Plos Computational Biology Publishes Research of Exceptional

Total Page:16

File Type:pdf, Size:1020Kb

Plos Computational Biology Publishes Research of Exceptional A peer-reviewed open-access journal published by the Public Library of Science www.ploscompbiol.org PLoS Computational Biology publishes research of exceptional significance that furthers our understanding of living systems at all scales — from molecules and cells, to patient populations and ecosystems — through the application of computational methods. • Run by an international Editorial Board led by Philip E. Bourne (University of California San Diego, USA). • Featuring high-quality Research Articles, invited Reviews, Tutorials, an outstanding Education section, Image credit: Toma Pigli and our popular Editorial “Ten Simple Rules” series. PLoS Computational Biology (2007) • Funder-compliant — Published articles are Topics include (but are not limited to): immediately deposited in PubMed Central and Molecular Biology subsequently cited in PubMed. Protein-Protein Interactions • Provides constructive peer review and rapid Computational Neuroscience publication. Regulatory Networks • Article-level metrics and web tools to facilitate Computational Immunology community discourse through notes, comments, Sequence Analysis and ratings. Protein Structure & Function Prediction • Highlighted in news outlets and blogs from around Population Biology the world. Cancer Genetics Microarray Data Analysis Gene Expression Synthetic Biology PLoS Computational Biology is published by the Public Machine Learning Library of Science (PLoS), a nonprofit organization committed to making the world’s scientific and medical literature a public resource. Everything we publish is freely available online through- out the world, for anyone to read, download, copy, distribute and use (with attribution). Barrier-free, open access, no permissions required. Image credit: Ryan Davey PLoS Computational Biology (2007) PUBLIC LIBRARY of SCIENCE www.plos.org A peer-reviewed open-access journal published by the Public Library of Science www.ploscompbiol.org Editorial Board Philip E. Bourne, Editor-in-Chief & Founding Editor Associate Editors Steven E. Brenner, Founding Editor Ad Aertsen Luhua Lai Chris P. Ponting Michael B. Eisen, Founding Editor Russ Altman Peter Latham Nathan Price Rustom Antia Douglas Lauffenburger Rama Ranganathan Fran Lewitter, Education Editor Manny Ares Thomas Lengauer Chris Rao Anand Asthagiri Michael Levitt Aviv Regev Olga Troyanskaya, ISCB Editor Joe Bader Wen-Hsiung Li Isidore Rigoutso Robert Murphy, Software Editor Daniel A. Beard Scott Markel Rob Russell Rolf Kötter, Reviews Editor Tim Behrens Andrew McCulloch Andrey Rzhetsky Carl Bergstrom Angela McLean David Searls Johanna McEntyre, Reviews Editor James Briggs Christian von Mering Eran Segal Edmund J. Crampin Lauren Ancel Meyers Eugene Shakhnovich Rob J. de Boer Satoru Miyano Adam Siepel Deputy Editors-in-Chief Roland Dunbrack Abigail Morrison Donna Slonim Jonathan Eisen William Stafford Noble Berend Snel Adam Paul Arkin Neil M. Ferguson Uwe Ohler Olaf Sporns Patricia Babbitt Christophe Fraser Christine Orengo Jörg Stelling Sebastian Bonhoeffer Roderic Guigó Christos A. Ouzounis Greg Tucker-Kellogg Barbara Bryant Boris Gutkin Vijay Pande Wyeth Wasserman Matt Jacobson Jason Papin Weixiong Zhang Karl Friston Lars Juhl Jensen Mercedes Pascual Lyle J. Graham Konrad Kording Yitzhak Pilpel Hanah Margalit Ruth Nussinov Editorial Advisory Board Burkhard Rost Peer Bork Roy Kishony Andrej Sali Wyeth Wasserman David Eisenberg Eugene Koonin Chris Sander Mark Gerstein Simon Levin Shoshana Wodak Trey Ideker John Mattick Examples of Highly Downloaded Content Unraveling Protein Networks with Power Graph Analysis (Research Article) Royer L, Reimann M, Andreopoulos B, Schroeder M www.ploscombiol.org/doi/pcbi.1000108 Broadband Criticality of Human Brain Network Synchronization (Research Article) Kitzbichler MG, Smith ML, Christensen SR, Bullmore E www.ploscompbiol.org/doi/pcbi.1000314 Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments Parter M, Kashtan N, Alon U www.ploscombiol.org/doi/pcbi. " ! Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web (Review) Hull D, Pettifer SR, Kell DB ! www.compbiol.org/doi/pcbi. he Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function (Tutorial) Punta M, Ofran Y www.ploscompbiol.org/ PLoS Computational Biology invites you to send us a postcard from the Pacific Symposium on Biocomputing (PSB). PLoS Conference Postcards represent a novel way to report important innovations and current research efforts presented at a scientific conference as told by upcoming members of the scientific community. Your “postcard” will focus on one of the highlights of PSB – a keynote, paper presentation, poster session, software demonstration, or tutorial. All Postcards will be considered by the Editors and those selected will be published in PLoS Computational Biology as part of an article summarizing the conference. PSB Conference Postcards Guidelines Any postdoctoral fellow or graduate student is eligible to be a reporter. Reporters may submit more than one report for consideration, but each report may only have one author. Your Conference Postcard should be between 800-1000 words; you may submit a maximum of one image. If the image is under copyright it is your responsibility to gain explicit permission to republish under the CCAL from the copyright holder. You should include: o A synopsis of what was presented. o Reasons why you think your chosen highlight is outstanding. o How it related to the theme of the meeting. o The impact it had on attendees. o Additional references considered useful. Any presentation at the conference deemed to be of exceptional significance to the broader community by the reporter is eligible to be reported. No permission from speakers is required beyond those obtained by PSB as regards live and postconference coverage of presentations. Please do not submit reports on presentations given by a close colleague. Preference will be given to reports that demonstrate evidence of additional research into the topic to support or counter the work presented, e.g., views of the work by other attendees gathered through personal interactions or blogs or information based on further discussions with the presenters. Reports accepted by the Editors for publication will be presented as a single article with author ordering determined by the PLoS Editors. PLoS Editors may request that the reporters make (generally minor) changes to the selected reports. As with all PLoS content, the Conference Postcards will be published under the Creative Commons Attribution License (CCAL) Agreement; made freely and fully available immediately upon publication; and deposited in PubMed Central and indexed in PubMed. Your submission should be sent to [email protected] with the report in the body of the email or attached as a Word document. Please list “PSB Postcards” as the subject of your email. Please list your name, institution, and the title of the session being reported. The closing date for submissions is: January 14th 2009 .
Recommended publications
  • Improving the Prediction of Transcription Factor Binding Sites To
    Improving the prediction of transcription factor binding sites to aid the interpretation of non-coding single nucleotide variants. Narayan Jayaram Research Department of Structural and Molecular Biology University College London A thesis submitted to University College London for the degree of Doctor of Philosophy 1 Declaration I, Narayan Jayaram confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Narayan Jayaram 2 Abstract Single nucleotide variants (SNVs) that occur in transcription factor binding sites (TFBSs) can disrupt the binding of transcription factors and alter gene expression which can cause inherited diseases and act as driver SNVs in cancer. The identification of SNVs in TFBSs has historically been challenging given the limited number of experimentally characterised TFBSs. The recent ENCODE project has resulted in the availability of ChIP-Seq data that provides genome wide sets of regions bound by transcription factors. These data have the potential to improve the identification of SNVs in TFBSs. However, as the ChIP-Seq data identify a broader range of DNA in which a transcription factor binds, computational prediction is required to identify the precise TFBS. Prediction of TFBSs involves scanning a DNA sequence with a Position Weight Matrix (PWM) using a pattern matching tool. This thesis focusses on the prediction of TFBSs by: (a) evaluating a set of locally-installable pattern-matching tools and identifying the best performing tool (FIMO), (b) using the ENCODE ChIP-Seq data to evaluate a set of de novo motif discovery tools that are used to derive PWMs which can handle large volumes of data, (c) identifying the best performing tool (rGADEM), (d) using rGADEM to generate a set of PWMs from the ENCODE ChIP-Seq data and (e) by finally checking that the selection of the best pattern matching tool is not unduly influenced by the choice of PWMs.
    [Show full text]
  • RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY
    RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press www.wseas.org Copyright © 2009, by WSEAS Press All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press. All papers of the present volume were peer reviewed
    [Show full text]
  • Applied Category Theory for Genomics – an Initiative
    Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4].
    [Show full text]
  • • La Gestion Efficace De L’Énergie • Le Réseautage Planétaire • Les Processus Géophysiques • L’Économie Globale, La Sécurité Et La Stabilité
    SupérieureS atiqueS athéM e M inaire D SéM The planet on which we live and the challenges that we face on this planet become increasingly complex as ecological, economic and social systems are large intertwined networks governed by dynamic processes and feedback loops. Mathematical models are indispensable in understanding and managing such systems since they provide insight into governing processes; they help predict future behavior; and they allow for risk-free evaluation of possible interventions. The goal of this thematic program is to tackle pressing and emerging challenges in population and ecosystem health, including understanding and controlling major transmissible diseases, optimizing and monitoring vaccination, predicting the impacts of climate change on invasive species, protecting biodiversity and managing ecosystems sustainably. This pan-Canadian program will bring together the international community of researchers who work on these topics in a series of workshops to foster exchange and stimulate cross-disciplinary research between all scientific areas involved, to discuss perspectives and directions for future advances in the field, including new models and methods and to foster tighter links between the research community, government agencies and policy makers. Three summer schools will introduce graduate students and postdoctoral fellows to the art of modeling living systems and to the latest tools and techniques to analyze these models. SCIENTIFIC COMMITTEE Jacques Bélair Mark Lewis (Montréal) Models and Methods in Ecology (Alberta) Frithjof Lutscher and Epidemiology Mathematical Modeling James Watmough (Ottawa) February 6-8, 2013 (UNB) of Indigenous Population Jianhong Wu CRM, Montréal (York) Organizers: Jacques Bélair (Montréal), Health Jianhong Wu (York) September 28-29, 2013 AISENSTADT CHAIRS BIRS Bryan Grenfell (Princeton), May 2013 Graphic Design: www.neograf.ca Simon A.
    [Show full text]
  • ISMB 2008 Toronto
    ISMB 2008 Toronto The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Linial, Michal, Jill P. Mesirov, B. J. Morrison McKay, and Burkhard Rost. 2008. ISMB 2008 Toronto. PLoS Computational Biology 4(6): e1000094. Published Version doi:10.1371/journal.pcbi.1000094 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11213310 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Message from ISCB ISMB 2008 Toronto Michal Linial1,2, Jill P. Mesirov1,3, BJ Morrison McKay1*, Burkhard Rost1,4 1 International Society for Computational Biology (ISCB), University of California San Diego, La Jolla, California, United States of America, 2 Sudarsky Center, The Hebrew University of Jerusalem, Jerusalem, Israel, 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 4 Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America the integration of students, and for the of ISMB. One meeting in South Asia support of young leaders in the field. (InCoB; http://incob.binfo.org.tw/) has ISMB has also become a forum for already been sponsored by ISCB, and reviewing the state of the art in the many another one in North Asia is going to fields of this growing discipline, for follow. ISMB itself has also been held in introducing new directions, and for an- Australia (2003) and Brazil (2006).
    [Show full text]
  • A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast
    A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast By Jessica M. Vera B.S. University of Wisconsin-Madison, 2007 A thesis submitted to the Faculty of the Graduate School in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Molecular, Cellular, and Developmental Biology 2015 This thesis entitled: A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast written by Jessica M. Vera has been approved for the Department of Molecular, Cellular, and Developmental Biology Tom Blumenthal Robin Dowell Date The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline iii Vera, Jessica M. (Ph.D., Molecular, Cellular and Developmental Biology) A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast Thesis Directed by Robin Dowell Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. I sought to ascertain the extent of conserved CUT expression across a variety of Saccharomyces yeast strains to further understand and characterize the nature of CUT expression. To this end I designed a Hidden Markov Model (HMM) to analyze strand-specific RNA sequencing data from nuclear exosome rrp6Δ mutants to identify and compare CUTs in four different yeast strains: S288c, Σ1278b, JAY291 (S.cerevisiae) and N17 (S.paradoxus).
    [Show full text]
  • Ontology-Based Methods for Analyzing Life Science Data
    Habilitation a` Diriger des Recherches pr´esent´ee par Olivier Dameron Ontology-based methods for analyzing life science data Soutenue publiquement le 11 janvier 2016 devant le jury compos´ede Anita Burgun Professeur, Universit´eRen´eDescartes Paris Examinatrice Marie-Dominique Devignes Charg´eede recherches CNRS, LORIA Nancy Examinatrice Michel Dumontier Associate professor, Stanford University USA Rapporteur Christine Froidevaux Professeur, Universit´eParis Sud Rapporteure Fabien Gandon Directeur de recherches, Inria Sophia-Antipolis Rapporteur Anne Siegel Directrice de recherches CNRS, IRISA Rennes Examinatrice Alexandre Termier Professeur, Universit´ede Rennes 1 Examinateur 2 Contents 1 Introduction 9 1.1 Context ......................................... 10 1.2 Challenges . 11 1.3 Summary of the contributions . 14 1.4 Organization of the manuscript . 18 2 Reasoning based on hierarchies 21 2.1 Principle......................................... 21 2.1.1 RDF for describing data . 21 2.1.2 RDFS for describing types . 24 2.1.3 RDFS entailments . 26 2.1.4 Typical uses of RDFS entailments in life science . 26 2.1.5 Synthesis . 30 2.2 Case study: integrating diseases and pathways . 31 2.2.1 Context . 31 2.2.2 Objective . 32 2.2.3 Linking pathways and diseases using GO, KO and SNOMED-CT . 32 2.2.4 Querying associated diseases and pathways . 33 2.3 Methodology: Web services composition . 39 2.3.1 Context . 39 2.3.2 Objective . 40 2.3.3 Semantic compatibility of services parameters . 40 2.3.4 Algorithm for pairing services parameters . 40 2.4 Application: ontology-based query expansion with GO2PUB . 43 2.4.1 Context . 43 2.4.2 Objective .
    [Show full text]
  • From DNA Sequence to Chromatin Dynamics: Computational Analysis of Transcriptional Regulation
    From DNA Sequence to Chromatin Dynamics: Computational Analysis of Transcriptional Regulation Thesis submitted for the degree of “Doctor of Philosophy” by Tommy Kaplan Submitted to the Senate of the Hebrew University May 2008 This work was carried out under the supervision of Prof. Nir Friedman and Prof. Hanah Margalit Abstract All cells of a living organism share the same DNA. Yet, they differ in structure, activities and interactions. These differences arise through a tight regulatory system which activates different genes and pathways to fit the cell’s specialization, condition, and requirements. Deciphering the regulatory mechanisms underlying a living cell is one of the fundamental challenges in biology. Such knowledge will allow us to better understand how cells work, how they respond to external stimuli, what goes wrong in diseases like cancer (which often involves disruption of gene regulation), and how it can be fought. In my PhD, I focus on regulation of gene expression from three perspectives. First, I present an innovative algorithm for identifying the target genes of novel transcription factors, based on their protein sequence (Chapter 1). Second, I consider how several transcription factors cooperate to process external stimuli and alter the behavior of the cell (Chapter 2). Finally, I study how the genomic position of nucleosomes and their covalent modifications modulate the accessibility of DNA to transcription factors, thus adding a fascinating dimension to transcriptional regulation (Chapters 3 and 4). To understand transcriptional regulation, one should first reconstruct the architecture of the cell’s regulatory map, thus identifying which genes are regulated by which transcription factors (TFs).
    [Show full text]
  • Ploidetect Enables Pan-Cancer Analysis of the Causes and Impacts of Chromosomal Instability
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.06.455329; this version posted August 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Ploidetect enables pan-cancer analysis of the causes and impacts of chromosomal instability Luka Culibrk1,2, Jasleen K. Grewal1,2, Erin D. Pleasance1, Laura Williamson1, Karen Mungall1, Janessa Laskin3, Marco A. Marra1,4, and Steven J.M. Jones1,4, 1Canada’s Michael Smith Genome Sciences Center at BC Cancer, Vancouver, British Columbia, Canada 2Bioinformatics training program, University of British Columbia, Vancouver, British Columbia, Canada 3Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada 4Department of Medical Genetics, Faculty of Medicine, Vancouver, British Columbia, Canada Cancers routinely exhibit chromosomal instability, resulting in tumors mutate, these variants are considerably more difficult the accumulation of changes in the abundance of genomic ma- to detect accurately compared to other types of mutations terial, known as copy number variants (CNVs). Unfortunately, and consequently they may represent an under-explored the detection of these variants in cancer genomes is difficult. We facet of tumor biology. 20 developed Ploidetect, a software package that effectively iden- While small mutations can be determined through base tifies CNVs within whole-genome sequenced tumors. Ploidetect changes embedded within aligned sequence reads, CNVs was more sensitive to CNVs in cancer related genes within ad- are variations in DNA quantity and are typically determined vanced, pre-treated metastatic cancers than other tools, while also segmenting the most contiguously.
    [Show full text]
  • AI and Bioinformatics
    AI Magazine Volume 25 Number 1 (2004) (© AAAI) Articles Editorial Introduction AI and Bioinformatics Janice Glasgow, Igor Jurisica, and Burkhard Rost ■ This article is an editorial introduction to the re- modern-day biology is far more complex than search discipline of bioinformatics and to the articles suggested by the simplified sketch presented in this special issue. In particular, we address the issue here. In fact, researchers in life sciences live off of how techniques from AI can be applied to many of the introduction of new concepts; the discov- the open and complex problems of modern-day mol- ecular biology. ery of exceptions; and the addition of details that usually complicate, rather than simplify, his special issue of AI Magazine focuses the overall understanding of the field. on some areas of research in bioinfor- Possibly the most rapidly growing area of re- Tmatics that have benefited from applying cent activity in bioinformatics is the analysis AI techniques. Undoubtedly, bioinformatics is of microarray data. The article by Michael Mol- a truly interdisciplinary field: Although some la, Michael Waddell, David Page, and Jude researchers continuously affect wet labs in life Shavlik (“Using Machine Learning to Design science through collaborations or provision of and Interpret Gene-Expression Microarrays”) tools, others are rooted in the theory depart- introduces some background information and ments of exact sciences (physics, chemistry, or provides a comprehensive description of how engineering) or computer sciences. This wide techniques from machine learning can be used variety creates many different perspectives and to help understand this high-dimensional and terminologies. One result of this Babel of lan- prolific gene-expression data.
    [Show full text]
  • Fall 2016 Is Available in the Laboratory of Dr
    RNA Society Newsletter Aug 2016 From the Desk of the President, Sarah Woodson Greetings to all! I always enjoy attending the annual meetings of the RNA Society, but this year’s meeting in Kyoto was a standout in my opinion. This marked the second time that the RNA meeting has been held in Kyoto as a joint meeting with the RNA Society of Japan. (The first time was in 2011). Particular thanks go to the local organizers Mikiko Siomi and Tom Suzuki who took care of many logistical details, and to all of the organizers, Mikiko, Tom, Utz Fischer, Wendy Gilbert, David Lilley and Erik Sontheimer, for putting together a truly exciting and stimulating scientific program. Of course, the real excitement in the annual RNA meetings comes from all of you who give the talks and present the posters. I always enjoy meeting old friends and colleagues, but the many new participants in this year’s meeting particularly encouraged me. (Continued on p2) In this issue : Desk of the President, Sarah Woodson 1 Highlights of RNA 2016 : Kyoto Japan 4 Annual Society Award Winners 4 Jr Scientist activities 9 Mentor Mentee Lunch 10 New initiatives 12 Desk of our CEO, James McSwiggen 15 New Volunteer Opportunities 16 Chair, Meetings Committee, Benoit Chabot 17 Desk of the Membership Chair, Kristian Baker 18 Thank you Volunteers! 20 Meeting Reports: RNA Sponsored Meetings 22 Upcoming Meetings of Interest 27 Employment 31 1 Although the graceful city of Kyoto and its cultural months. First, in May 2016, the RNA journal treasures beckoned from just beyond the convention instituted a uniform price for manuscript publication hall, the meeting itself held more than enough (see p 12) that simplifies the calculation of author excitement to keep ones attention! Both the quality fees and facilitates the use of color figures to and the “polish” of the scientific presentations were convey scientific information.
    [Show full text]
  • Microblogging the ISMB: a New Approach to Conference Reporting
    Message from ISCB Microblogging the ISMB: A New Approach to Conference Reporting Neil Saunders1*, Pedro Beltra˜o2, Lars Jensen3, Daniel Jurczak4, Roland Krause5, Michael Kuhn6, Shirley Wu7 1 School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Brisbane, Queensland, Australia, 2 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America, 3 Novo Nordisk Foundation Center for Protein Research, Panum Institute, Copenhagen, Denmark, 4 Department of Bioinformatics, University of Applied Sciences, Hagenberg, Freistadt, Austria, 5 Max-Planck-Institute for Molecular Genetics, Berlin, Germany, 6 European Molecular Biology Laboratory, Heidelberg, Germany, 7 Stanford Medical Informatics, Stanford University, Stanford, California, United States of America Cameron Neylon entitled FriendFeed for Claire Fraser-Liggett opened the meeting Scientists: What, Why, and How? (http:// with a review of metagenomics and an blog.openwetware.org/scienceintheopen/ introduction to the human microbiome 2008/06/12/friendfeed-for-scientists-what- project (http://friendfeed.com/search?q = why-and-how/) for an introduction. room%3Aismb-2008+microbiome+OR+ We—a group of science bloggers, most fraser). The subsequent Q&A session of whom met in person for the first time at covered many of the exciting challenges The International Conference on Intel- ISMB 2008—found FriendFeed a remark- for those working in this field. Clearly, ligent Systems for Molecular Biology
    [Show full text]