Welcome to the ISCB Community News Blog

This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
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Wednesday, November 26, 2014

Cytoscape Team at RSGw/DREAM

The Cytoscape team was thrilled to be a part of this year's Regulatory and Systems Genomics conference along with DREAM Challenges. Thanks to support from the National Resource for Network Biology (http://nrnb) and Agilent Technologies, we were able to host a number of unique events integrated into the meeting. The week started off with a sold-out Cytoscape workshop for new users, and a parallel workshop for Cytoscape app developers. These workshops included an introduction to network biology approaches, hands-on sessions with the latest Cytoscape 3.2.0 release, and professional app development training. The next day we shared a well-attended Cytoscape poster session with DREAM Challenges, mixing two communities of like-mined researchers. Finally, during the Systems Biology track, we integrated two Cytoscape App Expo sessions. Each session consisted of four 10-minute presentation about new Cytoscape Apps and how to apply them to systems biology research. All in all, a hugel y successful event with lots of great interactions. Thanks again to the RECOMB and ISCB co-organizers!
URL: http://gladstoneinstitutes.org

Contact Person: Alexander Pico, PhD (apico@gladstone.ucsf.edu)

Wednesday, November 19, 2014

A 45,000-Year-Old Leg Bone Reveals The Oldest Human Genome Yet

Researchers have successfully decoded the genes of a 45,000-year-old man from Siberia. The results offer clues about early human life outside of Africa as well as how humans interacted with Neanderthals and other groups around at the time.

The complete set of genes is the oldest genome of its kind, according to Svante Pääbo, a director at the Max Planck Institute for Evolutionary Anthropology in Leipzig. "It's almost twice as old as the next oldest genome that has been sequenced."

The work of Pääbo and his colleagues was published Wednesday in the journal Nature.

The DNA came from a human femur found in 2008 by a collector scouring the Irtysh River in western Siberia. The femur was handed over to a local paleontologist who in turn gave it to Pääbo's team in Leipzig.

When the age of the bone was revealed, the team couldn't believe it. "We were actually so amazed, we actually had it dated even twice, to make sure," Pääbo says.

Pääbo's team specializes in extracting ancient DNA from bones like these. They carefully set to work retrieving genetic material from bone cells in the femur. Because the bone came from a modern human, they had to take precautions to ensure it wasn't contaminated with their own genetic material.

The results provide a window into an unusual period in human existence.

Modern humans evolved in Africa around 200,000 years ago. They left the continent around 100,000 years ago. But researchers now know that other human-like people were already living in Europe and Asia. These included Neanderthals, large, muscular hominins that lived in the caves of Europe.

"What's exciting about this paper is that it's looking at a very ancient modern human who would have lived around the same time as Neanderthals," says Sarah Tishkoff, a geneticist at the University of Pennsylvania who was not involved with the work.

The bone shows that the Siberian man's DNA contained a tiny amount of Neanderthal genes. In other words, he had some Neanderthal ancestors. It's the latest in a series of papers showing that humans and Neanderthals bred.

Modern Asians, Europeans and Native Americans also have Neanderthal genes, but the Neanderthal gene sequences of the Siberian man were longer, indicating that interbreeding had taken place in the relatively recent past, between 50,000 and 60,000 years ago.

"They actually mixed with each other and did have children," Pääbo says.

As intriguing as the bone is, it leaves many questions about what happened next.

We know that humans thrived and that Neanderthals eventually went extinct, but we still don't know why, says Janet Kelso, a computational biologist at the Max Plank Institute in Leipzig, and a co-author on the paper. "The genetics just doesn't tell us anything about that."

Just as big a mystery is what happened to the Siberian man and his descendants.

Previously it was thought ancient humans hadn't lived so far north 45,000 years ago. And venturing into the region may have been a bad move, Pääbo suspects. The Siberian man's genetic code is distant from other groups of humans, suggesting his family may have gone extinct even before Neanderthals died out.
URL: http://www.npr.org/blogs/health/2014/10/22/358047524/a-45-000-year-old-leg-bone-reveals-the-oldest-human-genome-yet

Contact Person: Geoff Brumfiel (GeoffBrumfiel@npr.org)

Tuesday, November 11, 2014

ISCB announces 2015 Journal Subscriptions now available to ISCB Members

ISCB members can now subscribe to the 2015 issues of our Community Journal at discounted prices:

* Bioinformatics; ISCB Members receive a substantial discount, for more information click here
* Briefings in Bioinformatics Online and Print Discounts available to ISCB Members, for more information click here
* Briefings in Functional Genomics & Proteomics Online and Print Discounts available to ISCB Members for more information, click here
* Computers in Biology and Medicine Online and Print Discounts available to ISCB Members, for more information click here
* Computer Methods and Programs in Biomedicine Online and Print Discounts available to ISCB Members, for more information click here
* Human Molecular Genetics Online and Print Discounts available to ISCB Members, for more information click here
* Journal of Biomedical Informatics Online and Print Discounts available to ISCB Members, for more information click here
* Journal of Computational Biology Online Discount is available to ISCB members. for more information click here


Current members just login to your ISCB membership and select "Subscribe to Journals" from the menu on the left. New members can subscribe during their registration process.
URL: http://www.iscb.org

Contact Person: Suzi Smith (admin@iscb.org)

Wednesday, November 5, 2014

SPRINGER PUBLISHES "CANCER BIOINFORMATICS" BY UGA'S YING XU

Athens, GA - The Computational Systems Biology Lab of the University of Georgia's department of biochemistry and molecular biology is pleased to announce the release of "Cancer Bioinformatics" by Springer.  Authors Ying Xu (UGA), Juan Cui (University of Nebraska, Lincoln) and David Puett (UGA, retired) provide a framework for computational researchers studying the basics of cancer through comparative analyses of omic data. The book discusses how key cancer pathways can be analyzed and discovered to derive new insights into the disease and identifies diagnostic and prognostic markers for cancer.
 
Cancer has been typically studied at the cell level or with xenografted animals, outside of the microenvironmental stresses and pressures that shaped the development of the cancer.  This approach assumes that cancer will develop following the known rules of human biology.  Instead the authors leveraged the data from The Cancer Genome Atlas and found that cancer biology is fundamentally different from human biology.  Their book outlines a radically new framework for basic cancer biology, how cancer develops, and the many paths it can take to survive.  The authors also treat cancer as an evolving complex system, explore future case studies, and summarize the essential online data sources.
 
"Cancer Bioinformatics" is designed for practitioners and researchers working in cancer research and bioinformatics. It is also suitable as a secondary textbook for advanced-level students studying computer science, biostatistics or biomedicine.  You can access an online book review copy at no cost by visiting the book's web page at http://www.springer.com/computer/bioinformatics/book/978-1-4939-1380-0 and listen to a short podcast of lead author Ying Xu talking about cancer and hypoxia on WAMC's Academic Minute - http://academicminute.org/2014/10/ying-xu-university-of-georgia-hypoxia/. 
 
The CSBL is a part of UGA's Franklin College of Arts and Science department of biochemistry and molecular biology and is dedicated to developing a new framework studying cancer and in doing so enable other cancer researchers and computational biologists to join in and contribute.

URL: http://csbl.bmb.uga.edu/
Contact Person: Heather Jensen (hjensen@uga.edu)

Tuesday, November 4, 2014

IJCB: Call for papers

International Journal for Computational Biology (IJCB), which provides a rapid forum for the dissemination of original research articles as well as review articles in all areas of Computational Biology and Bioinformatics invites manuscripts. IJCB is a n official journal of Bioclues Organization, which in turn is an associate of ISCB.

International Journal for Computational Biology is published using an open access publication model, meaning that all interested readers are able to freely access the journal online at http://www.ijcb.in/ without the need for a subscription.

We are maintaining a mirror repository at www.bioinformatics.org for round the clock hassle free readership. Further we are in process of getting indexed with most of the world class citation and indexing databases for better impact and visibility of your research work.

The journal has a distinguished editorial board with extensive academic qualifications, ensuring that the journal maintains high scientific standards and has a broad international coverage. A current list of the journal\\\'s editors can be found at journal website.

Paper should be submitted through online manuscript submission system (Details of which has been given on journal website). Once a paper has been accepted for publication, it will undergo language copyediting, typesetting, and reference validation in order to provide the highest publication quality possible.

Please do not hesitate to contact me if you have any questions about the journal.

With kind regards

Editor-In-Chief
International Journal for Computational Biology (ISSN: 2278-8115)
Web: http://www.ijcb.in/
Email: ijcb@bioclues.org
URL: http://www.ijcb.in/

Contact Person: Chief Editor (ijcb@bioclues.org)