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Jenkins TP, Lopez Carranza N, Bray A, Beguir K, Laustsen AH. Can hackathons unlock a new talent pool from the developing world? Nat Biotechnol 2022; 40:1297-1298. [PMID: 35945432 DOI: 10.1038/s41587-022-01415-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
| | | | - Amy Bray
- Zindi Africa, Cape Town, South Africa
| | | | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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2
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Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. mSystems 2022; 7:e0146821. [PMID: 35258340 PMCID: PMC9052204 DOI: 10.1128/msystems.01468-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that are deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regard to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called "dark matter" is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to 40 distinct studies, comprising 963 samples, and covering 10 different human microbiomes including fecal, oral, lung, skin, and circulatory system microbiomes. We found that while the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. A rate of taxonomic characterization of 1.64% of unknown sequences being characterized per month was calculated from these taxonomically unknown sequences discovered in this study. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing. Our approach led to the discovery of several novel viral genomes that bear no similarity to sequences in the public databases. Some of these are widespread as they have been found in different microbiomes and studies. Hence, our study illustrates how the systematic characterization of unknown sequences can help the discovery of novel microbes, and we call on the research community to systematically collate and share the unknown sequences from metagenomic studies to increase the rate at which the unknown sequence space can be classified.
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Pickett BE, Connor R, Berhanu-Denka T, Bhalla S, Brover V, Chambers MJ, Chaudhary K, Cissé OH, Dillman A, Elmassry MM, Feldgarden M, Holloway E, Huang X, Klimke W, Inês Mendes C, Norred SE, Parkinson J, Sevilla S, Garcia Solache M, Surujon D, Torian U, Zalunin V, Busby B. Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence. F1000Res 2022. [DOI: 10.12688/f1000research.26452.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Virulence is a complex mix of microbial traits and host susceptibility that could ultimately lead to disease. The increased prevalence of multidrug resistant infections complicates treatment options, augmenting the need for developing robust computational methods and pipelines that enable researchers and clinicians to rapidly identify the underlying mechanism(s) of virulence in any given sample/isolate. Consequently, the National Center for Biotechnology and Information at the National Institutes of Health hosted an in-person hackathon in Bethesda, Maryland during July 2019 to assist with developing cloud-based methods to reduce reliance on local computational infrastructure. Groups of attendees were assigned tasks that are relevant to identifying relevant tools, constructing pipelines capable of identifying microbial virulence factors, and managing the associated data and metadata. Specifically, the assigned tasks consisted of the following: data indexing, metabolic functions, virulence factors, antimicrobial resistance, mobile elements in enterococci, and metatranscriptomics. The cloud-based framework established by this hackathon can be augmented and built upon by the research community to aid in the rapid identification of microbial virulence factors.
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Bonny P, Schaeffer J, Besnard A, Desdouits M, Ngang JJE, Le Guyader FS. Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams. Front Microbiol 2021; 12:770385. [PMID: 34917052 PMCID: PMC8669915 DOI: 10.3389/fmicb.2021.770385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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Affiliation(s)
- Patrice Bonny
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France.,Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon.,Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Marion Desdouits
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
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Braune K, Rojas PD, Hofferbert J, Valera Sosa A, Lebedev A, Balzer F, Thun S, Lieber S, Kirchberger V, Poncette AS. Interdisciplinary Online Hackathons as an Approach to Combat the COVID-19 Pandemic: Case Study. J Med Internet Res 2021; 23:e25283. [PMID: 33497350 PMCID: PMC7872325 DOI: 10.2196/25283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/02/2021] [Accepted: 01/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background The COVID-19 outbreak has affected the lives of millions of people by causing a dramatic impact on many health care systems and the global economy. This devastating pandemic has brought together communities across the globe to work on this issue in an unprecedented manner. Objective This case study describes the steps and methods employed in the conduction of a remote online health hackathon centered on challenges posed by the COVID-19 pandemic. It aims to deliver a clear implementation road map for other organizations to follow. Methods This 4-day hackathon was conducted in April 2020, based on six COVID-19–related challenges defined by frontline clinicians and researchers from various disciplines. An online survey was structured to assess: (1) individual experience satisfaction, (2) level of interprofessional skills exchange, (3) maturity of the projects realized, and (4) overall quality of the event. At the end of the event, participants were invited to take part in an online survey with 17 (+5 optional) items, including multiple-choice and open-ended questions that assessed their experience regarding the remote nature of the event and their individual project, interprofessional skills exchange, and their confidence in working on a digital health project before and after the hackathon. Mentors, who guided the participants through the event, also provided feedback to the organizers through an online survey. Results A total of 48 participants and 52 mentors based in 8 different countries participated and developed 14 projects. A total of 75 mentorship video sessions were held. Participants reported increased confidence in starting a digital health venture or a research project after successfully participating in the hackathon, and stated that they were likely to continue working on their projects. Of the participants who provided feedback, 60% (n=18) would not have started their project without this particular hackathon and indicated that the hackathon encouraged and enabled them to progress faster, for example, by building interdisciplinary teams, gaining new insights and feedback provided by their mentors, and creating a functional prototype. Conclusions This study provides insights into how online hackathons can contribute to solving the challenges and effects of a pandemic in several regions of the world. The online format fosters team diversity, increases cross-regional collaboration, and can be executed much faster and at lower costs compared to in-person events. Results on preparation, organization, and evaluation of this online hackathon are useful for other institutions and initiatives that are willing to introduce similar event formats in the fight against COVID-19.
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Affiliation(s)
- Katarina Braune
- Department of Paediatric Endocrinology and Diabetes, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Hacking Health Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | | | | | - Alvaro Valera Sosa
- Hacking Health Berlin, Berlin, Germany.,CityLAB Berlin, Building Health Lab, Berlin, Germany.,Department of Design and Typologies, Technische Universität Berlin, Berlin, Germany
| | | | - Felix Balzer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Anesthesiology and Intensive Care Medicine, Berlin, Germany.,Einstein Center Digital Future, Berlin, Germany
| | | | - Sascha Lieber
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Anesthesiology and Intensive Care Medicine, Berlin, Germany.,Executive Board, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Valerie Kirchberger
- Executive Board, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Akira-Sebastian Poncette
- Hacking Health Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Anesthesiology and Intensive Care Medicine, Berlin, Germany.,Einstein Center Digital Future, Berlin, Germany
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6
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Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, Canese K, Comeau DC, Funk K, Kim S, Klimke W, Marchler-Bauer A, Landrum M, Lathrop S, Lu Z, Madden TL, O’Leary N, Phan L, Rangwala SH, Schneider VA, Skripchenko Y, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2021; 49:D10-D17. [PMID: 33095870 PMCID: PMC7778943 DOI: 10.1093/nar/gkaa892] [Citation(s) in RCA: 410] [Impact Index Per Article: 136.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/25/2020] [Accepted: 10/08/2020] [Indexed: 11/14/2022] Open
Abstract
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 34 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface and NCBI datasets. Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.
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Affiliation(s)
- Eric W Sayers
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jeffrey Beck
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Devon Bourexis
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - James R Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kathi Canese
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Donald C Comeau
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kathryn Funk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Melissa Landrum
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stacy Lathrop
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Thomas L Madden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Nuala O’Leary
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lon Phan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yuri Skripchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jian Ye
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Barton W Trawick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
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7
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Martí-Carreras J, Gener AR, Miller SD, Brito AF, Camacho CE, Connor R, Deboutte W, Glickman C, Kristensen DM, Meyer WK, Modha S, Norris AL, Saha S, Belford AK, Biederstedt E, Brister JR, Buchmann JP, Cooley NP, Edwards RA, Javkar K, Muchow M, Muralidharan HS, Pepe-Ranney C, Shah N, Shakya M, Tisza MJ, Tully BJ, Vanmechelen B, Virta VC, Weissman JL, Zalunin V, Efremov A, Busby B. NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. Viruses 2020; 12:v12121424. [PMID: 33322070 PMCID: PMC7764237 DOI: 10.3390/v12121424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 02/05/2023] Open
Abstract
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
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Affiliation(s)
- Joan Martí-Carreras
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Alejandro Rafael Gener
- Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA
- Margaret M. and Albert B. Alkek Department of Medicine, Nephrology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
- School of Medicine, Universidad Central del Caribe, Bayamón, PR 00960, USA
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Sierra D. Miller
- Genetics & Molecular Biology, Millersville University, 40 Dilworth Rd, Millersville, PA 17551, USA;
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health (YSPH), 60 College Street, New Haven, CT 06510, USA;
| | - Christiam E. Camacho
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Ryan Connor
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Ward Deboutte
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - Cody Glickman
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - David M. Kristensen
- Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA;
| | - Wynn K. Meyer
- AAAS Science and Technology Policy Fellow, Office of Data Science Strategy, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, 31 Center Dr., Bethesda, MD 20894, USA;
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Alexis L. Norris
- Biotechnology Graduate Program, University of Maryland Global Campus, 1616 McCormick Drive, Largo, MD 20774, USA;
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14850, USA;
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Anna K. Belford
- Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA; (A.K.B.); (M.J.T.)
| | - Evan Biederstedt
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - James Rodney Brister
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Jan P. Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia;
| | - Nicholas P. Cooley
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - Robert A. Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia;
| | - Kiran Javkar
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20740, USA
| | - Michael Muchow
- Novel Microdevices, Nucleic Acids, Baltimore, MD 21202, USA;
| | - Harihara Subrahmaniam Muralidharan
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
- Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20740, USA
| | | | - Nidhi Shah
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
| | - Migun Shakya
- Bioscience Division, Bikini Atoll Road, Los Alamos National Laboratory, Los Alamos, NM 87545, USA;
| | - Michael J. Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA; (A.K.B.); (M.J.T.)
| | - Benjamin J. Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA;
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - Valerie C. Virta
- AAAS Science & Technology Policy Fellow, National Institutes of Health, Center for Information Technology, 6555 Rock Spring Drive, Bethesda, MD 20817, USA;
| | - JL Weissman
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA 90089, USA;
| | - Vadim Zalunin
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Alexandre Efremov
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Ben Busby
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
- DNANexus, 1975 W El Camino Real #204, Mountain View, CA 94040, USA
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
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