to resources such as the newly established Infectious Diseases and Ecological Systems (IDES) Computational Laboratory. Guelph is about one hour?s drive from Toronto and its many attractions and opportunities. Guelph has consistently been ranked as one of the top 10 places to live in Canada. The position is free from teaching obligations although there may be opportunities to teach undergraduate mathematics courses, depending on teaching needs of the department. Salary is commensurate with experience. The initial appointment is for one year with automatic renewal for a second year if performance is satisfactory. To apply, please send cover letter, research statement, representative publications, and a CV including names and contact details of three references to Professor Chris Bauch (cbauch at uoguelph dot ca). Applications received prior to February 10, 2011 will receive priority but applications will be considered until the position is filled. The appointment will start in Summer or Fall 2012. ---------------------------------------------------- From: Leo Cheng Date: Mon, Jan 9, 2012 at 4:07 PM Subject: Postdoc: Bioeng/Applied Maths, Auckland The Gastrointestinal research group at the Auckland Bioengineering Institute is seeking to employ a Research Scientist with a three-year appointment in the Research Fellow/Senior Research Fellow grade subject to experience. The primary focus of the applicant will be directed to modelling various aspects of gastrointestinal motility, supervision of existing graduate students and eventually develop a stream of research funding in their area of expertise. The research group is currently involved in collaborative work in a number of areas including: 1) high performance computational modelling of gastrointestinal cell electrophysiology, 2) soft-tissue mechanics, 3) signal processing, 4). image processing of confocal images of tissue, medical images (MRI/CT), and high resolution video. Applicants should hold a doctoral degree in the general fields of biomedical engineering, applied mathematics, computational physiology or related disciplines and ideally have 2 or more years research experience. For additional information see: http://tinyurl.com/gi-vacancy Please submit your application directly online (Vacancy Number: 13726): http://www.auckland.ac.nz/opportunities. Closing date is 23 Jan 2012. ---------------------------------------------------- From: Emilia Vynnycky Date: Thu, Jan 5, 2012 at 10:42 AM Subject: Research Fellow, Infectious Disease Modelling, LSHTM (London) Research Fellow in Infectious Disease Modelling Faculty of Epidemiology & Population Health Salary: £35,511 to £38,569 per annum inclusive Closing Date: Thursday 19 January 2012 Interview Date: Wednesday 25 January 2012 Reference: RW10 The London School of Hygiene & Tropical Medicine, an internationally renowned centre for research and postgraduate education in public health and tropical medicine, is seeking to recruit an enthusiastic Research Fellow to work on modelling M tuberculosis transmission and control in Africa as part of the CREATE consortium to design novel public health interventions to reduce the burden of HIV-related TB at the population level (http://www.tbhiv-create.org/). Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide, particularly in Africa, where the HIV epidemic has contributed to substantial increases in the burden of TB. The aim of the research is to understand the effect of a novel strategy of community-wide preventive treatment on control of tuberculosis in settings of high incidence. This will involve developing and parameterising mathematical models, using international data collected as part of major ongoing empirical studies under the CREATE consortium and funded by the Bill and Melinda Gates foundation. CREATE collaborators include the Aurum Institute for Health Research and the Desmond Tutu Centre, South Africa, the Municipal Health Secretariat of Rio de Janeiro, Brazil, the Zambart Project, Zambia and WHO, Geneva. The post involves a range of complex and original scientific work and requires a high degree of personal initiative. The post-holder will be based in a dynamic, supportive and stimulating group at LSHTM with close links to colleagues at HPA and collaborators in Africa. The initial appointment will be for a minimum of 12 months to the end of April 2013 with possible extension to March 2014. Starting salary will be in the range of £35,511 - £38,569 per annum inclusive. Applications should be made on-line via the website jobs.lshtm.ac.uk. The reference for this post is RW10. Applications should include the names and email contacts of 2 referees who can be contacted immediately if shortlisted. Any queries regarding the application process may be addressed to jobs@lshtm.ac.uk. For further details, please visit: http://jobs.lshtm.ac.uk/Vacancy.aspx?ref=RW10 ---------------------------------------------------- From: Henry Warchall Date: Fri, Jan 6, 2012 at 11:36 AM Subject: Assistant Director: Mathematical and Physical Sciences, NSF Dear Colleague: We are initiating a national search for the National Science Foundation's Assistant Director for Mathematical and Physical Sciences (MPS) and seek your assistance in the identification of candidates. The Assistant Director, MPS, leads a Directorate comprised of five divisions: Astronomical Sciences, Chemistry, Materials Research, Mathematical Sciences, and Physics; as well as the Office of Multidisciplinary Activities. Attached is a PDF version of this letter, which includes an information sheet summarizing the Directorate's activities and the responsibilities of the position, together with the criteria that will be used in the search. Employment may be on a temporary or permanent basis in the Federal Service or by temporary assignment under provisions of the Intergovernmental Personnel Act. We seek your help in identifying candidates with the following qualifications: outstanding leadership; a deep sense of scholarship; a grasp of the issues facing the mathematical and physical science communities in the areas of education and research; and the ability to serve effectively as a key member of the NSF management team. We are especially interested in identifying women, members of minority groups, and persons with disabilities for consideration. Recommendations of individuals from any sector -- academic, industry, or government -- are welcome. Please send your recommendations, including any supporting information that you can provide, to the AD/MPS Search Committee via e-mail (mpssrch@listserv.nsf.gov) or at the following address: National Science Foundation, Office of the Director, Suite 1205, 4201 Wilson Boulevard, Arlington, VA 22230. We would appreciate receiving your recommendations by January 15, 2012. Your assistance in this very important task is appreciated. Sincerely, Subra Suresh Cora B. Marrett Director Deputy Director National Science Foundation 4201 Wilson Boulevard, Suite 1205 Arlington, VA 22230 Enclosures Search Committee Review Criteria: [http://www.nsf.gov/od/searches/mps-111104/mps_review_criteria.jsp] Overview of the Directorate for Mathematical and Physical Sciences: [http://www.nsf.gov/od/searches/mps-111104/mps_info.jsp] PDF version of Letter and Enclosures: [ http://www.nsf.gov/od/searches/mps-111104/nsf_admpssearch_dearcolleagueletter_111104.pdf ] ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------