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Friday, October 31, 2014

Call for Applications: Research Collaboration Workshop for Women in Mathematical Biology

The National Institute for Mathematical and Biological Synthesis (NIMBioS) is now accepting applications for the Research Collaboration Workshop for Women in Mathematical Biology, to be held June 22-25, 2015, at NIMBioS.

Objectives: This collaborative workshop aims to help build a strong collaboration network of women working on problems in mathematical biology, by facilitating the formation of new collaborative research groups and encouraging them to continue to work together after the workshop. Junior women (tenure track faculty, post-docs and advanced graduate students) in biology, mathematics and related fields are encouraged to apply. The format of this workshop is designed to maximize the opportunities to collaborate:

There will be four teams. Each team will be led by two senior women researchers and will work collaboratively on a specific project. Team members will be chosen from applicants and will consist of junior researchers from both mathematics and biology. Team members can express their project preference in their application Each team will work intensely and present their findings at the end of
the workshop.

Each team is expected to continue their research and obtain results for a joint publication.

Projects: Aerodynamics of spider ballooning; sleep, circadian rhythms and pain; blood flow autoregulation in the kidney; and modeling the effects of antimicrobial therapy on gut microbiota and Clostridium difficile

Location: NIMBioS at the University of Tennessee, Knoxville

Co-Organizer: Anita Layton, Mathematics, Duke Univ.

For more information about the workshop and a link to the online application form, go to http://www.nimbios.org/education/WS_wwmb.html

Participation in the workshop is by application only; 3-4 participants will be selected for each team. Successful applicants will be notified within two weeks of the application deadline. If needed, financial support for travel, meals, and lodging is available for workshop attendees.

Application deadline: March 1, 2015

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, with additional support from The University of Tennessee, Knoxville.
URL: http://www.nimbios.org

Contact Person: Catherine Crawley, Ph.D. (ccrawley@nimbios.org)

Thursday, October 30, 2014

Top 10 papers reading list for 2013-14: call for nominations

Dear Colleagues,

Please help nominate papers in the field of Regulatory and Systems Genomics, that you've recently read and found to be of particular interest. Relevant areas include Motifs, Grammars, Networks, Systems, Variation, Disease, Personal Genomics, GWAS interpretation, Regulatory Evolution, Comparative genomics, Epigenomics, Physical modeling, Dataset Integration, Splicing regulation, transcriptional regulation, and all areas of gene and genome regulation at the systems level.

You can find the nomination form here: http://goo.gl/forms/ENlRYpOVhD

Please nominate papers that appeared between September 1st, 2013 and August 31st, 2014. You can of course nominate a paper from your own group, but we ask that if you are doing so, to also take the time to nominate at least one paper that was not co-authored by you.

The nomination process will close on November 5th.

Our goal is to identify seminal papers that introduced not only new biological insights, but also key computational methodologies for interpreting biological datasets that have had and will continue to have a lasting impact in the field of Regulatory and Systems Genomics. These will be honored at an awards ceremony in the 2014 RECOMB/ISCB Meeting on Regulatory and Systems Genomics in San Diego on November 9-14, 2014. http://www.iscb.org/recomb-regsysgen2014

Thank you for your help and for being part of our community,

Manolis Kellis and Saurabh Sinha
Co-organizers, RegSysGen Top 10 Papers Reading List
ISCB Special Interest Group On Regulatory & Systems Genomics (RegSys SIG)
http://cosi.iscb.org/wiki/RegSIG:Home
URL: http://cosi.iscb.org/wiki/RegSIG:Home

Contact Person: Manolis Kellis (sinhas@illinois.edu)

Tenth Annual Great Lakes Bioinformatics Conference : GLBIO 2015

Tenth Annual Great Lakes Bioinformatics Conference : GLBIO 2015

An official conference of the International Society for Computational Biology. Organized by the Great Lakes Bioinformatics Consortium. Co-hosted by Purdue University and the International Society for Computational Biology

The Great Lakes Bioinformatics Conference:
~ Provides an interdisciplinary forum for the discussion of research findings and methods.
~ Fosters long-term collaborative relationships and networking opportunities within the domain of computational approaches to biology.

GLBIO has established a strong reputation for building relationships among a nationally prominent bioscience research community, showcasing the North American Great Lakes region as a perfect place to conduct computer-aided research.

Every year, GLBIO organizers prepare a full agenda on the latest developments in bioinformatics and biologically relevant applications. From novice to expert, attendees partake in a variety of workshops, tutorials, presentations, posters, networking, and exhibits during the conference. 2015 program outline:

Monday, May 18: Afternoon tutorials and opening keynote

Tuesday, May 19 and Wednesday, May 20 : All day education including keynote speeches by

Bioinformatics community leaders, cutting edge research through poster sessions and tutorials on a variety of hot topics.
GLBIO 2014 was 2.5 days and consisted of the following presentations:
7 keynotes 7 tutorials
12 highlights talks 9 research talks 13 flash talks
102 poster presentations, presented in two sessions
1 educational panel 1 career symposium 1 sponsored tech talk

The most popular topics included scientific talks on the following topics:
• Applying bioinformatics approaches to further develop medical treatments for cancer Ecological bioinformatics
• Gene expression studies
• Genomic analysis and discovery and pathway analysis
• Machine learning
• Protein structures

Check out the latest schedules and updates at www.iscb.org/glbio2015

URL: http://www.iscb.org/glbio2015

Contact Person: Cori Dossett (glbio@conferencesdesigned.com)

Tuesday, October 28, 2014

Special Issue on Advances in Computational Methods for Genetic Diseases : Extended deadline

Due to Publisher policy, the deadline for the submission of papers has been extended. The new Issue schedule is the following:
_________________
IMPORTANT DATES
_________________
Manuscript Due Friday, 21 NOVEMBER 2014
First Round of Reviews, 13 FEBRUARY 2015
Publication Date, 10 APRIL 2015
URL: http://www.hindawi.com/journals/cmmm/osi

Contact Person: Antonino Staiano (antonino.staiano@uniparthenope.it)

Friday, October 24, 2014

Highlighting How Federally Funded Research Improves Health Ensures Continued Support for Science

FASEB Vice President for Science Policy Hud Freeze, PhD, is driven by the search for new treatments for patients with rare genetic diseases. Specific targets are mutations leading to defects called Congenital Disorders of Glycosylation (CDG). Dr. Freeze is equally passionate about the need to explain how finding cures starts with research to understand basic biological processes, much of which is funded by grants from the federal government. To ensure improved health, he and the FASEB leadership urge scientists to explain their work in public forums and to the media. Some examples of Dr. Freeze's efforts in this regard are linked here: 1) a San Diego TV show with a child suffering from a rare genetic disorder (http://link.brightcove.com/services/player/bcpid1649263564001?bckey=AQ~~,AAAAA5PNMME~,K3tOT-PuafsBOFardsNAXlIchcEkjy_p&bctid=3547868835001); and 2) a video from the Global Genes 2014 Rare Patient Advocacy Summit, session 9, from about minute 11 to 18:40 (http://globalgenes.org/2014summitvideos/).


Contact Person: Joseph Carey (jcarey@faseb.org)

NIH Group Analyzes Grant Processes at Other U.S. Agencies and in the United Kingdom

The National Institutes of Health (NIH) Scientific Management and Review Board (SMRB) on October 14 heard descriptions of the grant processes at other U.S. federal research agencies and at two funding organizations based in the United Kingdom.

Charged with providing guidance to the NIH Director on the organization of the NIH and the implementation of its funding portfolio, a SMRB Working Group since May has explored ways to streamline the grant review, award, and management process. Previous sessions featured presenters from NIH's Office of Extramural Research, the Center for Scientific Review, several NIH institutes and centers; and academic researchers with extensive service on peer review panels.

Sonny Ramaswamy, PhD, Director of the National Institute of Food and Agriculture at the U.S. Department of Agriculture (USDA) presented an overview of the grant-making arm of the agency and the average timelines for applications and awards. He said that the agency was struggling to find ways to shorten its process, which takes approximately 25 to 38 weeks on average. Dr. Ramaswamy flagged USDA's reliance on Requests for Applications (RFAs) or "solicited research" as a key difference between the NIH and USDA granting process, which adds approximately 14 to 16 weeks to the timeline to develop and announce the funding opportunity. Another key difference is that most USDA grants provide one year of funding, with some providing two years; NIH grants typically provide three to five years of support.

The National Science Foundation (NSF) grant review and award process, and potential expediting strategies, were discussed by the agency's Joanne Tornow, PhD, Deputy Assistant Director for Social, Behavioral, and Economic Sciences. She stated that 94 percent of NSF's FY 2013 budget went to extramural research. Of the 48,999 proposals received, the agency funded 10,829 new awards. Approximately three-quarters of all proposals are processed within six months of receipt, with potential bottlenecks caused by difficulty identifying reviewers, additional steps in the review process (e.g., site visit, review by the Director's Review Board or by the National Science Board, etc.), missing documentation, the agency processing a large volume of applications, or the uncertain status of the federal budget. Dr. Tornow noted that NSF has several pilot projects underway to test changes to specific aspects of the peer review process. These include virtual review panels and use of shorter preliminary proposals to reduce the number of full applications that need review.

Representatives of the U.K.'s Wellcome Trust and the Medical Research Council also described their grant processes. Both models incorporate face-to-face interviews with applicants in addition to written reviews.

Alyson Fox, PhD, Wellcome's Head of Grants Management, briefly described the application and review process for both its Investigator Awards, which are equivalent to the NIH R01 grant, and Intermediate Fellowships for postdoctoral scholars. Both processes take approximately 18 weeks with external reviewers engaged only after staff determine applications to be "shortlisted" for further review. During questions and answers, it appeared that this process would not be scalable to NIH, since Wellcome reviews only 160 to 180 applications per cycle for the Investigator Awards and 220 to 250 preliminary applications for the Intermediate Fellowship program.

Declan Mulkeen, PhD, Chief Science Officer for the Medical Research Council briefly described the approximately six month review process by which it funds 350 to 400 individual awards per year. Dr. Mulkeen noted that the process had been reduced from nine to 12 months by implementing shorter application forms and eliminating post-review resubmissions.
URL: http://

Contact Person: Yvette Seger (yseger@faseb.org)

News from NIH

The National Institutes of Health (NIH) recently released several notices of interest to the biological and biomedical research community, ranging from clarifying the role of graduate students and postdocs supported by research grants to the suspension of funding for certain types of research.

On October 10, NIH issued a notice that is particularly significant for postdoctoral scholars, the majority of whom are supported by research project grants. It recognizes their positions as both contributing to a research effort and as an opportunity to develop skills critical to becoming independent researchers. The notice reiterates the clarification released by the Council on Financial Assistance Reform (COFAR) and the Office of Management and Budget (OMB) regarding the dual role of graduate students and postdocs supported on federal research grants. The clarification states, "For non-Federal entities that educate and engage students in research, the dual role of students as both trainees and employees contributing to the completion of Federal awards for research must be recognized in the application of these principles."

An NIH Request for Information (RFI), also issued on October 10, seeks public input to inform the development of a program to facilitate the transition of physician-scientists to independent research careers. Proposed options include: modification of existing mentored career development awards, restructuring of institutional training or career development awards to fulfill the specific needs of physician-scientists, and development of a K99/R00 career transition award that better suits the career trajectory of physician-scientists to obtain input on perceived barriers and possible solutions to reinvigorate this dwindling workforce. The document builds upon the findings and recommendations of the Physician-Scientist Workforce Working Group that was presented the Advisory Committee to the Director, NIH, in June. Responses must be submitted via the RFI website and are due by November 3, 2014.

In accordance with an October 17 statement from the White House, NIH announced a funding pause for new "gain-of-function research" involving influenza, MERS, and SARS viruses. The three viruses were selected because of the significant risk they pose to public health. NIH defines gain-of-function research as any modification of a biological agent — like viruses, bacteria, or toxins — that gives it new or enhanced activity. Research affected under this announcement is limited to projects using any of the three viruses that are anticipated to enhance their pathogenicity or transmissibility via the respiratory system in mammals. The funding pause, which is expected to last nine months, will not impede efforts to characterize or test naturally-occurring versions of these viruses. During the pause, the government will carry out a deliberative process to assess the risks and benefits of such studies and will develop a new Federal policy regarding the funding of this research .
URL: http://

Contact Person: Yvette Seger (yseger@faseb.org)

Friday, October 10, 2014

Survey on credible practice of modeling and simulation in healthcare

With this invitation, we are asking you to complete a survey aimed to establish good practice guidelines in order to realize credibility of computational modeling and simulation (M&S) in healthcare. The survey can be found at:

https://stanforduniversity.qualtrics.com/SE/?SID=SV_4MeRluojMgdVR7n

The survey site will be available until February 15, 2015.

We sincerely appreciate your participation in this survey, which should take no longer than 10 minutes. Your participation is voluntary and your responses will be anonymous. You have been identified as a potential stakeholder in the M&S community. Your support will be instrumental in developing broadly applicable best practices in M&S, for their ultimate utilization in healthcare.

This survey is an initiative of the Committee on Credible Practice of Modeling & Simulation in Healthcare, to understand global and multidisciplinary perspectives in best practices to establish credibility of computational medicine. The Committee was formed as part of interactions within the Interagency Modeling and Analysis Group (IMAG) and Multiscale Modeling Consortium, which provide a platform to facilitate discussions between federal agencies in the United States and investigators within the United States and worldwide.

Please feel free to forward this invitation to others that may have an interest in providing their insight. Thank you for your support. If you have any questions, please feel free to contact me by phone, +1 (216) 445 9523, or by e-mail, erdemira@ccf.org.

Regards,

Ahmet

Ahmet Erdemir, PhD on behalf of Committee on Credible Practice of
Modeling & Simulation in Healthcare
http://wiki.simtk.org/cpms

URL:

Contact Person: Joy Ku (joyku@stanford.edu)

Wednesday, October 8, 2014

Call for Papers: Special issue on machine learning techniques in biological data mining

Dear colleague,

We invite you to submit a paper for a supplement to be published in Bioinformatics and Biology Insights in the next twelve months. The journal is extensively indexed and all published papers appear in Pubmed. The supplement focuses on current developments in machine learning techniques in biological data mining. In this supplement, we will discuss the use of machine-learning techniques to extract meaningful information from genetic and clinical data with the primary objective of answering pressing biomedical questions. Topics of interest include but are not limited to:

* Building predictive models for complex phenotypes from large-scale biological data
* Discovering biological networks and pathways underlying biological processes and diseases
* Processing of new/next-generation sequencing (NGS) data for genome structural variation analysis, discovery of biomarkers and mutations, and disease risk assessment
* Discovery of genotype-phenotype associations
* Novel methods and frameworks for mining and integrating big biological data
* Comparative genomics
* Metagenome analysis using sequencing data
* RNA-seq and microarray-based gene expression analysis
* Genome-wide analysis of non-coding RNAs
* Genome-wide regulatory motif discovery
* Correlating NGS with proteomics data analysis
* Functional annotation of genes and proteins
* Chemo-informatics: Drug discovery, Virtual screening and Combinatorial chemistry
* Knowledge discovery in clinical data and electronic medical records

If you are interested in contributing, please contact the guest editors Dr. Gaurav Pandey (gaurav.pandey@mssm.edu) and Dr. Gerard Dumancas (gerard.dumancas@okstate.edu) to discuss your contribution. In order to proceed, please submit a manuscript title and agreed submission date as soon as possible. Submissions must be received for peer review on or before June 1, 2015. We hope to hear from a lot of you!
URL: http://www.la-press.com/journal-bioinformatics-and-biology-insights-j39

Contact Person: Gaurav Pandey (pandey.gaurav@gmail.com)

Friday, October 3, 2014

Submission of manuscripts for publication

Journal of Biological and Food Science Research (JBFSR) with ISSN: 2277-0828 is currently accepting manuscripts for publication. JBFSR is an open access, international, multidisciplinary, blind peer-review journal which publishes high-quality solicited and unsolicited research and review articles in English, in all areas of bioinformatics, biology, microbiology, food science, botany, life science, biochemistry, optometry, zoology, industrial biology, industrial microbiology, clinical microbiology, laboratory science, cell and animal biology, genetics and molecular biology, medical sciences, dentistry, medical diagnosis and laboratory, computational biology, etc.

JBFSR is a rapid response journal that publishes an issue monthly. One of our objectives is to inform contributors (authors) of the decision on their manuscript(s) within a MONTH of submission. Following acceptance, a paper would be published in the next available issue. JBFSR provides immediate open access to published articles without any barrier.

Publishing your article with JBFSR means that the article will be available to millions of researchers in the field of Biological and Food Science Research because our large and diverse readership base comprises of millions of researchers. Majority of the journal's readers are academic lecturers, students, policy makers in the beverage industry, food and canning industry, and policy makers in government. Our journal support free downloading of published articles by scholars for use as materials for lecture, by government officials for policy making, and corporate researchers to favour corporate organizations world-wide. Also, JBFSR is a registered member of several local and international organizations? making it possible for the far and wide distribution of published articles. We ask you to support this initiative by publishing your paper(s) in this journal.

Authors should send their manuscript(s) as MS Word attachment to our editorial office through the following email address:
submit.jbfsr@onlineresearchjournals.org or
jbfsr.onlineresearch@yahoo.com; Instructions for authors and other details are available on our website www.onlineresearchjournals.org/JBFSR.
You may wish to visit
http://onlineresearchjournals.org/JBFSR/archive.htm for articles already published in this journal.
URL: http://www.onlineresearchjournals.org/JBFSR

Contact Person: Chairy Onyia (submit.jbfsr@onlineresearchjournals.org)

Thursday, October 2, 2014

Call for Bioclues Innovation, Research and Development (BIRD) awards for the year 2014

To encourage budding bioinformaticists in India who have had made outstanding contributions in the area of Bioinformatics and Functional Genomics, we have initiated the Bioclues Innovation, Research and Development (BIRD) awards in the year 2011. The call for the 2014 is now open. Do you have the following traits?

●Promoted international standards for R and D in India.

●Created novel models/opportunities or Bioinformatics-based tools.

●Mentored student researchers.

●S/he is less than 35 years and preferably a PhD in Bioinformatics or related field.

●Secured grants in organizing international events and activities in support of Bioinformatics.

●Have penchant for and respect Open Access

More at www.bioclues.org
URL: http://www.bioclues.org

Contact Person: Prashanth Suravajhala (prash@bioclues.org)