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Ann M. McCartney

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McCartney AM, McGovern HT, De Foe A. Predictors of Psychedelic Experience: A Thematic Analysis. J Psychoactive Drugs 2023;55:411-419. [PMID: 36197103 DOI: 10.1080/02791072.2022.2129885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/20/2022] [Accepted: 08/19/2022] [Indexed: 10/10/2022]

Altemose N, Glennis A, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science 2022;376:eabl4178. [PMID: 35357911 PMCID: PMC9233505 DOI: 10.1126/science.abl4178] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]

Affiliation(s)

Nicolas Altemose Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
A. Glennis Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
Andrey V. Bzikadze Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
Pragya Sidhwani Department of Biochemistry, Stanford University, Stanford, CA, USA
Sasha A. Langley Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
Gina V. Caldas Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
Savannah J. Hoyt Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Lev Uralsky Sirius University of Science and Technology, Sochi, Russia Vavilov Institute of General Genetics, Moscow, Russia
Fedor D. Ryabov Moscow Polytechnic University, Moscow, Russia
Colin J. Shew Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
Michael E. G. Sauria Department of Biology, Johns Hopkins University, Baltimore, MD, USA
Matthew Borchers Stowers Institute for Medical Research, Kansas City, MO, USA
Ariel Gershman Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
Alla Mikheenko Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Valery A. Shepelev Vavilov Institute of General Genetics, Moscow, Russia
Tatiana Dvorkina Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Olga Kunyavskaya Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Mitchell R. Vollger Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
Arang Rhie Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Ann M. McCartney Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Mobin Asri UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Ryan Lorig-Roach UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Kishwar Shafin UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Sergey Aganezov Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Daniel Olson Department of Computer Science, University of Montana, Missoula, MT. USA
Leonardo Gomes de Lima Stowers Institute for Medical Research, Kansas City, MO, USA
Tamara Potapova Stowers Institute for Medical Research, Kansas City, MO, USA
Gabrielle A. Hartley Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Marina Haukness UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Peter Kerpedjiev Reservoir Genomics, Oakland, CA
Fedor Gusev Vavilov Institute of General Genetics, Moscow, Russia
Kristof Tigyi UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Shelise Brooks NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Alice Young NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sergey Nurk Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sergey Koren Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sofie R. Salama UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Benedict Paten UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
Evgeny I. Rogaev Sirius University of Science and Technology, Sochi, Russia Vavilov Institute of General Genetics, Moscow, Russia Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
Aaron Streets Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA Chan Zuckerberg Biohub, San Francisco, CA, USA
Gary H. Karpen Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Abby F. Dernburg Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
Beth A. Sullivan Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
Aaron F. Straight Department of Biochemistry, Stanford University, Stanford, CA, USA
Travis J. Wheeler Department of Computer Science, University of Montana, Missoula, MT. USA
Jennifer L. Gerton Stowers Institute for Medical Research, Kansas City, MO, USA University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA
Evan E. Eichler Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Adam M. Phillippy Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Winston Timp Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
Megan Y. Dennis Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
Rachel J. O'Neill Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Justin M. Zook Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
Michael C. Schatz Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Pavel A. Pevzner Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA
Mark Diekhans UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Charles H. Langley Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
Ivan A. Alexandrov Vavilov Institute of General Genetics, Moscow, Russia Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
Karen H. Miga UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA

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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022;376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 887] [Impact Index Per Article: 443.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]

Affiliation(s)

Sergey Nurk Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Sergey Koren Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Arang Rhie Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Mikko Rautiainen Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Andrey V. Bzikadze Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
Alla Mikheenko Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
Mitchell R. Vollger Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Nicolas Altemose Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
Lev Uralsky Sirius University of Science and Technology; Sochi, Russia Vavilov Institute of General Genetics; Moscow, Russia
Ariel Gershman Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
Sergey Aganezov Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Savannah J. Hoyt Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Mark Diekhans UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Glennis A. Logsdon Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Michael Alonge Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Stylianos E. Antonarakis University of Geneva Medical School; Geneva, Switzerland
Matthew Borchers Stowers Institute for Medical Research; Kansas City, MO, USA
Gerard G. Bouffard NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Shelise Y. Brooks NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Gina V. Caldas Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
Nae-Chyun Chen Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Haoyu Cheng Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA Department of Biomedical Informatics, Harvard Medical School; Boston, MA
Chen-Shan Chin DNAnexus; Mountain View, CA, USA
William Chow Wellcome Sanger Institute; Cambridge, UK
Leonardo G. de Lima Stowers Institute for Medical Research; Kansas City, MO, USA
Philip C. Dishuck Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Richard Durbin Wellcome Sanger Institute; Cambridge, UK Department of Genetics, University of Cambridge; Cambridge, UK
Tatiana Dvorkina Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
Ian T. Fiddes Inscripta; Boulder, CO, USA
Giulio Formenti Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Robert S. Fulton Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
Arkarachai Fungtammasan DNAnexus; Mountain View, CA, USA
Erik Garrison UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA University of Tennessee Health Science Center; Memphis, TN, USA
Patrick G.S. Grady Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Tina A. Graves-Lindsay McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
Ira M. Hall Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
Nancy F. Hansen Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Gabrielle A. Hartley Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Marina Haukness UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Kerstin Howe Wellcome Sanger Institute; Cambridge, UK
Michael W. Hunkapiller Pacific Biosciences; Menlo Park, CA, USA
Chirag Jain Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
Miten Jain UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Erich D. Jarvis Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Peter Kerpedjiev Reservoir Genomics LLC; Oakland, CA
Melanie Kirsche Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Mikhail Kolmogorov Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
Jonas Korlach Pacific Biosciences; Menlo Park, CA, USA
Milinn Kremitzki McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
Heng Li Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA Department of Biomedical Informatics, Harvard Medical School; Boston, MA
Valerie V. Maduro Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Tobias Marschall Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
Ann M. McCartney Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Jennifer McDaniel Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Danny E. Miller Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
James C. Mullikin NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Eugene W. Myers Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
Nathan D. Olson Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Benedict Paten UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Paul Peluso Pacific Biosciences; Menlo Park, CA, USA
Pavel A. Pevzner Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
David Porubsky Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Tamara Potapova Stowers Institute for Medical Research; Kansas City, MO, USA
Evgeny I. Rogaev Sirius University of Science and Technology; Sochi, Russia Vavilov Institute of General Genetics; Moscow, Russia Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
Jeffrey A. Rosenfeld Cancer Institute of New Jersey; New Brunswick, NJ, USA
Steven L. Salzberg Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Valerie A. Schneider National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
Fritz J. Sedlazeck Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
Kishwar Shafin UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Colin J. Shew Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Alaina Shumate Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Ying Sims Wellcome Sanger Institute; Cambridge, UK
Arian F. A. Smit Institute for Systems Biology; Seattle, WA, USA
Daniela C. Soto Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Ivan Sović Pacific Biosciences; Menlo Park, CA, USA Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
Jessica M. Storer Institute for Systems Biology; Seattle, WA, USA
Aaron Streets Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA Chan Zuckerberg Biohub; San Francisco, CA, USA
Beth A. Sullivan Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
Françoise Thibaud-Nissen National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
James Torrance Wellcome Sanger Institute; Cambridge, UK
Justin Wagner Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Brian P. Walenz Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Aaron Wenger Pacific Biosciences; Menlo Park, CA, USA
Jonathan M. D. Wood Wellcome Sanger Institute; Cambridge, UK
Chunlin Xiao National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
Stephanie M. Yan Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Alice C. Young NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Samantha Zarate Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Urvashi Surti Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
Rajiv C. McCoy Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Megan Y. Dennis Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Ivan A. Alexandrov Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia Vavilov Institute of General Genetics; Moscow, Russia Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
Jennifer L. Gerton Stowers Institute for Medical Research; Kansas City, MO, USA Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
Rachel J. O’Neill Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Winston Timp Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Justin M. Zook Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Michael C. Schatz Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Evan E. Eichler Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Karen H. Miga UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
Adam M. Phillippy Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA

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Sherkow JS, Barker KB, Braverman I, Cook-Deegan R, Durbin R, Easter CL, Goldstein MM, Hudson M, Kress WJ, Lewin HA, Mathews DJH, McCarthy C, McCartney AM, da Silva M, Torrance AW, Greely HT. Ethical, legal, and social issues in the Earth BioGenome Project. Proc Natl Acad Sci U S A 2022;119:e2115859119. [PMID: 35042809 PMCID: PMC8795529 DOI: 10.1073/pnas.2115859119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open

Affiliation(s)

Jacob S Sherkow College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law DK-2300 Copenhagen S, Denmark
Katharine B Barker Global Genome Initiative and Global Genome Biodiversity Network, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
Irus Braverman University at Buffalo School of Law, The State University of New York at Buffalo, Buffalo, NY 14260
Robert Cook-Deegan School for the Future of Innovation in Society and Consortium for Science, Policy & Outcomes, College of Global Futures, Arizona State University, Washington, DC 20006
Richard Durbin Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
Carla L Easter Education and Community Involvement Branch, National Human Genome Research Institute, Bethesda, MD 20892
Melissa M Goldstein Department of Health Policy and Management, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
Maui Hudson Te Kotahi Research Institute, University of Waikato, Hamilton 3216, New Zealand Genomics Aotearoa, University of Otago, Dunedin 9016, New Zealand
W John Kress The Arnold Arboretum, Harvard University, Jamaica Plain, MA 02130 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
Harris A Lewin Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616 Department of Population Health and Reproduction, University of California, Davis, CA 95616
Debra J H Mathews Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205 Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
Catherine McCarthy Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
Ann M McCartney Genome Informatics Section, National Human Genomics Research Institute, Bethesda, MD 20892
Manuela da Silva Fiocruz Covid-19 Biobank, Fundação Oswaldo Cruz, Rio de Janeiro 21041-361, Brazil
Andrew W Torrance School of Law, University of Kansas, Lawrence, KS 66045
Henry T Greely Center for Law and the Biosciences, Stanford Law School, Stanford University, Stanford, CA 94305 Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305

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McCartney AM, Hilario E, Choi S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D. An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome. Mol Ecol Resour 2021;21:2125-2144. [PMID: 33955186 PMCID: PMC8362059 DOI: 10.1111/1755-0998.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022]

Abstract

We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths but perhaps lower coverage constructed more contiguous, kmers and gene-complete assemblies than short read length input data with higher coverage. The final genome assembly was constructed into 14 pseudochromosomes using an initial flye long read assembly, a racon/medaka/pilon combined polishing strategy, salsa2 and allhic scaffolding, juicebox curation, and Macadamia linkage map validation. We highlighted the importance of developing assembly workflows based on the volume and read length of sequencing data and established a robust set of quality metrics for generating high-quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by Hi-C data and that assembly scaffolding was more successful when the underlying contig assembly was of higher accuracy. These findings provide insight into how quality assessment tools can be implemented throughout genome assembly pipelines to inform the de novo reconstruction of a high-quality genome assembly for nonmodel organisms.

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McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biol Evol 2020;11:2678-2690. [PMID: 31400206 PMCID: PMC6764479 DOI: 10.1093/gbe/evz163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open

Affiliation(s)

Ann M McCartney Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
Edel M Hyland Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Institute for Global Food Security, Queens University Belfast, United Kingdom
Paul Cormican Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland
Raymond J Moran Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
Andrew E Webb Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland
Kate D Lee Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,School of Biological Sciences, University of Auckland, New Zealand.,School of Fundamental Sciences, Massey University, New Zealand
Jessica Hernandez-Rodriguez Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
Javier Prado-Martinez Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
Christopher J Creevey Institute for Global Food Security, Queens University Belfast, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
Julie L Aspden School of Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
James O McInerney Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
Tomas Marques-Bonet Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.,NAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallés, Barcelona, Spain
Mary J O'Connell Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom

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Florescu DF, McCartney AM, Qiu F, Langnas AN, Botha J, Mercer DF, Grant W, Kalil AC. Staphylococcus aureus infections after liver transplantation. Infection 2011;40:263-9. [PMID: 22124952 DOI: 10.1007/s15010-011-0224-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 11/08/2011] [Indexed: 02/07/2023]