---------------------------------------------------- Subject: SMB Digest v10i23 SMB Digest June 9, 2010 Volume 10 Issue 23 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: Conference: Synthetic Biology, 15-16 Dec, U of Evry-Val-d'Essonne NIMBioS Investigative Workshop on Modeling Wildlife Zoonoses NIMBioS Investigative Workshop on Solid Tumor Modeling CfP: 2010 International Workshop on Domain Driven Data Mining CfP: Computational Bioimaging, ISVC10, Nov 29 - Dec 1, Las Vegas NIMBioS News, May/June 2010 - Vol 2, Issue 3 Conference Postcards Postdocs: Laboratory of Biological Modeling, NIDDK, NIH Postdoc: Bioinformatics/Computational Biology, UNC Charlotte NIH Research Jobs - June Update SMBnet Reminders ---------------------------------------------------- From: Dominique Zeliszewski Date: Mon, Jun 7, 2010 at 5:06 AM Subject: Conference: Synthetic Biology, 15-16 Dec, U of Evry-Val-d'Essonne GenopoleŽ has the pleasure to announce the International Conference on SYNTHETIC BIOLOGY Bottom-up, Top-down and Cell-free approaches, Intellectual Property issues that will be held on December 15th and 16th, 2010 at the University of Evry-Val-d'Essonne, Evry, France Several approaches of Synthetic Biology research have been individualized - Top-down, Bottom-up, and Cell-free systems - all of these having produced many encouraging results. Our conference will allow the worldwide leaders in Synthetic Biology to show their latest advances. As Synthetic Biology moves forwards, new Intellectual Property Right models need to be defined, and the choice of these models will have a major impact in shaping the future of Synthetic Biology. A session will be devoted to Intellectual Property to address these issues. Our conference follows the Biomanufacturing Symposium also organized by GenopoleŽ on December 14th, in which some applications of Synthetic Biology will be presented. Submit your abstract or article before June 30th. Articles will be published in Biotechnology Journal after peer review. GenopoleŽ will award a limited number of grants to post-docs and PhD-students being the first author of an abstract selected for a poster or for a contributed talk. More information on http://syntheticbiology2010.genopole.fr Dominique ZELISZEWSKI Scientific communication Epigenomics Project/iSSB GenopoleŽ, CNRS UPS3201, UniverSud Paris, University of Evry Genopole Campus 1 - Genavenir 6 5 rue Henri Desbručres - F-91030 EVRY cedex Phone : 331 69 47 44 46- Fax : 331 69 47 44 37 dominique.zeliszewski@epigenomique.genopole.fr ---------------------------------------------------- From: Catherine Crawley Date: Tue, 08 Jun 2010 14:12:51 -0400 Subject: NIMBioS Investigative Workshop on Modeling Wildlife Zoonoses The National Institute for Mathematical and Biological Synthesis (NIMBioS) is now accepting applications for its Investigative Workshop: Mathematical Modeling of Wildlife and Virus Zoonoses to be held Nov. 8-10, 2010, at NIMBioS. Objectives: The focus of the workshop is to define, discuss, and develop approaches to collaboratively address critical gaps that remain in mathematical modeling of the ecology and natural history of zoonotic viruses, how they are maintained in their reservoirs, the processes and mechanisms that lead to transmission, host switching, and molecular events that lead to transfer and adaptation to a new host and post-transfer adaptation. Importantly, modeling efforts are essential to the discovery of new ecological paradigms and true understanding of the nature of episodic zoonotic epidemics or outbreaks such as those caused by RNA viruses, Ebola virus, SARS CoV, Nipah virus, and Machupo virus. By bringing together experts in mathematical models in conjunction with those engaged in experimental analyses of emerging viruses, the workshop will provide a venue to build collaborative efforts to integrate approaches that would result in the interpretation of ecological trends in the spread of zoonotic diseases, provide greater understanding of underlying causes of outbreaks, and provide guidelines for their control and prevention. Co-organizers: Colleen B. Jonsson (Univ. of Louisville); Linda J. S. Allen (Texas Tech Univ.); Pauline van den Driessche (Univ. of Victoria) Location: NIMBioS at the University of Tennessee, Knoxville For more information about the tutorial and a link to the online application form, go to http://www.nimbios.org/workshops/WS_zoonoses.html Application deadline: Aug. 6, 2010 ---------------------------------------------------- From: Catherine Crawley Date: Tue, 08 Jun 2010 14:19:56 -0400 Subject: NIMBioS Investigative Workshop on Solid Tumor Modeling The National Institute for Mathematical and Biological Synthesis (NIMBioS) is now accepting applications for its Investigative Workshop: Solid Tumor Modeling to be held Jan. 19-21, 2011, at NIMBioS. Objectives: The principal aim of this Investigative Workshop is to discuss current achievements and challenges in modeling solid tumors in the human body and to identify areas in modeling, computing, laboratory experimentation, and clinical diagnosis that should be pursued to improve our understanding of tumor development and ultimately treatment. The focus will be on modeling tumor level cancer progression. However, all pertinent systems that influence such growth will be open for discussion and analysis, including ongoing genetic mutation and genetic feedback, stem cells, angiogenesis and vascular dynamics, lymph system interaction, metastasis, mechanical properties of and interaction with host tissue, and immune system response. Specifically, we wish to identify the relative advantages of certain models (or modeling principles) in specific host tissue environments; the current state-of-the-art in modeling, from the points of view of biophysical relevance, mathematical suitability, and computational and technical advances; the perceived future directions and important challenges in next-generation tumor models; and the near-term feasibility of modeling in a clinical, patient-specific setting. Topics of discussion may include hybrid and multi-scale modeling, multiphase modeling, parameter estimation and relevant experimental and clinical data collection, and high-performance computing and visualization. Co-organizers: Vittorio Cristini (Univ. of Texas, Houston); John Lowengrub (Univ. of California, Irvine); Kasia Rejniak (Moffitt Cancer Center); Steven M. Wise (Univ. of Tennessee, Knoxville) Location: NIMBioS at the University of Tennessee, Knoxville For more information about the tutorial and a link to the online application form, go to http://www.nimbios.org/workshops/WS_tumor_modeling.html Application deadline: Oct. 15, 2010 The National Institute for Mathematical and Biological Synthesis (NIMBioS) 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: xinhua zhu Date: Sun, Jun 6, 2010 at 8:31 AM Subject: CfP: 2010 International Workshop on Domain Driven Data Mining Call for Papers - DDDM2010 July 23, 2010 - Due date for full workshop papers The 2010 International Workshop on Domain Driven Data Mining Sydney, Australia, December 13-17, 2010 In conjunction with the 2010 IEEE International Conference on Data Mining (ICDM 2010) URL: http://datamining.it.uts.edu.au/dddm/dddm10/ ---------------------------------------------------- From: Joăo Manuel R. S. Tavares Date: Tue, 8 Jun 2010 15:25:40 +0100 Subject: CfP: Computational Bioimaging, ISVC10, Nov 29 - Dec 1, Las Vegas Dear Colleague, Within the ISVC10 - 6th International Symposium on Visual Computing (http://www.isvc.net), to be held in Las Vegas, Nevada, USA, in November 29 - December 1, 2010, we are organizing the Special Track "ST5 - Computational Bioimaging" (http://www.isvc.net/ST5.pdf). ---------------------------------------------------- From: NIMBioS Date: Tue, Jun 8, 2010 at 9:16 AM Subject: NIMBioS News, May/June 2010 - Vol 2, Issue 3 See: http://campaign.constantcontact.com/render?v=001vuCdHl1qDg5K5nnHPt_aRyJvOz7vN8j0ov6U-KlgRiI-atFWVrjCXw6Ghl2XOKuQ1Mq0-EuAGio6AwfFV676g7w-aLyIiKtBqk9gODKHCHWs37pHqrNl_DRHqsSuAZzGGDiAzff6fps%3D ---------------------------------------------------- From: Raymond Mejia Date: Tue, 8 Jun 2010 14:30:53 -0400 (EDT) Subject: Conference Postcards The concept of a Conference Postcard has been introduced to provide an insightful description of important scientific results presented at a conference to those that were not present to savor it. (See http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000746 .) The SMB Digest includes notes and commentary on areas of mathematical biology, and has linked to these when they are beyond the scope of a digest. Hence, we encourage the readers to submit Conference Postcards to SMBnet@smb.org, and we shall include or link to these as appropriate. Best regards -- Ray ---------------------------------------------------- From: Vipul Periwal Date: Fri, Jun 4, 2010 at 1:09 PM Subject: Postdocs: Laboratory of Biological Modeling, NIDDK, NIH NIDDK, a major research component of the National Institutes of Health (NIH) and the Department of Health and Human Services (DHHS), is recruiting postdoctoral fellows in the Laboratory of Biological Modeling(LBM), located on the Main Campus in Bethesda, Maryland. The candidates will work with Dr. Vipul Periwal, Principal Investigator of the Mathematical Cell Modeling Section in the LBM. The research goals of the section are mainly focused on three areas: 1) quantitative analysis of tissue growth and development processes, 2) quantitative modeling of mitochondrial respiration and function, and its connections to mitochondrial dynamics, fission, fusion and mitophagy, and 3) insulin secretion and action on glucose utilization and lipolysis suppression. Candidates must have a Ph.D. with less than five years of postdoctoral research experience, as well as a strong research background in biophysics, applied mathematics or computational science. Interest and experience in biological modeling is desirable for this position. Salary is commensurate with experience and accomplishments (check here for stipend ranges). Initial appointment is one to two years, with extension up to five years. Positions are open until filled. Interested candidates should send curriculum vitae, statement of research interests, relevant publications, and contact information of three references to Dr. Vipul Periwal at vipulp AT mail.nih.gov OR LBM, NIDDK, Suite 4007, MSC 5621, 12A South Drive, Bethesda MD 20892-5621. HHS and NIH are Equal Opportunity Employers. The NIH is dedicated to building a diverse community in its training and employment programs. ---------------------------------------------------- From: Guo, Jun-tao Date: Fri, Jun 4, 2010 at 4:17 PM Subject: Postdoc: Bioinformatics/Computational Biology, UNC Charlotte A postdoctoral research associate position in bioinformatics and computational biology will be available in September of 2010 at the University of North Carolina at Charlotte. The successful candidate will have the opportunity to participate in an NSF-funded research project. The goal of the project is to develop computational methods for genomic scale prediction of transcription factor (TF) binding sites, through modeling protein-DNA interactions. Applicants should be strongly motivated and have a Ph.D. in Bioinformatics/Computational Biology, Computational Chemistry, Computer Science, Statistics, or a related field. Working experience with Monte Carlo simulation will be a plus. Strong ability in programming is required. The initial appointment is for one year and may be extended. Interested candidates should send an updated CV to Dr. Jun-tao Guo (jguo4@uncc.edu), Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223 ---------------------------------------------------- From: "Owens, Roland (NIH/OD) [E]" Date: Wed, 2 Jun 2010 19:01:39 -0400 Subject: NIH Research Jobs - June Update Tenured or Tenure-Track Epidemiologist Hormonal and Reproductive Epidemiology Branch, NCI DCEG (deadline: August 15*) The Hormonal and Reproductive Epidemiology Branch (HREB, http://dceg.cancer.gov/hreb), a component of NCI's intramural Division of Cancer Epidemiology and Genetics (DCEG), is recruiting an epidemiologist to develop an independent research program focused on one or more hormonally-related cancers (e.g., breast, prostate, endometrial, etc.). It is expected that the successful candidate will develop a distinctive interdisciplinary program that complements ongoing investigations and builds on the existing strengths of NCI's intramural research program. Current research includes the evaluation of novel risk factors, identification of common susceptibility genetic loci, molecular profiling of tumors to evaluate etiologic heterogeneity and determinants of prognosis, identification of early markers of risk, measurement of circulating and local levels of endogenous hormones using novel assays, and assessment of other biomarkers. Candidates must have a doctorate in epidemiology, or a medical degree or doctorate in a biologically-related discipline (with additional training or post-doctoral experience in epidemiology). They must have at least two years of post-doctoral research experience and an established record of publications that demonstrates their ability to design, conduct, analyze and interpret data from molecular epidemiology studies. Candidates should have knowledge of and demonstrated capacity to apply state-of-the-art epidemiologic, statistical and laboratory methods in at least one of the following areas of research: risk prediction, mechanisms of carcinogenesis, natural history of cancer precursors, hormonal carcinogenesis, genetic susceptibility, or pathologic/molecular tumor characterization. Collaboration with biostatisticians, laboratory investigators and physicians (pathologists, radiologists and clinicians) is central to the success of our research. Candidates must document the strong communication skills that will be required to write effective research papers, present work at scientific meetings, and convey information clearly to staff, collaborators, consultants and contractors. Candidates must also be sufficiently experienced to function independently, both in the development of their own research efforts, and in the mentoring and supervision of less experienced investigators. Appropriate office space and resources will be provided. Salary is competitive and commensurate with research experience and accomplishments, and a full Civil Service package of benefits (including retirement, health insurance, life insurance, and a thrift savings plan) is available. Candidates may be eligible for the NIH Loan Repayment Program (http://www.LRP.NIH.gov). This position is not restricted to U.S. citizens. Interested individuals should send a cover letter, curriculum vitae, brief summary of research interests, experience and future plans, copies of no more than 3 selected publications, and three letters of reference to: Ms. Judy Schwadron; Division of Cancer Epidemiology and Genetics; National Cancer Institute; 6120 Executive Blvd., Room EPS 8073; Rockville, MD 20852-7242. Or e-mail: schwadrj@mail.nih.gov. The closing date of the advertisement is August 15, 2010; however, the search will continue until a qualified candidate is found. A completed package of your application is required in order to be considered for this position. DHHS and NIH are Equal Opportunity Employers. Systems Biology/Bioinformatics Staff Scientist Neuro-Oncology Branch, NCI-NINDS (deadline: open-ended) The Neuro-Oncology Branch, a trans-institute program of the National Cancer Institute and the National Institute of Neurological Disorders and Stroke of the National Institutes of Health is seeking an outstanding candidate to work in the area of cancer genomics, bioinformatics and systems biology, particularly on computational modeling of signaling and gene networks in cancer cells. Ongoing projects include the integration of -omics and clinical data in the exploration of signaling and transcriptional networks that govern cell differentiation, proliferation and migration in primary brain tumors, cancer tumor stem cells and normal embryonic neural stem cells and the translation of those discoveries to patients through the highly integrated clinical brain tumor research program. Applicants should have a strong background in mathematical and computational modeling and be expected to carry out an interdisciplinary project with experimental groups. The Staff Scientist candidate will take a lead role in the mentorship and scientific management of a team of bioinformatics research fellows. The following skills and qualifications are required: 1) PhD in computer science, mathematics, bioinformatics, or related fields, and at least 3 years of post-doctoral training in bioinformatics and/or systems biology; 2) experience in machine learning and network generation algorithms; 3) basic knowledge of cell/molecular biology; 4) experience in genome-wide genetic and gene expression data analysis. Please send curriculum vitae, statement of research interests and two letters of reference to: Howard A. Fine, Chief; Neuro-Oncology Branch, National Cancer Institute; MSC 8200, Room 225; 9030 Old Georgetown Road; Bethesda, MD 20892-8200 or to smithj9@mail.nih.gov. Candidates may be U.S. citizens, resident aliens, or nonresident aliens. DHHS, NIH, the National Cancer Institute and the National Institute of Neurological Disorders and Stroke are Equal Employment Opportunity and Affirmative Action employers that value and foster diversity throughout the entire organization. Chief Laboratory of Computational Medicine, NEI (deadline: open-ended) The NEI seeks to develop a new program in computational analysis that fully employs human genomic, transcriptomic, proteomic, metabolomic, neurophysiological and clinical data sets to reconstruct biological networks characteristic of normal and disease states. The magnitude, diversity, rich information content, and hierarchical connectivity of these data sets require the utilization and development of novel quantitative tools. The goal is to understand human disease at a molecular level in order to develop mechanism-based therapeutic interventions. We invite applications for head of a new laboratory of Computational Medicine within the NEI Intramural Research Program. This initiative seeks to integrate and translate knowledge from genetics and biology to a wide range of disease processes using systems, network, statistical and bioinformatics approaches. * Examples in ocular biology amenable to a systems approach would include neuro-immune interactions, gene regulatory networks during disease pathogenesis, protein interaction pathways, neuron-glial-vascular biological networks in the retina, neuronal networks in the CNS, and developmental conditions and disorders. * The research program has interest in developing novel computational methodologies for analyzing large genetic, biological, biomedical, neuronal, and functional data sets. Particular attention will be paid to genotype-phenotype correlations, gene-gene and gene-environment interactions. In parallel, we will actively seek to develop disease intermediate phenotypes that reflect the underlying biology and pathophysiology of disease. * Data sets from large clinical trials, genetic studies (including GWAS), expression profiling in normal and disease conditions, and from the eyeGENE human research repository for monogenic ophthalmic diseases will be developed to reconstruct and understand ocular biological networks that link genetic perturbations, small molecule interactions, and physiological processes, to predict normal and disease states The NEI/NIH provides an exceptional environment of dedicated scientists as well as a wide range of resources. We currently envision that this program will be located in the newly constructed Porter Neuroscience complex that houses a diverse set of investigators from many different Institutes. The successful candidate will be expected to recruit tenure-track faculty in areas that may include computational medicine or neuroscience, network biology, genetic or molecular epidemiology, cell and molecular biology, statistical genetics, bioinformatics, and biostatistics into the new Laboratory of Computational Medicine. Applicants should have a MD, MD/PhD or PhD and an outstanding record of accomplishments in genetics, epidemiology, neuroscience, cell and molecular biology, biostatistics, or a related quantitative discipline. Senior scientists would have the opportunity to maintain their participation in existing collaborative research in non-eye diseases if desired. This position will remain open until filled. Applicants should submit curriculum vitae, bibliography, copies of their five most significant publications, a summary of research accomplishments, names of three references, and a detailed experimental plan for the development of this program. These materials should be sent to: The Office of the Scientific Director, National Eye Institute, Attention: Ms. Mica Gordon (gordonmi@nei.nih.gov), NIH Building 31, 31 Center Drive, Room 6A22, Bethesda, MD, 20892. The National Eye Institute does not discriminate in employment on the basis of race, color, religion, sex, national origin, political affiliation, sexual orientation, marital status, disability, age, membership in an employee organization, or other non-merit factor. DHHS and NIH are Equal Opportunity Employers. An asterisk next to the closing date in the postings above indicates that applications will continue to be accepted and considered until the position is filled. Below are such positions that still might be accepting applications, listed by the most recent. Tenure-Track Investigator Statistical Genetics, NIMH The Division of Intramural Research Programs (DIRP), National Institute of Mental Health (NIMH), National Institutes of Health (NIH), seeks a highly accomplished Tenure Track Investigator to develop an independent research program in statistical genetics. (Applications from tenured investigators will be considered.) The candidate will have the opportunity for collaboration with scientists in diverse research areas in genetics (e.g., genetic epidemiology, biostatistics, statistical genetics, molecular genetics), as well as neuroscience and relevant clinical disciplines. The position comes with a budget and staff. The strong scientific environment and outstanding resources at NIMH make this a unique opportunity for a high-achieving scientist. The position also offers unparalleled opportunities for interdisciplinary collaborations with scientists throughout the NIH. The successful candidate will be expected to strengthen the current program by establishing a program in statistical genetics that applies and develops statistical methods to analyze the role of genes in the etiology of complex disorders, particularly neuropsychiatric disorders. Applicants should have a Ph.D. in statistics, population genetics, mathematics, genetic epidemiology, or related fields. The applicant should have experience and interest in statistical analysis of human genetic data, and in developing new methods or adapting traditional statistical methods to identify the role of genes in the etiology of complex disorders. Salary is commensurate with experience and accomplishments, and a full Civil Service package of benefits (including retirement, health, life, and long-term care insurance, as well as a Thrift Savings Plan, etc.) is available. NIMH is a major research component of the National Institutes of Health and the Department of Health and Human Services, which have nationwide responsibility for improving the health and well-being of all Americans. Interested applicants should send curriculum vitae, bibliography, statement of research interests, accomplishments, and goals, together with 3 letters of reference to: Chair, Search Committee for Statistical Geneticist, NIMH, NIH, Bldg. 10, Rm. 4N-222, 9000 Rockville Pike, Bethesda, MD 20892; or e-mail to: steyerm@mail.nih.gov. Review of applications will begin March 31, 2010, but applications will continue to be accepted and considered until the position is filled. NIH and DHHS are Equal Opportunity Employers. Link to Fellowships, Staff Scientist and Tenured/Tenure-Track Research Positions http://www.training.nih.gov/ Link to NIH Jobs http://www.jobs.nih.gov/ Searchable database of all NIH intramural research projects http://intramural.nih.gov/search/index.tml ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------