Biome’s first year: a review

Posted by Biome on 6th May 2014 - 1 Comment


Biome logo scopeWith the number of journals and articles published within them on the rise, it’s difficult enough to keep up with key advances in your own field, let alone in a broader scope of disciplines. A year ago BioMed Central launched Biome to help.

Designed for the research community to catch some of the most interesting and significant publications across the breadth of medical and biological fields that our open access journals cover, Biome also gives a voice to the communities of life scientists, medical researchers and clinicians that these journals serve.

Biome takes the format of an online magazine – it doesn’t publish any research itself, but highlights some of the most significant advances published in our journals and elsewhere, providing succinct, accessible guides to the research and its importance.

As well as being launched with the needs of researchers in mind, we also want to hear their views too. Biome’s Q&As, perspectives, debates, podcasts and videos therefore give a voice to those active in the fields of biology and medicine.

As open access publishing continues to grow, secondary sources – magazines, blogs and news media – are an important route for discovering research that you can access in full. As all of the research published by BioMed Central is made available in this way, what gets covered in Biome is instantly available to read in its entirety, just one click away.

To mark our first anniversary, here are a few highlights from the year…

 

A focus on original research

 

Methane-enzyme_Science-Photo-Library-C0150946-367x300Our Research Synopses provide concise summaries of original research, and this year we’ve covered areas as diverse as methane eating bacteria and the evolution of butterfly wing patterns, to drug delivery across the blood-brain barrier and newly found risk factors for cardiovascular disease.

When looking at research to highlight in the magazine, we often find ourselves wanting to ask some of the broader questions raised: “What is surprising about the findings? What will be the impact of this research? What’s the next challenge?”… and that’s exactly what our Author Q&As aim to do.

When Steve Horvath published research on an ‘epigenetic clock’ in Genome Biology last year, we spoke with him about the potential impact of the tool on diagnosing and characterizing disease, while Greg Gibson and Atul Butte discussed the possible application of genome sequencing in healthy people for ‘wellness’, following research in Genome Medicine.

We asked Kenneth Stedman why his discovery of a new class of DNA RNA hybrid viral genome in a boiling lake raised new questions about viral evolution, and looked at the chances of pandemic in the event that an influenza virus escapes from a lab with Alessandro Vespignani and Stefano Merler.

In clinical research, Munir Pirmohamed and Rosalind Smyth looked at off label drug prescriptions for children, and whether they are causing adverse reactions, and Frank Duffy explains how electroencephalography might be able to differentiate individuals with Asperger’s Syndrome from those with Autism Spectrum Disorder.

ORF logo cropWe also provide a regular round-up of the best open access research elsewhere in ‘Open Reading Frame’, with weekly summaries alternating in focus between biology and medicine.

 

Perspectives from the field

 

As well as looking at specific research articles, Biome also looks to opinion leaders for comment and debate on questions of topical interest, often coinciding with publications or article series in BioMed Central journals.

Handshake (edited w cross)_Flickr_Aidan JonesFollowing the recent publication of two large studies on the unintended effects of statins, Michael Blaha weighed up the risks and benefits of prescribing them to a higher proportion of the population, and Leroy Hood gave his perspective on how participatory medicine has the potential to revolutionise these types of decisions.

Given the currently different standpoints taken by US and European guidelines on when to start antiretroviral HIV therapy, we invited Caroline Sabin and Steven Deeks to debate the issue.

We’ve also looked at differing attitudes towards standard PSA screening for prostate cancer, and physician-certified versus computer-coded verbal autopsies in resource-limited settings, and intend to continue with this multiple perspective format in areas of dispute.

In the genomics field, Rich Roberts explained why single-molecule real-time sequencing hasn’t been well received, and why he thinks there is a need for re-evaluation (as well as why the Nobel winning research wasn’t the highlight of his career!), while Itai Yanai told us how and why the latest methods in single-cell transcriptomics will change biological research.

Elaine Mardis discussed promising avenues in next-generation sequencing for cancer care, and challenges in the clinical translation of these advances. Frank Slack more specifically looked at how miRNAs might be exploited for cancer diagnosis, and Carl-Henrik Heldin discussed the potential of targeting the PDGF pathway in tumour treatment. Taking the broader view, Jenny Chang discussed what critical gaps in breast cancer research should be prioritised for effective translation to prevention and treatment strategies.

To coincide with a Genome Biology series on plant genomics, leading plant scientist Dale Sanders told Biome his views on genetically modified crops. Addressing recent advances in plant genome editing, Sophien Kamoun considered the impact of CRISPR and how this technology may influence the current debate on the safety of genetically modified crops.

 

Podcasts

 

Our journaHeadphonesls provide in-depth overviews of research topics through thematic article collections, often working with leading scientists in these fields, as guest Editors or authors, who have inspiring stories about their work. Biome has been collaborating with these journals to produce podcasts giving an overview of the field, and a flavour of what’s covered in more depth in the series.

This year we’ve tackled what some have hailed as central principles of a forthcoming paradigm shift in healthcare, the tailoring of healthcare interventions to the individual, or personalised medicine, and the increased involvement of the patient in their own monitoring and treatment in a move to a participatory model of healthcare.

With public interest in traumatic brain injury growing considerably in recent years (and recent funding from the US National Football League and Department of Defence attracting much media attention), Alzheimer’s Research & Therapy’s series on the issue is certainly timely. We spoke about recent developments in this field, and challenges ahead, with some of the researchers publishing in the series.

We’ve also spoken to seminal researchers, from an in depth interview with the father of DNA fingerprinting Alec Jeffreys, to ‘anecdotes from the field’ from Raymond Gosling (the first person to crystallize DNA) who recalls a trip to inspect an early model of DNA by Watson and Crick, and William Frankland (the oldest practising scientist in the UK and seminal allergy researcher) who told us about a close scrape with a South American insect during his foray into self-experimentation.

Other podcasts have looked at the use of plant genomics to tackle the future food crisis, surprising discoveries in the field of epigenetics, and the ongoing search for biomarkers for Alzheimer’s diagnosis.

 

Community matters

 

We called the magazine ‘Biome’ as we liked how the word evokes images of diverse ecosystems and communities (as well as having an obvious link with ‘BioMed Central’!). Biome aims to cover issues of importance in the day-to-day life of both clinicians and academics, as well as looking at the research cycle itself.

Peer review_Flickr_AJ CannAt a time when long established conventions of peer review are being questioned, Greg Petsko asks where the solution to ‘the sting of peer review’ will come from, and in our video ‘Is peer review broken?’ we discuss some of the current problems and emerging solutions. The experience of an author using a third party peer review service is given in this podcast, and one of our journal Editors who, after initial alarm that such public discussion was happening about a manuscript currently under submission in her journal, discusses the benefits of ‘open’ peer review conducted on blogs and twitter.

In the last year transparency of clinical trials has been a key issue, with recent small but significant steps in Europe towards ensuring that clinical trials are registered, and data coming from them made available. Ben Goldacre, who has been particularly vocal in support of the AllTrials campaign, and in bringing this debate to the public, spoke with us about the importance of clinical trial transparency.

Firm support for AllTrials also came from the Cochrane Collaboration, who celebrated their 20th Anniversary last year, and published an anniversary reviews series with Systematic Reviews. To coincide with the series, this podcast looks at Cochrane’s successes and future plans in improving access to high-quality and up-to-date research evidence for healthcare decision making. Sally Hopewell outlined just how improvements to the reporting of health research in the first instance could increase its value.

Coinciding with BioMed Central’s move to open up data, by applying the CC0 waiver to data published in our journals, Carole Goble commented on the importance of truly open data for the scientific enterprise.

At the heart of our journal community are our journal Editors, and in various forms we have spoken with them about their careers in science. Starting with the Editors-in-Chief of Epigenetics & Chromatin, Frank Grosveld and Steven Henikoff, who survey the field of epigenetics and where they see it going, and most recently Ravinder Maini, Editor-in-Chief of Arthritis Research & Therapy, who discusses the future of rheumatic disease treatment. Have a look at the Community section for more video and written interviews.

 

What’s next?

 

We’ve several exciting developments coming up for Biome. We’re soon to  launch a new feature type called ‘Clinical Insights’, which aims to give clinicians short overviews of the latest medical research findings and what this evidence means to their practice. These will mostly cover randomised controlled trials, systematic reviews and meta-analyses). This ties into our larger plans for a renewed focus on evidence based medicine, in addition to peer review and open data.

We’ve also got some new website features on the way to make it easier to find the content that’s relevant to you. Sign up for updates to receive further details!

 

How to receive updates

 

We send a monthly mailing of highlights, sign up from the Biome website, or register for updates via BioMed Central. If you sign up by registering with BioMed Central, we’ll send you a version of the mailing tailored to your interests (biology or medicine).

You can also follow us on twitter @biomemagazine, or follow our RSS feed.iTunes logo
You can subscribe to our podcasts via iTunes or the RSS feed, or our page on PodBean, and have the latest podcasts delivered to you automatically.

 

Ciaran O’Neill & Lux Fatimathas

 

Acknowledgements

 

We gratefully acknowledge the contribution of Michaela Torkar in launching Biome, Stephanie Harriman, Maria Kowalczuk, Elizabeth Moylan, Shreeya Nanda and Jigisha Patel for their continuing work on the magazine, and all who contribute. A full list of contributors is available here.