PLOS Genetics’ Tenth Anniversary

2015 marks the tenth anniversary of publishing cutting-edge research at PLOS Genetics. Since the inaugural issue on the 25th of July 2005, PLOS Genetics has been dedicated to supporting the scientists that make up the genetics community with ethical rigour, thorough peer reviewing and lively scientific discussion. As the years have gone by we have seen a wealth of expertise rotate through our Editorial Board, and we are delighted to have worked so closely with much of our community.

Image credit: Flickr vpisteve CC BY

Image Credit: Flickr vpisteve CC BY

On the occasion of our tenth anniversary we are highlighting and celebrating many aspects of PLOS Genetics. In order to recognise the outstanding work published in PLOS Genetics, the Editors are awarding a prize for the best Research Article of 2014. Articles will be nominated by the wider community and our Editors-in-Chief and Section Editors will select a winner from the nominated works. To reflect the journal’s aims of publishing high quality research and fostering community engagement, the winner will be chosen based upon scientific excellence and community impact. Nominations will open in a few weeks, so keep a lookout for updates! In the meantime, why not refresh your memory and browse through our 2014 volume?

As well as celebrating recent publications we want to acknowledge the richness of research that we have published over the years. We are launching a collection of the ten most downloaded articles in PLOS Genetics’ history to form a PLOS Genetics Tenth Anniversary Collection. Each article in the collection will be accompanied by a commentary, written by an expert in the field, and the collection will include a reflective editorial from our Editors-in-Chief, looking back upon the past decade.

The first ever cover image for PLOS Genetics from July 2005. Image Credit: Photograph by Erwin and Peggy Bauer, USFWS; line graphic by Felice Macera.

The first ever cover image for PLOS Genetics from July 2005. Image Credit: Photograph by Erwin and Peggy Bauer, USFWS; line graphic by Felice Macera.

PLOS Genetics owes much of its success to our outstanding Editorial Board. These individuals work tirelessly to encourage, assess and improve our submissions, whilst being vital members of the genetics community and making outstanding scientific contributions in their respective fields.  To celebrate ten years of hard work, research, and immense dedication from our Editorial Board, we are inviting our editors to contribute to PLOS Biologue. In these posts, our editors reflect on how their areas of research have developed and changed over the last ten years, and explain what their hopes are for future research. The first post in this series is from Beth Sullivan on the last ten years of chromosome biology, which provides an exciting insight into the challenges and achievements this field has seen over the decade. The second post has been written by John Greally, and focuses on the future of epigenetics research. He suggests that isolated EWAS needs to be replaced with a new approach, involving the concurrent testing of the epigenome, transcriptome and genome.

To keep the discussion going, John Greally will be hosting a tweetchat on July 29 at 11-12 EDT. Members of the genetics community will be on Twitter discussing the future of epigenetics research and how to support progress. Be part of the conversation at #epig20.

Our twitter followers have been active in our anniversary celebrations by tweeting their favourite papers and images. The public has voted to select the Anniversary Image which will grace all our celebration activities. The winning image was announced earlier today, and you can read more about it here. This image will take pride of place on our homepage, and we will also be featuring articles from the PLOS Genetics archive over the anniversary period.

We appreciate the hard work and dedication shown by all of our contributors, and it was a delight to be able to thank our reviewers at the close of last year. The readers, authors, reviewers and editors of PLOS Genetics have come together to create and nourish this journal over the past ten years, and these celebrations are as much about you as about the journal.  As 2015 continues we will take the opportunity to reflect, plan for the future, and celebrate with the genetics community. Watch this space!

Category: Announcement, Community, Genetics, News, PLOS Genetics, Publishing | Leave a comment

Winner of the PLOS Genetics issue image campaign

 

E-cadherin

Claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse (October 2014). Image Credit: Tia DiTommaso

Earlier this month we launched a campaign to solicit people’s favourite PLOS Genetics issue images, published over the last ten years, from a selection of five. The winning image depicts claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse and was featured as PLOS Genetics’ October 2014 issue image. Submitted by Tia DiTommaso et al, in their paper entitled ‘Keratin 76 Is Required for Tight Junction Function and Maintenance of the Skin Barrier’, this image depicts claudin 1 in green, E-cadherin in red and keratin 14 in blue, and the work highlights the role of Keratin 76 in wound repair and barrier activity in the skin. Find out more about the research behind the image in this post from the authors, published as part of our ‘Understanding Images’ series. The image will be featured on the journal’s Twitter account and homepage during PLOS Genetics’ tenth anniversary week.

Thank you to all who voted!

 

Author: Jessica Miller, Publications Assistant, PLOS Genetics

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What’s your favourite PLOS Genetics issue image?

PLOS Genetics is celebrating its ten year anniversary in July. Over the last decade, we have seen some eye-catching issue images and we would like to know which one is your favourite. The winning image will then be featured on the PLOS Genetics’  homepage and Twitter account during the journal’s tenth anniversary week.

Take a look at the five images below, and let us know which is your favourite (or tell us about one you like which isn’t included) by taking the following survey: https://www.surveymonkey.com/r/2X6R2XZ

Journal issue images are chosen by the Editors-in-Chief each month, and this selection was picked by the journal staff here in Cambridge, UK.

The last day of the survey is Friday 24th July, so vote soon!

 

Early sensory development in the inner ear

Early sensory development in the inner ear (January 2006). Image Credit: Amy Kiernan

Rolled thumb print

Rolled thumb print (September 2007). Image Credit: Sarah E. Medland

 

 

 

 

 

 

 

 

C albicans

Candida albicans colony morphology (December 2009). Image Credit: Oliver Homann and Jeanselle Dea

Drosophila testis

Reporter construct expression in Drosophila testis and male genital tract (June 2013). Image Credit: Helen White-Cooper

 

 

 

 

 

 

 

 

Claudin 1

Claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse (October 2014). Image Credit: Tia DiTommaso

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J. Andrew Bangham (1947 – 2014): Enterprising scientist who broke new ground in computational biology and image analysis

Andrew teaching in Italy

Andrew Bangham, former Professor in Computer Science at the University of East Anglia, Norwich, was a pioneering researcher with the rare ability to integrate diverse disciplines: from computer science and electrophysiology to plant development and visual art. He is best known for developing the theory of ‘sieves’, which find frequent application in modern computer vision including artistic rendering of images, and for interdisciplinary approaches to modelling plant growth and development. He was also an inspirational teacher who cultivated and encouraged talent during the birth and flowering of computer science.

Andrew was born just after the war into a scientific and artistic family. He was the eldest son of medical doctors Rosalind and Alec Bangham, and grew up outside Cambridge where Alec (later FRS) was a researcher at the Babraham Institute of Animal Physiology. Andrew’s village upbringing was filled with sailing, photography and painting; his uncle Patrick Heron had a strong influence on Andrew’s later interest in the perception of colour.

Andrew found his vocation soon after finishing high school. Unsure whether he would have the sufficient grades to study medicine, his father arranged for him to spend six months in the US, working with eminent physiologist Dan Tosteson at Duke University in North Carolina. He took to experimental research like a duck to water. Fired up by his experiences at Duke, and by the publication of his first paper, Andrew arrived at University College London (UCL) to study physiology.

The late 1960s and early 1970s were a tremendously exciting time for electrophysiology and UCL had multiple Nobel prize-winning physiologists working there. After his undergraduate degree—during which he met his future wife Kate, a medical student—he stayed on at UCL to complete a PhD in the Biophysics Department, where he worked on the electrophysiology of mitochondria. Further developing the lipid film techniques first acquired in the Tosteson lab, Andrew shared his work with colleagues at Cambridge and at the University of East Anglia (UEA).This led to an invitation to join the UEA Biology Department in 1973, in order to continue studying the electrical properties of cells and tissues.

Computational methods were still in their infancy, and Andrew became one of the first to use computers to address physiological questions. He wrote computer programmes to interpret the very noisy electrical traces produced by his experiments, inventing new filtering techniques to pick out signals in the noise. In the 1970s, the challenges of using computing in research were not purely technical, but also financial. Andrew established new ways of raising research money, setting up contracts to do modelling for local commercial companies on the University’s mainframe computers.

Through this work he was eventually able to buy a state-of-the-art Sun computer, which offered enough computing power for work on a new class of information filters, which he would later call ‘sieves’. By analogy with physical sieves, which pass objects depending on their size, computational sieves filter signals using medians—in contrast to the more conventional mean-based filters. Andrew realized that the potential for sieves was in the growing field of computer vision.

Eventually he decided to devote himself full-time to computational problems, moving in mid-1980s from UEA’s Biology Department to its School of Information Systems. Undaunted by the need to master a whole new field of mathematics known as mathematical morphology, Andrew formulated a new theoretical treatment for computer vision. He extended his funding approach to his new department by setting up contacts between numerous research groups and local and national companies, such as the local Norwich shoe company Start-rite, Britain’s Post Office, and the Independent Television Commission.

Andrew also realised that his median sieves allowed him to extract striking colour patterns from photographs, reminiscent of the paintings by Heron. Andrew became deeply interested in the relationship between median sieves and the ways in which human brains interpret visual signals. He developed software—later known as PhotoArtmaster—that offered tools for the digital alteration and analysis of photographs, and which he sold through his company Fo2Pix.

Patterns of growth in the Snapdragon model. Image Credit: Bangham et al.

Patterns of growth in the Snapdragon model. Image Credit: Bangham et al.

Throughout this period of entrepreneurship and programming, Andrew retained a strong interest in biology. In the mid-1990s he began collaborating with Professor Enrico Coen at the John Innes Centre, who shared Andrew’s passion for understanding pattern and form. They tackled the problem of how the petals of the garden snapdragon grow using a combination of computational and experimental approaches. Inspired by these experiences, Andrew established UEA’s D’Arcy Thompson Centre for Computational Biology.

A passionate sailor, and devoted to his family, Andrew had a broad network of friends, colleagues and students in Norwich and beyond. At a celebration of his scientific work at the John Innes Centre, speaker after speaker talked of Andrew’s influential role in their work, of his enthusiasm, and of his ability to articulate the links between individual problems and whole scientific fields. Colleagues described him as the unusual combination of unconventional thinker, wonderful host, inspiring teacher and supportive colleague.

Andrew, Enrico and colleagues published their work on the genetic control of tissue growth in PLOS Computational Biology and PLOS Biology:

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002071

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000537

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Human Disease Epigenomics 2.0

It might be hard to believe, but 2015 marks ten years of PLOS Genetics! To celebrate ten years of hard work, research, and immense dedication from our Editorial Board, we are featuring posts from ten of our editors. Next in the series is a forward looking post from John Greally, Associate Editor at PLOS Genetics, exploring what the future might hold for epigenetics.

John Greally, Associate Editor at PLOS Genetics Image Credit: Trésor Parisien CC BY

John Greally, Associate Editor at PLOS Genetics Image Credit: Trésor Parisien CC BY

The study of how genes are regulated and how their regulation affects human disease has the potential to generate insights into mechanisms that aren’t based on variation in DNA sequence, and could even show that temporally remote events can be “remembered” by the cell.  Currently the method used by epigeneticists to examine these regulatory processes is an epigenome-wide-association study (EWAS).  However, it is increasingly clear that the isolated EWAS is not sustainable as a robust means of gaining desired insights, and needs to be re-thought substantially.  The human disease epigenomics 2.0 approach is a way of thinking about increasing the interpretability and value of these studies.

It’s worth generalizing about the typical EWAS.  These studies are usually designed as cross-sectional, comparing affected cases and unaffected controls at one time point rather than longitudinally over time.  As another general rule, the same type of tissue or cells is usually compared in all individuals, recognizing that different cell types have different patterns of epigenetic and transcriptional regulation [1].  DNA methylation is the regulatory process almost universally studied in EWASs.

Epigenetic studies are mostly focused on testing the abundant 5-methylcytosine (5mC) modification, where a methyl group is attached to a carbon at position 5 in cytosine, but with a variable contribution of the minor 5-hydroxymethylcytosine (5hmC) modification where a hydroxyl group is added to the methyl group at the position 5.  At present, most assays used do not discriminate 5hmC from 5mC [2], so ‘DNA methylation’ studies are generally measuring a combination of both 5mC and 5hmC.  An increasingly wide range of human phenotypes is being tested for epigenetic dysregulation [3], based on the idea that a change in DNA methylation at the same site(s) in multiple affected cases when compared with controls is indicative of cellular changes characterizing the disease phenotype.

There is, however, growing concern that EWASs are not delivering reliable results, due to our recognition that DNA methylation is influenced by a number of factors.  While any genome-wide assay is subject to technical and experimental variability, DNA methylation is also influenced by a number of biological influences.  If the people studied have differences in the relative proportions of subtypes of cells in their samples from which DNA is extracted, that can affect the overall DNA methylation pattern generated [4, 5].  If a locus in the genome is transcribed to form RNA in some people and not others, this also has the potential to change DNA methylation at that locus [6, 7].  The normal differences that exist in DNA sequence between individuals represent an especially strong influence, accounting for between 22-80% of DNA methylation differences between individuals [8-10].  Analytically, there are some measures being taken to diminish the effects of cell subtype heterogeneity in particular [11], but less progress with the other sources of variability.  If an EWAS has not tested for the contribution of major sources of variability, we cannot interpret the reason for any observed DNA methylation changes with any confidence.

There is not much we can do with current studies that were not designed to address these problems.  We can, however, do better in our prospective design of new studies.  A human disease epigenomics 2.0 era would involve the concurrent testing of the epigenome, transcriptome and genome, using cells in which the subtype composition can be determined, generating a rich dataset in which expression and methylation quantitative trait loci (eQTLs and mQTLs) allow insights into the effects of DNA sequence variability.

Image Credit: John Greally

The network of interactions involving the epigenome (represented here by DNA methylation) includes transcription, cell subtype proportions and DNA sequence variability. As a further intriguing possibility, if DNA sequence variation causes unrecognised cell subtype lineage commitment effects (as lineage quantitative trait loci, linQTLs), it would follow that the presumed effects of DNA sequence variability upon gene expression and DNA methylation (eQTLs and mQTLs) may instead reflect effects upon cell subtype proportions. Image Credit: Greally Lab CC BY

The potential then exists to use this characterization of interactions in control subjects as the foundation for understanding the deviations from these patterns in individuals affected by a disease, thereby defining epigenetic changes that are not accounted for by recognized confounding effects.  Performing DNA methylation, transcriptional and genotyping studies in the same cells is certainly more expensive than testing DNA methylation alone.  However, if isolated DNA methylation studies are not generating interpretable information, these would be cheaper but wasteful experiments.  Furthermore, even the DNA methylation changes that are due to cell subtype, transcriptional or DNA sequence differences are potentially valuable as pathophysiological insights.  A systematic change in representation of a cell subtype is potentially mechanistically contributory to a disease, as is a transcriptional difference between groups, while a DNA methylation difference attributable to an mQTL will have identified a genotypic association with the disease.  These byproducts of the integrative human disease epigenomics 2.0 approach should be sought specifically, even if they do not test a starting hypothesis of independent epigenetic perturbations.

The first wave of EWASs has revealed DNA methylation changes associated with a wide range of phenotypes [3].  We now also appreciate that the ability to interpret these studies is constrained by our lack of information about known influences on DNA methylation.  The isolated EWAS now needs to be supplanted by the more rigorous human disease epigenomics 2.0 approach, so that we generate fully interpretable data and robust insights into this exceptionally interesting alternative mechanism of human phenotypes.

COMPETING INTERESTS

Dr. Greally serves as chair of the scientific advisory board of Medyear (a division of Personiform Inc.) which provides an electronic personal health exchange service to patients.

REFERENCES

  1. Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, et al. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res. 2013;41(8):4423-32. Epub 2013/03/14. doi: 10.1093/nar/gkt143. PubMed PMID: 23482391; PubMed Central PMCID: PMC3632130.
  2. Plongthongkum N, Diep DH, Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014;15(10):647-61. doi: 10.1038/nrg3772. PubMed PMID: 25159599.
  3. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013;10(10):949-55. Epub 2013/10/01. doi: 10.1038/nmeth.2632. PubMed PMID: 24076989.
  4. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86. Epub 2012/05/10. doi: 10.1186/1471-2105-13-86. PubMed PMID: 22568884; PubMed Central PMCID: PMC3532182.
  5. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014;15(2):R31. doi: 10.1186/gb-2014-15-2-r31. PubMed PMID: 24495553; PubMed Central PMCID: PMC4053810.
  6. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 2007;39(1):61-9. Epub 2006/11/28. doi: 10.1038/ng1929. PubMed PMID: 17128275.
  7. Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011;21(11):1833-40. Epub 2011/10/01. doi: 10.1101/gr.116509.110. PubMed PMID: 21957152; PubMed Central PMCID: PMC3205568.
  8. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011;12(1):R10. Epub 2011/01/22. doi: 10.1186/gb-2011-12-1-r10. PubMed PMID: 21251332; PubMed Central PMCID: PMC3091299.
  9. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011;7(8):e1002228. Epub 2011/08/20. doi: 10.1371/journal.pgen.1002228. PubMed PMID: 21852959; PubMed Central PMCID: PMC3154961.
  10. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 2010;6(5):e1000952. Epub 2010/05/21. doi: 10.1371/journal.pgen.1000952. PubMed PMID: 20485568; PubMed Central PMCID: PMC2869317.
  11. Houseman EA, Molitor J, Marsit CJ. Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics. 2014;30(10):1431-9. doi: 10.1093/bioinformatics/btu029. PubMed PMID: 24451622; PubMed Central PMCID: PMC4016702.
Category: Biology, Community, Debate, Epigenetics, Genetics, Genomics, PLOS Genetics, Research | Tagged , , , , | 1 Comment

Spinal Cord Injury, Gut Microbiome, and White-Plague Coral Disease: the PLOS Comp Biol June Issue

Here are some highlights from June’s PLOS Computational Biology

 

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

June Issue Image: Handmade painting representing FAAH bound to the membrane. Image Credit: Painting by Giulia Palermo with digital manipulation by O'Reilly Science Art, LLC

June Issue Image: Handmade painting representing FAAH bound to the membrane. Credit: Painting by Giulia Palermo with digital manipulation by O’Reilly Science Art, LLC

The community of bacteria that live in our intestines (called the “gut microbiome”) is important to normal intestinal function, and the destruction of this community has a causative role in diseases including obesity, diabetes, and even neurological disorders. Reka Albert and colleagues use a mathematical model to identify how the normal bacterial community interacts and how this community changes with antibiotic treatment and C. difficile infection.

 

A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury

 

People with spinal cord injury are predisposed to pressure ulcers. These ulcers remain a significant burden in cost of care and quality of life, despite improved mechanistic understanding and advanced interventions. Yoram Vodovotz and colleagues create a virtual pressure ulcer as a platform to test therapies and determine the mechanisms most correlated with unfavourable outcomes. Their analysis reveals that inflammation is an important determinant of ulcer severity and overall tissue damage.

 

Coral colonies from the genus Favia infected with white-plague disease. Credit:  Zvuloni et al.

Coral colonies from the genus Favia infected with WPD. Credit: Zvuloni et al.

 

Modeling the Impact of White-Plague Coral Disease in Climate Change Scenarios

 

Coral reefs are deteriorating at alarming rates, with coral disease outbreaks increasing in prevalence and in special distribution. Anomalously high ocean temperatures are thought to significantly contribute to this problem. Yael Artzy-Randrup and colleagues have collected a unique dataset of a White Plague Disease (WPD) outbreak from the coral reef of Eilat (Israel, Red Sea). By fitting a novel epidemiological model to the data, they characterize the dynamics of WPD, and study the possible effects of future increasing sea-surface temperatures on disease dynamics.

Category: Climate, Community, Infectious disease, Microbiology, PLOS Computational Biology | Tagged , , , , | Leave a comment

Calling All Bloggers for ISMB/ECCB 2015

ISMB/ECCB 2015 in Dublin, Ireland, is fast approaching and we invite you to be involved in the live coverage of the event.

 

In previous years, ISMB has been way ahead of the social media curve with microblogging in 2008, one year before the launch of Flickr, one year after the launch (in the USA) of the Apple original iPhone 1, and just two years after Twitter was founded. Now at the last count, Twitter has averaged at 236 million users, three million blogs come online each month, and Tumblr owners publish approximately 27,778 new blog posts every minute. We all know that, in like-fashion, social media is a growing aspect of conferences, — read more in our Ten Simple Rules for Live Tweeting at Scientific Conferences, –and we think ISMB is a great venue for progress.

Sean MacEntee/Flickr

Sean MacEntee/Flickr

How can you be involved?

We want you to take live blogging to ISMB/ECCB. If you are planning to attend the conference in Dublin and you blog or tweet, or even if you would like to try it for the first time, we want to hear from you – Everyone can get involved.

Our invitation extends to attendees from all backgrounds and experience who could contribute blog posts covering the conference. In addition we are looking for a number of ‘super bloggers’ who can commit to blogging two to three high-quality posts or who would be interested in interviewing certain speakers at the conference. If you are speaking at ISMB/ECCB and would like to be involved, please do also get in touch.

In acknowledgment of your time and effort, each contributor will receive a select PLOS Computational Biology 10th Anniversary t-shirt (only available at ISMB/ECCB 2015) and your work will be shared on the PLOS Medium.com page, making it easier for all to contribute and collaborate.

 

What are the next steps?

If you’re active on Twitter or the blogosphere and want to help us share the latest and greatest from ISMB/ECCB 2015 conference, please email us at ploscompbiol@plos.org with a bit about your background and how you’d like to contribute. See you in Dublin!

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ISMB/ECCB 2015

Heading to Dublin for ISMB/ECCB 2015? Swing by Booth 1 and say hello to PLOS!

Many of the journal’s academic editors will be in attendance, and PLOS Computational Biology staff Gary Beardmore and Bethany Coates will be manning the booth, alongside Catherine Nancarrow, Senior Managing Editor, and Mei-Yan Leung, Product Marketing Manager. They’re keen to answer your questions, talk about your research, and hear your thoughts on Open Access and the journal’s role in the community.

We will also be running a live blog, with guest bloggers relating their experiences of ISMB/ECCB 2015 and interviewing some of the speakers. If you are interested in taking part, please e-mail ploscompbiol@plos.org or drop by Booth 1.

PLOS/Kifayathullah Liakath-Ali

PLOS/Kifayathullah Liakath-Ali

We will have special PLOS Computational Biology 10th Anniversary t-shirts available from the booth, featuring a design by this year’s winner Kifayathullah Liakath-Ali. Numbers are limited however, so come early to snag one before they’re gone!

Keep an eye out for PLOS Computational Biology editors across the conference and follow us on Twitter for live updates on events in which they are involved. Here are some to get you started:

 

Friday 10th July

Sunday 12th July

  • Michael Levitt gives a keynote presentation on the Birth & Future of Multiscale Modeling of Macromolecules
  • Francis Oulette, Gabrielle Rustici, Annette McGrath, and Dave Clements host a workshop on Experience Exchange: Focus on NGS Course.

Monday 13th July

  • Donna Slonim presents her paper ‘Finding Novel Molecular Connections between Developmental Processes and Disease’.
  • Marc Marti-Renom presents a special session on ‘Assessing the limits of restraint-based 3D modelling of genomes and genomic domains’.
  • Later in the day Philip Bourne and Niklas Blomberg talk data with their special session on ‘Elixir – Towards unifying a computational biology ecosystem’.
  • Steven Brenner will lead one of ISMB’s theme presentations on ‘Widespread degradation of transcripts by splicing and nonsense-mediated mRNA decay (NMD) includes ultraconserved targets whose regulation by alternative splicing and NMD is conserved between kingdoms’.

Tuesday 14th July

  • David Searls will be giving a special presentation on ‘James Joyce’s Ulysses: A bioinformatics perspective.

 

There’s still time to register for ISMB/ECCB 2015 online if you’ve not yet done so. We look forward to seeing you in Dublin!

 

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PLOS Computational Biology’s 10th Anniversary

This post marks a very important date for PLOS Computational Biology and highlights how we are celebrating.

Image credit: Cade Buchana / Flickr

Ten years ago, on June 24th 2005, the inaugural issue of PLOS Computational Biology was published, making this our 10th anniversary!

To mark this momentous occasion, the journal is launching a special anniversary collection. The collection showcases some of the best of PLOS Computational Biology – high-quality research articles; the feature series, “Ten Simple Rules”; and an editorial by Founding Editor-in-Chief Philip E. Bourne and Founding Editors Steven E. Brenner and Michael B. Eisen, – Ten Years of PLOS Computational Biology: A Decade of Appreciation and Innovation – in which they reflect on the journal’s evolution and offer a few thoughts for the next ten years.

The first Issue Image.  Image credit:Image Credit: Drawn by Barker and Pagel using BioLayout software.

The first Issue Image.
Image credit:Image Credit: Drawn by Barker and Pagel using BioLayout software.

The collection also contains a PLOS Computational Biology “Taster”; here readers can sample a flavour of PLOS Computational Biology and the kinds of articles we publish. Covering Software, Education, About My Lab, Topic Pages and a Focus Feature, we’re sure you’ll find something to pique your interest.

Our tenth anniversary is the perfect time to reflect on the journal’s progress. The collaboration with ISCB – and the participation of its membership – has been critical to the success of the journal. In the collection, you can read the newly published Message from ISCB which describes the growth of computational biology as a discipline, reaching into every facet of scientific research from the viewpoints of experts in the field – Philip Bourne, Win Hide, Janet Kelso, Scott Markel, Ruth Nussinov and Janet Thornton.

PLOS Computational Biology is, by definition and at its heart, a community journal. The Editorial Board of academics, who are active members of the communities we serve, keeps PLOS Computational Biology at the cutting edge of research. The journal’s success is due in no small part to the rigour and quality of our editorial board, guest editors and reviewers. It was our pleasure to publicly thank our reviewers this year for their contribution, but we would also like to take this opportunity to thank everybody who submits, reads, and edits the articles we publish. Together, we have developed a journal that is by the community and for the community.

ploscb10

Winning design of the 10th Anniversary T-shirt Competition. Image credit: Kifayathullah Liakath-Ali

The collection is joined in our celebrations by our PLOS Computational Biology 10th Anniversary T-shirt competition, through which the favourite T-shirt design of the past ten years was voted for by our readership. The T-shirts will be first available at ISMB in Dublin on July 11th-14th, so be sure to visit PLOS at Booth 1, say happy birthday and pick up a T-shirt from PLOS staff. You can keep up to date with all these celebrations and more @PLOSCompBiol via our anniversary hashtag #PLOSCB10.

 

As we close out this special year, we’ll be adding more 10th anniversary content, so watch this space…

 

 

 

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PLOS Genetics editors – David Kwiatkowski and Peter McKinnon

The first post in our PLOS Genetics’ editors series introduces David Kwiatkowski, Brigham and Women’s Hospital and Harvard Medical School, USA and Peter McKinnon, St Jude Children’s Research Hospital, USA, who are Section Editors for Cancer Genetics. David and Peter began their roles on PLOS Genetics in October 2014 and February 2014, respectively. Here they provide an introduction to their background and research, tell us about their positions on the PLOS Genetics Editorial Board, and explain how they feel their role fits into the mission of PLOS Genetics and PLOS as a whole.

 

David Kwiatkowski:

Kwiatkowski,David at lab dec 2013 029

David Kwiatkowski. Image credit: David Kwiatkowski.

I am an oncologist and geneticist, with some research specialisms; however, I maintain a broad range of interests across the field of cancer genetics. Growing up, I loved and was very good at mathematics which led me to undertake a BSc and PhD in Mathematics at Caltech and the Massachusetts Institute of Technology, respectively. Subsequently, I decided that I wanted to pursue something more practical and went to medical school. During medical training, I became interested in Medical Oncology, which appealed to me due to the possibility of treating and curing an otherwise fatal disease, and the intensity of the patient-doctor relationship.

Fellowship training introduced me to biomedical research, and I felt a natural affinity for genetics, which was an expanding field at the time. Mostly by chance my research led me to study Tuberous Sclerosis Complex (TSC) from a genetic perspective, and this disorder, which results in non-cancerous tumours, became my lifelong research interest. It has been gratifying in TSC research to see the progression from gene identification, to pathway definition, to therapeutic success, although there is still a long way to go. I have continued to practice as a thoracic oncologist at the Dana Farber Cancer Institute, USA.

About five years ago, I undertook a mini-sabbatical at the Broad Institute with Gad Getz and Matthew Meyerson.  The era of modern cancer genetics was just beginning and the sabbatical gave me the opportunity to learn computational and statistical methods, in addition to participating in several projects run by The Cancer Genome Atlas (TCGA).

I am one of two Senior Editors in the Cancer Genetics section of PLOS Genetics, along with Peter McKinnon. My favorite part of this role is the weekly calls, in which we review new submissions, typically about five new manuscripts. This review pushes me to stay current on all aspects of cancer genetics, and the interaction and discussion with Peter is always fun. It is also gratifying to attempt to accelerate the review process as much as I can, and it is always satisfying when a review has been completed and the letter sent to the author, especially when it is an acceptance!

The mission of PLOS is to advance Open Access scientific research, and I am pleased to play a role in advancing this objective. It is also worth noting that PLOS maintains very high standards of manuscript review and conflicts of interest, which means that Peter or I recuse ourselves from any role in the review of manuscripts in which we have any possible competing interests.

 

 

Peter McKinnon:

pmckinnon

Peter McKinnon. Image credit: The University of Tennessee Health Science Center

I grew up in a small town in Australia and wanted to become a research scientist focusing on chemistry. An early and important start for me was an after school job in an old-style English pharmacy (in Australia they are referred to as a Chemist shop; so what better start than to get a job doing ‘chemistry’). This Chemist shop was from the turn of the 20th century, and still had shelf upon shelf filled with large exotic glass bottles with chemical names gold-etched in Latin, making it feel that I was immersed in chemistry. The reality was that the job mostly entailed counting pills into bottles for prescriptions, and very occasionally watching the pharmacist formulating some old-style skin creams. Upon entering University, I maintained my interest and specialised in biological chemistry, and eventually molecular biology. For the last two decades, my scientific work has focussed on understanding the processes of DNA damage signalling, and its relationship to human disease, with an emphasis on the nervous system. These topics overlap broadly with DNA repair, neuroscience and cancer.

As an editor for PLOS Genetics, I see my role as helping to maintain the high quality content the journal publishes. This mainly involves acting as a co-Senior Editor with David Kwiatkowski for the Cancer Genetics section and we aim to identify exciting and topical papers that provide a range of new findings of broad relevance to genetics research and cancer. One of the great things about being an editor is the opportunity to see such a large amount of high-calibre science. David and I work by consensus when we are evaluating papers, and I believe that having the two of us discuss each manuscript is important to ensure balance and fairness as we decide which manuscripts should be sent out for review. We aim to continue to ensure that PLOS Genetics is a high-quality journal that researchers consider when deciding where to submit an exciting new story for publication.

Category: Cancer, PLOS Genetics, Uncategorized | Tagged , , , , | 2 Comments