PLOS PROGRESS UPDATE 2014/2015 FROM THE CHAIRMAN AND CEO

PLOS is dedicated to the transformation of research communication through collaboration, transparency, speed and access. Since its founding, PLOS has demonstrated the viability of high quality, Open Access publishing; launched the ground- breaking PLOS ONE, a home for all sound science selected for its rigor, not its “significance”; developed the first Article- Level Metrics (ALMs) to demonstrate the value of research beyond the perceived status of a journal title; and extended the impact of research after its publication with the PLOS data policy, ALMs and liberal Open Access licensing.

But challenges remain. Scientific communication is far from its ideal state. There is still inconsistent access, and research is oered at a snapshot in time, instead of as an evolving contribution whose reliability and significance are continually evaluated through its lifetime.

The current state demands that PLOS continue to establish new standards and expectations for scholarly communication. These include a faster and more ecient publication experience, more transparent peer review, assessment though the lifetime of a work, better recognition of the range of contributions made by collaborators and placing researchers and their communities back at the center of scientific communication.

To these ends, PLOS is developing ApertaTM, a system that will facilitate and advance the submission and peer review process for authors, editors and reviewers. PLOS is also creating richer and more inclusive forums, such as PLOS Paleontology and PLOS Ecology Communities and the PLOS Science Wednesday redditscience Ask Me Anything.

Progress is being made on early posting of manuscripts at PLOS. PLOS Computational Biology Topic Pages allow authors and editors to collaborate in a timely and transparent way. They then publish the work in both the journal and, along with the peer reviews and author responses, on Wikipedia for visibility and discussion.

What began as a movement to make research accessible and free now provides millions of readers around the world increasing opportunities to make important, positive impacts on global health, scientific discovery and science education.

Chairman , Chief Executive O cer 1 Gary Ward, Elizabeth Marincola Transparent and Continual PLOS HIGHLIGHTS Assessment Advances Science

Ongoing Engagement Extends New Research Available 100 PERCENT O PEN ACCESS the Lifetime of Research Sooner Accelerates Science Advances in digital technologies have created PLOS believes that the early availability of + opportunities to alter the way people work, research findings, expert commentary and YEARS communicate and cooperate. Leveraging the broad informed scientific opinion benefits basic 12 AS A LEADER IN OPEN ACCESS PUBLISHING readership and technology of Wikipedia and scientists, clinicians, policymakers and the editorial rigor of PLOS Computational Biology, public through improved decision making. Topic Pages [1] allow PLOS authors and editors a To allow for fast and timely release of PEER- collaborative, timely and transparent approach to information to the community at the height REVIEWED authoring, reviewing and editing. Manuscripts of the Ebola epidemic, two manuscripts JOURNALS created and revised on the journal’s Wiki undergo a submitted to PLOS Neglected Tropical 7 peer review process made transparent to the public Diseases describing the social pathways of by publishing the work—as both a journal article [2] transmission and factors leading to the and a Wikipedia page—together with the peer emergence of Ebola in West Africa were reviews and author responses. Access to the work conditionally accepted before rigorous peer on Wikipedia increases visibility and invites review and posted on the blog ‘Speaking of discussion. Eight Topic Pages have been created Medicine.’ On completion of the peer review with Wikipedia versions of articles updated as process, the articles [3] were published [4] discoveries are made, allowing the research record in the journal. to evolve.

2 Recognized Author Contributions respectful dialogue and constructive commenting. Industry Collaboration on PLOS—A TOP TEN PLOS supports these experiments through its editor PLOS ONE— Enhance Discovery Peer Review Ensures Integrity Measuring Article Impact BIOMEDICAL PUBLISHER and reviewer training available in the Academic To encourage appropriate recognition of researchers Editor Knowledge Base. PLOS joined other publishers and the Committee On 0.10 for contributing resources such as antibodies and Publication Ethics (COPE) to improve the integrity Scientists in the UK identify their model organisms, authors of PLOS Biology and and eectiveness of peer review by developing an 0.08 best work for the UK’s 2014 PLOS Genetics articles gained the ability to industry-wide response to inappropriate and Research Excellence Framework participate in the cross-publisher Resource orchestrated manipulation of the review process. whereby materials described 0.06 (REF), a periodic assessment of Identification Initiative The response includes a statement with published research articles. A total in an article are assigned a persistent and unique recommendations for individual publishers on of 2,403 PLOS articles across a machine-readable resource identifier. The identifier 0.04 retracting articles published on the basis of wide range of disciplines that links to a curated description of the resource, and manipulated reviews, and guidelines to ensure the provide new understanding of other articles or online sources citing that resource, integrity of the scientific record, public trust in the 0.02

CALCULATED CITATION FREQUENCY CITATION CALCULATED disease processes, clinical insights via the SciCrunch web portal. In addition to scientific literature and author confidentiality. or important basic scientific incentivizing appropriate credit, this facilitates better

0.00 research discoveries were submitted resource management, reproducibility and discovery. 0 10 20 30 40 50 60 to the assessment, reflecting high- SCOPUS CITATIONS quality research by UK university “The balance tips towards the requirement Training Improves scientists published in PLOS journals. for transparency. Readers need 23,464 articles published in 2012 Assessment Quality to be able to judge whether writers are • 10% of articles ≥19 citations Assessment at multiple stages along a research commenting outside their areas of expertise.” • Median citations =7 project’s lifecycle provides a comprehensive

Hilda Bastian Courtesy of Martin Fenner. Scopus citation counts as of July 13, 2015 for approach toward faster publication of quality work. PLOS ONE articles published in 2012 Editor, PubMed Health and PubMed Commons Training in how to critique research, the ability to Academic Editor, PLOS Medicine more rigorously capture the intellectual eort of commenting and acknowledgments of contributions will stimulate a stronger post-publication culture [5]. Towards this goal, those scientists engaged in discovery—from basic science [6] to translational research [7]—in discussion through blogs [8] can play a role in creating and enriching a scientific environment enhanced by critical thinking, 3 Recognized Author Contributions respectful dialogue and constructive commenting. Industry Collaboration on PLOS supports these experiments through its editor OPENNESS FOSTERS Enhance Discovery Peer Review Ensures Integrity and reviewer training available in the Academic INCREASED PUBLIC To encourage appropriate recognition of researchers Editor Knowledge Base. ENGAGEMENT PLOS joined other publishers and the Committee On for contributing resources such as antibodies and Publication Ethics (COPE) to improve the integrity model organisms, authors of PLOS Biology and and eectiveness of peer review by developing an PLOS Genetics articles gained the ability to The Public Engagement in Science industry-wide response to inappropriate and ARTICLE HIGHLIGHTS* participate in the cross-publisher Resource Collection [9] investigates through orchestrated manipulation of the review process. Identification Initiative whereby materials described case studies the conditions under ARTICLES PUBLISHED The response includes a statement with in an article are assigned a persistent and unique which the public is motivated to recommendations for individual publishers on machine-readable resource identifier. The identifier engage in scientific issues and retracting articles published on the basis of links to a curated description of the resource, and + decision making related to bio- manipulated reviews, and guidelines to ensure the other articles or online sources citing that resource, 33,000 science innovation. Recent articles integrity of the scientific record, public trust in the via the SciCrunch web portal. In addition to address open collaboration [10] scientific literature and author confidentiality. incentivizing appropriate credit, this facilitates better involving broadened participant resource management, reproducibility and discovery. groups to improve local 11.6 MILLION environmental governance; Training Improves MONTHLY ARTICLE VIEWS increased transparency [11] in the grant review process to bolster Assessment Quality confidence for public spending on Assessment at multiple stages along a research 1.9+ MILLION research; incremental changes [12] project’s lifecycle provides a comprehensive MONTHLY ARTICLE DOWNLOADS to improve transparency of peer approach toward faster publication of quality work. review for grant funding Training in how to critique research, the ability to applications; and the fundamental more rigorously capture the intellectual eort of technical and structural elements commenting and acknowledgments of contributions COLLECTIONS of a trust-centric framework [13] will stimulate a stronger post-publication LAUNCHED 18 for genomic data. culture [5]. Towards this goal, those scientists engaged in discovery—from basic science [6] to A R TICLES translational research [7]—in discussion through 135,000+ PUBLISHED ‡ blogs [8] can play a role in creating and enriching a *2014 scientific environment enhanced by critical thinking, ‡ 4 Through 2014 COMMUNITY HIGHLIGHTS* GLOBAL REPRESENTATION AUTHOR SATISFACTION‡

25 BLOGS 6,900+ EDITORS 90,000+ REVIEWERS 93% MILLION PLOS AUTHORS WOULD UNIQUE VISITORS SUBMIT TO PLOS AGAIN 2.1TO PLOS BLOGS 190,000+ TWITTER FOLLOWERS 94% + PLOS AUTHORS WOULD NOBEL LAUREATES 190 COUNTRIES RECOMMEND PLOS TO A 57 AS AUTHORS W ITH AUTHORS COLLEAGUE

*As of August 1, 2015 Through 2014 ‡2014 Author Survey

5 POST-PUBLICATION One PLOS, Many Communities DISCUSSION VENUES EXPAND AUDIENCE

The value of scientific research resides in more than just the final publication. PLOS Science Richer and More Inclusive Wednesday on redditscience Venues for Interaction provides a venue for an interactive post-publication conversation and and Information Dissemination a place for select PLOS authors to Discussion of published research takes place online communicate their science and through PLOS Communities—venues that advance interact with the eight million discovery through opportunities to share research, member extended community of place findings into context and enable participants to readers, researchers and student stay current on the most relevant work by engaging scientists. The weekly Ask Me in online dialogue. In joining the existing Anything (AMA) series is open to PLOS Neuroscience and PLOS Synthetic Biology anyone with an internet connection Communities, PLOS Ecology and and an interest in science or the PLOS Paleontology support the robust engagement “It makes [the research] more visible, and story behind the science. Top of authors in these disciplines. These Communities gives a chance for people who really AMAs covered computer models for artificial intelligence, inflation are led by independent researchers acting as want to engage with science to engage bias in science publications and community blog editors working in cooperation with with it in a way that’s a little more personal the importance of vaccination PLOS sta and Academic Editors. Together they than what’s oered by a form open collectives of early and mid-career related to the 2014-2015 measles newspaper article or a blog post.” researchers and noted bloggers who interview outbreak. In its first eight weeks, authors, highlight articles, provide conference Andrew Farke the series generated 500,000 coverage and facilitate research-based debates and PLOS Science Wednesday on redditscience page views and 2,000 comments Ask Me Anything participant discussions directly on PLOS-hosted web properties and questions for authors, while PLOS Paleontology Community Editor and and through social media networks. PLOS ONE Academic Editor bringing more readers to their Augustyn Family Curator of Paleontology PLOS articles. Archived AMA Raymond M. Alf Museum of Paleontology transcripts are Open Access and 6 available for remix and reuse. Collaborative Blogging Active Participation Strengthens SCIENTISTS SHARE THE Generates Greater Reach Feedback Loops for Researchers IMPORTANCE OF RESEARCH TO SOCIETY The rapidly changing scientific communication To develop the collective voice of communities landscape oers opportunities for interaction among while preserving the individual perspective, PLOS

researchers at conferences and beyond. provides blogs on matters of interest to diverse In a forum for active scientists to Field Reports blogging sites, hosted on plos.org, audiences. The PLOS Blogs Network features sta speak directly to the public allow live collaborative blogging and tweeting to and community scientists and science writers about why basic research in their bring conference coverage to colleagues near and contributing on topics ranging from the discipline- field is important, PLOS Pathogens’ far, amplifying dissemination of research and specific ‘ ,’ focused on genomics DNA Science Research Matters [14] series meeting highlights. At the Society for Neuroscience research, to the broad interest ‘Public Health provides an opportunity for Annual Meeting, nearly 50 contributor attendees Perspectives.’ Timely blogs include ‘SciComm,’ an individual scientists to communicate posted highlights of research news from conference open platform for opinion and discussion on the how diverse fundamental research presentations. Attendees of the American Society art and science of science communication and into pathogens assures real and of Tropical Medicine and Hygiene Annual Meeting ‘Absolutely, Maybe,’ an independent blog exploring compelling impact on public health provided coverage of research discussions and hot topics in biomedical research. Recent posts and human knowledge. The series keynotes—by Bill Gates and representatives of the cover meta-analysis, scientists working together launched with perspectives from World Health Organization—for international online and the integration of social media into the journal’s Editors-in-Chief scientists including many prevented from attending public television health documentaries. whose curiosity-driven research due to travel restrictions on Ebola-aected countries, led them to get involved in in an eort coordinated by PLOS Neglected start-up biotech [15] companies Tropical Diseases sta and community editors. and joint ventures [16] with pharmaceutical companies, demonstrating the diverse ways basic science can have practical and unpredicted application.

7 Metrics Enhancements Improve Assessment

ALM Reports Increase Usability

As more Article-Level Metrics (ALM) data are collected and made available, users can more almreports.plos.org quickly and easily understand their relevance and meaning in graphical presentation format. ALM Reports allow users to collect metrics for any set of PLOS articles as well as to summarize and visualize the results. The latest iteration of the visualization tool features three interactive formats that support granular assessment of large article sets by subject area, usage over time and author location to identify potential collaborators and users of the research content. A faceted search allows comprehensive discovery across the entire corpus of over 135,000 PLOS articles with results narrowed by journal, article type and publication date.

“Views and shares on social media (such as Twitter and Facebook) are important metrics Visualization example of article usage by subject area. because they are nearly instantaneous measures of impact (compared to citations) and they imply there is a public interest in the research.”

Chris Rands

PLOS Genetics author Project Manager, Science 8 PHG Foundation, Cambridge, United Kingdom Stakeholders Encourage Deeper IMPROVING THE Understanding of Metrics READER EXPERIENCE

The ability to know where published work is

attracting attention beyond academia and to On each article, the redesigned understand its influence before it has accumulated ALM signpost provides better scholarly citation are author and funder interests visibility of views, cites, saves and addressed by use of ALMs. In their expert shares of individual articles commentary [17] on the potential of metrics to together with improved display provide a deeper understanding of the impact of the and feedback options for subject work they support, the Wellcome Trust recommends area terms. An updated format for ALM developers work in concert with funders for the the journal homepages highlights further benefit of all stakeholders. In turn, the Higher content and incorporates some of Education Funding Council for England (HEFCE) the striking images that accompany report on the role of metrics in research and PLOS articles. Other improvements performance assessment adopted many of the focus on quality assurance and recommendations made by PLOS in May 2014 to typesetting processes, including take a rigorous and quantitative approach while implementation of a single column developing necessary guidelines to protect against PDF design that enables a more misuse. The report calls on publishers to reduce the ecient composition process and emphasis on journal impact factors and ensures readability of PLOS articles recommends that data on quantitative indicators across a variety of devices. be openly available for analysis. Additional improvements serve as the pillars of future initiatives and integrations. “Meaningful work is published in many places and the impact of each study cannot be dictated by the title of the journal in which it appears.”

Damian Pattinson

9 Editorial Director, PLOS ONE Standards Enable Reproducibility

Streamlined Data Deposition and other research outputs, discovery and PLOS Medicine by John Ioannidis—with Improves Access reproducibility are cumbersome and variable. PLOS over 87,000 views—on how to make more is collaborating with Technical and Human published research true suggests benefits The PLOS Data Repository Integration Partner infrastructures for Open Research (THOR) grant from enhancing a culture of replication Program simplifies data deposition, provides consortium partners ORCID, DataCite, Dryad, and reproducibility practices in research confidential access to data for editors and peer Zenodo, PubMed Central and others to ensure the science. PLOS’ most viewed article to reviewers during the review process and allows increasingly complex network of digital identifiers date, with over 1.3 million views, is a public access to these data for readers following and systems developing around research studies is PLOS Medicine Essay on the implications publication. Researchers deposit data and submit linked and that digital identifiers are recognized of bias in research claims: “Why Most their manuscript through a single, streamlined across diverse systems. Published Research Findings Are False” [20]. workflow to ensure the article and its underlying The article is one of 15 must-reads on the data are fully paired—published and linked together. Expert Insights Enhance UC Berkeley Summer Reading List for Dryad and FlowRepository currently support incoming students. integration, laying the foundation for additional Research Replication repositories in the future. PLOS worked with Dryad Reproducibility is crucial for success of the scientific to develop an Application Programming Interface endeavor and a key topic of interest to an expansive (API) that facilitates metadata exchange between readership; a 2014 study [18] describing the inability journals and the repository, making the process more of authors to replicate their previously published reliable and scalable. findings made the front page of redditscience with over 850 comments. An Education article in Community Standards Facilitate PLOS Computational Biology defines [19] scientific communities and the value they bring to facilitating Reproducibility the exchange and development of ideas and Without a discoverable relationship between expertise, including those related to fostering datasets, their contributors, associated publications reproducible research, and an Essay [6] in 10 GUIDES TO ADDRESS Resources Foster CAREER CHALLENGES Early Career Researchers With nearly 50 articles, the Ten Simple Rules Collection [21] professional development for a successful career. published in PLOS Computational Communicating Insights for Biology has amassed over The PLOS Early Career Travel Award Program Professional Development 1.8 million page views to date. recognizes eorts of PLOS authors in the early Articles in the series provide quick, PLOS encourages the next generation of scientists to stages of their career and supports opportunities for concentrated guides for mastering couple creative ingenuity with rigorous inquiry in their them to present their research findings to a wider some of the professional challenges research. ‘The Student Blog’ is a platform to foster audience. Selected recipients provided thoughtful research scientists face in their these skills while providing a forum to connect and creative written perspectives regarding the careers. Favorite recent articles students with colleagues and PLOS authors. Written by hindrances to early career researchers for reflect the interests and concerns a geographically disperse team of students from a communicating their science as well as solutions for of young professionals: variety of institutions, disciplines and levels of change. Approaching a New Job [22]; education, the blog provides insight into the current Live Tweeting at Scientific state of science education and work by early career Conferences [23]; Better researchers and their community, with posts covering (Scientific) Figures [24]; Win a Nobel Prize [25]; Successful student perspectives on deep brain stimulation, “As technology has evolved, the teaching of Cross-Disciplinary Collaboration public misunderstanding of current scientific topics science communication should reflect this. [26] and (Empirical) Rules for and the importance of the World Health Organization In addition to traditional formal writing and Writing Science [27]. in global health emergencies. presentation, universities should include tasks that provide students with the skills and confidence to become involved in social Awards Program Recognizes media (Facebook, Twitter), blogs, scientific Ideas to Improve Research forums and media audiences.”

Communication Denice Higgins, PhD

Experience in becoming eective science Forensic Odontologist and Post-doctoral Research Associate, The University of Adelaide, Australia communicators is an important component of PLOS Early Career Travel Award Recipient 11 Open Access Advances Science

Global Policies Enable Access Foundations Launch

With passage of AB609, the first state Open Access Progressive Policies legislation, California became the first in the country To make all outputs of the research that it supports to ensure that state Department of Public Health freely accessible and fully usable to the public, the funded research is publically available, setting the Bill & Melinda Gates Foundation required that as of stage for the acceleration of scientific discovery, January 2015, all articles and associated data sets innovation and economic growth. PLOS led the derived from their funding must be made available coalition that brought this legislation to the public. under a CC BY 4.0 license, with no embargo period Around the world, governments released policies for allowed beginning in 2017. To promote greater institutions, funders and researchers to shift transparency and accessibility of materials, the scholarly communication toward Open Access. Ford Foundation adopted an open licensing policy Denmark created a for all researchers to publish plan for all grant-funded projects and research, and in an any government-funded research Open Access by eort to help speed the pace of discovery and 2021 while The Netherlands’ vision targets 2024. In innovation around the globe, the Wikimedia the US, broad release of government access and Foundation adopted a pilot Open Access policy. data policies reflect that of the National Institutes of Health.

“Published research resulting from our funding should be promptly and broadly disseminated. We have adopted an Open Access policy that enables the unrestricted access and reuse of all peer-reviewed published research funded, in whole or in part, by the foundation, including any underlying data sets.”

Bill & Melinda Gates Foundation

12 Open Access Policy 13 with current andfuture publishingindustry practices, and data miningfor research purposesiscompatible T Mining Allows Discovery Unrestricted Text and Data adoption oftheAPCmodel. organization in Germany, willeasewidespread the largest independentresearch funding University, CopernicusPublishing, Publications, Bielefeld working group comprised administration amongmemberinstitutions ofthe information transfer ofbest practices incost infrastructures for eective payments. Strategic reduced administrative costs andcompatible including suggestions ontheultimate goalsof customized recommendations onhow to proceed, the cost ofpublication. The ESAC Charge (APC)funds.AnAPCisafee that osets when administering ArticleProcessing institutions ororganizations to assess their needs includes aquizandscoring matrix that enables Eciency andStandards for ArticleCharges (ESAC) An Open Access Implementation Charge ManagementImproves Ecient ArticleProcessing o supportpolicies andpublic awareness that text online tool developed by theworking group the MaxPlankDigitalLibaryandDFG, of PLOS, tool provides Co-Action seven languages. global scalebenefitfrom theguidetranslated into conducted thepilot.Scientificcommunities ona Infrastructure Services for OpenAccess (IS4OA) Preservation andAccess (SHERPA) and Securing aHybridEnvironment for Research Access Association ScholarlyPublishers (OASPA), Copernicus Publications, inconsultation withOpen and Academic Resources Coalition (SPARC) and journals’ policies.PLOS, theScholarly Publishing updated basedonareal-world pilotcovering 100 implementation from opento closedaccess was terminology anddescribesaspectrumof Spectrum The popular“HowOpenIsIt? Understanding ofOpenAccess Updated GuideIncreases Global is available for maximumdiscovery andreusability. ideas contained withinensures that journalcontent promote machinereadability ofthefacts, data and scientific literature together withstandards that legal repercussions. Unrestricted access to the data miningofdigitalcontent ontheweb without action to enableresearchers to carryouttext and Age Declaration onKnowledge Discovery intheDigital PLOS participated inconstruction ofThe Hague , asetoffive core principlesandaroadmap for guide that standardizes OpenAccess ® ” OpenAccess

NUMBER OF ARTICLES includes BMC,Copernicus, Ecancermedicalscience, eLife, Frontiers, 100,000 140,000 Open Access Articles Growth inPublished 120,000 40,000 60,000 80,000 Hindawi, JMIRPublications, MDPI,PeerJ, PLOS, SpringerOpen 20,000 Data from OASPA; OA-only journalsusingaCC BY license 0 00 02 04 06 YEAR 08 10 12 14 Curated Content Accelerates Discovery: Collections

Research to Improve International Expertise Global Health for Deeper Understanding

A partnership [28] between PLOS Medicine and the Maternal In one of the largest collections of new material published by Health Task Force at Harvard School of Public Health PLOS, experts from the World Health Organization (WHO) produced a series of article collections focused on the better and the World Bank Group document and monitor progress understanding of how and when to comprehensively towards a healthcare environment in which all people who integrate maternal and infant health care. From Argentina to need health services receive them—without excessive Zimbabwe, articles come from authors in over 400 financial hardship. The PLOS Medicine Monitoring Universal institutions around the world, ensuring global participation in Health Coverage (UHC) Collection [30] includes an and access to comprehensive maternal health data, Overview [31], 13 country case studies written by national programmatic experiences and critical areas of debate experts and five technical reviews that provide insights and consensus. The 2014 Collection, Integrating related to the measurement of financial protection, service Health Care to Meet the Needs of the coverage and equity. The Collection provides in-depth Mother—Infant Pair [29], emphasizes analysis on interlinked components and integration of UHC the importance of simultaneous monitoring into the overall monitoring of healthcare systems’ considerations of treatment and performance. The accompanying Editorial, “The PLOS prevention in the integration of ‘Monitoring Universal Health Coverage Collection: Managing care. A ‘Speaking of Medicine’ Expectations” [32], places this global eort by WHO and post highlights key articles World Bank in historical context and describes its limitations. over three years.

14 Improved Diagnoses Integrated Content for from Dedicated Resources Broader Dissemination

The Special Programme in Research and Training in Tropical To provide a complete picture of the latest research and Diseases (TDR) was formed in 1974 in response to the World commentary to the public in historical context, PLOS is Health Assembly’s call for increased eort and strengthened able to leverage additional collection formats that may training to combat diseases of poverty, particularly in be sourced externally. As in the case of the Ebola developing countries. Resulting tools provide improvements outbreak, Perspectives [35], Commentary [36], blog posts, in malaria control, tuberculosis diagnosis and assessment of Editorials [37] and Primers [38] published across the impact of climate change on vector-borne diseases. The PLOS, early research rapidly published in TDR Reflects on 40 Years Collection [33] published in PLOS Currents: Outbreaks [39] and older articles that PLOS Neglected Tropical Diseases provides perspectives and provide background [40] are pulled together into historical profiles written by current and former sta at TDR a PLOS Resources on Ebola flipboard. on 40 years of disease and policy research and implementation. An Historical Profile [34] on bringing community viewpoints into research and application is highlighted on the WHO website.

15 Global Media Extends Article Reach and Impact

“When HIV Infects the Brain” “Hope for Ebola Epidemic End in Liberia” “California Trees Nailed as the March 26, 2015 January 15, 2015 Source of Mystery Infections” PLOS Pathogens PLOS Biology August 22, 2014 PLOS Pathogens

“Is Redoing Scientific Research the “Deep Sea ‘Mushroom’ May Be New Branch of Life” “Watch Death Valley’s Rocks Best Way to Find Truth?” September 3, 2014 Walk Before Your Eyes” January 13, 2015 PLOS ONE August 27, 2014 PLOS Medicine PLOS ONE

“New Algorithms Search for Signs “Tracking Worms Troubles to “BPA Disrupts Sperm Development, of Consciousness in Brain Injury Patients” Monitor a Country’s Health” Linked to Declining Male Fertility” October 16, 2014 May 4, 2015 January 23, 2015 PLOS Computational Biology PLOS Neglected Tropical Diseases PLOS Genetics

16 PLOS publishes a suite of influential Open 10-YEAR ANNIVERSARIES Access journals from diverse areas of science and medicine that contain rigorously peer-reviewed research articles, together with expert commentary, analysis and 2014 educational material. PLOS journals fully comply PLOS Medicine with Open Access mandates from funders, institutions and policymakers; upon publication all articles 2015 are immediately deposited in PubMed Central. Together with high-quality reporting of interesting research itself, PLOS Computational Biology deep dives into key topics with Collections, Perspectives PLOS Genetics PLOS Pathogens and Editorials bring readers to the more than 135,000 articles published in PLOS journals since 2003.

17 PLOS Biology

The search for eective Alzheimer’s disease progressed with the identification [41] of an An integrative approach combining the analysis of An Essay [48] considering the nature of evolution inhibitor targeting an enzyme involved in learning modern bird development and dinosaur fossil data and the concept of language proposes a recent and and memory found to be overactive in the disease. clarified [45] how wrist bones evolved during the rapid emergence of language, in evolutionary terms. In a mouse model of Alzheimer’s, treatment with dinosaur—bird transition and resolved previous The authors explain the development of simple the novel compound—a tyrosine phosphatase disparities challenging support for the dinosaur— phrases and ultimately sentences as a series of inhibitor—improved cognitive function. bird link. A description [46] of how the wrist was merged word sets of increasing size and complexity. A Synopsis [42] summarizes the significance remodeled bone by bone and honed for flight The Perspective “Life in a World without of the work. discusses the benefits of combining paleontology Microbes” [49] considers life without the human and embryology to piece together evolution. Widespread poor practice of data representation gut microbiome, a hypothetical scenario of a in the scientific literature as described in a An industrial revolution may be on its way to the radically dierent world lacking bacteria and Perspective [43] struck a chord with readers, with laboratory with the increasing availability of 3-D archaea to regulate the environment, and the deadly 100,000 page views in less than a month following printers in combination with designs and assembly implications of eliminating microbial eukaryotes and With a readership that encompasses the scientific community publication—the most meteoric rise in Article-Level instructions placed in Open Access repositories that viruses. This work was widely viewed in the era of Metrics (ALMs) to date for PLOS Biology. The article include the National Institutes of Health 3-D Print what some have called the age of the microbiome. as well as educators, policymakers and members of the public, presents data on the misuse of the bar graph and Exchange and peer-reviewed journals. A Community PLOS Biology publishes articles of exceptional significance, Moving from the stomach to the head, scientists includes Excel templates for creating scatterplots Page [47] details how the Open Labware movement discovered [50] that the mammalian circadian originality and relevance in all areas of biological science, with the discussion continuing post-publication, as originated, its current state, capabilities and clock in the brain is synchronized not only by the engaged readers added code for generating plots resources, as well as lessons learned from from molecules to ecosystems, including work at the interface presence of light but also by the color information in other statistical software. The work is part of the introducing the concept to educators in sub-Saharan of other disciplines, such as chemistry, medicine, physics contained in that light. The work, implying a more PLOS Reporting Guidelines Collection [44]. Africa and Latin America. A PLOS Science and mathematics. In addition to primary research, the journal complex sensory mechanism than previously Wednesday on redditscience Ask Me Anything with realized for telling time of day, is accompanied by publishes Primers, Perspectives and Community Pages. the authors received nearly 800 comments. a Primer [51] explaining the research.

18 PLOS Biology

The search for eective Alzheimer’s disease progressed with the identification [41] of an An integrative approach combining the analysis of An Essay [48] considering the nature of evolution inhibitor targeting an enzyme involved in learning modern bird development and dinosaur fossil data and the concept of language proposes a recent and and memory found to be overactive in the disease. clarified [45] how wrist bones evolved during the rapid emergence of language, in evolutionary terms. In a mouse model of Alzheimer’s, treatment with dinosaur—bird transition and resolved previous The authors explain the development of simple the novel compound—a tyrosine phosphatase disparities challenging support for the dinosaur— phrases and ultimately sentences as a series of inhibitor—improved cognitive function. bird link. A description [46] of how the wrist was merged word sets of increasing size and complexity. A Synopsis [42] summarizes the significance remodeled bone by bone and honed for flight The Perspective “Life in a World without of the work. discusses the benefits of combining paleontology Microbes” [49] considers life without the human and embryology to piece together evolution. Widespread poor practice of data representation gut microbiome, a hypothetical scenario of a in the scientific literature as described in a An industrial revolution may be on its way to the radically dierent world lacking bacteria and Perspective [43] struck a chord with readers, with laboratory with the increasing availability of 3-D archaea to regulate the environment, and the deadly 100,000 page views in less than a month following printers in combination with designs and assembly implications of eliminating microbial eukaryotes and publication—the most meteoric rise in Article-Level instructions placed in Open Access repositories that viruses. This work was widely viewed in the era of Metrics (ALMs) to date for PLOS Biology. The article include the National Institutes of Health 3-D Print what some have called the age of the microbiome. presents data on the misuse of the bar graph and Exchange and peer-reviewed journals. A Community Moving from the stomach to the head, scientists includes Excel templates for creating scatterplots Page [47] details how the Open Labware movement discovered [50] that the mammalian circadian with the discussion continuing post-publication, as originated, its current state, capabilities and clock in the brain is synchronized not only by the engaged readers added code for generating plots resources, as well as lessons learned from presence of light but also by the color information in other statistical software. The work is part of the introducing the concept to educators in sub-Saharan contained in that light. The work, implying a more PLOS Reporting Guidelines Collection [44]. Africa and Latin America. A PLOS Science complex sensory mechanism than previously Wednesday on redditscience Ask Me Anything with realized for telling time of day, is accompanied by the authors received nearly 800 comments. a Primer [51] explaining the research.

19 PLOS Medicine

The journal celebrated its 10th Anniversary in 2014 garnered widespread media coverage, comment leaders, doctors and polio survivors working to at a Symposium with guest speakers John Ioannidis from the World Sugar Research Organization and an reverse local opposition to polio vaccination. speaking on truth in published research and Hilda author rebuttal recommending scrutiny of industry In the aftermath of the massive earthquake that Bastian discussing post-publication evaluation. opposition to current policy proposals. On Speaking devastated Haiti in 2010, an ongoing epidemic of Complete presentations and an interview with of Medicine, the Executive Director of the Center cholera introduced by United Nations peacekeepers Ioannidis are available on the PLOS Video Channel. for Science in the Public Interest remarks on the reached over 730,000 cases and 8,700 deaths. debate in the context of sugary beverages and 2015 A malaria clinical trials partnership published a An Essay [56] calls for measures such as pre- national dietary guidelines. milestone [52] in the development of a vaccine with deployment screening and treatment to prevent the work receiving the Charles C. Shepard Science A statement calling for public access to data from the spread of drug-resistant malaria by UN Award in the category of ‘Prevention and Control’ for all clinical trials went live on the World Health peacekeeping troops reassigned from areas best manuscript published in a reputable, peer- Organization (WHO) website in concert with an where resistance is prevalent. reviewed journal by a Center for Disease Control or Essay [54] in PLOS Medicine by WHO leaders An Essay [57] from Bernard Pécoul and colleagues Agency for Toxic Substances and Disease Registry explaining that conduct of human research without from Médecins Sans Frontières, Wellcome Trust, scientist. The impact of this trial demonstrating safety publication and dissemination of the results is An influential venue for research and commentary on the major Institut Pasteur and other public health experts and even partial vaccine ecacy in infants and unethical and a Perspective on practical approaches challenges to human health worldwide, PLOS Medicine publishes called for the creation of a global biomedical children in seven African countries cannot be under- to achieving transparency by Ben Goldacre, research and development (R&D) fund for innovation articles across all areas of medical science with potential to estimated as there currently is no licensed malaria co-founder of AllTrials.net. in drug research for Ebola, antibiotics and other directly and substantially inform clinical practice or health policy, vaccine. The article acquired more than 12,000 views A Health in Action article—which provides a venue drugs for neglected diseases. The publication of the in the first two weeks following publication. including research that provides mechanistic insights into disease for groups or individuals not regularly represented essay coincided with the World Health Assembly in processes. The journal emphasizes work that advances A study [53] documenting more than a decade-long in a medical journal to describe important issues Geneva and the WHO Ebola R&D summit. understanding of conditions or risk factors impacting human eort in the 1960s–1970s by the sugar industry to from their perspective—reports [55] on a coalition health through clinical, epidemiological or translational research. influence national dental health research and policy campaign in Nigeria involving imams and other

20 PLOS Medicine

The journal celebrated its 10th Anniversary in 2014 garnered widespread media coverage, comment leaders, doctors and polio survivors working to at a Symposium with guest speakers John Ioannidis from the World Sugar Research Organization and an reverse local opposition to polio vaccination. speaking on truth in published research and Hilda author rebuttal recommending scrutiny of industry In the aftermath of the massive earthquake that Bastian discussing post-publication evaluation. opposition to current policy proposals. On Speaking devastated Haiti in 2010, an ongoing epidemic of Complete presentations and an interview with of Medicine, the Executive Director of the Center cholera introduced by United Nations peacekeepers Ioannidis are available on the PLOS Video Channel. for Science in the Public Interest remarks on the reached over 730,000 cases and 8,700 deaths. debate in the context of sugary beverages and 2015 A malaria clinical trials partnership published a An Essay [56] calls for measures such as pre- national dietary guidelines. milestone [52] in the development of a vaccine with deployment screening and treatment to prevent the work receiving the Charles C. Shepard Science A statement calling for public access to data from the spread of drug-resistant malaria by UN Award in the category of ‘Prevention and Control’ for all clinical trials went live on the World Health peacekeeping troops reassigned from areas best manuscript published in a reputable, peer- Organization (WHO) website in concert with an where resistance is prevalent. reviewed journal by a Center for Disease Control or Essay [54] in PLOS Medicine by WHO leaders An Essay [57] from Bernard Pécoul and colleagues Agency for Toxic Substances and Disease Registry explaining that conduct of human research without from Médecins Sans Frontières, Wellcome Trust, scientist. The impact of this trial demonstrating safety publication and dissemination of the results is Institut Pasteur and other public health experts and even partial vaccine ecacy in infants and unethical and a Perspective on practical approaches called for the creation of a global biomedical children in seven African countries cannot be under- to achieving transparency by Ben Goldacre, research and development (R&D) fund for innovation estimated as there currently is no licensed malaria co-founder of AllTrials.net. in drug research for Ebola, antibiotics and other vaccine. The article acquired more than 12,000 views A Health in Action article—which provides a venue drugs for neglected diseases. The publication of the in the first two weeks following publication. for groups or individuals not regularly represented essay coincided with the World Health Assembly in A study [53] documenting more than a decade-long in a medical journal to describe important issues Geneva and the WHO Ebola R&D summit. eort in the 1960s–1970s by the sugar industry to from their perspective—reports [55] on a coalition influence national dental health research and policy campaign in Nigeria involving imams and other

21 PLOS ONE

Without the publication of negative, null and generation of scientists as well as bring diagnostic within five years. A genetic sequencing study [67] inconclusive results the research record is techniques to developing countries. The article is of supercentenarians, an exploration of human incomplete. These missing pieces in the scientific accompanied by assembly instructions and video longevity, was widely covered by the media. literature—when published and discoverable—help and received international media coverage. A conferences page on ‘EveryONE,’ the ocial blog prevent duplication of research endeavors and Four species described in PLOS ONE were chosen of PLOS ONE, provides an integrated location for accelerate research progress. The PLOS Missing for inclusion in the Top Ten New Species for 2015 information regarding scientific meetings that PLOS Pieces Collection [58] highlights the importance of curated by the International Institute for Species attends, including when and where to meet with publishing all sound science, including negative Exploration. One of the more popular discoveries is journal sta; key PLOS articles are also curated findings, which are valuable to the community in Dendrogramma [61], a deep sea mushroom-like according to the focus of each conference. Blog context of previous work and as a measure against organism that may be a novel classification of life. post highlights on EveryONE include top research unnecessary research eorts. Others include a dinosaur [62] with bird-like videos from published articles and a post that The mystery of the sliding rocks in Death Valley features, unique reproductive practices by a places in context two articles on patient-reported National Park may now be solved [59] with the first frog [63] that gives birth to live tadpoles and outcomes (PRO) in clinical trials. The articles The world’s largest journal, PLOS ONE publishes scientifically observations of rocks in motion, made using GPS distinct practices by a wasp [64] that uses dead document insucient guidance [68] for protocol sensors and time-lapse photography. The article ants as a nest protection strategy. writers in a broad sampling of protocols and rigorous research in all areas of science and medicine including captured the global imagination, with international incomplete PRO information [69] on clinical trials interdisciplinary work as well as replication studies and A widely-shared study [65] was the first to compare media coverage in more than 60 unique outlets and registered with the UK National Institute for all sizes of plastic afloat at sea—more than 5 trillion negative results, vital components of the scientific record. over 215,000 views less than one year following Health Research Health Technology pieces weighing over 250,000 tons. Circular currents publication. Assessment program. Publication criteria require research be conducted and reported known as ocean gyres may shred large plastic items according to high technical and ethical standards rather The Foldscope [60], an origami-based paper into smaller microplastics that are then ejected than subjective assessment of significance, providing a faster microscope that costs under $1 and assembles in across the ocean. 10 minutes, has the potential to excite the next path for disseminating research to the public. Research [66] that caught the attention of readers suggests that for older adults, being unable to

22 identify scents may be a predictor of mortality PLOS ONE

Without the publication of negative, null and generation of scientists as well as bring diagnostic within five years. A genetic sequencing study [67] inconclusive results the research record is techniques to developing countries. The article is of supercentenarians, an exploration of human incomplete. These missing pieces in the scientific accompanied by assembly instructions and video longevity, was widely covered by the media. literature—when published and discoverable—help and received international media coverage. A conferences page on ‘EveryONE,’ the ocial blog prevent duplication of research endeavors and Four species described in PLOS ONE were chosen of PLOS ONE, provides an integrated location for accelerate research progress. The PLOS Missing for inclusion in the Top Ten New Species for 2015 information regarding scientific meetings that PLOS Pieces Collection [58] highlights the importance of curated by the International Institute for Species attends, including when and where to meet with publishing all sound science, including negative Exploration. One of the more popular discoveries is journal sta; key PLOS articles are also curated findings, which are valuable to the community in Dendrogramma [61], a deep sea mushroom-like according to the focus of each conference. Blog context of previous work and as a measure against organism that may be a novel classification of life. post highlights on EveryONE include top research unnecessary research eorts. Others include a dinosaur [62] with bird-like videos from published articles and a post that The mystery of the sliding rocks in Death Valley features, unique reproductive practices by a places in context two articles on patient-reported National Park may now be solved [59] with the first frog [63] that gives birth to live tadpoles and outcomes (PRO) in clinical trials. The articles observations of rocks in motion, made using GPS distinct practices by a wasp [64] that uses dead document insucient guidance [68] for protocol sensors and time-lapse photography. The article ants as a nest protection strategy. writers in a broad sampling of protocols and captured the global imagination, with international incomplete PRO information [69] on clinical trials A widely-shared study [65] was the first to compare media coverage in more than 60 unique outlets and registered with the UK National Institute for all sizes of plastic afloat at sea—more than 5 trillion over 215,000 views less than one year following Health Research Health Technology pieces weighing over 250,000 tons. Circular currents publication. Assessment program. known as ocean gyres may shred large plastic items The Foldscope [60], an origami-based paper into smaller microplastics that are then ejected microscope that costs under $1 and assembles in across the ocean. 10 minutes, has the potential to excite the next Research [66] that caught the attention of readers suggests that for older adults, being unable to

23 identify scents may be a predictor of mortality PLOS Computational Biology

In honor of the journal’s tenth year, the diseases around the globe, an important the focus of a PLOS Science Wednesday on 10th Anniversary Collection [70] showcases the consideration for halting infectious disease outbreaks redditscience Ask Me Anything on computational wide range of articles published with a retrospective before they reach epidemic or pandemic stages. The models for artificial intelligence. In a separate study, look [71] at the journal by Founding Editors Philip E. work fueled a public dialogue, was featured by the scientists discovered distinctive neural network Bourne, Steven E. Brenner and Michael B. Eisen and global media and was the subject of a radio signatures [77] in the brains of people in a a discussion of advances to come [72] by interview on NPR Science Friday. The article is vegetative state, which could improve clinical Editor-in-Chief Ruth Nussinov. A message [73] from accompanied by an author interview and comment assessment and help identify patients who are aware the International Society for Computational Biology from the editor on the emerging field of Digital despite being unable to communicate. The work celebrates the successful collaboration between the Epidemiology, the intersection of science, everyday inspired comment and extensive media coverage. organization and the journal. technology and public health. Investigators also approached a key problem in Focus Features serve as a nexus of work of central Key articles described development of computational understanding gene regulatory networks through concern in the field, addressing key areas of methods for genetic analysis. A team of scientists application of the bioinformatics program computational biology, from research to how the developed SciClone [75] to identify the number iRegulon [78]. The method identifying master Research, special features and practical career advice are regular journal can best serve the biological community. The and genetic composition of tumor subclones for regulators of biological processes and mapping their first covers the “ ,” an increasingly improved tracking of tumor evolution and to identify downstream gene targets was highlighted in a features of PLOS Computational Biology. The journal Ethics of Big Data important consideration for researchers. Additionally, the spatial origin of cells resistant to therapy. sequencing industry blog. publishes work on the application of computational methods a guide [19] to building a successful bioinformatics Ultimately deep sequencing combined with an “Web-Based Computational Chemistry Education to biological problems in order to provide substantial insights community discusses the benefits to the exchange understanding of intra-tumor heterogeneity can lead with CHARMMing” [79] in the PLOS Computational into living systems at all scales, from the nano to the macro, and development of ideas and expertise, to improved therapeutic strategies. Biology Education Collection [80] describes the interactions and engagement with professionals and across multiple disciplines, from molecular science, Research demonstrating that modular neural development, implementation and use of web-based from other fields, coordinated funding activities and neuroscience and physiology to ecology and population biology. networks [76] have high overall performance lessons to introduce students and other newcomers more. suggests that a benefit of modularity in animal to computer simulations of biological macro- Analyzing page views of Wikipedia articles brains may be to help organisms evolve to learn new molecules. The lessons take the form of interactive facilitates the ability to monitor and forecast [74] skills without forgetting old ones. The work was step-by-step instructions for performing common 24 molecular simulation tasks. PLOS Computational Biology

In honor of the journal’s tenth year, the diseases around the globe, an important the focus of a PLOS Science Wednesday on 10th Anniversary Collection [70] showcases the consideration for halting infectious disease outbreaks redditscience Ask Me Anything on computational wide range of articles published with a retrospective before they reach epidemic or pandemic stages. The models for artificial intelligence. In a separate study, look [71] at the journal by Founding Editors Philip E. work fueled a public dialogue, was featured by the scientists discovered distinctive neural network Bourne, Steven E. Brenner and Michael B. Eisen and global media and was the subject of a radio signatures [77] in the brains of people in a a discussion of advances to come [72] by interview on NPR Science Friday. The article is vegetative state, which could improve clinical Editor-in-Chief Ruth Nussinov. A message [73] from accompanied by an author interview and comment assessment and help identify patients who are aware the International Society for Computational Biology from the editor on the emerging field of Digital despite being unable to communicate. The work celebrates the successful collaboration between the Epidemiology, the intersection of science, everyday inspired comment and extensive media coverage. organization and the journal. technology and public health. Investigators also approached a key problem in Focus Features serve as a nexus of work of central Key articles described development of computational understanding gene regulatory networks through concern in the field, addressing key areas of methods for genetic analysis. A team of scientists application of the bioinformatics program computational biology, from research to how the developed SciClone [75] to identify the number iRegulon [78]. The method identifying master journal can best serve the biological community. The and genetic composition of tumor subclones for regulators of biological processes and mapping their first covers the “Ethics of Big Data,” an increasingly improved tracking of tumor evolution and to identify downstream gene targets was highlighted in a important consideration for researchers. Additionally, the spatial origin of cells resistant to therapy. sequencing industry blog. a guide [19] to building a successful bioinformatics Ultimately deep sequencing combined with an “Web-Based Computational Chemistry Education community discusses the benefits to the exchange understanding of intra-tumor heterogeneity can lead with CHARMMing” [79] in the PLOS Computational and development of ideas and expertise, to improved therapeutic strategies. Biology Education Collection [80] describes the interactions and engagement with professionals Research demonstrating that modular neural development, implementation and use of web-based from other fields, coordinated funding activities and networks [76] have high overall performance lessons to introduce students and other newcomers more. suggests that a benefit of modularity in animal to computer simulations of biological macro- Analyzing page views of Wikipedia articles brains may be to help organisms evolve to learn new molecules. The lessons take the form of interactive facilitates the ability to monitor and forecast [74] skills without forgetting old ones. The work was step-by-step instructions for performing common 25 molecular simulation tasks. PLOS Genetics

2015 marks the 10th Anniversary for PLOS Genetics the position of these points and therefore overall The series Deep Reads continues to provide the and to recognize the valued contributions of its face shape. The concept sparked Formal genetics and genomics community a place to Editorial Board, select members will reflect on Comment [83] and extensive global and foreign explore how the discipline is portrayed outside the developments in their area of research and language media coverage. scientific literature, in relationship to the wider projections for future research in posts on public. Book topics that influenced today’s genetics In a Review [84] of machine learning and predictive ‘PLOS Biologue.’ The first in this series covers the researchers include the use of DNA in tracking modeling for clinical outcomes, the authors discuss last ten years of chromosome biology, providing patterns of human migration, mechanisms of concerns and challenges of machine learning- insight into the challenges and achievements over the heredity and evolution and species diversity. An based models for optimum prediction of complex decade. original series on PLOS Biologue, Understanding phenotypic traits. Genotype to phenotype prediction Images, brings greater appreciation and insight to In the journal, researchers identified ICARUS1 [81], a has relevance in prediction of medical treatment research articles through detailed explanation of universal gene required for cell proliferation and outcomes and of economically beneficial traits in select monthly issue images. The series initiated with plant growth at high temperatures, a discovery that agriculture. an image of the tight junctions in hair follicle skin cells. might be important in optimizing plant growth as Current estimates on how much of the human rising temperatures across the world are predicted Based on extreme-high depth coverage of By publishing outstanding original contributions in genetics genome is functional range from less than 5% to to have negative impact on agricultural productivity. mitochondrial DNA (mtDNA) sequencing of and genomic biology, PLOS Genetics reflects the full breadth, nearly 80%. In a study [85] based on variation in human mother-father-child trio DNA samples, no Scientists discovered gene variants that may be rates of sequence turnover across functional interdisciplinary nature and impact of these fields on evidence of paternal transmission of mtDNA was predictors [82] of facial shape based on 3-D images elements, approximately 8% of human DNA was science and medicine. The journal’s emphasis is to reflect the detected [86], findings that agree with the accepted of faces from populations with mixed European and found to be necessary. A PLOS Biologue post interests of a broad genetics community by highlighting studies dogma of exclusive maternal transmission of West African ancestry, in combination with genetic describes the relevance of the findings in context of mtDNA. A companion Perspective [87] puts the with significant biological insight across a wide range analysis and superimposed maps of more than 7,000 previous larger estimates by the Encyclopedia of controversy in context and compares two models of systems and fields, including human and model organisms. detection points. The author’s predictive modeling DNA Elements (ENCODE) consortium and analyzes of paternal DNA reduction for non-transmission of considers how genes, sex and racial ancestry aect the article’s Article-Level Metrics (ALMs), boosted paternal mtDNA. by a general interest science website story that was shared over 12,000 times on social media. 26 PLOS Genetics

2015 marks the 10th Anniversary for PLOS Genetics the position of these points and therefore overall The series Deep Reads continues to provide the and to recognize the valued contributions of its face shape. The concept sparked Formal genetics and genomics community a place to Editorial Board, select members will reflect on Comment [83] and extensive global and foreign explore how the discipline is portrayed outside the developments in their area of research and language media coverage. scientific literature, in relationship to the wider projections for future research in posts on public. Book topics that influenced today’s genetics In a Review [84] of machine learning and predictive ‘PLOS Biologue.’ The first in this series covers the researchers include the use of DNA in tracking modeling for clinical outcomes, the authors discuss last ten years of chromosome biology, providing patterns of human migration, mechanisms of concerns and challenges of machine learning- insight into the challenges and achievements over the heredity and evolution and species diversity. An based models for optimum prediction of complex decade. original series on PLOS Biologue, Understanding phenotypic traits. Genotype to phenotype prediction Images, brings greater appreciation and insight to In the journal, researchers identified ICARUS1 [81], a has relevance in prediction of medical treatment research articles through detailed explanation of universal gene required for cell proliferation and outcomes and of economically beneficial traits in select monthly issue images. The series initiated with plant growth at high temperatures, a discovery that agriculture. an image of the tight junctions in hair follicle skin cells. might be important in optimizing plant growth as Current estimates on how much of the human rising temperatures across the world are predicted Based on extreme-high depth coverage of genome is functional range from less than 5% to to have negative impact on agricultural productivity. mitochondrial DNA (mtDNA) sequencing of nearly 80%. In a study [85] based on variation in human mother-father-child trio DNA samples, no Scientists discovered gene variants that may be rates of sequence turnover across functional evidence of paternal transmission of mtDNA was predictors [82] of facial shape based on 3-D images elements, approximately 8% of human DNA was detected [86], findings that agree with the accepted of faces from populations with mixed European and found to be necessary. A PLOS Biologue post dogma of exclusive maternal transmission of West African ancestry, in combination with genetic describes the relevance of the findings in context of mtDNA. A companion Perspective [87] puts the analysis and superimposed maps of more than 7,000 previous larger estimates by the Encyclopedia of controversy in context and compares two models detection points. The author’s predictive modeling DNA Elements (ENCODE) consortium and analyzes of paternal DNA reduction for non-transmission of considers how genes, sex and racial ancestry aect the article’s Article-Level Metrics (ALMs), boosted paternal mtDNA. by a general interest science website story that was shared over 12,000 times on social media. 27 PLOS Neglected Tropical Diseases

Dengue is the most common mosquito-transmitted Mapping Tool (NTDmap.org)” describes [89] the The 40 Years of the APOC Partnership viral disease. To help public health ocials prioritize creation of an innovative tool which allows users to Collection [92] marks the anniversary of the resources and improve decision making, an visualize the geographic distribution of selected landmark African Onchocerciasis Control Program, international collaboration of health policy experts NTDs. Since cost-eectiveness of intervention is one of the most successful private-public propose strategies [88] surrounding better data greatest when targeted to areas with a high burden partnerships for health in Africa. Collection articles collection. Improved measurements of the global of multiple diseases, distribution maps are essential present the challenges, solutions and lessons distribution of Dengue and the resulting economic for planning and implementing interventions, as well learned from the success of disease control with burden should accompany current development in as for visualization of program progress in advocacy programs launched in 1974 that now reach more tools for diagnosis, vaccination, vector control and eorts. than 100 million people annually across Africa. treatment. A research article assessing interactions [90] In keeping with its mission of scientific capacity In “Outbreak of Ebola Virus Disease in Guinea: between schistosomiasis and malaria transmission in building in disease endemic countries and Where Ecology Meets Economy” [37], Editor Daniel sub-Saharan Africa concludes that mass recognizing the benefits of providing early career Bausch and colleague Lara Schwarz discuss the schistosomiasis treatment and control programs in researchers with tools to successfully communicate The first journal devoted to chronic infectious diseases that interrelated ecological and economic factors that regions where both pathogens are highly prevalent their work, PLOS NTDs organizes free manuscript may underlie the Ebola outbreak, from poverty to may have indirect benefits on reducing malaria writing workshops geared toward helping young primarily occur in rural and poor urban areas of low- and drought to poor healthcare systems. The Editorial is transmission, perhaps as a result of general scientists understand the publication process and middle-income countries, PLOS Neglected Tropical Diseases the sixth most viewed article in PLOS NTDs’ history, reduction of immune burden. best practices for manuscript writing. The workshop (PLOS NTDs) is dedicated to advancing research in receiving extensive media coverage including program provides materials and support for A Viewpoint [91] by researchers at the Smithsonian The Washington Post and This Week in Virology. seminars conducted by volunteer members of the pathology, epidemiology, treatment, control and prevention Tropical Research Institute in Panama discusses the PLOS NTDs Editorial Board, with resources and of NTDs, as well as public policy. The journal promotes From Innovation to Application articles provide implications of the appearance in North America of information freely available. Since the formalization the eorts of scientists, health practitioners and public health authors opportunity to discuss novel technologies, the tropical viruses Dengue and Chikungunya as a of the program in 2014, the journal has supported including drugs, vaccines and diagnostics. result of geographic expansion of an invasive experts from endemic countries, building capacity in the nearly a dozen workshops in five countries spanning “Integrating Data and Resources on Neglected mosquito variety across Panama. Chikungunya is a areas most in need. four continents. Tropical Diseases for Better Planning: The NTD worldwide emerging pathogen that causes fever, 28 fatigue and joint swelling in humans. PLOS Neglected Tropical Diseases

Dengue is the most common mosquito-transmitted Mapping Tool (NTDmap.org)” describes [89] the The 40 Years of the APOC Partnership viral disease. To help public health ocials prioritize creation of an innovative tool which allows users to Collection [92] marks the anniversary of the resources and improve decision making, an visualize the geographic distribution of selected landmark African Onchocerciasis Control Program, international collaboration of health policy experts NTDs. Since cost-eectiveness of intervention is one of the most successful private-public propose strategies [88] surrounding better data greatest when targeted to areas with a high burden partnerships for health in Africa. Collection articles collection. Improved measurements of the global of multiple diseases, distribution maps are essential present the challenges, solutions and lessons distribution of Dengue and the resulting economic for planning and implementing interventions, as well learned from the success of disease control with burden should accompany current development in as for visualization of program progress in advocacy programs launched in 1974 that now reach more tools for diagnosis, vaccination, vector control and eorts. than 100 million people annually across Africa. treatment. A research article assessing interactions [90] In keeping with its mission of scientific capacity In “Outbreak of Ebola Virus Disease in Guinea: between schistosomiasis and malaria transmission in building in disease endemic countries and Where Ecology Meets Economy” [37], Editor Daniel sub-Saharan Africa concludes that mass recognizing the benefits of providing early career Bausch and colleague Lara Schwarz discuss the schistosomiasis treatment and control programs in researchers with tools to successfully communicate interrelated ecological and economic factors that regions where both pathogens are highly prevalent their work, PLOS NTDs organizes free manuscript may underlie the Ebola outbreak, from poverty to may have indirect benefits on reducing malaria writing workshops geared toward helping young drought to poor healthcare systems. The Editorial is transmission, perhaps as a result of general scientists understand the publication process and the sixth most viewed article in PLOS NTDs’ history, reduction of immune burden. best practices for manuscript writing. The workshop receiving extensive media coverage including program provides materials and support for A Viewpoint [91] by researchers at the Smithsonian The Washington Post and This Week in Virology. seminars conducted by volunteer members of the Tropical Research Institute in Panama discusses the PLOS NTDs Editorial Board, with resources and From Innovation to Application articles provide implications of the appearance in North America of information freely available. Since the formalization authors opportunity to discuss novel technologies, the tropical viruses Dengue and Chikungunya as a of the program in 2014, the journal has supported including drugs, vaccines and diagnostics. result of geographic expansion of an invasive nearly a dozen workshops in five countries spanning “Integrating Data and Resources on Neglected mosquito variety across Panama. Chikungunya is a four continents. Tropical Diseases for Better Planning: The NTD worldwide emerging pathogen that causes fever, 29 fatigue and joint swelling in humans. PLOS Pathogens

A proof-of-concept study [93] of the first responsible for the majority of urinary tract concise and practical insights tailored to early career hematopoietic stem cell transplant in simian human infections, providing a potential therapeutic researchers. Select additions to the series bridging immunodeficiency virus-infected rhesus macaques alternative or complement to antibiotics. current research to traditional textbook content provided evidence that anti-retroviral therapy and describe the impact of the Syrian civil war on The sources of four subtypes of environmentally- irradiation therapy are not eective for long-term infectious disease in the region [99]; the skin acquired human pathogens causing infections in treatment of HIV. A unified interpretation of the microbiome, related diseases and research [100]; Canada, Washington, Oregon and HIV/AIDS patients results has yet to emerge, demonstrating the and modeling of virulence evolution [101]. in southern California were identified [96] as three ongoing need to understand why there is only one novel tree species. This unique discovery, in part the PLOS Pathogens marked several disease awareness person thought to be cured of HIV to date. Media work of a middle school student, was highlighted in days with topical posts on Speaking of Medicine. coverage placed this work in perspective for a AllGov California and US News & World Report. World Pneumonia Day featured an author interview general audience. covering vaccines, the importance of continued Scientists discovered [97] that shed glycoprotein of A gut microbe in mosquitos that serve as vectors for clinical research in the elderly population and more; Ebola virus triggers immune activation in non-infected dengue and malaria pathogens makes the mosquito World Oral Health Day highlighted journal content immune cells, increasing vascular permeability even less susceptible [94] to infection and thus less likely and the role of the oral microbial community; Committed to educating the pathogens community as well as in the absence of whole virus. The massive release to transmit disease. Researchers also found that the and World Malaria Day presented a discussion of the public at large, PLOS Pathogens publishes outstanding of pro- and anti-inflammatory cytokines by infected bacterium secretes metabolites with anti-pathogenic challenges for drug development and the path to macrophages and dendritic cells may be central to primary research, compelling analysis and educational content properties that could potentially be developed into malaria control, elimination and eradication. the excessive and dysregulated inflammatory host to significantly advance the understanding of bacteria, prevention or treatment therapies. reactions to infection, contributing to high virus fungi, parasites, prions, viruses and their interactions with host An experimental drug that stabilizes transcription pathogenicity. organisms. The journal provides a forum for interdisciplinary factor Hypoxia Inducible Factor-1α protects [95] The ongoing Pearls Collection [98], short educational human bladder cells and mice against a pathogen community and fosters exchange of ideas across all articles addressing topics of relevance and areas of pathogens research through Opinion pieces on topical, importance that span the pathogens field, provides emerging or controversial issues. 30 PLOS Pathogens

A proof-of-concept study [93] of the first responsible for the majority of urinary tract concise and practical insights tailored to early career hematopoietic stem cell transplant in simian human infections, providing a potential therapeutic researchers. Select additions to the series bridging immunodeficiency virus-infected rhesus macaques alternative or complement to antibiotics. current research to traditional textbook content provided evidence that anti-retroviral therapy and describe the impact of the Syrian civil war on The sources of four subtypes of environmentally- irradiation therapy are not eective for long-term infectious disease in the region [99]; the skin acquired human pathogens causing infections in treatment of HIV. A unified interpretation of the microbiome, related diseases and research [100]; Canada, Washington, Oregon and HIV/AIDS patients results has yet to emerge, demonstrating the and modeling of virulence evolution [101]. in southern California were identified [96] as three ongoing need to understand why there is only one novel tree species. This unique discovery, in part the PLOS Pathogens marked several disease awareness person thought to be cured of HIV to date. Media work of a middle school student, was highlighted in days with topical posts on Speaking of Medicine. coverage placed this work in perspective for a AllGov California and US News & World Report. World Pneumonia Day featured an author interview general audience. covering vaccines, the importance of continued Scientists discovered [97] that shed glycoprotein of A gut microbe in mosquitos that serve as vectors for clinical research in the elderly population and more; Ebola virus triggers immune activation in non-infected dengue and malaria pathogens makes the mosquito World Oral Health Day highlighted journal content immune cells, increasing vascular permeability even less susceptible [94] to infection and thus less likely and the role of the oral microbial community; in the absence of whole virus. The massive release to transmit disease. Researchers also found that the and World Malaria Day presented a discussion of of pro- and anti-inflammatory cytokines by infected bacterium secretes metabolites with anti-pathogenic challenges for drug development and the path to macrophages and dendritic cells may be central to properties that could potentially be developed into malaria control, elimination and eradication. the excessive and dysregulated inflammatory host prevention or treatment therapies. reactions to infection, contributing to high virus An experimental drug that stabilizes transcription pathogenicity. factor Hypoxia Inducible Factor-1α protects [95] The ongoing Pearls Collection [98], short educational human bladder cells and mice against a pathogen articles addressing topics of relevance and importance that span the pathogens field, provides

31 Reinvesting to Transform Research Communication

PLOS experienced increased submissions year over year resulting in over 33,000 research articles published in 2014. This brings the total number of Open Access articles published by the organization to more than 135,000. The 2014 financial year brought gross revenue and support to PLOS of $48.5 million and an increase in net assets of $4.89 million. Expenses neared $40.7 million, driven by investments in two key areas:

• Development of resources to create Aperta, a submission • Enhancement and implementation of sophisticated system that will provide a more ecient publishing content management systems for optimum handling experience. Aperta will provide a foundation for of web and article content, as well as architectural additional innovations. The spending associated with advances to the publishing platform, Ambra™ . these R&D investments has been capitalized due to the multi-year nature of their anticipated future use.

PLOS believes that lack of funds should not be a barrier to Open Access publication. Globally authors have benefited from the increased availability of institutional, government and foundation Open Access funds in 2014. To supplement these funds, PLOS supported those who were still unable to pay all or part of their publication fees with assistance totaling almost $3.0 million; included in this amount is the PLOS Global Participation Initiative providing assistance to authors from low- and middle-income countries. PLOS also expanded to over 40 institutions its Institutional Account program through which PLOS administers payment on behalf of participating institutions and their authors.

32 6% 8% BALANCE SHEET STATEMENT OF ACTIVITIES ($000’s) ($000’s)

ASSETS 2014 REVENUE AND SUPPORT 2014 17% Current Assets Contributions 62 Cash and cash equivalents 1,838 Publication fees, gross 47,137 Program and accounts receivable, net 1,333 Membership fee 20 Prepaid expenses and other 739 Advertising and other 1,301 Total current assets 3,909 Total gross revenue and support 48,520 69% Less: Publication Fee Assistance 2,962 Noncurrent Assets Total net revenue and support 45,557 Investments 27,298 Expenses Total Expenses Plus Publication Loan Receivable 54 Publishing 33,011 Fee Assistance $46.5 Million Property and equipment, net 2,288 General and administrative 7,655 Deposits 8 Total expenses 40,666 Total noncurrent assets 32,682 Increase in net assets 4,892 ● 69% Publishing Total assets 36,591 Efforts related to editorial and production operations and advocacy, including staffing, productivity tools and LIABILITIES AND NET ASSETS 2014 enhancement of Ambra Current Liabilities PLOS Supporters ● 6% Publication Fee Assistance Accounts payable 2,891 Fee assistance provided by PLOS to Accrued liabilities 1,539 GRANTS authors unable to pay all or part of their Deferred revenue 863 Alfred P. Sloan Foundation article publication fees; including those Total current liabilities 5,293 qualifying under the PLOS Global Open Society Foundations Deferred rent liability 669 Participation Initiative William K. Bowes, Jr. Foundation Total liabilities 5,962 ● 8% Research & Development SPONSORSHIPS Efforts include innovations in content Net Assets management systems and publishing BioMed Central 30,010 architectures, enhancements to PLOS Unrestricted Copernicus Publications Temporarily restricted 618 Article-Level Metrics (ALMs) and eLife development of Aperta® inclusive of Total net assets 30,629 Frontiers capitalized development Total liabilities and net assets 36,591 Maternal Health Task Force at the Harvard School ● 17% General & Administrative of Public Health Non-publishing costs that support staff and outsourced services in human Scholarly Publishing and Academic resources, legal and accounting; also Resources Coalition 33 includes rent and bank fees Open Access Scholarly Publishers Association PLOS Board of Directors and Management

as of August 1, 2015

Board of Directors Rosalind L. Smyth Susan Au Editorial Boards Institute of Child Health, Director, Finance & Accounting Patrick O. Brown University College London PLOS Biology Stanford University School Paula Carter plosbiology.org/static/edboard of Medicine Gary E. Ward (Chairman) Director, Project University of Vermont Management Oce PLOS Medicine Michael W. Carroll plosmedicine.org/static/edboard American University John Chodacki PLOS ONE Washington College of Law Director, Product Management Senior Sta plosone.org/static/edboard Michael B. Eisen Christine Ferguson Elizabeth Marincola PLOS Computational Biology University of California, Berkeley Joint Chief Editor, PLOS Biology Chief Executive Ocer Ruth Nussinov, Editor-in-Chief Howard Hughes Medical Institute Emma Ganley Richard Hewitt ploscompbiol.org/static/edboard Heather Joseph Joint Chief Editor, PLOS Biology Chief Financial Ocer PLOS Genetics Scholarly Publishing and Academic James Harney Gregory S. Barsh and Resources Coalition (SPARC) Véronique Kiermer Director, Business Systems Executive Editor Gregory P. Copenhaver, David Liddle Integration Editors-in-Chief US Venture Partners CJ Rayhill plosgenetics.org/static/edboard Catherine Nancarrow Chief Technology Ocer Robin Lovell-Badge Senior Managing Editor, PLOS Neglected Tropical Diseases Medical Research Council, Darlene Yaplee PLOS Journals Peter J. Hotez and Serap Aksoy, National Institute for Medical Chief Marketing Ocer Editors-in-Chief Damian Pattinson Research, UK plosntds.org/static/edboard Ray Campbell Editorial Director, PLOS ONE Elizabeth Marincola General Counsel & Secretary PLOS Pathogens Larry Peiperl Chief Executive Ocer Kasturi Haldar and Grant McFadden, Katie Sharabati Chief Editor, PLOS Medicine Editors-in-Chief Meredith T. Niles Director, Human Resources plospathogens.org/static/edboard University of Vermont Helen Atkins Acting Publisher 34 34. Shaping the Research Agenda plosntds.org/doi/pntd.0003350 54. Rationale for WHO's New Position Calling for Prompt Reporting and 69. Systematic Evaluation of the Patient-Reported Outcome (PRO) Content 87. Keeping in Shape the Dogma of Mitochondrial DNA Maternal References 35. The Individualised versus the Public Health Approach to Treating Ebola Public Disclosure of Interventional Clinical Trial Results of Clinical Trial Protocols plosone.org/doi/pone.0110229 Inheritance plosgenetics.org/doi/pgen.1005179 plosmedicine.org/doi/pmed.1001819 plosmedicine.org/doi/pmed.1001858 70. PLOS Computational Biology: 10th Anniversary Collection 88. Approaches to Refining Estimates of Global Burden and Economics of 36. Commentary: Containing the Ebola Outbreak – the Potential and 55. From Intense Rejection to Advocacy: How Muslim Clerics Were ploscollections.org/ploscompbiol10years Dengue plosntds.org/doi/pntd.0003306 1. PLOS Computational Biology: Topic Pages Collection 18. The Influence of Partner-Specific Memory Associations on Picture Challenge of Mobile Network Data plos.io/1U2UniV Engaged in a Polio Eradication Initiative in Northern Nigeria 71. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation 89. Integrating Data and Resources on Neglected Tropical Diseases for ploscollections.org/topicpages Naming: A Failure to Replicate Horton (2007) plosmedicine.org/doi/pmed.1001687 37. Outbreak of Ebola Virus Disease in Guinea: Where Ecology Meets and Innovation ploscompbiol.org/doi/pcbi.1004317 Better Planning: The NTD Mapping Tool (NTDmap.org) plosone.org/doi/pone.0109035 2. Inferring Horizontal Gene Transfer ploscompbiol.org/doi/pcbi.1004095 Economy plosntds.org/doi/pntd.0003056 56. Screening and Treating UN Peacekeepers to Prevent the Introduction 72. Advancements and Challenges in Computational Biology plosntds.org/doi/pntd.0003400 19. A Quick Guide for Building a Successful Bioinformatics Community of Artemisinin-Resistant Malaria into Africa 3. Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and 38. Characterizing the Transmission Dynamics and Control of Ebola Virus ploscompbiol.org/doi/pcbi.1004053 90. Impact of Schistosoma mansoni on Malaria Transmission in ploscompbiol.org/doi/pcbi.1003972 plosmedicine.org/doi/pmed.1001822 Some Implications for Containment plosntds.org/doi/pntd.0003567 Disease plosbiology.org/doi/pbio.1002057 73. Computational Biology: Moving into the Future One Click at a Time Sub-Saharan Africa plosntds.org/doi/pntd.0003234 20. Why Most Published Research Findings Are False 57. A Global Biomedical R&D Fund and Mechanism for Innovations of 4. What Factors Might Have Led to the Emergence of Ebola in West 39. Insights into the Early Epidemic Spread of Ebola in Sierra Leone ploscompbiol.org/doi/pcbi.1004323 91. Geographic Expansion of the Invasive Mosquito Aedes albopictus across plosmedicine.org/doi/pmed.0020124 Public Health Importance plosmedicine.org/doi/pmed.1001831 Africa? plosntds.org/doi/pntd.0003652 Provided by Viral Sequence Data plos.io/1fBYvUn 74. Global Disease Monitoring and Forecasting with Wikipedia Panama—Implications for Control of Dengue and Chikungunya Viruses 21. PLOS Computational Biology: Ten Simple Rules Collection 58. PLOS ONE: The Missing Pieces: A Collection of Negative, Null and plosntds.org/doi/pntd.0003383 5. A Stronger Post-Publication Culture Is Needed for Better Science 40. Wave-Like Spread of Ebola Zaire plosbiology.org/doi/pbio.0030371 ploscompbiol.org/doi/pcbi.1003892 Inconclusive Results ploscollections.org/missingpieces plosmedicine.org/doi/pmed.1001772 plos.io/ZVqyyG 92. PLOS Neglected Tropical Diseases: 40 Years of the APOC Partnership 41. Inhibitor of the Tyrosine Phosphatase STEP Reverses Cognitive Deficits 75. SciClone: Inferring Clonal Architecture and Tracking the Spatial and 22. Ten Simple Rules for Approaching a New Job 59. Sliding Rocks on Racetrack Playa, Death Valley National Park: First Collection ploscollections.org/APOC 6. How to Make More Published Research True in a Mouse Model of Alzheimer's Disease Temporal Patterns of Tumor Evolution ploscompbiol.org/doi/pcbi.1003665 ploscompbiol.org/doi/pcbi.1003660 Observation of Rocks in Motion plosone.org/doi/pone.0105948 plosmedicine.org/doi/pmed.1001747 plosbiology.org/doi/pbio.1001923 76. Neural Modularity Helps Organisms Evolve to Learn New Skills without 93. Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus 23. Ten Simple Rules of Live Tweeting at Scientific Conferences 60. Foldscope: Origami-Based Paper Microscope Macaques after Autologous Hematopoietic Stem Cell Transplant 7. The Economics of Reproducibility in Preclinical Research 42. A Novel Phosphatase Inhibitor May Be a STEP Toward Ameliorating Forgetting Old Skills ploscompbiol.org/doi/pcbi.1004128 ploscompbiol.org/doi/pcbi.1003789 plosone.org/doi/pone.0098781 plospathogens.org/doi/ppat.1004406 plosbiology.org/doi/pbio.1002165 Cognitive Dysfunction plosbiology.org/doi/pbio.1001924 77. Spectral Signatures of Reorganised Brain Networks in Disorders of 24. Ten Simple Rules for Better Figures 61. Dendrogramma, New Genus, with Two New Non-Bilaterian Species 94. Chromobacterium Csp_P Reduces Malaria and Dengue Infection in 8. Exploring the Complex Pattern of Information Spreading in Online Blog 43. Beyond Bar and Line Graphs: Time for a New Data Presentation Consciousness ploscompbiol.org/doi/pcbi.1003887 ploscompbiol.org/doi/pcbi.1003833 from the Marine Bathyal of Southeastern Australia (Animalia, Vector Mosquitoes and Has Entomopathogenic and In Vitro Anti- Communities plosone.org/doi/pone.0126894 Paradigm plosbiology.org/doi/pbio.1002128 78. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Metazoa incertae sedis)—with Similarities to Some Medusoids from the pathogen Activities plospathogens.org/doi/ppat.1004398 25. Ten Simple Rules to Win a Nobel Prize ploscompbiol.org/doi/pcbi.1003731 9. PLOS Biology: Public Engagement in Science Collection 44. PLOS: Reporting Guidelines Collection Precambrian Ediacara plosone.org/doi/pone.0102976 Motif and Track Collections ploscompbiol.org/doi/pcbi.1004084 95. Role of Hypoxia Inducible Factor-1α (HIF-1α) in Innate Defense against ploscollections.org/publicengagement ploscollections.org/reportingguidelines 79. Web-Based Computational Chemistry Education with CHARMMing I: 62. A New Large-Bodied Oviraptorosaurian Theropod Dinosaur from the Uropathogenic Escherichia coli Infection 26. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration ploscompbiol.org/doi/pcbi.1003719 10. Committing to Place: The Potential of Open Collaborations for Trusted 45. New Developmental Evidence Clarifies the Evolution of Wrist Bones in Latest Cretaceous of Western North America Lessons and Tutorial plospathogens.org/doi/ppat.1004818 ploscompbiol.org/doi/pcbi.1004214 Environmental Governance plosbiology.org/doi/pbio.1002081 the Dinosaur–Bird Transition plosbiology.org/doi/pbio.1001957 plosone.org/doi/pone.0092022 80. PLOS Computational Biology: Education Collection 96. Cryptococcus gattii VGIII Isolates Causing Infections in HIV/AIDS 27. Ten Simple (Empirical) Rules for Writing Science ploscollections.org/compbioleducation 11. The Transformative Nature of Transparency in Research Funding 46. Resolving the Flap over Bird Wrists plosbiology.org/doi/pbio.1001958 63. A Novel Reproductive Mode in Frogs: A New Species of Fanged Frog Patients in Southern California: Identification of the Local Environmental plosbiology.org/doi/pbio.1002027 ploscompbiol.org/doi/pcbi.1004205 47. Open Labware: 3-D Printing Your Own Lab Equipment with Internal Fertilization and Birth of Tadpoles 81. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Source as Arboreal plospathogens.org/doi/ppat.1004285 28. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health plosone.org/doi/pone.0115884 Proliferation and Growth at High Temperatures in Arabidopsis thaliana 12. Grant Application Review: The Case of Transparency plosbiology.org/doi/pbio.1002086 97. Shed GP of Ebola Virus Triggers Immune Activation and Increased plosbiology.org/doi/pbio.1002010 ploscollections.org/maternalhealth plosgenetics.org/doi/pgen.1005085 48. How Could Language Have Evolved? plosbiology.org/doi/pbio.1001934 64. A Unique Nest-Protection Strategy in a New Species of Spider Wasp Vascular Permeability plospathogens.org/doi/ppat.1004509 13. Redefining Genomic Privacy: Trust and Empowerment 29. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health plosone.org/doi/pone.0101592 82. Modeling 3D Facial Shape from DNA 49. Life in a World without Microbes plosbiology.org/doi/pbio.1002020 98. PLOS Pathogens: Pearls Collection ploscollections.org/pearls Year 3 (2013-14) - "Integrating Health Care to Meet the Needs of the plosgenetics.org/doi/pgen.1004224 plosbiology.org/doi/pbio.1001983 65. Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Mother–Infant Pair" plos.io/1hDc3Rn 50. Colour As a Signal for Entraining the Mammalian Circadian Clock 99. War and Infectious Diseases: Challenges of the Syrian Civil War 14. Introducing “Research Matters” plospathogens.org/doi/ppat.1005014 Pieces Weighing over 250,000 Tons Afloat at Sea 83. Let's Face It—Complex Traits Are Just Not That Simple plosbiology.org/doi/pbio.1002127 plospathogens.org/doi/ppat.1004438 30. PLOS Medicine: Monitoring Universal Health Coverage Collection plosone.org/doi/pone.0111913 plosgenetics.org/doi/pgen.1004724 15. The Curious Road from Basic Pathogen Research to Clinical Translation ploscollections.org/uhc2014 51. A Colourful Clock plosbiology.org/doi/pbio.1002160 100. The Skin Microbiome: A Focus on Pathogens and Their Association with 84. Regularized Machine Learning in the Genetic Prediction of Complex plospathogens.org/doi/ppat.1004997 66. Olfactory Dysfunction Predicts 5-Year Mortality in Older Adults Skin Disease plospathogens.org/doi/ppat.1004436 31. Monitoring Progress towards Universal Health Coverage at Country and 52. Ecacy and Safety of the RTS,S/AS01 Malaria Vaccine during 18 plosone.org/doi/pone.0107541 Traits plosgenetics.org/doi/pgen.1004754 16. From Cell and Organismal Biology to Drugs Global Levels plosmedicine.org/doi/pmed.1001731 Months after Vaccination: A Phase 3 Randomized, Controlled Trial in 101. Theory and Empiricism in Virulence Evolution plospathogens.org/doi/ppat.1005002 67. Whole-Genome Sequencing of the World’s Oldest People 85. 8.2% of the Human Genome Is Constrained: Variation in Rates of Children and Young Infants at 11 African Sites plospathogens.org/doi/ppat.1004387 32. The PLOS “Monitoring Universal Health Coverage” Collection: plosone.org/doi/pone.0112430 Turnover across Functional Element Classes in the Human Lineage 17. Alternative Perspectives on Impact: The Potential of ALMs and plosmedicine.org/doi/pmed.1001685 Managing Expectations plosmedicine.org/doi/pmed.1001732 plosgenetics.org/doi/pgen.1004525 Altmetrics to Inform Funders about Research Impact 68. Patient-Reported Outcome (PRO) Assessment in Clinical Trials: 53. Sugar Industry Influence on the Scientific Agenda of the National plosbiology.org/doi/pbio.1002003 33. PLOS Neglected Tropical Diseases: TDR Reflects on 40 Years Collection A Systematic Review of Guidance for Trial Protocol Writers 86. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Institute of Dental Research’s 1971 National Caries Program: A Historical ploscollections.org/tdr plosone.org/doi/pone.0110216 Evidence of Paternal Transmission in Humans Analysis of Internal Documents plosmedicine.org/doi/pmed.1001798 35 plosgenetics.org/doi/pgen.1005040 34. Shaping the Research Agenda plosntds.org/doi/pntd.0003350 54. Rationale for WHO's New Position Calling for Prompt Reporting and 69. Systematic Evaluation of the Patient-Reported Outcome (PRO) Content 87. Keeping in Shape the Dogma of Mitochondrial DNA Maternal 35. The Individualised versus the Public Health Approach to Treating Ebola Public Disclosure of Interventional Clinical Trial Results of Clinical Trial Protocols plosone.org/doi/pone.0110229 Inheritance plosgenetics.org/doi/pgen.1005179 plosmedicine.org/doi/pmed.1001858 plosmedicine.org/doi/pmed.1001819 70. PLOS Computational Biology: 10th Anniversary Collection 88. Approaches to Refining Estimates of Global Burden and Economics of 36. Commentary: Containing the Ebola Outbreak – the Potential and 55. From Intense Rejection to Advocacy: How Muslim Clerics Were ploscollections.org/ploscompbiol10years Dengue plosntds.org/doi/pntd.0003306 1. PLOS Computational Biology: Topic Pages Collection 18. The Influence of Partner-Specific Memory Associations on Picture Challenge of Mobile Network Data plos.io/1U2UniV Engaged in a Polio Eradication Initiative in Northern Nigeria 71. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation 89. Integrating Data and Resources on Neglected Tropical Diseases for ploscollections.org/topicpages Naming: A Failure to Replicate Horton (2007) plosmedicine.org/doi/pmed.1001687 37. Outbreak of Ebola Virus Disease in Guinea: Where Ecology Meets and Innovation ploscompbiol.org/doi/pcbi.1004317 Better Planning: The NTD Mapping Tool (NTDmap.org) plosone.org/doi/pone.0109035 2. Inferring Horizontal Gene Transfer ploscompbiol.org/doi/pcbi.1004095 Economy plosntds.org/doi/pntd.0003056 56. Screening and Treating UN Peacekeepers to Prevent the Introduction 72. Advancements and Challenges in Computational Biology plosntds.org/doi/pntd.0003400 19. A Quick Guide for Building a Successful Bioinformatics Community of Artemisinin-Resistant Malaria into Africa 3. Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and 38. Characterizing the Transmission Dynamics and Control of Ebola Virus ploscompbiol.org/doi/pcbi.1004053 90. Impact of Schistosoma mansoni on Malaria Transmission in ploscompbiol.org/doi/pcbi.1003972 plosmedicine.org/doi/pmed.1001822 Some Implications for Containment plosntds.org/doi/pntd.0003567 Disease plosbiology.org/doi/pbio.1002057 73. Computational Biology: Moving into the Future One Click at a Time Sub-Saharan Africa plosntds.org/doi/pntd.0003234 20. Why Most Published Research Findings Are False 57. A Global Biomedical R&D Fund and Mechanism for Innovations of 4. What Factors Might Have Led to the Emergence of Ebola in West 39. Insights into the Early Epidemic Spread of Ebola in Sierra Leone ploscompbiol.org/doi/pcbi.1004323 91. Geographic Expansion of the Invasive Mosquito Aedes albopictus across plosmedicine.org/doi/pmed.0020124 Public Health Importance plosmedicine.org/doi/pmed.1001831 Africa? plosntds.org/doi/pntd.0003652 Provided by Viral Sequence Data plos.io/1fBYvUn 74. Global Disease Monitoring and Forecasting with Wikipedia Panama—Implications for Control of Dengue and Chikungunya Viruses 21. PLOS Computational Biology: Ten Simple Rules Collection 58. PLOS ONE: The Missing Pieces: A Collection of Negative, Null and plosntds.org/doi/pntd.0003383 5. A Stronger Post-Publication Culture Is Needed for Better Science 40. Wave-Like Spread of Ebola Zaire plosbiology.org/doi/pbio.0030371 ploscompbiol.org/doi/pcbi.1003892 Inconclusive Results ploscollections.org/missingpieces plosmedicine.org/doi/pmed.1001772 plos.io/ZVqyyG 92. PLOS Neglected Tropical Diseases: 40 Years of the APOC Partnership 41. Inhibitor of the Tyrosine Phosphatase STEP Reverses Cognitive Deficits 75. SciClone: Inferring Clonal Architecture and Tracking the Spatial and 22. Ten Simple Rules for Approaching a New Job 59. Sliding Rocks on Racetrack Playa, Death Valley National Park: First Collection ploscollections.org/APOC 6. How to Make More Published Research True in a Mouse Model of Alzheimer's Disease Temporal Patterns of Tumor Evolution ploscompbiol.org/doi/pcbi.1003665 ploscompbiol.org/doi/pcbi.1003660 Observation of Rocks in Motion plosone.org/doi/pone.0105948 plosmedicine.org/doi/pmed.1001747 plosbiology.org/doi/pbio.1001923 76. Neural Modularity Helps Organisms Evolve to Learn New Skills without 93. Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus 23. Ten Simple Rules of Live Tweeting at Scientific Conferences 60. Foldscope: Origami-Based Paper Microscope Macaques after Autologous Hematopoietic Stem Cell Transplant 7. The Economics of Reproducibility in Preclinical Research 42. A Novel Phosphatase Inhibitor May Be a STEP Toward Ameliorating Forgetting Old Skills ploscompbiol.org/doi/pcbi.1004128 ploscompbiol.org/doi/pcbi.1003789 plosone.org/doi/pone.0098781 plospathogens.org/doi/ppat.1004406 plosbiology.org/doi/pbio.1002165 Cognitive Dysfunction plosbiology.org/doi/pbio.1001924 77. Spectral Signatures of Reorganised Brain Networks in Disorders of 24. Ten Simple Rules for Better Figures 61. Dendrogramma, New Genus, with Two New Non-Bilaterian Species 94. Chromobacterium Csp_P Reduces Malaria and Dengue Infection in 8. Exploring the Complex Pattern of Information Spreading in Online Blog 43. Beyond Bar and Line Graphs: Time for a New Data Presentation Consciousness ploscompbiol.org/doi/pcbi.1003887 ploscompbiol.org/doi/pcbi.1003833 from the Marine Bathyal of Southeastern Australia (Animalia, Vector Mosquitoes and Has Entomopathogenic and In Vitro Anti- Communities plosone.org/doi/pone.0126894 Paradigm plosbiology.org/doi/pbio.1002128 78. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Metazoa incertae sedis)—with Similarities to Some Medusoids from the pathogen Activities plospathogens.org/doi/ppat.1004398 25. Ten Simple Rules to Win a Nobel Prize Motif and Track Collections ploscompbiol.org/doi/pcbi.1003731 9. PLOS Biology: Public Engagement in Science Collection 44. PLOS: Reporting Guidelines Collection Precambrian Ediacara plosone.org/doi/pone.0102976 ploscompbiol.org/doi/pcbi.1004084 95. Role of Hypoxia Inducible Factor-1α (HIF-1α) in Innate Defense against ploscollections.org/publicengagement ploscollections.org/reportingguidelines 79. Web-Based Computational Chemistry Education with CHARMMing I: 62. A New Large-Bodied Oviraptorosaurian Theropod Dinosaur from the Uropathogenic Escherichia coli Infection 26. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration Lessons and Tutorial ploscompbiol.org/doi/pcbi.1003719 10. Committing to Place: The Potential of Open Collaborations for Trusted 45. New Developmental Evidence Clarifies the Evolution of Wrist Bones in Latest Cretaceous of Western North America plospathogens.org/doi/ppat.1004818 ploscompbiol.org/doi/pcbi.1004214 Environmental Governance plosbiology.org/doi/pbio.1002081 the Dinosaur–Bird Transition plosbiology.org/doi/pbio.1001957 80. PLOS Computational Biology: Education Collection plosone.org/doi/pone.0092022 96. Cryptococcus gattii VGIII Isolates Causing Infections in HIV/AIDS 27. Ten Simple (Empirical) Rules for Writing Science ploscollections.org/compbioleducation 11. The Transformative Nature of Transparency in Research Funding 46. Resolving the Flap over Bird Wrists plosbiology.org/doi/pbio.1001958 63. A Novel Reproductive Mode in Frogs: A New Species of Fanged Frog Patients in Southern California: Identification of the Local Environmental plosbiology.org/doi/pbio.1002027 ploscompbiol.org/doi/pcbi.1004205 47. Open Labware: 3-D Printing Your Own Lab Equipment with Internal Fertilization and Birth of Tadpoles 81. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Source as Arboreal plospathogens.org/doi/ppat.1004285 28. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health Proliferation and Growth at High Temperatures in Arabidopsis thaliana 12. Grant Application Review: The Case of Transparency plosbiology.org/doi/pbio.1002086 plosone.org/doi/pone.0115884 97. Shed GP of Ebola Virus Triggers Immune Activation and Increased plosbiology.org/doi/pbio.1002010 ploscollections.org/maternalhealth plosgenetics.org/doi/pgen.1005085 48. How Could Language Have Evolved? plosbiology.org/doi/pbio.1001934 64. A Unique Nest-Protection Strategy in a New Species of Spider Wasp Vascular Permeability plospathogens.org/doi/ppat.1004509 13. Redefining Genomic Privacy: Trust and Empowerment 29. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health plosone.org/doi/pone.0101592 82. Modeling 3D Facial Shape from DNA 49. Life in a World without Microbes plosbiology.org/doi/pbio.1002020 98. PLOS Pathogens: Pearls Collection ploscollections.org/pearls Year 3 (2013-14) - "Integrating Health Care to Meet the Needs of the plosgenetics.org/doi/pgen.1004224 plosbiology.org/doi/pbio.1001983 65. Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Mother–Infant Pair" plos.io/1hDc3Rn 50. Colour As a Signal for Entraining the Mammalian Circadian Clock 99. War and Infectious Diseases: Challenges of the Syrian Civil War 14. Introducing “Research Matters” plospathogens.org/doi/ppat.1005014 Pieces Weighing over 250,000 Tons Afloat at Sea 83. Let's Face It—Complex Traits Are Just Not That Simple plosbiology.org/doi/pbio.1002127 plospathogens.org/doi/ppat.1004438 30. PLOS Medicine: Monitoring Universal Health Coverage Collection plosone.org/doi/pone.0111913 plosgenetics.org/doi/pgen.1004724 15. The Curious Road from Basic Pathogen Research to Clinical Translation ploscollections.org/uhc2014 51. A Colourful Clock plosbiology.org/doi/pbio.1002160 100. The Skin Microbiome: A Focus on Pathogens and Their Association with 84. Regularized Machine Learning in the Genetic Prediction of Complex plospathogens.org/doi/ppat.1004997 66. Olfactory Dysfunction Predicts 5-Year Mortality in Older Adults Skin Disease plospathogens.org/doi/ppat.1004436 31. Monitoring Progress towards Universal Health Coverage at Country and 52. Ecacy and Safety of the RTS,S/AS01 Malaria Vaccine during 18 plosone.org/doi/pone.0107541 Traits plosgenetics.org/doi/pgen.1004754 16. From Cell and Organismal Biology to Drugs Global Levels plosmedicine.org/doi/pmed.1001731 Months after Vaccination: A Phase 3 Randomized, Controlled Trial in 101. Theory and Empiricism in Virulence Evolution plospathogens.org/doi/ppat.1005002 67. Whole-Genome Sequencing of the World’s Oldest People 85. 8.2% of the Human Genome Is Constrained: Variation in Rates of Children and Young Infants at 11 African Sites plospathogens.org/doi/ppat.1004387 32. The PLOS “Monitoring Universal Health Coverage” Collection: plosone.org/doi/pone.0112430 Turnover across Functional Element Classes in the Human Lineage 17. Alternative Perspectives on Impact: The Potential of ALMs and plosmedicine.org/doi/pmed.1001685 Managing Expectations plosmedicine.org/doi/pmed.1001732 plosgenetics.org/doi/pgen.1004525 Altmetrics to Inform Funders about Research Impact 68. Patient-Reported Outcome (PRO) Assessment in Clinical Trials: 53. Sugar Industry Influence on the Scientific Agenda of the National plosbiology.org/doi/pbio.1002003 33. PLOS Neglected Tropical Diseases: TDR Reflects on 40 Years Collection A Systematic Review of Guidance for Trial Protocol Writers 86. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Institute of Dental Research’s 1971 National Caries Program: A Historical ploscollections.org/tdr plosone.org/doi/pone.0110216 Evidence of Paternal Transmission in Humans Analysis of Internal Documents plosmedicine.org/doi/pmed.1001798 36 plosgenetics.org/doi/pgen.1005040 34. Shaping the Research Agenda plosntds.org/doi/pntd.0003350 54. Rationale for WHO's New Position Calling for Prompt Reporting and 69. Systematic Evaluation of the Patient-Reported Outcome (PRO) Content 87. Keeping in Shape the Dogma of Mitochondrial DNA Maternal plosone.org/doi/pone.0110229 35. The Individualised versus the Public Health Approach to Treating Ebola Public Disclosure of Interventional Clinical Trial Results of Clinical Trial Protocols Inheritance plosgenetics.org/doi/pgen.1005179 plosmedicine.org/doi/pmed.1001858 plosmedicine.org/doi/pmed.1001819 70. PLOS Computational Biology: 10th Anniversary Collection 88. Approaches to Refining Estimates of Global Burden and Economics of ploscollections.org/ploscompbiol10years 36. Commentary: Containing the Ebola Outbreak – the Potential and 55. From Intense Rejection to Advocacy: How Muslim Clerics Were Dengue plosntds.org/doi/pntd.0003306 1. PLOS Computational Biology: Topic Pages Collection 18. The Influence of Partner-Specific Memory Associations on Picture Challenge of Mobile Network Data plos.io/1U2UniV Engaged in a Polio Eradication Initiative in Northern Nigeria 71. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation 89. Integrating Data and Resources on Neglected Tropical Diseases for ploscollections.org/topicpages Naming: A Failure to Replicate Horton (2007) plosmedicine.org/doi/pmed.1001687 ploscompbiol.org/doi/pcbi.1004317 37. Outbreak of Ebola Virus Disease in Guinea: Where Ecology Meets and Innovation Better Planning: The NTD Mapping Tool (NTDmap.org) plosone.org/doi/pone.0109035 2. Inferring Horizontal Gene Transfer ploscompbiol.org/doi/pcbi.1004095 Economy plosntds.org/doi/pntd.0003056 56. Screening and Treating UN Peacekeepers to Prevent the Introduction 72. Advancements and Challenges in Computational Biology plosntds.org/doi/pntd.0003400 19. A Quick Guide for Building a Successful Bioinformatics Community of Artemisinin-Resistant Malaria into Africa ploscompbiol.org/doi/pcbi.1004053 3. Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and 38. Characterizing the Transmission Dynamics and Control of Ebola Virus 90. Impact of Schistosoma mansoni on Malaria Transmission in ploscompbiol.org/doi/pcbi.1003972 plosmedicine.org/doi/pmed.1001822 Some Implications for Containment plosntds.org/doi/pntd.0003567 Disease plosbiology.org/doi/pbio.1002057 73. Computational Biology: Moving into the Future One Click at a Time Sub-Saharan Africa plosntds.org/doi/pntd.0003234 20. Why Most Published Research Findings Are False 57. A Global Biomedical R&D Fund and Mechanism for Innovations of ploscompbiol.org/doi/pcbi.1004323 4. What Factors Might Have Led to the Emergence of Ebola in West 39. Insights into the Early Epidemic Spread of Ebola in Sierra Leone 91. Geographic Expansion of the Invasive Mosquito Aedes albopictus across plosmedicine.org/doi/pmed.0020124 Public Health Importance plosmedicine.org/doi/pmed.1001831 Africa? plosntds.org/doi/pntd.0003652 Provided by Viral Sequence Data plos.io/1fBYvUn 74. Global Disease Monitoring and Forecasting with Wikipedia Panama—Implications for Control of Dengue and Chikungunya Viruses 21. PLOS Computational Biology: Ten Simple Rules Collection 58. PLOS ONE: The Missing Pieces: A Collection of Negative, Null and ploscompbiol.org/doi/pcbi.1003892 plosntds.org/doi/pntd.0003383 5. A Stronger Post-Publication Culture Is Needed for Better Science 40. Wave-Like Spread of Ebola Zaire plosbiology.org/doi/pbio.0030371 Inconclusive Results ploscollections.org/missingpieces plosmedicine.org/doi/pmed.1001772 plos.io/ZVqyyG 92. PLOS Neglected Tropical Diseases: 40 Years of the APOC Partnership 41. Inhibitor of the Tyrosine Phosphatase STEP Reverses Cognitive Deficits 75. SciClone: Inferring Clonal Architecture and Tracking the Spatial and 22. Ten Simple Rules for Approaching a New Job 59. Sliding Rocks on Racetrack Playa, Death Valley National Park: First ploscompbiol.org/doi/pcbi.1003665 Collection ploscollections.org/APOC 6. How to Make More Published Research True in a Mouse Model of Alzheimer's Disease Temporal Patterns of Tumor Evolution ploscompbiol.org/doi/pcbi.1003660 Observation of Rocks in Motion plosone.org/doi/pone.0105948 plosmedicine.org/doi/pmed.1001747 plosbiology.org/doi/pbio.1001923 76. Neural Modularity Helps Organisms Evolve to Learn New Skills without 93. Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus 23. Ten Simple Rules of Live Tweeting at Scientific Conferences 60. Foldscope: Origami-Based Paper Microscope ploscompbiol.org/doi/pcbi.1004128 Macaques after Autologous Hematopoietic Stem Cell Transplant 7. The Economics of Reproducibility in Preclinical Research 42. A Novel Phosphatase Inhibitor May Be a STEP Toward Ameliorating Forgetting Old Skills ploscompbiol.org/doi/pcbi.1003789 plosone.org/doi/pone.0098781 plospathogens.org/doi/ppat.1004406 plosbiology.org/doi/pbio.1002165 Cognitive Dysfunction plosbiology.org/doi/pbio.1001924 77. Spectral Signatures of Reorganised Brain Networks in Disorders of 24. Ten Simple Rules for Better Figures 61. Dendrogramma, New Genus, with Two New Non-Bilaterian Species ploscompbiol.org/doi/pcbi.1003887 94. Chromobacterium Csp_P Reduces Malaria and Dengue Infection in 8. Exploring the Complex Pattern of Information Spreading in Online Blog 43. Beyond Bar and Line Graphs: Time for a New Data Presentation Consciousness ploscompbiol.org/doi/pcbi.1003833 from the Marine Bathyal of Southeastern Australia (Animalia, Vector Mosquitoes and Has Entomopathogenic and In Vitro Anti- Communities plosone.org/doi/pone.0126894 Paradigm plosbiology.org/doi/pbio.1002128 78. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Metazoa incertae sedis)—with Similarities to Some Medusoids from the pathogen Activities plospathogens.org/doi/ppat.1004398 25. Ten Simple Rules to Win a Nobel Prize Motif and Track Collections ploscompbiol.org/doi/pcbi.1003731 9. PLOS Biology: Public Engagement in Science Collection 44. PLOS: Reporting Guidelines Collection Precambrian Ediacara plosone.org/doi/pone.0102976 ploscompbiol.org/doi/pcbi.1004084 95. Role of Hypoxia Inducible Factor-1α (HIF-1α) in Innate Defense against ploscollections.org/publicengagement ploscollections.org/reportingguidelines 79. Web-Based Computational Chemistry Education with CHARMMing I: 62. A New Large-Bodied Oviraptorosaurian Theropod Dinosaur from the Uropathogenic Escherichia coli Infection 26. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration Lessons and Tutorial ploscompbiol.org/doi/pcbi.1003719 10. Committing to Place: The Potential of Open Collaborations for Trusted 45. New Developmental Evidence Clarifies the Evolution of Wrist Bones in Latest Cretaceous of Western North America plospathogens.org/doi/ppat.1004818 ploscompbiol.org/doi/pcbi.1004214 Environmental Governance plosbiology.org/doi/pbio.1002081 plosbiology.org/doi/pbio.1001957 80. PLOS Computational Biology: Education Collection the Dinosaur–Bird Transition plosone.org/doi/pone.0092022 96. Cryptococcus gattii VGIII Isolates Causing Infections in HIV/AIDS 27. Ten Simple (Empirical) Rules for Writing Science ploscollections.org/compbioleducation 11. The Transformative Nature of Transparency in Research Funding 46. Resolving the Flap over Bird Wrists plosbiology.org/doi/pbio.1001958 63. A Novel Reproductive Mode in Frogs: A New Species of Fanged Frog Patients in Southern California: Identification of the Local Environmental plosbiology.org/doi/pbio.1002027 ploscompbiol.org/doi/pcbi.1004205 47. Open Labware: 3-D Printing Your Own Lab Equipment with Internal Fertilization and Birth of Tadpoles 81. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Source as Arboreal plospathogens.org/doi/ppat.1004285 28. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health Proliferation and Growth at High Temperatures in Arabidopsis thaliana 12. Grant Application Review: The Case of Transparency plosbiology.org/doi/pbio.1002086 plosone.org/doi/pone.0115884 97. Shed GP of Ebola Virus Triggers Immune Activation and Increased plosbiology.org/doi/pbio.1002010 ploscollections.org/maternalhealth plosgenetics.org/doi/pgen.1005085 48. How Could Language Have Evolved? plosbiology.org/doi/pbio.1001934 64. A Unique Nest-Protection Strategy in a New Species of Spider Wasp Vascular Permeability plospathogens.org/doi/ppat.1004509 13. Redefining Genomic Privacy: Trust and Empowerment 29. Maternal Health Task Force (MHTF)-PLOS Collection on Maternal Health plosone.org/doi/pone.0101592 82. Modeling 3D Facial Shape from DNA 49. Life in a World without Microbes plosbiology.org/doi/pbio.1002020 98. PLOS Pathogens: Pearls Collection ploscollections.org/pearls Year 3 (2013-14) - "Integrating Health Care to Meet the Needs of the plosgenetics.org/doi/pgen.1004224 plosbiology.org/doi/pbio.1001983 65. Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Mother–Infant Pair" plos.io/1hDc3Rn 50. Colour As a Signal for Entraining the Mammalian Circadian Clock 99. War and Infectious Diseases: Challenges of the Syrian Civil War 14. Introducing “Research Matters” plospathogens.org/doi/ppat.1005014 Pieces Weighing over 250,000 Tons Afloat at Sea 83. Let's Face It—Complex Traits Are Just Not That Simple plosbiology.org/doi/pbio.1002127 plospathogens.org/doi/ppat.1004438 30. PLOS Medicine: Monitoring Universal Health Coverage Collection plosone.org/doi/pone.0111913 plosgenetics.org/doi/pgen.1004724 15. The Curious Road from Basic Pathogen Research to Clinical Translation ploscollections.org/uhc2014 51. A Colourful Clock plosbiology.org/doi/pbio.1002160 100. The Skin Microbiome: A Focus on Pathogens and Their Association with 84. Regularized Machine Learning in the Genetic Prediction of Complex plospathogens.org/doi/ppat.1004997 66. Olfactory Dysfunction Predicts 5-Year Mortality in Older Adults Skin Disease plospathogens.org/doi/ppat.1004436 31. Monitoring Progress towards Universal Health Coverage at Country and 52. Ecacy and Safety of the RTS,S/AS01 Malaria Vaccine during 18 plosone.org/doi/pone.0107541 Traits plosgenetics.org/doi/pgen.1004754 16. From Cell and Organismal Biology to Drugs Global Levels plosmedicine.org/doi/pmed.1001731 Months after Vaccination: A Phase 3 Randomized, Controlled Trial in 101. Theory and Empiricism in Virulence Evolution plospathogens.org/doi/ppat.1005002 67. Whole-Genome Sequencing of the World’s Oldest People 85. 8.2% of the Human Genome Is Constrained: Variation in Rates of Children and Young Infants at 11 African Sites plospathogens.org/doi/ppat.1004387 32. The PLOS “Monitoring Universal Health Coverage” Collection: plosone.org/doi/pone.0112430 Turnover across Functional Element Classes in the Human Lineage 17. Alternative Perspectives on Impact: The Potential of ALMs and plosmedicine.org/doi/pmed.1001685 Managing Expectations plosmedicine.org/doi/pmed.1001732 plosgenetics.org/doi/pgen.1004525 Altmetrics to Inform Funders about Research Impact 68. Patient-Reported Outcome (PRO) Assessment in Clinical Trials: 53. Sugar Industry Influence on the Scientific Agenda of the National plosbiology.org/doi/pbio.1002003 33. PLOS Neglected Tropical Diseases: TDR Reflects on 40 Years Collection A Systematic Review of Guidance for Trial Protocol Writers 86. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Institute of Dental Research’s 1971 National Caries Program: A Historical ploscollections.org/tdr plosone.org/doi/pone.0110216 Evidence of Paternal Transmission in Humans Analysis of Internal Documents plosmedicine.org/doi/pmed.1001798 37 plosgenetics.org/doi/pgen.1005040 Page 19: Liran Samuni. PLOS Biology. 2014. 12(9) Image Credits Don McCullough, Flickr.com Benjamin Blonder. PLOS Biology. 2014. (12)9

Cover: Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, et al. Page 20: David Pacey, Flickr.com PLOS Genetics. 2015. 11(3)

Mayer FL, Hube B, Wilson D. PLOS Pathogens. 2012. 8(3) Page 21: James Gathany, Center for Disease Control. LoggaWiggler, Pixabay.com Simon Davis/UK Department for International Development (DFID). PLOS Medicine. 2015. 12(1) Cecil Fox, Wikimedia Commons. PLOS Medicine Cancer Research Collection. 2015. 7(23) Page 22: Simpson SD, Harrison HB, Claereboudt MR, Planes S. PLOS ONE. 2014. DOI: J. Peter Etchells and Simon R. Turner. PLOS Genetics. 2012. 8(11) 10.1371/journal.pone.0107610

Page 2: Jeremiah Busch. PLOS Biology. 2013. 11(5) Page 23: Patrut A, von Reden KF, Danthu P, Leong Pock-Tsy JM, Patrut RT, Lowy DA. PLOS ONE. 2015. DOI: 10.1371/journal.pone.0121170 Page 3: Annelies te Selle. PLOS Computational Biology. 2015. 11(5) Hone DWE, Farke AA, Watabe M, Shigeru S, Tsogtbaatar K. PLOS ONE. 2014. DOI: 10.1371/journal.pone.0113306 Page 7: Damien Caillaud. PLOS Biology. 2010. 8(10) Sue-Ann Watson. PLOS ONE. 2015. DOI: 10.1371/journal.pone.0128405 de Souza W, Crepaldi PH, Teixeira DE, Benchimol M. PLOS Neglected Tropical Diseases. 2012. 6(8) Page 24: Kifayathullah Liakath-Ali. PLOS Collection: PLOS Computational Biology 10th Anniversary. 2015. 3(15) Page 8: Fifty most viewed PLOS articles published August 1, 2014–July 31, 2015. almreports.plos.org accessed September 1, 2015 Page 25: Daniel Rubenstein. PLOS. 2015

Page 9: Marco Todesco and Detlef Weigel. PLOS Genetics. 2014. 10(7) Srivas Chennu. PLOS. 2014. Ian Sane, Flickr.com. PLOS Biology. 2015. 13(3) Page 26: Yuan S, Li F, Meng Q, Zhao Y, Chen L, et al. PLOS Genetics. 2014. 11(5)

Page 10: LoggaWiggler. Pixabay.com Page 27: Dialynas G, Shrestha OK, Ponce JM, Zwerger M, Thiemann DA, et al. PLOS Genetics. 2015. 11(5) Page 11: Christian Schnettelker, Flickr.com. PLOS Medicine. 2015. 12(2) Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, et al. Page 12: Margaret McFall-Ngai. PLOS Biology. 2014. 12(2) PLOS Genetics. 2015. 11(3) Adrienne Roeder. PLOS Biology. 2010. 8(5) Furumizu C, Alvarez JP, Sakakibara K, Bowman JL. PLOS Genetics. 2015. 11(2)

Page 13: Lin Chen and Donghui Zhang. PLOS Neglected Tropical Diseases. 2013. 7(1) Page 28: James Gathany/CDC, Wikimedia Commons

Page 14: Jack Zalium, Flickr.com. Maternal Health Task Force (MHTF)-PLOS Page 29: Daniel G. Bausch and Lara Schwarz. PLOS Neglected Tropical Diseases. 2014. 8(7) Collection: Maternal Health; Year 3. 2013-2014. 1(24) Frederique Jacquerioz. PLOS Neglected Tropical Diseases. 2014. 8(7) PLOS. PLOS Collection: Monitoring Universal Health Coverage. 2014. 7(22) Page 30: Rodrigo J. Gonzalez. PLOS Pathogens. 2015. 11(1) Page 15: WHO/TDR/Andy Craggs. PLOS Collection: TDR Reflects on 40 Years of Research and Training in Tropical Diseases. 2015. 8(10) Page 31: Litvintseva AP, Brandt ME, Mody RK, Lockhart SR. PLOS Pathogens. 2015. 11(5)

Center for Disease Control Helen Springer-Frauenho. PLOS Pathogens. 2014. 10(10)

39 Skelly PJ, Da’dara AA, Li XH, Castro-Borges W, Wilson RA. PLOS Pathogens. 2014. Page 18: National Institute of Allergy and Infectious Diseases. PLOS Biology. 2015. 13(1) 10(8) References (continued)

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