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1. FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

Author

Robert M Harris, Brown Ct, Jones A, Poten R, Melissa A. Haendel, Stephan C. Schürer, Jennie Larkin, Mary Shimoyama, Vivien Bonazzi, Susanna-Assunta Sansone, Amanda Charbonneau, Paul Avillach, Megan L. Wojciechowicz, Avi Ma'ayan, Linhua Wang, Kimberly Robasky, Jared L. Nedzel, Clarke Djb, Gamble M, Juergen Klenk, Denis Torre, Jason Williams, Daniel J. Cooper, de Miranda Azevedo R, Claris Castillo, Brian M. Schilder, Michel Dumontier, Moshe C. Silverstein, Zachary N Flamholz, Sherry L. Jenkins, Kathleen M. Jagodnik, Peter McQuilton, Stan Ahalt, and Ray Idaszak

Subjects
0303 health sciences, Guiding Principles, Computer science, Best practice, Interoperability, Findability, Rubric, 02 engineering and technology, Bookmarklet, World Wide Web, 03 medical and health sciences, Workflow, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Use case, 030304 developmental biology
Abstract

As more datasets, tools, workflows, APIs, and other digital resources are produced by the research community, it is becoming increasingly difficult to harmonize and organize these efforts for maximal synergistic integrated utilization. The Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge by making these digital resources follow common standards and best practices so that they can become more integrated and organized. Faced with the question of how to make digital resources more FAIR, it has become imperative to measure what it means to be FAIR. The diversity of resources, communities, and stakeholders have different goals and use cases and this makes assessment of FAIRness particularly challenging. To begin resolving this challenge, the FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual, semi- and fully-automated FAIR assessment capabilities. The FAIRshake toolkit contains a database that lists registered digital resources, with their associated metrics, rubrics, and assessments. The FAIRshake toolkit also has a browser extension and a bookmarklet that enables viewing and submitting assessments from any website. The FAIR assessment results are visualized as an insignia that can be viewed on the FAIRshake website, or embedded within hosting websites. Using FAIRshake, a variety of bioinformatics tools, datasets listed on dbGaP, APIs registered in SmartAPI, workflows in Dockstore, and other biomedical digital resources were manually and automatically assessed for FAIRness. In each case, the assessments revealed room for improvement, which prompted enhancements that significantly upgraded FAIRness scores of several digital resources.

Published
2019
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2. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Author

Melissa A. Haendel, Ray Idaszak, Robert M Harris, Peter McQuilton, Lily Wang, Mary Shimoyama, Kimberly Robasky, Zachary N Flamholz, Jason Williams, Stephan C. Schürer, Stanley C. Ahalt, Rudy Poten, Meredith Gamble, Kathleen M. Jagodnik, Sherry L. Jenkins, Megan L. Wojciechowicz, Avi Ma'ayan, Ricardo de Miranda Azevedo, Denis Torre, Vivien Bonazzi, Amanda Charbonneau, Paul Avillach, Claris Castillo, Jennie Larkin, Michel Dumontier, Brian M. Schilder, Daniel J. Cooper, C. Titus Brown, Daniel J.B. Clarke, Susanna-Assunta Sansone, Jared L. Nedzel, Alex Jones, Moshe C. Silverstein, Juergen Klenk, RS: FSE DACS IDS, and Institute of Data Science

Subjects
Histology, Guiding Principles, Computer science, Interoperability, MEDLINE, Biochemistry, Online Systems, Article, Pathology and Forensic Medicine, Insignia, World Wide Web, 03 medical and health sciences, 0302 clinical medicine, Research community, Digital resources, Humans, Molecular Biology, 030304 developmental biology, 0303 health sciences, Internet, Information Dissemination, Rubric, Cell Biology, Variety (cybernetics), Health Resources, Generic health relevance, Biochemistry and Cell Biology, 030217 neurology & neurosurgery, Biotechnology
Abstract

As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR assessments are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness.

Published
2019

3. Should biomedical research be like Airbnb?

Author

Vivien Bonazzi and Philip E. Bourne

Subjects
0301 basic medicine, Biomedical Research, Data management, Scientific Misconduct, Social Sciences, Cloud computing, Efficiency, 0302 clinical medicine, Learning and Memory, Sociology, Medicine and Health Sciences, Psychology, Biology (General), Social Change, Data Management, Scope (project management), General Neuroscience, Communication Barriers, Health services research, Software Development, Software Engineering, Social Communication, Research Assessment, Reproducibility, Professions, Social Networks, Perspective, Workforce, Engineering and Technology, The Internet, Health Services Research, Periodicals as Topic, General Agricultural and Biological Sciences, Network Analysis, Computer and Information Sciences, QH301-705.5, Biology, Trust, Research and Analysis Methods, General Biochemistry, Genetics and Molecular Biology, World Wide Web, 03 medical and health sciences, Human Learning, Technology Transfer, Research Support as Topic, Animals, Humans, Learning, Social media, Internet, General Immunology and Microbiology, business.industry, Information Dissemination, Software development, Cognitive Psychology, Biology and Life Sciences, Cloud Computing, Computing Methods, United States, Communications, Health Care, 030104 developmental biology, National Institutes of Health (U.S.), People and Places, Database Management Systems, Scientists, Cognitive Science, Population Groupings, business, Commons, Social Media, 030217 neurology & neurosurgery, Software, Program Evaluation, Neuroscience
Abstract

The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH) and elsewhere, as an example of the move towards platforms for research.

Published
2017

4. A framework for human microbiome research

Author

Rosamond Rhodes, Asif T. Chinwalla, Tessa Madden, Ashlee M. Earl, Maria C. Rivera, Candace N. Farmer, Jonathan M. Goldberg, Karthik Kota, Victor Felix, Nicholas B. King, Shibu Yooseph, Erica Sodergren, Monika Bihan, Martin J. Blaser, Dirk Gevers, Dan Knights, Pamela Sankar, Anup Mahurkar, Heather Huot Creasy, Veena Bhonagiri, Thomas M. Schmidt, Curtis Huttenhower, Mina Rho, Todd J. Treangen, Thomas J. Sharpton, I. Min A. Chen, Bo Liu, Sarah K. Highlander, Catherine C. Davis, Susan M. Huse, Richard A. Gibbs, Noam J. Davidovics, Patricio S. La Rosa, Carsten Russ, Wesley C. Warren, Richard K. Wilson, Patrick Minx, Jean E. McEwen, Alyxandria M. Schubert, Scott Anderson, Bonnie P. Youmans, Jamison McCorrison, Kathie A. Mihindukulasuriya, Vandita Joshi, Peter J. Mannon, Brandi L. Cantarel, Joseph F. Petrosino, Jack D. Sobel, Chandri Yandava, Sharvari Gujja, Janet K. Jansson, David J. Dooling, Daniel McDonald, Rob Knight, Granger G. Sutton, Gary C. Armitage, Larry J. Forney, Robert S. Fulton, Yuan Qing Wu, Jonathan Crabtree, Susan Kinder-Haake, Lu Wang, Liang Ye, Victor M. Markowitz, Narmada Shenoy, Elizabeth A. Lobos, Ruth M. Farrell, Tatiana A. Vishnivetskaya, Patrick S. G. Chain, Jacques Ravel, Katherine H. Huang, Sergey Koren, Yan Ding, Christina Giblin, Jason R. Miller, Michelle G. Giglio, Gina A. Simone, Chad Nusbaum, Lynn M. Schriml, Matthew C. Ross, Daniel D. Sommer, Sandra L. Lee, Theresa A. Hepburn, Michael Holder, Shaila Chhibba, Patrick D. Schloss, Omry Koren, Lan Zhang, Catrina Fronick, Richard R. Sharp, Diana Tabbaa, Yuzhen Ye, Dennis C. Friedrich, Christie Kovar, Owen White, A. Scott Durkin, Michael Feldgarden, Gary L. Andersen, Makedonka Mitreva, Todd Wylie, Nihar U. Sheth, Sheila Fisher, John Martin, Jose C. Clemente, Xiang Qin, James Versalovic, Dana A. Busam, Bruce W. Birren, Jeremy Zucker, Yu-Hui Rogers, Shannon Dugan, Kristine M. Wylie, Katherine P. Lemon, Floyd E. Dewhirst, Nicola Segata, Konstantinos Liolios, Anthony A. Fodor, Elizabeth L. Appelbaum, Ramana Madupu, W. Michael Dunne, Katherine S. Pollard, Leslie Foster, Olukemi O. Abolude, Yue Liu, Nikos C. Kyrpides, Christopher Wellington, Yanjiao Zhou, Lita M. Proctor, Tsegahiwot Belachew, Mircea Podar, Julia A. Segre, Holli A. Hamilton, Aye Wollam, Paul Spicer, Lei Chen, Sarah Young, Beltran Rodriguez-Mueller, Todd Z. DeSantis, Sean M. Sykes, Toby Bloom, Kelvin Li, Shane Canon, Catherine Jordan, Manolito Torralba, Brandi Herter, R. Dwayne Lunsford, Krishna Palaniappan, Jeroen Raes, Hongyu Gao, Barbara A. Methé, Kjersti Aagaard, Amy L. McGuire, Jonathan Friedman, Matthew D. Pearson, Jason Walker, Mary A. Cutting, Jonathan H. Badger, Diane E. Hoffmann, Tulin Ayvaz, Michael Fitzgerald, Brian J. Haas, Ravi Sanka, Doyle V. Ward, Kris A. Wetterstrand, Mark A. Watson, Christopher Smillie, Lucinda Fulton, Zhengyuan Wang, Lisa Begg, James R. White, Konstantinos Mavrommatis, Lucia Alvarado, Pamela McInnes, Emily L. Harris, Harindra Arachchi, Craig Pohl, Catherine A. Lozupone, Ruth E. Ley, Clinton Howarth, Yiming Zhu, Huaiyang Jiang, Gregory A. Buck, Carl C. Baker, Kimberley D. Delehaunty, Cristyn Kells, Katarzyna Wilczek-Boney, Kim C. Worley, Cesar Arze, J. Fah Sathirapongsasuti, Carolyn Deal, Sandra W. Clifton, Ken Chu, Rachel L. Erlich, Elaine R. Mardis, Cecil M. Lewis, Niall Lennon, Margaret Priest, Scott T. Kelley, Kymberlie Hallsworth-Pepin, Jane Peterson, Allison D. Griggs, Michelle O'Laughlin, Heidi H. Kong, Joshua Orvis, Maria Y. Giovanni, Sahar Abubucker, Dawn Ciulla, Sean Conlan, Chien Chi Lo, Antonio Gonzalez, Georgia Giannoukos, Jennifer R. Wortman, Paul Brooks, Jacques Izard, Chad Tomlinson, Donna M. Muzny, Shital M. Patel, Eric J. Alm, George M. Weinstock, Irene Newsham, Jeffrey G. Reid, Karoline Faust, Qiandong Zeng, Elena Deych, Nathalia Garcia, Mathangi Thiagarajan, James A. Katancik, Vivien Bonazzi, Robert C. Edgar, Christian J. Buhay, Indresh Singh, Johannes B. Goll, Ioanna Pagani, Vincent Magrini, Wendy A. Keitel, Emma Allen-Vercoe, Teena Mehta, Jeffery A. Schloss, William D. Shannon, Mihai Pop, Matthew B. Scholz, Valentina Di Francesco, Rebecca Truty, Karen E. Nelson, Kevin Riehle, Lora Lewis, Joseph L. Campbell, Laurie Zoloth, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Friedman, Jonathan, Smillie, Chris Scott, and Alm, Eric J.

Subjects
Adult, Male, Adolescent, Statistics as Topic, Population, Computational biology, Biology, Genome, Article, Young Adult, 03 medical and health sciences, Human health, 0302 clinical medicine, RNA, Ribosomal, 16S, Humans, Microbiome, education, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Bacteria, Human microbiome, Reference Standards, Metagenomics, 030220 oncology & carcinogenesis, Earth Microbiome Project, Metagenome, Female, Human Microbiome Project
Abstract

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Published
2012

5. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Author

Jed A. Fuhrman, Justin Kuczynski, Dawn Field, Renzo Kottmann, Jack A. Gilbert, Dan Knights, Lynn M. Schriml, Patrick D. Schloss, Linda A. Amaral-Zettler, Jeroen Raes, Ruth E. Ley, Mark J. Bailey, Jacques Ravel, Andreas Wilke, David A. Relman, Martin J. Blaser, Wolfgang Ludwig, Lindsay K. Newbold, Rob Knight, Josh D. Neufeld, Frederic D. Bushman, Pier Luigi Buttigieg, Peer Bork, Scott T. Kelley, Michelle I. Smith, Norman Morrison, Christopher I. Hunter, Rohini Sinha, Omry Koren, Catherine A. Lozupone, Christian L. Lauber, Diana R. Nemergut, Tanya Yatsunenko, George M. Weinstock, Patrick S. G. Chain, Sara Nakielny, Elizabeth K. Costello, Timothy F. Booth, Anjanette Johnston, Brian D. Muegge, Sarah K. Highlander, Christian Quast, Susanna Assunta-Sansone, Aymé Spor, Bruce W. Birren, Sujeevan Ratnasingham, Peter Sterk, Andrew S. Whiteley, Antonio Gonzalez, Owen White, Robert P. Guralnick, Pelin Yilmaz, Jeffrey I. Gordon, Emily S. Charlson, Doug Wendel, Dirk Gevers, Eamonn Maguire, Erica Sodergren, Ilene Karsch-Mizrachi, Joseph F. Petrosino, Elmar Pruesse, Folker Meyer, Andrew L. Kau, Jörg Peplies, Giriprakash Palanisamy, Richard A. Gibbs, Jerry Kennedy, Doyle V. Ward, Nikos C. Kyrpides, Karen E. Nelson, Wolfgang Hankeln, Manimozhiyan Arumugam, Philippe Rocca-Serra, Philip Hugenholtz, James M. Tiedje, Robert Larsen, Jesse Stombaugh, Rachel E. Gallery, Lita M. Proctor, Janet K. Jansson, Todd Z. DeSantis, Vivien Bonazzi, Anna Oliver, Laura K. Baumgartner, Robert Vaughan, James R. Cole, Joonhong Park, Frank Oliver Glöckner, Donna Lyons, Heather Huot-Creasy, Teresa M. Legg, Norman R. Pace, Noah Fierer, Jennifer R. Wortman, Barbara A. Methé, Inigo San Gil, Guy Cochrane, Peter Dawyndt, and Department of Bio-engineering Sciences

Subjects
Sequence analysis, Biomedical Engineering, Information Storage and Retrieval, Bioengineering, Computational biology, Environment, Biology, Applied Microbiology and Biotechnology, Marker gene, Article, DNA sequencing, chemistry.chemical_compound, Molecular marker, Databases, Genetic, Humans, Sequence (medicine), Genetics, Whole genome sequencing, Internet, fungi, Nucleic acid sequence, Genetic Variation, Genes, rRNA, Sequence Analysis, DNA, Checklist, mimimarks, chemistry, Metagenomics, Molecular Medicine, Programming Languages, Biomarkers, Software, Biotechnology
Abstract

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2011

6. The NIH Human Microbiome Project

Author

Valentina Di Francesco, Jean E. McEwen, Carl C. Baker, Jeffery A. Schloss, Samir Zakhari, Susan Garges, Bracie Watson, Tsegahiwot Belachew, Kris A. Wetterstrand, Matthew E. Portnoy, Michael H. Sayre, A. Roger Little, Beena Akolkar, Carolyn Deal, Lindsey Grandison, Jane Peterson, Michael Wright, Lisa Begg, Jag H. Khalsa, Pamela Starke-Reed, Rachelle Salomon, Jennifer S. Read, Hannah Peavy, Robert W. Karp, T. Kevin Howcroft, Christina Giblin, Chris Mullins, Cindy D. Davis, Pamela McInnes, Christopher Wellington, Lu Wang, R. Dwayne Lunsford, Melody Mills, Hagit David, Maria Y. Giovanni, Carol H. Pontzer, Vivien Bonazzi, Michael C. Humble, and Mark S. Guyer

Subjects
Resource, Knowledge management, National Health Programs, Biology, Bioinformatics, Human health, Resource (project management), RNA, Ribosomal, 16S, Genetics, Humans, Microbiome, Genetics (clinical), Skin, Mouth, Bacteria, NIH Roadmap, business.industry, Human microbiome, Sequence Analysis, DNA, United States, Gastrointestinal Tract, National Institutes of Health (U.S.), Metagenomics, Earth Microbiome Project, Vagina, Metagenome, Female, business, Human Microbiome Project
Abstract

The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites from each of at least 250 “normal” volunteers; (2) to determine whether there are associations between changes in the microbiome and health/disease by studying several different medical conditions; and (3) to provide both a standardized data resource and new technological approaches to enable such studies to be undertaken broadly in the scientific community. The ethical, legal, and social implications of such research are being systematically studied as well. The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome. The history and implementation of this new program are described here.

Published
2009

7. A preliminary comparison of the mouse and human genomes

Author

Cheryl A. Evans, Mark Yandell, Jian Wang, Hamilton O. Smith, George L. Gabor Miklos, Joseph H. Nadeau, Kendra Biddick, Granger G. Sutton, Arthur L. Delcher, Xiangqun H. Zheng, Ron Wides, Steven L. Salzberg, Jeffrey Hoover, Vivien Bonazzi, William H. Majoros, Mark Raymond Adams, Robert A. Holt, Fu Lu, Peter W. Li, Richard J. Mural, Eugene W. Myers, Aaron L. Halpern, Doug Rusch, and J. Craig Venter

Subjects
Comparative genomics, Genetics, Genome evolution, Cot analysis, Sequence assembly, Human genome, General Medicine, Computational biology, Biology, Genome, Synteny, Reference genome
Abstract

Accurate annotated assemblies of the mouse and human genomes enable a detailed comparison of the organization and evolution of the two genomes. We have completed several assemblies of both the mouse, with and without public data, and human genomes. Analysis of these assemblies suggests the mouse genome is about 10% smaller than the human genome primarily because of a difference in the content of repetitive DNA between the two genomes. More than 300,000 positions in these two genomes can be aligned with one another based on short segments of sequence similarity. These conserved segments significantly enhance the resolution of the resultant comparative maps and can be used to divide the genomes into regions of conserved-shared synteny. The genes found in such regions are highly conserved as is their relative order and orientation. Comparison of the human and mouse genome is expected to be key to deciphering the important biological information encoded in the mammalian genome. A prerequisite to comparing complex genomes such as those of mouse and human is the availability of annotated assemblies of both genomes that are comparable in quality and completeness. Since February 2001, we have assembled, annotated and delivered to our subscribers two versions of the human genome and two versions of the mouse genome. A third assembly of the human genome is being completed and will be delivered by fall of 2002. These annotated assemblies provide the starting materials for the genome-wide comparisons of the mouse and human reported here. We will begin with a description of the first Celera whole genome assembly of the mouse to provide a general basis of the quality and completeness of these data and then will report the results of a preliminary comparison between these two genomes.

Published
2002

8. The Celera Discovery SystemTM

Author

Marc Nodell, Anthony R. Kerlavage, Peter W. Li, Frank Mayberry, Jinghui Zhang, Vivien Bonazzi, Charles Lawrence, Richard J. Mural, Paul Thomas, Matteo di Tommaso, and Mark Yandell

Subjects
Transcription, Genetic, Sequence analysis, Information Storage and Retrieval, Sequence Homology, Sequence alignment, Biology, Genome, Article, Mice, Annotation, Search engine, Databases, Genetic, Computer Graphics, Genetics, Animals, Chromosomes, Human, Humans, RNA, Messenger, Hidden Markov model, Conserved Sequence, Internet, Information retrieval, Multiple sequence alignment, business.industry, Chromosome Mapping, Genetic Variation, Proteins, Markov Chains, ComputingMethodologies_PATTERNRECOGNITION, Mutation, The Internet, business, Sequence Alignment, Forecasting
Abstract

The Celera Discovery System™ (CDS) is a web-accessible research workbench for mining genomic and related biological information. Users have access to the human and mouse genome sequences with annotation presented in summary form in BioMolecule Reports for genes, transcripts and proteins. Over 40 additional databases are available, including sequence, mapping, mutation, genetic variation, mRNA expression, protein structure, motif and classification data. Data are accessible by browsing reports, through a variety of interactive graphical viewers, and by advanced query capability provided by the LION SRS™ search engine. A growing number of sequence analysis tools are available, including sequence similarity, pattern searching, multiple sequence alignment and Hidden Markov Model search. A user workspace keeps track of queries and analyses. CDS is widely used by the academic research community and requires a subscription for access. The system and academic pricing information are available at http://cds.celera.com.

Published
2002

9. More on the sequencing of the human genome

Author

J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, Lesley Kline, Shashi Koduru, Amy Love, Felecia Mann, David May, Steven McCawley, Tina McIntosh, Ivy McMullen, Mee Moy, Linda Moy, Brian Murphy, Keith Nelson, Cynthia Pfannkoch, Eric Pratts, Vinita Puri, Hina Qureshi, Matthew Reardon, Robert Rodriguez, Yu-Hui Rogers, Deanna Romblad, Bob Ruhfel, Richard Scott, Cynthia Sitter, Michelle Smallwood, Erin Stewart, Renee Strong, Ellen Suh, Reginald Thomas, Ni Ni Tint, Sukyee Tse, Claire Vech, Gary Wang, Jeremy Wetter, Sherita Williams, Monica Williams, Sandra Windsor, Emily Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, Karena Zaveri, Josep F. Abril, Roderic Guigó, Michael J. Campbell, Kimmen V. Sjolander, Brian Karlak, Anish Kejariwal, Huaiyu Mi, Betty Lazareva, Thomas Hatton, Apurva Narechania, Karen Diemer, Anushya Muruganujan, Nan Guo, Shinji Sato, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz, Brian Walenz, Shibu Yooseph, David Allen, Anand Basu, James Baxendale, Louis Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Yen-Hui Chiang, My Coyne, Carl Dahlke, Anne Deslattes Mays, Maria Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, Carl Fosler, Harold Gire, Stephen Glanowski, Kenneth Glasser, Anna Glodek, Mark Gorokhov, Ken Graham, Barry Gropman, Michael Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, Donald Jennings, Catherine Jordan, James Jordan, John Kasha, Leonid Kagan, Cheryl Kraft, Alexander Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel Ma, William Majoros, Joe McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, Ngoc Nguyen, Marc Nodell, Sue Pan, Jim Peck, Marshall Peterson, William Rowe, Robert Sanders, John Scott, Michael Simpson, Thomas Smith, Arlan Sprague, Timothy Stockwell, Russell Turner, Eli Venter, Mei Wang, Meiyuan Wen, David Wu, Mitchell Wu, Ashley Xia, Ali Zandieh, and Xiaohong Zhu

Subjects
Male, Cancer genome sequencing, Chromosomes, Artificial, Bacterial, Databases, Factual, Clinical Biochemistry, Genome, Gene Duplication, Databases, Genetic, Human Genome Project, Genetics, Multidisciplinary, Chromosome Mapping, Exons, Genomics, Genome project, Physical Chromosome Mapping, Phenotype, Genetic Techniques, Perspective, DNA, Intergenic, Female, Algorithms, Pseudogenes, Personal genomics, Genome evolution, Retroelements, Hybrid genome assembly, Biology, ENCODE, Polymorphism, Single Nucleotide, Evolution, Molecular, Sequence-tagged site, Species Specificity, Gene density, Consensus Sequence, Animals, Humans, Genome size, Repetitive Sequences, Nucleic Acid, Whole genome sequencing, Comparative genomics, Genome, Human, Biochemistry (medical), Computational Biology, Genetic Variation, Proteins, Sequence Analysis, DNA, Introns, Chromosome Banding, Genes, CpG Islands, Reference genome
Abstract

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Published
2003

10. Structure, function and diversity of the healthy human microbiome

Author

Catherine A. Lozupone, Paul Spicer, Margaret Priest, Todd J. Treangen, Niall J. Lennon, Thomas M. Schmidt, Sandra W. Clifton, Ken Chu, Vandita Joshi, Catherine C. Davis, Omry Koren, Yuanqing Wu, Christie Kovar, Jonathan Friedman, Matthew D. Pearson, Scott T. Kelley, Brandi L. Cantarel, Patrick S. G. Chain, Chad Nusbaum, Jonathan Crabtree, Lu Wang, Bonnie P. Youmans, James A. Katancik, George M. Weinstock, Granger G. Sutton, Lisa Begg, Candace N. Farmer, Victor Felix, Barbara A. Methé, Elena Deych, Martin J. Blaser, Amy L. McGuire, Pamela McInnes, Xiang Qin, James Versalovic, James R. White, Yan Ding, Christian J. Buhay, Jason R. Miller, Susan M. Huse, Wm. Michael Dunne, Vivien Bonazzi, Jeremy Zucker, Ioanna Pagani, Robert C. Edgar, Dana A. Busam, Gina A. Simone, Michael Feldgarden, Vincent Magrini, Richard A. Gibbs, Noam J. Davidovics, Indresh Singh, Lucinda Fulton, Lucia Alvarado, Rob Knight, Emma Allen-Vercoe, Teena Mehta, Patricio S. La Rosa, Carsten Russ, Joshua Orvis, Sahar Abubucker, Jacques Ravel, Richard R. Sharp, Dirk Gevers, Wesley C. Warren, Pamela Sankar, Chad Tomlinson, Donna M. Muzny, Jean E. McEwen, Nihar U. Sheth, Sheila Fisher, Katherine H. Huang, Dennis C. Friedrich, Gary C. Armitage, John Martin, Richard K. Wilson, Katarzyna Wilczek-Boney, Catrina Fronick, Patrick Minx, Rebecca Truty, William D. Shannon, Matthew B. Scholz, Kris A. Wetterstrand, Maria Y. Giovanni, Katherine P. Lemon, Floyd E. Dewhirst, Shaila Chhibba, Anthony A. Fodor, Lan Zhang, Patrick D. Schloss, Lynn M. Schriml, Doyle V. Ward, Diana Tabbaa, Jose C. Clemente, Larry J. Forney, Kimberley D. Delehaunty, Cesar Arze, Sharvari Gujja, Lita M. Proctor, Christopher Smillie, Elizabeth L. Appelbaum, Konstantinos Liolios, Chandri Yandava, David J. Dooling, Emily L. Harris, Katherine S. Pollard, Clinton Howarth, Tatiana A. Vishnivetskaya, Sarah Young, Huaiyang Jiang, Karoline Faust, Janet K. Jansson, Kymberlie Hallsworth-Pepin, Owen White, Thomas J. Sharpton, Yiming Zhu, Yanjiao Zhou, Julia A. Segre, Jason Walker, Heidi H. Kong, Toby Bloom, Mathangi Thiagarajan, Tulin Ayvaz, I. Min A. Chen, Bo Liu, Kim C. Worley, Jennifer R. Wortman, Susan Kinder Haake, Manolito Torralba, Makedonka Mitreva, Kjersti Aagaard, J. Fah Sathirapongsasuti, Carolyn Deal, Jeroen Raes, Olukemi O. Abolude, Yue Liu, Rachel L. Erlich, Gary L. Andersen, Nicola Segata, Christopher Wellington, Todd Wylie, Kristine M. Wylie, Tsegahiwot Belachew, Jonathan H. Badger, Mark A. Watson, Aye Wollam, Zhengyuan Wang, Michelle G. Giglio, Kelvin Li, Diane E. Hoffmann, Cristyn Kells, Daniel D. Sommer, Victor M. Markowitz, Chien Chi Lo, Karen E. Nelson, Brian J. Haas, Ruth M. Farrell, Craig Pohl, Harindra Arachchi, Nicholas B. King, Gregory A. Buck, Konstantinos Mavromatis, Qiandong Zeng, Krishna Palaniappan, Kathie A. Mihindukulasuriya, Dan Knights, Anup Mahurkar, Nathalia Garcia, Mary A. Cutting, Theresa A. Hepburn, Mina Rho, Catherine Jordan, Christina Giblin, Dawn Ciulla, Shital M. Patel, Eric J. Alm, Kevin Riehle, Irene Newsham, Sarah K. Highlander, Jamison McCorrison, Nikos C. Kyrpides, Mircea Podar, Beltran Rodriguez-Mueller, Lora Lewis, Robert S. Fulton, Yuzhen Ye, Joseph L. Campbell, Laurie Zoloth, R. Dwayne Lunsford, Ramana Madupu, A. Scott Durkin, Maria C. Rivera, Sergey Koren, Shibu Yooseph, Ruth E. Ley, Erica Sodergren, Cecil M. Lewis, Heather Huot Creasy, Joseph F. Petrosino, Jacques Izard, Jack D. Sobel, J. Paul Brooks, Jeffrey G. Reid, Antonio Gonzalez, Narmada Shenoy, Elizabeth A. Lobos, Georgia Giannoukos, Matthew C. Ross, Allison D. Griggs, Yu-Hui Rogers, Leslie Foster, Wendy A. Keitel, Lei Chen, Alyxandria M. Schubert, Scott Anderson, Peter J. Mannon, Shane Canon, Hongyu Gao, Mihai Pop, Holli A. Hamilton, Tessa Madden, Michelle Oglaughlin, Karthik Kota, Monika Bihan, Veena Bhonagiri, Michael Holder, Daniel McDonald, Liang Ye, Sandra L. Lee, Rosamond Rhodes, Asif T. Chinwalla, Ashlee M. Earl, Shannon Dugan, Sean Conlan, Johannes B. Goll, Jonathan M. Goldberg, Valentina Di Francesco, Curtis Huttenhower, Brandi Herter, Todd Z. DeSantis, Sean M. Sykes, Michael Fitzgerald, Elaine R. Mardis, Jane Peterson, Bruce W. Birren, Ravi Sanka, Carl C. Baker, Jeffery A. Schloss, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Alm, Eric J., Friedman, Jonathan, and Smillie, Christopher S.

Subjects
Adult, Male, Adolescent, Ecology (disciplines), Biology, Bioinformatics, 03 medical and health sciences, Young Adult, RNA, Ribosomal, 16S, Humans, Microbiome, Ecosystem, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Bacteria, 030306 microbiology, Gastrointestinal Microbiome, Human microbiome, Biodiversity, Phenotype, Evolutionary biology, Health, Earth Microbiome Project, Metagenome, Enterotype, Female, Oral Microbiome, Metagenomics, Metabolic Networks and Pathways, Human Microbiome Project
Abstract

Author Manuscript date: 2013 February 05., Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Published
2012

11. The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Author

Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R. Cole, Linda Amaral-Zettler, Jack A. Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce W. Birren, Martin J. Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth K. Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel E. Gallery, Richard A. Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth M. Glass, Antonio Gonzalez, Jeffrey I. Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian L. Lauber, Teresa Legg, Ruth E. Ley, Catherine A. Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara A. Methé, Folker Meyer, Sara Nakielny, Karen E. Nelson, Diana Nemergut, Josh D. Neufeld, Norman R. Pace, Giriprakash Palanisamy, Jörg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David A. Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James M. Tiedje, Doyle V. Ward, George M. Weinstock, Doug Wendel, Owen White, Andreas Wilke, Jennifer Wortmann, and Frank Oliver Glöckner

Subjects
Ecology, Bioinformatics, Earth & Environment, Data Standards, Genetics & Genomics, Microbiology, Biotechnology
Abstract

We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2010
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12. The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Author

Frank Oliver Glöckner, Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James Cole, Linda Amaral-Zettler, Jack Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce Birren, Martin Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel Gallery, Richard Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth Glass, Antonio Gonzalez, Jeffrey Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian Lauber, Teresa Legg, Ruth Ley, Catherine Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara Methé, Folker Meyer, Sara Nakielny, Karen Nelson, Diana Nemergut, Josh Neufeld, Norman Pace, Giriprakash Palanisamy, Jörg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James Tiedje, Doyle Ward, George Weinstock, Doug Wendel, Owen White, Andreas Wilke, and Jennifer Wortmann

Subjects
General Materials Science
Published
2010

13. The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Author

Folker Meyer, J.R. Wortman, Patrick D. Schloss, Jed A. Fuhrman, S. Highlander, James R. Cole, Dawn Field, Renzo Kottmann, Robert P. Guralnick, Linda A. Amaral-Zettler, W. Ludwig, Anjanette Johnston, L.K. Neubold, Teresa M. Legg, Lynn M. Schriml, Doug Wendel, Todd Z. DeSantis, Bruce W. Birren, Emily S. Charlson, Eamonn Maguire, George M. Weinstock, Norman R. Pace, Noah Fierer, I. San Gil, Doyle V. Ward, D.A. Relman, Wolfgang Hankeln, Rachel E. Gallery, Joonhong Park, Jane Peterson, Jerry Kennedy, D. Nemergut, S. Ratnasingham, Karen E. Nelson, Rohini Sinha, Laura K. Baumgartner, Aymé Spor, Peer Bork, Christopher I. Hunter, Ruth E. Ley, Frank Oliver Glöckner, Christian Quast, J.D. Neufeld, Christian L. Lauber, Patrick S. G. Chain, Jesse Stombaugh, Martin J. Blaser, Donna Lyons, Elizabeth K. Costello, Jeroen Raes, Heather Huot-Creasy, Giri Palanisamy, Justin Kuczynski, Vivien Bonazzi, Pier Luigi Buttigieg, Rob Knight, Scott T. Kelley, J. Jansson, Owen White, Richard A. Gibbs, Philippe Rocca-Serra, Ilene Karsch-Mizrachi, Antonio Gonzalez, Jacques Ravel, A. Whitely, Robert Larsen, Michelle G. Giglio, Nikos C. Kyrpides, Peter Sterk, Pelin Yilmaz, Jack A. Gilbert, Dan Knights, Philip Hugenholtz, Elmar Pruesse, Erica Sodergren, Manimozhiyan Arumugam, S. Nakieny, Catherine A. Lozupone, Lita M. Proctor, Anna Oliver, J. Peplies, Robert Vaughan, Barbara Methé, Dirk Gevers, James M. Tiedje, Frederic D. Bushman, J. Petrosino, J.I. Gordon, Norman Morrison, Susanna Assunta-Sansone, A. Wikle, Omry Koren, Guy Cochrane, and Peter Dawyndt

Subjects
Genetic diversity, Ecology, Tree of life, Biosphere, Computational biology, Biology, Data science, DNA sequencing, Data sequences, Biology and Microbiology, Data and Information, General Materials Science, Gene, Sequence (medicine)
Abstract

We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2010

14. The NIH Big Data to Knowledge (BD2K) initiative

Author

Michelle Dunn, Vivien Bonazzi, Philip E. Bourne, Mark S. Guyer, Beth Russell, George A. Komatsoulis, Eric D. Green, and Jennie Larkin

Subjects
business.industry, Statement (logic), media_common.quotation_subject, education, Big data, Library science, Health Informatics, Context (language use), Data science, Excellence, Common fund, Medicine, business, Brief Communications on Big Data, health care economics and organizations, media_common
Abstract

Understanding the human condition is a Big Data problem. This statement is nicely illustrated by the articles that follow from seven of the Centers for Data Excellence that have been funded by the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. BD2K is a trans-NIH program, funded by all Institutes and Centers at NIH as well as the NIH Common Fund; it is overseen by the NIH Office of Data Science within the NIH Office of the Director. The beginnings of BD2K have been described previously,1 and the purpose here is to provide an overall context, from …

Published
2015

15. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Author

Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien Bonazzi, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi, Chain, Patrick S.G., Charlson, Emily, Costello, Elizabeth K., Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A., Gallery, Rachel E., Gevers, Dirk, Gibbs, Richard A., Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I., Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L., Kelley, Scott T., Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L., Legg, Teresa, Ley, Ruth E., Lozupone, Catherine A., Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A., Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E., Nemergut, Diana, Neufeld, Josh D., Newbold, Lindsay K., Oliver, Anna E., Pace, Norman R., Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A., Assunta-Sansone, Susanna, Schloss, Patrick D., Schriml, Lynn, Sinha, Rohini, Smith, Michelle I., Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M., Ward, Doyle V., Weinstock, George M., Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R., Yatsunenko, Tanya, Glöckner, Frank Oliver, Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien Bonazzi, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi, Chain, Patrick S.G., Charlson, Emily, Costello, Elizabeth K., Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A., Gallery, Rachel E., Gevers, Dirk, Gibbs, Richard A., Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I., Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L., Kelley, Scott T., Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L., Legg, Teresa, Ley, Ruth E., Lozupone, Catherine A., Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A., Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E., Nemergut, Diana, Neufeld, Josh D., Newbold, Lindsay K., Oliver, Anna E., Pace, Norman R., Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A., Assunta-Sansone, Susanna, Schloss, Patrick D., Schriml, Lynn, Sinha, Rohini, Smith, Michelle I., Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M., Ward, Doyle V., Weinstock, George M., Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R., Yatsunenko, Tanya, and Glöckner, Frank Oliver

Abstract

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2011

16. A Framework for Human Microbiome Research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Vivien Bonazzi, J., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Deych, Elena, Dooling, David J., Dugan, Shannon P., Farmer, Candace N., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huse, Susan M., Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, R. Dwayne, Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Pamela Sankar, J., Sathirapongsasuti, Fah, Schloss, Jeffery A., Schloss, Patrick D., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., White, Owen, Huttenhower, Curtis, FitzGerald, Michael G., Martin, John C., Young, Sarah K., Anderson, Scott, Chu, Ken, Dewhirst, Floyd Everett, Ding, Yan, Dunne, Wm. Michael, Durkin, A. Scott, Edgar, Robert C., Erlich, Rachel L., Farrell, Ruth M., Goldberg, Jonathan M., Harris, Emily L., Huang, Katherine H., Izard, Jacques Georges, Knights, Dan, Lee, Sandra L., Lemon, Katherine Paige, Lennon, Niall, Liu, Bo, Liu, Yue, McDonald, Daniel, Miller, Jason R., Pearson, Matthew, Schmidt, Thomas M., Smillie, Chris Scott, Sykes, Sean M., Wang, Lu, White, James R., Ye, Liang, Zhang, Lan, Zucker, Jeremy Daniel Hofeld, and Wilson, Richard K.

Abstract

A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

Published
2012
Full Text
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