Transcriptional control in flies

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In a paper recently published in Genome Biology, Boris Adryan (Cambridge University) and Sarah Teichmann (LMB) have presented evidence that calls in to question currently-held beliefs about how transcription factors (TFs) coordinate gene expression during development to specify the fates of the different tissues in the body.

It has been assumed that transcription factors are expressed in the manner of a cascade, with one TF turning on the expression of others resulting in groups of TFs acting in a cooperative manner to specify cell fate. In this study, Adryan and Teichmann have analysed gene expression data from Drosophila melanogaster development to investigate when every transcription factor is expressed. 95% of TFs were expressed at some time during …

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Novel format for gene variant reporting

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The Locus Reference Genomic (LRG) sequence format, recently reported in Genome Medicine, allows a single fixed record containing a reference DNA sequence and all relevant transcripts and protein sequences to be associated with an updateable layer of gene variant coordinates, which should reduce errors in reporting and lead to improved communication about genomic variants.

Nature
Genetics
this month stated that the LRG agreement has provided a platform which allows the editors to adjust journal policy, mandating the use of Human Genome Variation Society (HGVS) allele naming conventions in manuscripts submitted to Nature Genetics.

Dalgleish and colleagues propose that variants associated with human genetic disease can be documented using this format, which was designed for the specific purpose …

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The Genome Biology 10th birthday special issue

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Genome Biology, which has been proudly publishing some of the most exciting research from all areas of genomics for the past 10 years, celebrates its birthday this year. To mark this, we have commissioned a series of reviews from areas of particular interest in the genomics field and from scientists who have helped shape these fields over the last decade.

As such, this month’s issue of Genome Biology contains more than the usual research highlights, reviews and cutting edge scientific research. This month you will also find an editorial from Editor Clare Garvey on ‘A decade and genome of change’, in which Clare discusses the humble beginnings of Genome Biology. First published in 2000, the …

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Macha online – a guest post from Computer Aid

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Computer Aid International’s Stephen Campbell visited the community of Macha to see the impact of the Internet and the research it enables, on an African community.

You won’t find the community of Macha on many maps. It’s 50 miles from the nearest road in the Southern Province of Zambia, itself a land-locked southern African country - it’s pretty much the last place you’d expect to find a community logged on to the Internet.
 
Taking advantage of a satellite link installed by John Hopkins University Malaria Research Institute, the LinkNet Cooperative (formed three years ago by the community and staffed by talented self-taught local youngsters, none of whom have graduated beyond grade 12) has established the largest wireless Mesh Network in …

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Fun at FASEB

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This week BioMed Central exhibited at the Experimental Biology meeting in Anaheim, USA where 10,000 delegates descended upon the Convention Centre which was conveniently located next door to Disneyland.

This meeting provided the ideal opportunity to celebrate the relaunch of our new improved BMC Biology incorporating Journal of Biology. To mark the occasion, the journal’s Editor-in-Chief, Miranda Robertson, hosted a party on Monday night. We were thrilled that Greg Petsko, President of the American Society for Biochemistry and Molecular Biology and Angelo Azzi, President of the International Union of Biochemistry and Molecular Biology came along. We were also fortunate to be joined by the distinguished Editors-in-Chief of three of our journals, Hin Wing Yeung (Chinese Medicine), Kuan-Teh Jeang (Retrovirology) …

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Meeting the challenges of supplement publishing

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Publishing supplements in journals is a practice that frequently comes under scrutiny due to the external sources of funding involved.  Some journals choose to avoid publishing supplements altogether to protect against any potential perception that industry involvement might lead to lost objectivity.  In an editorial in the latest issue of Arthritis Research & Therapy however, the Editors set out how supplements can be published without risking scientific integrity.

Editorial
   
Challenges and opportunities of publishing
supplements at Arthritis Research & Therapy

Frances Mulvany, Jo Baker, Peter E Lipsky,
Ravinder N Maini
Arthritis
Research & Therapy
2010, 12:113
(28 April 2010)

They outline the rigorous peer-review process that supplement articles undergo before publication, and the full …

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New standards for comparative effectiveness research

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Optimizing patient care when resources are limited is an ongoing
global challenge. Meeting this challenge requires an unbiased tool
for assessing the relative effectiveness of health care interventions. In an editorial co-published this week in Trials, editors from several medical journals set out guidelines for the conduct, reporting and publication of comparative effectiveness research.

Comparative effectiveness research – defined by the United States Institute of Medicine as research that "compares the benefits and harms of alternative methods to prevent, diagnose, treat, and monitor a clinical condition, or to improve the delivery of care" – generates evidence to inform the decisions taken by clinicians, patients and policy makers about patient care. The standards outlined in this editorial aim to …

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Improvements always possible: EQUATOR promoting transparent reporting

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In a recent commentary published in BMC Medicine, researchers from the EQUATOR network (Enhancing the QUAlity and Transparency Of health Research) talk about improving the reporting of healthcare studies. Transparency and quality of reporting for biomedical research seriously affects the value and utility of literature.  Not only that, but shortcomings in both of these are a waste of increasingly scarce resources being invested in this research.
 
The commentary further discusses the goals and progress of EQUATOR, as well as outlining some of the ways that all those involved can act – including authors, institutions, funding agencies, and journals. The network is an international initiative with the aim of advancing high quality reporting in health research through, …

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BioMed Central journals indexed in ACM and CINAHL

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Selected BioMed Central journals have recently been added to two specialist indexing services, ACM and CINAHL.

ACM indexes a wide range of journals relevant to computing and recently accepted the following journals:

Algorithms for Molecular Biology
Automated Experimentation
BioData Mining
BMC Bioinformatics
Source Code for Biology and Medicine

CINAHL, a literature service focusing on nursing and allied healthcare, already indexes over 30 BioMed Central journals and recently added the following titles:

Asia Pacific Family Medicine
Head & Neck Oncology
Health & Quality of Life Outcomes
Human Resources for Health
Journal of Cardiovascular Magnetic Resonance
Tobacco Induced Diseases

In addition, all of these titles are included in PubMed, PubMed Central and a wide range of other databases. Full details of all …

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Evolution and cancer: a mathematical biology approach

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 “Cancer is, in some sense, a condensed-time laboratory of evolution” says Marek Kimmel, in an Editorial to introduce a new thematic series published in Biology Direct.

The series brings together cancer researchers and mathematicians to provide insight into the various ways that evolutionary mechanisms relate to cancer, and how these mechanisms can be modeled mathematically. Articles in the series focus on three broad themes; carcinogenesis and the emergence of cancer, evolution and progression of cancer cells and structures, and implications for therapy.

A broad spectrum of areas where evolutionary forces such as mutation and selection are at work are considered; from the level of gene regulation and DNA repair mechanisms disrupted in cancer, to the development of resistance …

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