Public Library of Science - In the News

Call for Designs: The PLoS Computational Biology 2010 T-shirt

Cecy Marden — Tue, 16 Mar 2010 08:13:51 -0700

This year’s ISMB will be the debut of the newest addition to the PLoS T-shirt collection and we want you to design it.

We have heard tales of PLoS T-shirts being spotted across the globe; from Hawaiian mountain-tops to the historic streets of Cambridge, England – we know you enjoy wearing them. We want the T-shirt to feature an eye-catching design which appeals to the computational biology community and encapsulates a recent advance or innovation in the field.

Unleash your inner artist and send us the design for 2010. The T-shirt design specifications file below contains all the information you need to format your design appropriately; please follow the specifications closely as we will be unable to consider any images which do not meet them.

Please send your design and any queries to contribute[at]plos.org by April 9th 2010.

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PLoS Computational Biology at ISMB

Cecy Marden — Thu, 11 Mar 2010 03:32:58 -0800

At the end of last month we were pleased to hear that our workshop proposal, entitled ‘Where and How to Get Published’ had been accepted by Intelligent Systems for Molecular Biology (ISMB) 2010. We hope that a wide range of perspectives on how best to get research published will make this workshop invaluable to those just starting out on their careers. We are very excited that our involvement in the International Society for Computational Biology’s annual meeting is set to continue and more details will follow when the timing of the workshop is confirmed in May.

Attendees should also be on the look out for our Conference Postcards; we look forward to hearing from some of you about the most outstanding sessions or posters of this summer’s ISMB.

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PLoS Pathogens featured in This Week in Virology

Patrick Reilly — Wed, 10 Feb 2010 09:08:12 -0800

In their Feb. 7, 2010 TWiV podcast Alan Dove, Rich Condit, and Vincent Racaniello, PLoS Pathogens Community Editor, consider ‘recent outbreaks of mumps in the UK, US, and Israel, protection of mice against 2009 H1N1 influenza A virus by 1918-like and classical swine H1N1 vaccines, and a virus-like particle vaccine for chikungunya virus.’

They discuss the recent PLoS Pathogens article “Protection of Mice against Lethal Challenge with 2009 H1N1 Influenza A Virus by 1918-Like and Classical Swine H1N1 Based Vaccines”, co-written by long-time Pathogens editor Adolfo García-Sastre, as well as well as a review piece also published in the journal, “Crossing the Line: Selection and Evolution of Virulence Traits.” Download the podcast here!

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PLoS ONE indexed by Web of Science

Mark Patterson — Tue, 05 Jan 2010 12:16:28 -0800

Today we learned that by the end of this week PLoS ONE (in keeping with all other PLoS journals) will be indexed by the Web of Science – this is an important literature discovery tool that many people use and so we are pleased to be indexed. PLoS ONE is also indexed by a host of other services such as PubMed, MEDLINE, PubMed Central, Scopus, Google Scholar, the Chemical Abstracts Service (CAS), EMBASE, AGRICOLA, PsycINFO, Zoological Records, FSTA (Food Science and Technology Abstracts), GeoRef, and RefAware.

Initially, coverage in the Web of Science will include new PLoS ONE articles plus those published in 2008 and 2009, and will be expanded to the articles published in 2006 (when PLoS ONE was launched) and 2007 in the coming weeks. Inclusion in the Web of Science also means that in June 2010 PLoS ONE will receive journal-level citation data from Thomson Reuters including a 2- and 5-year Impact Factor and Eigenfactor metrics.

As we have previously indicated, PLoS believes that research articles are best assessed on their own merits, rather than on the basis of the journal (and its impact factor) where the work happens to be published. While we are happy that PLoS ONE articles will become more discoverable as a result of their inclusion in the Web of Science, we will continue to push forward with our Article-Level Metrics program.

Naturally, we understand that inclusion in the Web of Science is significant for many academics whose research output is still measured by traditional means. We hope that this news encourages even more scientists to publish their work in PLoS journals, to benefit from the article-level metrics that are provided for every PLoS article (for example, this PLoS ONE article), and to ensure that all interested users have open access to their research.

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Presentations from the first OASPA Conference

Mark Patterson — Mon, 05 Oct 2009 06:58:35 -0700

From September 14-16, 2009, the Open Access Scholarly Publishers Association (OASPA) held its inaugural conference in Lund, Sweden. The talks from the meeting are now available online.

OASPA was launched officially last year, on OA Day. The aim of OASPA is to develop a community of OA publishers, large and small, to foster high standards, and to promote the broader adoption of OA publishing.

In Lund, OASPA constituted its first official Board, and PLoS is delighted to be included as a Board member. The first President of OASPA is Caroline Sutton of Co-Action Publishing.

There are some terrific talks to watch and listen to from the meeting, including "Ten Challenges for Open Access Journals" from Peter Suber.

Many thanks to Kaveh Bazargan of River Valley, for generously recording the event and making it available.

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The history behind lactose intolerance, revealed.

Patrick Reilly — Thu, 03 Sep 2009 11:29:04 -0700

The study, published August 28, explains how Europeans evolved to drink milk as adults (lactase persistence). The findings suggest that lactase persistence began around 7,500 years ago, and further confirm that the ability to drink milk as an adult has been a coevolutionary process between genetics and agricultural development.

Yuval Itan and colleagues develop a simulation model of the spread of lactase persistence, dairying, and farmers in Europe, combining genetic and archaeological data using newly developed statistical approaches. They study a single genetic variant strongly associated with lactase persistence, ?13,910*T, which they find to have been favored by natural selection within the past 10,000 years. By matching this with the historical timeline of humans’ beginning to drink fresh milk due to animal domestication, the researchers were able to map this lactase persistence.

The group infers that lactase persistence/dairying coevolution began around 7,500 years ago between the central Balkans and central Europe. However, they also determine that populations inhabiting higher latitudes didn’t progress towards adult milk consumption any more quickly, despite an increased requirement for dietary vitamin D. The authors note that this work exemplifies the possibility of integrating genetic and archaeological data to address important questions on human evolution.

This study has garnered a wide range of coverage, including:

-Scientific American

-USA Today

-United Press International

And more

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Leishmania gets by your immune system with a little help from its friends

Patrick Reilly — Fri, 28 Aug 2009 16:38:02 -0700

On August 21st, Matthew Rogers and colleagues published an article in PLoS Pathogens which shows that the parasite Leishmania tricks host immune defense cells into feeding it rather than killing it. This development may help in the search for an effective vaccine against leishmaniasis, a painful, disfiguring, potentially fatal disease that afflicts approximately 12 million people worldwide.

Using a mouse model, Rogers et al demonstrated that the parasite secretes a gel-like substance within the sand-flies that are primary transmitters of the disease. This gel must be regurgitated in order for the fly to bite and feed on its target, allowing the gel, along with the parasites, to enter the target’s skin. This gel actually attracts the macrophages (white blood cells) meant to eat and digest invading pathogens. That these cells then feed the parasites rather than destroy them allows the Leishmania parasite to establish an infection with little resistance.

The story was covered by the BBC, Tropika, Wellcome Trust, Red Orbit, Medical News Today, and Cordis News.

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PLoS Computational Biology at ISMB/ECCB 09

Evie Browne — Mon, 01 Jun 2009 10:37:13 -0700

As an official journal of the International Society for Computational Biology, PLoS Computational Biology is once again delighted to be participating in the ISMB/ECCB conference for 2009, this year held in Stockholm, Sweden, June 27^th – July 2^nd, where you’ll find us at Booth 12 in the exhibition hall.

This year we’ll be presenting two sessions:

1. Future of Scientific Publishing (Monday, June 29^th 14:15 – 18:45 pm)

This year, BioLINK—a special interest group run for many years in association with ISMB—has devoted the final part of their program to PLoS Computational Biology and the ISCB Publications Committee to discuss developments and desires in scientific publishing. Our four distinguished speakers will be David Shotton (Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article), Anita de Waard (From Proteins to Hypotheses—Some Experiments in Semantic Enrichment), Dietrich Rebholz-Schuhmann (ELIXIR Scientific Literature Interdisciplinary Interactions), and PLoS Computational Biology Editor-in-Chief Philip E. Bourne (OpenID vs. ResearcherID). This afternoon session is open to BioLINK and ISMB/ECCB delegates and will be followed by a Publishers’ Panel discussion with representatives from major publishers, including PLoS, Oxford University Press, Nature, Wiley-Blackwell, Cambridge University Press, and BioMed Central.

You can also read more about the session here.

2. Special Session on Advances and Challenges in Computational Biology (Wednesday, July 1^st 10:45 am – 12:40 pm)

Brought to you through the eyes of three of PLoS Computational Biology’s editors, this session covers recent scientific advances made possible by computation and mathematics in different fields—Synthetic Biology (Adam Arkin), Computational Neuroscience (Abigail Morrison), and Infectious Diseases (Christophe Fraser). Addressing themes such as drivers of research directions, scientific impact, reproducibility, model validation, co-operation amongst researchers, the need for tools to enable sharing (such as common description languages), and interfacing with scientists who are not focused on computational approaches, this session aims to provide a wide-reaching overview of common issues faced by computational biologists in different areas.

Meet the Team—Booth 12

PLoS Computational Biology team members Evie Browne, Publications Manager, and Rosemary Dickin, Publications Assistant, will answer your questions about PLoS, open access, the NIH Public Access Policy, and publishing your work in PLoS Computational Biology, the leading journal in its field. Don't forget to visit us at Booth 12 and collect some FREE PLoS goodies:

T-Shirts—Sign up for our e-mail content alerts and receive our 2009 t-shirt (while supplies last).
Buttons/Badges designed for our authors, editorial board members, readers, and supporters.
Postcards, to remind yourself and your colleagues why you should publish in PLoS Computational Biology.

We look forward to seeing you very soon.

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PLoS Computational Biology editors win awards

Evie Browne — Tue, 28 Apr 2009 04:00:27 -0700

PLoS Computational Biology is pleased to acknowledge two of our editors, Philip E. Bourne and Lars Jensen, who have won prestigious awards in recent weeks.

Philip E. Bourne, PLoS Computational Biology Editor-in-Chief, was honoured with the Benjamin Franklin Award, given by the Bioinformatics Organization at the 2009 Bio-IT World Conference & Expo in Boston. We are particularly pleased to note that this award is given for Open Access in the Life Sciences and is in part due to Phil’s work with PLoS, along with his involvement and leadership roles in such innovative projects as the Protein Data Bank and Scivee.tv. Professor Bourne is a founding editor of PLoS Computational Biology, and his leadership has been a driving force for Open Access in this field and throughout the sciences. Read more about the presentation here.

A PLoS Computational Biology Associate Editor, Lars Jensen, is part of the team which won the Elsevier Grand Challenge, a competition to “describe and prototype a tool to improve the interpretation and identification of meaning in (online) journals and text databases relating to the life sciences.” Dr Jensen’s team from the European Molecular Biology Laboratory have developed Reflect, a program which can tag gene, protein, or small molecule names on any website. The competition itself has stimulated developments in science and science publishing, and we look forward to seeing new ways to improve, use and re-use journal content.

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Solving the Romanov Mystery, Anthrax's American History, Usage Maps of Science and a Self-Healing Caterpillar

Rebecca Walton — Mon, 16 Mar 2009 10:10:52 -0700

PLoS ONE’s biggest news buzz last week was created by a study from an international team of researchers led by Michael Coble of the Armed Forces DNA Identification Laboratory. The researchers report the results of forensic DNA tests, which confirm that skeletal remains of two individuals discovered in Russia in 2007 belong to the two missing children of the last Tsar of Russia—the Crown Prince, Alexei Romanov and one of his sisters. The Tsar, Nicholas II, his wife Alexandra, their five children and four family employees were murdered by the Bolsheviks in 1918 to prevent them from being rescued by the White Russian Army, who were loyal to the Tsar. After a failed attempt to hide the remains in a nearby mine shaft, the Bolsheviks first tried to cremate two of the children (discovered in 2007) and then buried the remaining nine bodies in a mass grave (officially discovered in 1991).

There was extensive coverage of the story in the news and in the blogosphere, and the study was highlighted on the CNN front page and on the ScienceBlogs homepage on March 12. Other coverage includes: the Los Angeles Times, National Geographic, the Independent, the Telegraph, Greg Laden’s blog, the Intersection and 80beats.

A second historical “mystery” was solved by a paper published on Friday by Leo Kenefic and colleagues, which suggests that Columbus wasn’t to blame for introducing anthrax to the Americas. Although Europeans introduced many diseases which had serious impacts on the indigenous populations when invading the Americas, the new study shows, however, that anthrax was actually introduced thousands of years earlier, during the Stone Age. New Scientist and USA Today both posted nice write-ups on the study.

Johan Bollen’s new article, Clickstream Data Yields High-Resolution Maps of Science, also picked up some media attention on its publication last week, with its intricate maps created from citation data, giving a detailed, contemporary view of scientific activity and correct the under-representation of the social sciences and humanities that is commonly found in citation data. Figure 5 from the paper is a fantastic image and was reused in several of the stories and posts highlighting the paper. As well as a New York Times article, Nature News, the USA Today science blog, Wired News, the Scholarly Kitchen and the Edge of Vision also covered the study.

Finally, I was intrigued by the title of Carl Zimmer’s recent post on the Loom, Woolly Bear, Heal Thyself, which of course refers to a type of caterpillar, which can, according to a study by Michael Singer, self-medicate, in response to disease or to parasites. Another blog post on the study appears on Evolving Ideas and National Geographic and ScienceNOW have both run stories on the article.

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