PLOS Computational Biology Associate Editor Handbook Second Edition Version 2.6
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Progress Update July 2011
PUBLIC LIBRARY of SCIENCE PUBLIC LIBRARY of SCIENCE www.plos.org 3URJUHVV8SGDWH 2010 Progress Update July 2011 www.plos.org Welcome to the 2010 PLoS Progress Update, aimed at keeping our authors, reviewers, editors, and supporters fully apprised of developments at PLoS over our most recent Highlights year. You can sign up to read future updates here. If you would like 1. Message from a fuller historical picture of how far we’ve come, you can read the the Founders 2009 Progress Update and the first full Progress Report. 2. Publishing Initiatives 3. Influential 1. Message from the Founders Research 4. A Growing It’s been another exciting year for PLoS, focused on establishing more open, Organization efficient, and effective ways to accelerate progress in science and medicine 5. The Evolving and leading a transformation in research communication. Open Access Landscape PLoS reached a truly significant milestone in 2010 when, seven years 6. The First PLoS after entering the publishing business, our annual operating revenues Forum exceeded expenses for the first time. Although we are delighted that PLoS and others have now shown that Open Access (OA) is a viable and 7. Customer Service sustainable business model, we have a long way to go before universal 8. Financial Summary access is achieved for all. 9. 2011 and Beyond The significant progress that we’ve made toward this goal could not have 10. Major Support been achieved without the leadership of our co-founder Harold Varmus, in 2010 who announced during the year that he was stepping aside as Chairman 11. -
When Is Open Access Not Open Access?
Editorial When Is Open Access Not Open Access? Catriona J. MacCallum ince 2003, when PLoS Biology Box 1. The Bethesda Statement on Open-Access Publishing was launched, there has been This is taken from http:⁄⁄www.earlham.edu/~peters/fos/bethesda.htm. a spectacular growth in “open- S 1 access” journals. The Directory of An Open Access Publication is one that meets the following two conditions: Open Access Journals (http:⁄⁄www. 1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, doaj.org/), hosted by Lund University worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit Libraries, lists 2,816 open-access and display the work publicly and to make and distribute derivative works, in any digital journals as this article goes to press medium for any responsible purpose, subject to proper attribution of authorship2, as (and probably more by the time you well as the right to make small numbers of printed copies for their personal use. read this). Authors also have various 2. A complete version of the work and all supplemental materials, including a copy of “open-access” options within existing the permission as stated above, in a suitable standard electronic format is deposited subscription journals offered by immediately upon initial publication in at least one online repository that is supported traditional publishers (e.g., Blackwell, by an academic institution, scholarly society, government agency, or other well- Springer, Oxford University Press, and established organization that seeks to enable open access, unrestricted distribution, many others). In return for a fee to interoperability, and long-term archiving (for the biomedical sciences, PubMed Central the publisher, an author’s individual is such a repository). -
Current Topics in Computational Molecular Biology Edited by Tao Jiang Ying Xu Michael Q. Zhang a Bradford Book the MIT Press
Current Topics in Computational Molecular Biology edited by Tao Jiang Ying Xu Michael Q. Zhang A Bradford Book The MIT Press Cambridge, Massachusetts London, England Contents Preface vii I INTRODUCTION 1 1 The Challenges Facing Genomic Informatics 3 Temple F. Smith H COMPARATIVE SEQUENCE AND GENOME ANALYSIS 9 2 Bayesian Modeling and Computation in Bioinformatics Research 11 Jun S. Liu 3 Bio-Sequence Comparison and Applications 45 Xiaoqiu Huang 4 Algorithmic Methods for Multiple Sequence Alignment 71 Tao Jiang and Lusheng Wang 5 Phylogenetics and the Quartet Method 111 Paul Kearney 6 Genome Rearrangement 135 David Sankoff and Nadia El-Mabrouk 7 Compressing DNA Sequences 157 Ming Li HI DATA MINING AND PATTERN DISCOVERY 173 8 Linkage Analysis of Quantitative Traits 175 Shizhong Xu , 9 Finding Genes by Computer: Probabilistic and Discriminative Approaches 201 Victor V. Solovyev 10 Computational Methods for Promoter Recognition 249 Michael Q. Zhang 11 Algorithmic Approaches to Clustering Gene Expression Data 269 Ron Shamir and Roded Sharan 12 KEGG for Computational Genomics 301 Minoru Kanehisa and Susumu Goto vi Contents 13 Datamining: Discovering Information from Bio-Data 317 Limsoon Wong IV COMPUTATIONAL STRUCTURAL BIOLOGY 343 14 RNA Secondary Structure Prediction 345 Zhuozhi Wang and Kaizhong Zhang 15 Properties and Prediction of Protein Secondary Structure 365 Victor V. Solovyev and Ilya N. Shindyalov 16 Computational Methods for Protein Folding: Scaling a Hierarchy of Complexities 403 Hue Sun Chan, Huseyin Kaya, and Seishi Shimizu 17 Protein Structure Prediction by Comparison: Homology-Based Modeling 449 Manuel C. Peitsch, Torsten Schwede, Alexander Diemand, and Nicolas Guex 18 Protein Structure Prediction by Protein Threading and Partial Experimental Data 467 Ying Xu and Dong Xu 19 Computational Methods for Docking and Applications to Drug Design: Functional Epitopes and Combinatorial Libraries 503 Ruth Nussinov, Buyong Ma, and Haim J. -
Scientific Production in the PLOS Journals Sibele Fausto*, Rogério Mugnaini**
Beyond traditional metrics at the University of São Paulo: scientific production in the PLOS journals Sibele Fausto*, Rogério Mugnaini** *[email protected], **[email protected] Escola de Comunicações e Artes, University of São Paulo, Av. Prof. Lúcio M. Rodrigues, 443, São Paulo, SP, CEP 05608-020 (Brazil) INTRODUCTION In the evolution of the Open Access Movement, there have been pioneering initiatives to provide free and open access to published scientific content, such as the creation of the BioMed Central (BMC) and the Public Library of Science (PLOS) in early 2000. These set out a new funding model for journals where the liability for publishing costs is transferred from the readers to the authors. The PLOS was also innovative since it led to the creation of Article-Level Metrics - ALM (Fenner & Lin, 2013) and expanded by issuing a series of new titles - PLOS Biology in 2003; PLOS Medicine in 2004, PLOS Computational Biology, PLOS Genetics and PLOS Pathogens in 2005, PLOS ONE in 2006 and more recently PLOS Currents. As a result, today the set of PLOS journals is widely recognized and prestigious. Recently (on June 18, 2013), PLOS introduced a new search engine - PLOS-ALM Reports (http://almreports.plos.org/) (Allen, 2013) which allows more detailed investigations to be carried out in all the PLOS journals showing consolidated alternative measures of visibility and impact earned by published articles. Since the University of São Paulo is considered to be "Brazil's leading academic institution in research and graduate education" (Schwartzman, 2006), this study is an attempt to find evidence of the USP performance that goes beyond traditional metrics, by using the alternative indicators provided by PLOS-ALM and making a comparison with other articles in the PLOS journals that come from Brazil. -
Bonnie Berger Named ISCB 2019 ISCB Accomplishments by a Senior
F1000Research 2019, 8(ISCB Comm J):721 Last updated: 09 APR 2020 EDITORIAL Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient [version 1; peer review: not peer reviewed] Diane Kovats 1, Ron Shamir1,2, Christiana Fogg3 1International Society for Computational Biology, Leesburg, VA, USA 2Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel 3Freelance Writer, Kensington, USA First published: 23 May 2019, 8(ISCB Comm J):721 ( Not Peer Reviewed v1 https://doi.org/10.12688/f1000research.19219.1) Latest published: 23 May 2019, 8(ISCB Comm J):721 ( This article is an Editorial and has not been subject https://doi.org/10.12688/f1000research.19219.1) to external peer review. Abstract Any comments on the article can be found at the The International Society for Computational Biology (ISCB) honors a leader in the fields of computational biology and bioinformatics each year with the end of the article. Accomplishments by a Senior Scientist Award. This award is the highest honor conferred by ISCB to a scientist who is recognized for significant research, education, and service contributions. Bonnie Berger, Simons Professor of Mathematics and Professor of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology (MIT) is the 2019 recipient of the Accomplishments by a Senior Scientist Award. She is receiving her award and presenting a keynote address at the 2019 Joint International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology in Basel, Switzerland on July 21-25, 2019. Keywords ISCB, Bonnie Berger, Award This article is included in the International Society for Computational Biology Community Journal gateway. -
Scientometrics1
Scientometrics1 Loet Leydesdorff a and Staša Milojević b a Amsterdam School of Communication Research (ASCoR), University of Amsterdam, Kloveniersburgwal 48, 1012 CX Amsterdam, The Netherlands; [email protected] b School of Informatics and Computing, Indiana University, Bloomington 47405-1901, United States; [email protected]. Abstract The paper provides an overview of the field of scientometrics, that is: the study of science, technology, and innovation from a quantitative perspective. We cover major historical milestones in the development of this specialism from the 1960s to today and discuss its relationship with the sociology of scientific knowledge, the library and information sciences, and science policy issues such as indicator development. The disciplinary organization of scientometrics is analyzed both conceptually and empirically. A state-of-the-art review of five major research threads is provided. Keywords: scientometrics, bibliometrics, citation, indicator, impact, library, science policy, research management, sociology of science, science studies, mapping, visualization Cross References: Communication: Electronic Networks and Publications; History of Science; Libraries; Networks, Social; Merton, Robert K.; Peer Review and Quality Control; Science and Technology, Social Study of: Computers and Information Technology; Science and Technology Studies: Experts and Expertise; Social network algorithms and software; Statistical Models for Social Networks, Overview; 1 Forthcoming in: Micheal Lynch (Editor), International -
Making Institutional Repositories Work “Making Institutional Repositories Work Sums It up Very Well
Making Institutional Repositories Work “Making Institutional Repositories Work sums it up very well. This book, the first of its kind, explains how IRs work and how to get the greatest re- sults from them. As many of us know, numerous IRs launched with high hopes have in fact languished with lackluster results. Faculty have little in- terest, and administrators see little promise. But the many chapter authors of this very well edited book have made their IRs successful, and here they share their techniques and successes. This is a necessary book for anyone contemplating starting an IR or looking to resurrect a moribund one.” — Richard W. Clement Dean, College of University Libraries & Learning Sciences University of New Mexico “This volume presents an interesting cross-section of approaches to in- stitutional repositories in the United States. Just about every view and its opposite makes an appearance. Readers will be able to draw their own con- clusions, depending on what they see as the primary purpose of IRs.” — Stevan Harnad Professor, University of Québec at Montréal & University of Southampton “Approaching this volume as one of ‘those of us who have been furiously working to cultivate thriving repositories,’ I am very excited about what this text represents. It is a broad compilation featuring the best and brightest writing on all the topics I’ve struggled to understand around re- positories, and it also marks a point when repository management and de- velopment is looking more and more like a core piece of research library work. Callicott, Scherer, and Wesolek have pulled together all the things I wished I’d been able to read in my first year as a scholarly communication librarian. -
Will Sci-Hub Kill the Open Access Citation Advantage and (At Least for Now) Save Toll Access Journals?
Will Sci-Hub Kill the Open Access Citation Advantage and (at least for now) Save Toll Access Journals? David W. Lewis October 2016 © 2016 David W. Lewis. This work is licensed under a Creative Commons Attribution 4.0 International license. Introduction It is a generally accepted fact that open access journal articles enjoy a citation advantage.1 This citation advantage results from the fact that open access journal articles are available to everyone in the word with an Internet collection. Thus, anyone with an interest in the work can find it and use it easily with no out-of-pocket cost. This use leads to citations. Articles in toll access journals on the other hand, are locked behind paywalls and are only available to those associated with institutions who can afford the subscription costs, or who are willing and able to purchase individual articles for $30 or more. There has always been some slippage in the toll access journal system because of informal sharing of articles. Authors will usually send copies of their work to those who ask and sometime post them on their websites even when this is not allowable under publisher’s agreements. Stevan Harnad and his colleagues proposed making this type of author sharing a standard semi-automated feature for closed articles in institutional repositories.2 The hashtag #ICanHazPDF can be used to broadcast a request for an article that an individual does not have access to.3 Increasingly, toll access articles are required by funder mandates to be made publically available, though usually after an embargo period. -
Mapping Scientometrics (1981-2001)
Mapping Scientometrics (1981 -2001) Chaomei Chen College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. Email: [email protected] Katherine McCain College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. Email: kate .mccai n@cis .drexel . ed u Howard White College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. Email: [email protected] Xia Lin College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. Email: xia .I in@cis . d rexel. edu We investigate an integrated approach to co-citation analysis could lead to a clearer picture of the scientometric studies with emphasis to the use of cognitive content of publications (Braam, Moed, & Raan, information visualization and animation 1991a, 1991b). techniques. This study draws upon citation and In Little Science, Big Science, Derek de Solla Price co-citation patterns derived from articles (1963) raised some of the most fundamental questions that published in the journal Scientornetrics (1981- have led to the scientometric study today: Why should we 2001). The modeling and visualization takes an not turn the tools of science on science itself? Why not evolutionary and historical perspective. The measure and generalize, make hypotheses, and derive design of the visualization model adapts a virtual conclusions? He used the metaphor of studying the landscape metaphor with document cocitation behavior of gas in thermodynamics as an analogue of the networks as the base map and annual citation science of science. Thermodynamics studies the behavior of rates as the thematic overlay. The growth of gas under various conditions of temperature and pressure, citation rates is presented through an animation but the focus is not on the trajectory of a specific molecule. -
Estimated Costs of Implementing an Open Access Policy at a Private Foundation
bioRxiv preprint doi: https://doi.org/10.1101/128413; this version posted August 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Estimated costs of implementing an open access policy at a private foundation 1 2 Carly Strasser and Eesha Khare 1 Gordon and Betty Moore Foundation, Palo Alto, California, USA 2 Harvard University, Cambridge, Massachusetts, USA Corresponding author: Carly Strasser1 Email address: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/128413; this version posted August 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Background: The Gordon and Betty Moore Foundation (GBMF) was interested in understanding the potential effects of a policy requiring open access to peer-reviewed publications resulting from the research the foundation funds. Methods: We collected data on more than 2000 publications in over 500 journals that were generated by GBMF grantees since 2001. We then examined the journal policies to establish how two possible open -
Catalyzed Synthesis of Zinc Clays by Prebiotic Central Metabolites
bioRxiv preprint doi: https://doi.org/10.1101/075176; this version posted September 14, 2016. 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. Catalyzed Synthesis of Zinc Clays by Prebiotic Central Metabolites Ruixin Zhoua, Kaustuv Basub, Hyman Hartmanc, Christopher J. Matochad, S. Kelly Searsb, Hojatollah Valib,e, and Marcelo I. Guzman*,a *Corresponding Author: [email protected] aDepartment of Chemistry, University of Kentucky, Lexington, KY, 40506, USA; bFacility for Electron Microscopy Research, McGill University, 3640 University Street, Montreal, Quebec H3A 0C7, Canada; cEarth, Atmosphere, and Planetary Science Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; dDepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA; eDepartment of Anatomy & Cell Biology, 3640 University Street, Montreal H3A 0C7, Canada The authors declare no competing financial interest. Number of text pages: 20 Number of Figures: 9 Number of Tables: 0 bioRxiv preprint doi: https://doi.org/10.1101/075176; this version posted September 14, 2016. 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. Abstract How primordial metabolic networks such as the reverse tricarboxylic acid (rTCA) cycle and clay mineral catalysts coevolved remains a mystery in the puzzle to understand the origin of life. -
Regional Reinfection by Dengue: a Network Approach Using Data from Mexico
bioRxiv preprint doi: https://doi.org/10.1101/475137; this version posted November 23, 2018. 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. Regional reinfection by Dengue: a network approach using data from Mexico Mayra N´u~nez-L´opeza;∗, Luis Alarc´on-Ramosb, and Jorge X. Velasco-Hern´andezc aDepartamento de Matem´aticas Aplicadas, ITAM R´ıoHondo 1, CDMX 01080, M´exico bDepartamento de Matem´aticas Aplicadas y Sistemas, UAM-Cuajimalpa, Av.Vasco de Quiroga 4871, CDMX 05300, M´exico and cInstituto de Matem´aticas, UNAM-Juriquilla, Boulevard Juriquilla No. 3001, Quer´etaro, 76230, M´exico Most of the recent epidemic outbreaks in the world have a strong immigration component as a trigger rather than the dynamics implied by the basic reproduction number. In this work we present and discuss an approach to the problem of pathogen reinfections in a given area that associates people mobility and transmission of dengue, using a Markov-chain Susceptible-Infected-Susceptible (SIS) metapopulation model over a network. Our model postulates a parameter that we have named the effective inoculum size which represents a local measure of the population size of infected hosts that arrive at a given location as a function of population size, current incidence at neighboring locations and the connectivity of the patches. This parameter can be interpreted as an indicator of outbreak risk of any location.