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169 results for Phillippy,+Adam+M.

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ArticlesPeer ReviewedFull Text
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Author / Creator:Rhie, Arang ; Walenz, Brian P. ; Koren, Sergey ; Phillippy, Adam M.
Publisher:England: BioMed Central
Journal title:Genome Biology, 2020-09, Vol.21 (1), p.245-245, Article 245
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ArticlesPeer ReviewedFull Text
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Author / Creator:Jain, Chirag ; Rodriguez-R, Luis M ; Phillippy, Adam M ; Konstantinidis, Konstantinos T ; Aluru, Srinivas
Publisher:London: Nature Publishing Group
Journal title:Nature communications, 2018-11, Vol.9 (1), p.1-8
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ArticlesPeer ReviewedFull Text
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Author / Creator:Treangen, Todd J ; Ondov, Brian D ; Koren, Sergey ; Phillippy, Adam M
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2014-11, Vol.15 (11), p.524-524, Article 524
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ArticlesPeer ReviewedFull Text
MUMmer4: A fast and versatile genome alignment system
Author / Creator:Marçais, Guillaume ; Delcher, Arthur L. ; Phillippy, Adam M. ; Coston, Rachel ; Salzberg, Steven L. ; Zimin, Aleksey
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2018-01, Vol.14 (1), p.e1005944
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ArticlesPeer ReviewedFull Text
Long-read mapping to repetitive reference sequences using Winnowmap2
Author / Creator:Jain, Chirag ; Rhie, Arang ; Hansen, Nancy F. ; Koren, Sergey ; Phillippy, Adam M.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2022-06, Vol.19 (6), p.705-710
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ArticlesPeer ReviewedFull Text
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Author / Creator:Dilthey, Alexander T. ; Jain, Chirag ; Koren, Sergey ; Phillippy, Adam M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-07, Vol.10 (1), p.3066-12, Article 3066
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ArticlesPeer ReviewedFull Text
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Author / Creator:Ghurye, Jay ; Rhie, Arang ; Walenz, Brian P. ; Schmitt, Anthony ; Selvaraj, Siddarth ; Pop, Mihai ; Phillippy, Adam M. ; Koren, Sergey
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-08, Vol.15 (8), p.e1007273
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ArticlesPeer ReviewedFull Text
Interactive metagenomic visualization in a Web browser
Author / Creator:Ondov, Brian D ; Bergman, Nicholas H ; Phillippy, Adam M
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2011-09, Vol.12 (1), p.385-385, Article 385
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ArticlesPeer ReviewedFull Text
Mash Screen: high-throughput sequence containment estimation for genome discovery
Author / Creator:Ondov, Brian D. ; Starrett, Gabriel J. ; Sappington, Anna ; Kostic, Aleksandra ; Koren, Sergey ; Buck, Christopher B. ; Phillippy, Adam M.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2019-11, Vol.20 (1), p.232-232, Article 232
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ArticlesPeer ReviewedFull Text
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Author / Creator:Koren, Sergey ; Schatz, Michael C ; Walenz, Brian P ; Martin, Jeffrey ; Howard, Jason T ; Ganapathy, Ganeshkumar ; Wang, Zhong ; Rasko, David A ; McCombie, W Richard ; Jarvis, Erich D ; Phillippy, Adam M
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2012-07, Vol.30 (7), p.693-700
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ArticlesPeer ReviewedFull Text
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Author / Creator:Nasko, Daniel J. ; Koren, Sergey ; Phillippy, Adam M. ; Treangen, Todd J.
Publisher:England: BioMed Central
Journal title:Genome Biology, 2018-10, Vol.19 (1), p.165-165, Article 165
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ArticlesPeer ReviewedFull Text
The structure, function and evolution of a complete human chromosome 8
Author / Creator:Logsdon, Glennis A. ; Vollger, Mitchell R. ; Hsieh, PingHsun ; Mao, Yafei ; Liskovykh, Mikhail A. ; Koren, Sergey ; Nurk, Sergey ; Mercuri, Ludovica ; Dishuck, Philip C. ; Rhie, Arang ; de Lima, Leonardo G. ; Dvorkina, Tatiana ; Porubsky, David ; Harvey, William T. ; Mikheenko, Alla ; Bzikadze, Andrey V. ; Kremitzki, Milinn ; Graves-Lindsay, Tina A. ; Jain, Chirag ; Hoekzema, Kendra ; Murali, Shwetha C. ; Munson, Katherine M. ; Baker, Carl ; Sorensen, Melanie ; Lewis, Alexandra M. ; Surti, Urvashi ; Gerton, Jennifer L. ; Larionov, Vladimir ; Ventura, Mario ; Miga, Karen H. ; Phillippy, Adam M. ; Eichler, Evan E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2021-05, Vol.593 (7857), p.101-107
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ArticlesPeer ReviewedFull Text
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
Author / Creator:Kronenberg, Zev N. ; Rhie, Arang ; Koren, Sergey ; Concepcion, Gregory T. ; Peluso, Paul ; Munson, Katherine M. ; Porubsky, David ; Kuhn, Kristen ; Mueller, Kathryn A. ; Low, Wai Yee ; Hiendleder, Stefan ; Fedrigo, Olivier ; Liachko, Ivan ; Hall, Richard J. ; Phillippy, Adam M. ; Eichler, Evan E. ; Williams, John L. ; Smith, Timothy P. L. ; Jarvis, Erich D. ; Sullivan, Shawn T. ; Kingan, Sarah B.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-04, Vol.12 (1), p.1935-10, Article 1935
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ArticlesPeer ReviewedFull Text
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
Author / Creator:Liu, Zhanjiang ; Liu, Shikai ; Yao, Jun ; Bao, Lisui ; Zhang, Jiaren ; Li, Yun ; Jiang, Chen ; Sun, Luyang ; Wang, Ruijia ; Zhang, Yu ; Zhou, Tao ; Zeng, Qifan ; Fu, Qiang ; Gao, Sen ; Li, Ning ; Koren, Sergey ; Jiang, Yanliang ; Zimin, Aleksey ; Xu, Peng ; Phillippy, Adam M. ; Geng, Xin ; Song, Lin ; Sun, Fanyue ; Li, Chao ; Wang, Xiaozhu ; Chen, Ailu ; Jin, Yulin ; Yuan, Zihao ; Yang, Yujia ; Tan, Suxu ; Peatman, Eric ; Lu, Jianguo ; Qin, Zhenkui ; Dunham, Rex ; Li, Zhaoxia ; Sonstegard, Tad ; Feng, Jianbin ; Danzmann, Roy G. ; Schroeder, Steven ; Scheffler, Brian ; Duke, Mary V. ; Ballard, Linda ; Kucuktas, Huseyin ; Kaltenboeck, Ludmilla ; Liu, Haixia ; Armbruster, Jonathan ; Xie, Yangjie ; Kirby, Mona L. ; Tian, Yi ; Flanagan, Mary Elizabeth ; Mu, Weijie ; Waldbieser, Geoffrey C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2016-06, Vol.7 (1), p.11757-11757, Article 11757
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ArticlesPeer ReviewedFull Text
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Author / Creator:Low, Wai Yee ; Tearle, Rick ; Liu, Ruijie ; Koren, Sergey ; Rhie, Arang ; Bickhart, Derek M. ; Rosen, Benjamin D. ; Kronenberg, Zev N. ; Kingan, Sarah B. ; Tseng, Elizabeth ; Thibaud-Nissen, Françoise ; Martin, Fergal J. ; Billis, Konstantinos ; Ghurye, Jay ; Hastie, Alex R. ; Lee, Joyce ; Pang, Andy W. C. ; Heaton, Michael P. ; Phillippy, Adam M. ; Hiendleder, Stefan ; Smith, Timothy P. L. ; Williams, John L.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-04, Vol.11 (1), p.2071-14, Article 2071
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ArticlesPeer ReviewedFull Text
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Author / Creator:Kim, Juwan ; Lee, Chul ; Ko, Byung June ; Yoo, Dong Ahn ; Won, Sohyoung ; Phillippy, Adam M. ; Fedrigo, Olivier ; Zhang, Guojie ; Howe, Kerstin ; Wood, Jonathan ; Durbin, Richard ; Formenti, Giulio ; Brown, Samara ; Cantin, Lindsey ; Mello, Claudio V. ; Cho, Seoae ; Rhie, Arang ; Kim, Heebal ; Jarvis, Erich D.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-09, Vol.23 (1), p.204-204, Article 204
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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Author / Creator:Bickhart, Derek M. ; Watson, Mick ; Koren, Sergey ; Panke-Buisse, Kevin ; Cersosimo, Laura M. ; Press, Maximilian O. ; Van Tassell, Curtis P. ; Van Kessel, Jo Ann S. ; Haley, Bradd J. ; Kim, Seon Woo ; Heiner, Cheryl ; Suen, Garret ; Bakshy, Kiranmayee ; Liachko, Ivan ; Sullivan, Shawn T. ; Myer, Phillip R. ; Ghurye, Jay ; Pop, Mihai ; Weimer, Paul J. ; Phillippy, Adam M. ; Smith, Timothy P. L.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2019-08, Vol.20 (1), p.153-153, Article 153
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ArticlesPeer ReviewedFull Text
Genome assembly forensics: finding the elusive mis-assembly
Author / Creator:Phillippy, Adam M ; Schatz, Michael C ; Pop, Mihai
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology (Online Edition), 2008-03, Vol.9 (3), p.R55-1917, Article R55
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Reply to ‘Errors in long-read assemblies can critically affect protein prediction’
Author / Creator:Koren, Sergey ; Phillippy, Adam M. ; Simpson, Jared T. ; Loman, Nicholas J. ; Loose, Matthew
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2019-02, Vol.37 (2), p.127-128
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Effect of sequence depth and length in long-read assembly of the maize inbred NC358
Author / Creator:Ou, Shujun ; Liu, Jianing ; Chougule, Kapeel M. ; Fungtammasan, Arkarachai ; Seetharam, Arun S. ; Stein, Joshua C. ; Llaca, Victor ; Manchanda, Nancy ; Gilbert, Amanda M. ; Wei, Sharon ; Chin, Chen-Shan ; Hufnagel, David E. ; Pedersen, Sarah ; Snodgrass, Samantha J. ; Fengler, Kevin ; Woodhouse, Margaret ; Walenz, Brian P. ; Koren, Sergey ; Phillippy, Adam M. ; Hannigan, Brett T. ; Dawe, R. Kelly ; Hirsch, Candice N. ; Hufford, Matthew B. ; Ware, Doreen
Publisher:London: Nature Publishing Group UK
Journal title:Nature biotechnology, 2020-05, Vol.11 (1), p.2288-10, Article 2288
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Showing 1 to 20 of 169 results

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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

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The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

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MUMmer4: A fast and versatile genome alignment system

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Long-read mapping to repetitive reference sequences using Winnowmap2

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Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

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Interactive metagenomic visualization in a Web browser

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Mash Screen: high-throughput sequence containment estimation for genome discovery

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Hybrid error correction and de novo assembly of single-molecule sequencing reads

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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

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The structure, function and evolution of a complete human chromosome 8

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

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The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

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False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

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Genome assembly forensics: finding the elusive mis-assembly

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Reply to ‘Errors in long-read assemblies can critically affect protein prediction’

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Effect of sequence depth and length in long-read assembly of the maize inbred NC358

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