Genome Biology – lots of exciting software this month

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The August issue of Genome Biology is now available on our website, and it’s a bumper issue this month. As well as several high-quality research articles (such as the wallaby genome sequence, the transcriptome of regenerating heads in planarians and a comprehensive screen for substrates of the Chk1 checkpoint kinase), we have a number of exciting computational methods for analyzing high throughput genomics data.

Kim and Salzberg present TopHat-Fusion, a modified version of the popular TopHat package for analyzing RNA-seq datasets, that can identify transcripts from fusion genes. As fusion genes are often important in carcinogenesis (such as the canonical BCR-Abl fusion from the Philadelphia chromosome in some leukemias), this has important medical applications.

Uwe Ohler …

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Towards interoperable bioinformatics web services for integrated applications

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The generation of unprecedented amounts of genomic-scale data on a daily basis has created an awareness of the need for more effective interaction between biological researchers and the bioinformatics tools they use. A comprehensive report from the 2nd Database Center for Lifescience (DCBLS) BioHackathon, held in March 2009, was published last month in Journal of Biomedical Semantics. At this meeting, software developers and genome biologists were brought together to discuss issues regarding incomplete interoperability between individual data and analytical tools. The ultimate goal of the meeting was to collaboratively evaluate the feasibility of addressing real-world biological problems by utilizing web services to create data “mashups” with existing tools in the hope of developing stable and usable …

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Companion articles explore the kangaroo genome

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Accompanying the publication of the tammar wallaby genome sequence in  Genome Biology, BioMed Central also has a pouchful of companion articles in a cross-journal article series.

The focus of several of these studies is on the insights that the genome sequence offers into marsupial immune systems. Emily Wong and colleagues present a database of immune genes identified from several marsupial and monotreme species. This gives researchers a new tool for exploring immune function in these groups and more broadly in understanding the evolution of the mammalian  immune system. In another study, Wong et al. also compare the genes expressed in the twin thymus glands of wallabies to understand the immune function of each organ, finding that both are …

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Tying the kangaroo genome down

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If the date is January 22nd and you happen to be a tammar wallaby, the chances are high that it will be your birthday – as well as the anniversary of your conception. In between these two events, you will have spent eleven months in suspended animation, followed by a short one month gestation (in which you only grew to the size of a kidney bean).

These quirks of tammar reproduction are just some of the many fascinating biological features whose underlying genetics may now be explained, thanks to the publication in Genome Biology of the tammar wallaby genome and transcriptome sequences.

The article, which is accompanied by a number of companion articles in BMC Genomics, BMC Molecular Biology, BMC

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Implementing computerized clinical decision support systems

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Quality of care studies document that physicians often inconsistently diagnose clinical problems and inappropriately prescribe clinical care. A new thematic series published in Implementation Science and edited by R. Brian Haynes (McMaster University) assesses the use of computerized clinical decision support systems (CCDSSs) to address these issues.

CCDSSs match the characteristics of patients to a computerized medical knowledge base, and may consistently and appropriately provide recommendations to clinicians for consideration. The knowledge base for CCDSSs was typically that of expert opinion in the early days of the computer era. Nowadays the knowledge base is more commonly evidence-based, grounded in strong findings from clinical research that show, for example, that treatment A is better than treatment B for a …

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Medical Tourism – Concepts, Ethics, And Practices

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Thematic Series Editors: Silke Schicktanz, University of Goettingen & Tulsi Patel, Delhi School of Economics, New Delhi, India

Modern medical care in today’s global world market is accessible in many different locations, including the non-western countries. The provision of apparently reliable medical care in Asia at a fraction of the cost incurred in Western countries has created lucrative business opportunities. This phenomenon of seeking medical care through inter-cultural travel, known as ‘medical tourism’, incurs a host of potential moral, ethical, economic, and legal benefits, questions, risks, and problems. Philosophy, Ethics and Humanities in Medicine is dedicating a thematic issue to medical tourism that aims to explore medical tourism from an interdisciplinary perspective. We encourage submission of speculative papers, …

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Open access journals supported by a €1 million Dutch open access fund

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The Netherlands Organisation for Scientific Research (NWO), the main Dutch science funding body, has launched a €1 million open access fund to help Dutch scientists establish new open access journals or convert existing journals to open access. This initiative is the fruit of a wider open access initiative that started in 2010 when the NWO committed €5 million to encourage open access development. The deadline for submitting proposals is Tuesday 4 October 2011. Further information regarding this funding can be found at www.nwo.nl/openaccess (English).

NWO joins other major European funding bodies in supporting open access. Several initiatives, on a national and European level, have recently been put in place to accelerate open access …

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Perioperative Medicine is now accepting submissions!

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Perioperative Medicine is an exciting new journal that publishes highly topical clinical research relating to the perioperative care of surgical patients.

Its essence is the distillation, examination and application of clinical evidence to improve surgical outcome. Modern perioperative medicine is a true multidisciplinary specialty and the journal welcomes research in all areas relevant to perioperative medicine from any healthcare professional.

The journal is led by Editors-in-Chief Monty Mythen and Mark Hamilton, from University College Hospital and St George’s Hospital, London, UK, who also co-chair the Evidence-Based Perioperative Medicine (EBPOM) series of conferences. They are joined by an internationally renowned Editorial Board

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Predicting genetic risk for disease

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A lot has been written about the potential for
genomic information to revolutionize medicine. Much of the excitement centers
around the idea that if we know an individual’s genome we can use this
information to predict risk of a particular disease and then give specific
treatment. In a research article published
in the latest issue of Genome Medicine,
Cecile Janssens, Muin Khoury and colleagues improve current models of
genetic risk, taking us one step nearer to this aim.

Genetic risk prediction is a very active area of
research,  boosted by the number of
genetic variants associated with common diseases that have been recently discovered
through genome-wide association studies. Previous studies looked at how single
mutations affect risk, …

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Report from the Publishing Open Data Working Group meeting, 17th June 2011

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On 17th June BioMed Central held a Publishing Open Data Working Group meeting, proposed in the spring, in London, UK. This post is a summary report from the meeting, including the next steps for the stakeholders involved. The meeting has also been reported by Alex Ball on the Digital Curation Centre blog. Many thanks to all the attendees acknowledged below for their contributions. While an important reason for convening the meeting was to stimulate debate amongst authors, editors, publishers, funders and librarians, it’s excellent to report that there are a number of mutually agreeable ways forward on all three of the meeting’s proposed goals. Please note that the actions and views stated do not necessarily represent the views …

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