BMC series blog

Invitation to submit to Cancer Bioinformatics thematic series

'Cancer Bioinformatics: Bioinformatic Methods, Network Biomarkers and Precision Medicine' is a special thematic series to be published across BMC Bioinformatics, BMC Cancer, Genome Medicine and Journal of Clinical Bioinformatics (JCBi).

Cancer remains one of the leading causes of death across the globe. Most cancer treatments work for only a subset of patients and there is still a great need for disease-specific biomarkers and individualized medicine, since a large proportion of patients receive ineffective treatments. It is essential that we develop accurate tools for delivering the right treatment to the right patient in the right time, based on biological characterization of each patient’s tumor. There is still a lack of tools for aiding early diagnosis, prognosis prediction, or predicting response to treatment. Increasing evidence that genomic, proteomic, and metabolomic analyses can be utilized to understand molecular mechanisms of cancer has led to increasing work within this area.

This series will specifically focus on new developments in cancer bioinformatics and computational systems biology and will present biologically interesting discoveries on cancer using computational methods, in addition to exploring the potential of clinical applications to improve the outcomes of patients with cancer.

Potential topics include, but are not limited to:

    * Algorithms for clinical biomarker selection
    * Integrative approaches
    * Systems biology and network-based approaches
    * Novel approaches to clinical trials
    * Deep sequencing and proteomic profiling
    * Epigenetic mechanisms and RNAs
    * Drug discovery and development
    * Individualized medicine


Submission of original research, methodology, software, and database articles are encouraged until 1st November 2012 but will be processed as soon as they come in.

Please direct any questions to Xiangdong Wang (Series Editor) at editorial@jclinbioinformatics.com. Please submit your manuscript here: BMC Bioinformatics, BMC Cancer, Genome Medicine and Journal of Clinical Bioinformatics, and state clearly in the covering letter that it is intended for this thematic series.

Posted by Charles Jensen at 15:25    Comments (0)

 

BMC-series journals on track for Impact Factor

BMC Biophysics, BMC Ecology and BMC Endocrine Disorders have all recently been accepted for indexing by Thomson Reuters and are on course to receive their first Impact Factors. We are delighted that these journals have been selected for indexing, joining the many other journals in the BMC series  to have an Impact Factor.

BMC Endocrine Disorders has been tracked from publications in 2009 and is due to receive its first Impact Factor in 2012. A recent blog post discusses one of the special thematic collections in BMC Ecology, which has likely contributed to the increased visibility and recognition of the journal.

This is great news too for BMC Biophysics, considering it is less than a year since the journal re-launched on the BioMed Central platform. Since re-launch the journal has recruited a new Editorial Board consisting of world-renowned experts in the field.

In 2011 we published many interesting articles, including one from our Section Editor, Gerhard Gompper, which is an important theoretical contribution to the field. In it, the authors introduce and analyze a discrete filament-motor protein model of subcellular microtubule self-assembly in fission yeast, which demonstrates spontaneous generation of a number of steady states, including spindles, nematics, and asters. We think this study highlights the power and flexibility of online open access publishing in biophysics, as the authors were able to directly link the article’s text to their video figures. View their hypnotic animations of microtubule vortices here. 

The journal has already had a strong start to 2012 by publishing an exciting article by Qin et al. describing the structural determination of the EphA4 ligand binding domain, providing the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity. An accompanying commentary by Ruth Nussinov and Buyong Ma in our flagship biology journal BMC Biology says: “These snapshots of multiple conformations of the free EphA4 LDB provide a unique insight into the conformational dynamics of EphA4 and the Eph-ephrin signaling pathways.”

After such a great start we are looking forward to what 2012 has in store for these journals and would invite you to submit your next research article to BMC Biophysics, BMC Ecology and BMC Endocrine Disorders.

Shane Canning

Journal Development Editor

Simon Harold

Executive Editor

Posted by Shane Canning at 10:00    Comments (0)

 

Bacterial symbionts – the key to fighting pests and diseases?

Arthropods such as insects can be devastatingly efficient pests and disease vectors, posing significant challenges to the agricultural and medical communities. Pesticides used to be a common solution to dealing with pests but, with more stringent environmental regulations on pesticides and increasing pest resistance to the chemicals, new solutions are required.

Many arthropods have evolved a symbiotic relationship with bacteria and this association could potentially be exploited to control pests and disease  vectors. This biological control approach, called symbiont-based control strategies, would be preferable to chemical controls due to their lower environmental impact.

In order to exploit the arthropod- bacterial symbiosis, more knowledge of the relationship is required. BMC Microbiology has published a supplement – Arthropod symbiosis: from fundamental studies to pest and disease management consisting of the latest interdisciplinary research in this field. The articles in the supplement look at bacterial symbiosis with pests such as the Anopheles mosquito that spreads malaria, tsetse fly that spreads sleeping sickness and the cereal weevil that devastates cereal crops.

Currently in their initial stages of development, symbiont-based control strategies have the potential to increase global health and food resources by removing arthropod disease vectors and agricultural pests.

Posted by Srimathy Sriskantharajah at 16:03    Comments (0)

 

BMC Ecology starts 2012 on a high!

The year 2011 was a successful one for BMC Ecology and 2012 is off to an excellent start with the news that the journal has been accepted for tracking by Thomson Reuters and will receive its first Impact Factor in 2015. We are delighted with this result as it reflects the growth and increased visibility of the journal in its field and the hard work and support given by our Editorial Board and in-house team.

To support and drive the further growth of BMC Ecology, we are now working with external Section Editors on the journal and are pleased to welcome Nick Royle, Josef Settele, Jean Clobert, Michel Baguette, and Mike Bonsall to the journal in these roles. We look forward to working with them on developing their sections in the future and benefiting from their experience and expertise.

In addition to these successes BMC Ecology celebrated the 2011 UN Year of Forests with the publication of a thematic series entitled ‘Forests: Looking to the Future’ in conjunction with another of BioMed Central’s open access journals, Carbon Balance and Management. The series published a number of articles, including a review by Raf Aerts and one of BMC Ecology’s Associate Editors Olivier Honnay on forest restoration, which has been highly accessed, and an article by Tiina Sarkinen and colleagues on the effective mapping of dry forest biomes. The series has generated a lot of interest and we are pleased with the promotion that has given the journal, in particular the coverage on Twitter at the Forests 2011 conference in Belgium which was happening at the same time.

We are looking forward to what the rest of 2012 brings. 

Posted by Genevieve Horne at 15:38    Comments (0)

 

Conferences: From bone to brain

 November was a busy month for conferences, and two of those attended by BioMed Central included the 75th annual meeting of the American College of Rheumatology and  the Association of Rheumatology Health Professionals (ACR/ARHP),  and Neuroscience 2011, the Society for Neuroscience's (SfN) 41st annual meeting.

This year, ACR/ARHP was held in Chicago, Illinois from 5th-9th November and was attended by over 16,000 delegates. The conference themes covered all aspects of rheumatology from basic science to clinical applications, and popular topics included advances in juvenile idiopathic arthritis (JIA), advances in treatment of gout, osteoarthritis and systemic lupus erythematosus, as well as non-pharmacological interventions for musculoskeletal disorders. We met with many of our board members for Arthritis Research and Therapy, BMC Musculoskeletal Disorders, Pediatric Rheumatology and Journal of Foot and Ankle Research.  Some of our Editorial Board members delivered stimulating talks on the clinical phenotypes of JIA (Alberto Martini, Editor-in-Chief of Pediatric Rheumatology), heart disease and updated guidelines on rheumatoid arthritis (Jasvinder Singh, Section Editor of BMC Musculoskeletal Disorders) and Yusuf Yazici (Section Editor of BMC Musculoskeletal Disorders) discussed the comparative efficacy of biologic agents in rheumatoid arthritis. In addition, Editorial Adviser Anthony Woolf who is the current chairman for the Bone and Joint Decade group, spoke about how to encourage policymakers to take musculoskeletal conditions seriously.

Neuroscience 2011 was held on the following week, from 12th-16th November in Washington, DC and was attended by over 32,000 people.This is the ‘must-attend’ event for neuroscientists from all over the world, and was overseen by the current president of SfN, Susan G Amara, who is also Editorial Adviser for BMC Neuroscience. Presidential lectures were delivered by Editorial Advisers for BMC Neuroscience Cori Bargmann and Mu-ming Poo, and a very well received special lecture on neuronal networks of motor control  was given by Thomas Jessel.This annual SfN event is always a great place to meet with our Editorial Board members, and this year we had the pleasure of meeting many of them, including (but not limited to) Section Editors for BMC Neuroscience (Robert Gerlai, Anthony Kline, Maurizio Popoli, Mark Rasenick and Ramesh Raghupathi), as well as Editors-in-Chief of Journal of Neuroinflammation, Molecular Autism, Molecular Brain, Molecular Neurodegeneration, Molecular Pain and Neural Development.

We hope to see you all again at key conferences next year!

Posted by Sabina Alam at 10:46    Comments (0)

 

BMC Cancer turns ten

  This year saw BMC Cancer turn ten.  When the journal published its first volume of 20 articles in 2001 it was one of only a handful of open access titles operating in the field and was exclusively run by a small team of in-house editors.  A decade later, the journal’s in-house team is supported by an international group of Section Editors, Deputy Section Editors, Associate Editors and Editorial Advisers numbering in the hundreds and has published nearly 3,000 articles.

To mark the end of its 10th year, BMC Cancer is publishing a special anniversary collection of commissioned articles.  With contributions from Carlos Caldas, Ian Cree, Shoukat Dedhar and many others, the collection highlights the advances in the field over the past 10 years and looks forward to the developments that we might expect to see in the next decade.

Congratulations to BMC Cancer for reaching this milestone and here’s to the next 10 years.

Philip Dooner          

Journal Development Editor

Posted by Christna Chap at 10:13    Comments (0)

 

New thematic series to highlight the end of 2011 - UN Year of Forests

2011 has been the UN International Year of Forests and to highlight this, two of BioMed Central’s open access journals, BMC Ecology and Carbon Balance and Management, have joined forces to create a thematic series showcasing the latest research into these crucial ecosystems.

The two journals’ differing scopes are reflected in the different research themes highlighted in the series. Co Editor-in-Chief of Carbon Balance and Management, Georgii Alexandrov, introduces the thematic series in his editorial and discusses the importance of Land-Use/Land-Cover Change models in setting forest conservation targets. In a separate article, BMC Ecology’s Associate Editor Olivier Honnay reviews the use of a biodiversity-ecosystem functioning perspective in forest restoration. This approach, and its emphasis on functional rather than taxonomic diversity, may lead to a more pragmatic approach to forest restoration where a species’ function, rather than its origin, is assessed when selecting tree species to include.

Non-native tree species are also discussed in research by Annabel J Porte and colleagues who studied the invasive maple species, Acer negundo, which displays higher phenotypic plasticity than native species under non-limiting resource environments, explaining how these trees are able to spread throughout the resource rich forests of Europe.

Further articles published by Carbon Balance and Management in the thematic series include research by Dr Grant Domke et al. on the importance of incorporating density reductions and structural loss adjustments when assessing forest biomass and carbon stock estimates, and a timely review by Dr Martin Herold et al. discussing the best options for monitoring past carbon emissions from forest degradation.

Finally, BMC Ecology presents research by Tiina Särkinen and colleagues on the seasonally dry tropical forests (SDTF) of South America. Current biome maps for these areas vary considerably and highlight the difficulty in mapping highly discontinuous and fragmented vegetation like SDTF over large areas. Potential new methods for modeling these areas are presented with the hope that the generation of more reliable maps will allow further research into these threatened forests.

Over the forthcoming months we will be adding new articles to the series and we hope you enjoy reading them and keeping up to date with developments in this important area of research.

Philippa Harris
Senior Executive Editor
BMC Ecology

Genevieve Horne
Senior Journal Development Editor
BMC Ecology and Carbon Balance and Management

Posted by Philippa Harris at 17:20    Comments (0)

 

A guide to the MDCK variety pack

In a Commentary published in BMC Cell Biology, Joseph Dukes, Paul Whitley and Andrew Chalmers present a useful guide to the Madin-Darby Canine Kidney (MDCK) cells, a line that is regarded as a model system for studying protein trafficking, polarity and junctions in epithelial cells. These cells come in a variety of different strains and, in spite of their widespread use among cell biologists, researchers often fail to report in the literature which strain they used, and sometimes provide inaccurate information, which has made it increasingly difficult for researchers new to MDCK cells to choose the right strain for their experiment. In the context of the recent emphasis on cell line authentication, Dukes and colleagues provide a short guide to the different MDCK strains available, with a description of their specific properties and features and a list of suppliers.

You can read the whole Commentary here.

Posted by Dafne Solera at 16:26    Comments (0)

 

Companion articles explore the kangaroo genome

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 functionally equivalent.

A third study, by Hannah Siddle and colleagues looks in detail at the immune genes of the wallaby major histocompatability complex (MHC). They find that there have been extensive changes in the organization of these genes since the split of the Australasian and American  marsupials, with the wallaby Class I MHC genes having been scattered across a number of genomic  locations and the Class II split into two separate clusters.

In a publication in EvoDevo Brandon Menzies and colleagues demonstrate that the wallaby placenta secretes hormones structurally and functionally similar to the pituitary hormones prolactin, luteinizing hormone and growth hormone. This suggests that these pituitary hormones may be an ancestral feature of the reproduction of all mammals.

Hop over to the series homepage to read more, and the rest of the articles.

The Tammar Wallaby embryo and fetus at day 18 (a,b), 23(c) and 25(d) of gestation. The joey is born on day 26. Taken from Menzies et al. EvoDevo

Posted by Tim Sands at 16:29    Comments (0)

 

BMC Biophysics meets the Queen of the Danube

How appropriate for the 8th European Biophysics Congress to be held in a city like Budapest, the so-called “Queen of the Danube”. Here is a place unified at the banks of this great river—Buda to west, Pest to the east—and here is where Biology meets Physics, unified in a single discipline.

Like the city itself this union is not a new one, with co-hosts the European Biophysics Societies Association (EBSA) and the Hungarian Biophysical Society celebrating their 27th and 50th anniversary, respectively.

In the face of such history, BMC Biophysics is a relatively new addition to the field. The journal has recently relaunched from its previous incarnation as PMC Biophysics, and is now a member of the BMC-series journals, with an expanded Editorial Board.

As one of the few dedicated biophysics journals to be entirely open access, this is an exciting time for the field to embrace open data, and the associated benefits of free and open dissemination of research.

BMC Biophysics will consider all articles across the entire field of biophysics, with no restriction on article types. We particularly welcome submissions with a strong focus on physics, as well as contributions to the field of computational biophysics, and biophysical methods including software articles. As an online publisher we are not restricted by page limits, and are happy to handle non-standard figure-types—such as videos—as additional files.

The EBSA Congress was a wonderful showcase for the breadth of scope that this field has to offer, and BMC Biophysics was delighted to be able to catch up with its current outgoing president, and Section Editor for the journal, Professor Alberto Diaspro. Professor Diaspro was enthused by how the conference has developed since its inception 16 years ago, and to see the huge developments that have occurred in the field over this time.

In his opening lecture to the popular “Imaging and Optical Microscopy” session, he talked at length of the latest advances in super-resolution nanoscopy, and the “resolution obsession” that drives the field (or “vive la resolution” as Holger Stark of the Max Planck Institute puts it). We are delighted to welcome Professor Diaspro to the journal’s Editorial Board, and look forward to working together as the field develops further.

Other notable highlights of the congress included sessions on “Neuronal Systems and Optogenetics” and “Nucleic Acid and Chromatin Structure and Function” (jointly hosted by BMC Biophysics Section Editors Jörg Langowski and Sanford Leuba), as well as a number of exciting plenary addresses. These included an opening address by Nobel laureate Ada Yonath, who emphasised strongly the need for a greater presence for women researchers across all scientific disciplines.

This call was appropriately met in the EBSA Prize-winning lecture that followed, with recipient Kinneret Keren discussing her excellent research on cell movement. In it, she likened the biophysical problem of actin dynamics to the equivalent of attempting to fit the world’s population into a city the size of Budapest, and then expecting them to self-organise at the speed of 600 km/h. I’m not sure how the Queen of the Danube would feel about that.

Simon Harold PhD

Executive Editor

BMC Biophysics

Posted by Simon Harold at 13:24    Comments (0)

 

The first Chinese Rhesus macaque genome

The Rhesus macaque (Macaca mulatta) is an Asian monkey that shares 93% of its DNA sequence with humans and, due to this similarity, is an important species for scientific study. Until now, work on the Rhesus macaque has largely focused on the Indian subspecies, but an article published in Genome Biology reports, for the first time, the genome sequence of a Chinese Rhesus macaque. Rhesus macaqueIn the article, researchers from the BGI (China’s premier genomics institute) and the Kunming Institute of Zoology identify millions of DNA sequence variations between the Indian and Chinese Rhesus macaque genomes, including 5.5 million one letter variations known as single nucleotide polymorphisms, or SNPs. A website to enable browsing of these SNPs accompanies the article and provides a valuable new resource cataloging the differences between the two subspecies. Our understanding of genomic diversity in the Rhesus macaque is also enhanced by a recent article published in BMC Genomics, which compares the genome sequences of three Indian Rhesus macaques, identifying 3 million SNPs. Together, the Genome Biology and BMC Genomics datasets represent a significant advance in primate genomics and will inform future research in fields ranging from human evolution to HIV virology.

Posted by Blog Maintenance at 13:16    Comments (0)

 

European Consultation on Scientific Information in the digital age

The European Commission (EC) has announced a consultation on ‘scientific information in the digital age’. The consultation is running until 9th September 2011 so if you’re as interested in open access and open data as we are then the EC wants to hear your opinion on the following issues: - how scientific articles could become more accessible to researchers and society at large - how research data can be made widely available and how it could be re-used - how permanent access to digital content can be ensured and what barriers are preventing the preservation of scientific output The EC is hoping to push for improved knowledge circulation in the European research area and this initiative is being spearheaded by Commissioner for Research and Innovation, Máire Geoghegan-Quinn and Vice President for the Digital Agenda Neelie Kroes, who reiterated the importance of open access in the following statement: "The results of publicly funded research should be circulated as widely as possible as a matter of principle. The broad dissemination of knowledge, within the European Research Area and beyond, is a key driver of progress in research and innovation, and thus for jobs and growth in Europe. Our vision is Open Access to scientific information so that all of us benefit as much as possible from investments in science. To accelerate scientific progress, but also for education, for innovation and for other creative re-use. For the same reason we must preserve scientific records for future generations". This Consultation will result in a Communication and a Recommendation on the access to and preservation of scientific literature, specifically with regards to research funded by the EU. Europe has always been a leader in scientific innovation and the EC feels that this is progress is aided by fast and easy access to scientific information, something that open access publishing contributes to greatly.

Posted by Blog Maintenance at 13:15    Comments (0)

 

Epidemiology of major depression: Global patterns

With major depression being one of the leading causes of disability worldwide, impacting on many different areas of life, including pregnancy and work absence, treatment and management of this debilitating condition garners a lot of attention. However, from a public health perspective, better understanding the patterns and causes of depression will help guide initiatives to reduce the impact of depression on individuals and society. In a new research article (link) published this week in BMC Medicine, Bromet and colleagues from around the world present the results of their multi-national study looking at the epidemiology of major depressive episode from 18 countries (including low/medium and high income nations), reporting on prevalence, impairment and demographic aspects. Although they find differences between low/medium-income and high income countries, they also find patterns that are not country or income specific. Visit the BMC Medicine website to read the full article(link) and find out what other interesting insights the authors are able to make into this global problem, as well as their suggestions for moving forward in this field of research.

Posted by Blog Maintenance at 13:14    Comments (0)