P
Patrick Marks
Researcher at Pacific Biosciences
Publications - 31
Citations - 10928
Patrick Marks is an academic researcher from Pacific Biosciences. The author has contributed to research in topics: Genomics & Human genome. The author has an hindex of 20, co-authored 30 publications receiving 9592 citations. Previous affiliations of Patrick Marks include University of Illinois at Urbana–Champaign.
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Journal ArticleDOI
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chen-Shan Chin,David Alexander,Patrick Marks,Aaron Klammer,James P Drake,Cheryl Heiner,Alicia Clum,Alex Copeland,John Huddleston,Evan E. Eichler,Stephen Turner,Jonas Korlach +11 more
TL;DR: This work presents a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.
Journal ArticleDOI
Real-Time DNA Sequencing from Single Polymerase Molecules
John Eid,Adrian Fehr,Jeremy Gray,Khai Luong,John Lyle,Geoff Otto,Paul Peluso,David R. Rank,Primo Baybayan,Brad Bettman,Arkadiusz Bibillo,Keith Bjornson,Bidhan Chaudhuri,Fred Christians,Ronald L. Cicero,Sonya Clark,Ravindra V. Dalal,Alex DeWinter,John Dixon,Mathieu Foquet,Alfred Gaertner,Paul Hardenbol,Cheryl Heiner,Kevin Hester,David P. Holden,Gregory J. Kearns,Xiangxu Kong,Ronald Kuse,Yves Lacroix,Steven Lin,Paul Lundquist,Congcong Ma,Patrick Marks,Mark Maxham,Devon Murphy,Insil Park,Thang Pham,Michael Phillips,Joy Roy,Robert Sebra,Gene Shen,Jon M. Sorenson,Austin B. Tomaney,Kevin Travers,Mark Trulson,John Vieceli,Jeffrey Wegener,Dawn Wu,Alicia Yang,Denis Zaccarin,Peter Zhao,Frank Zhong,Jonas Korlach,Stephen Turner +53 more
TL;DR: Single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs) are presented.
Journal ArticleDOI
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Grace X.Y. Zheng,Billy T. Lau,Michael Schnall-Levin,Mirna Jarosz,John Bell,Christopher Hindson,Sofia Kyriazopoulou-Panagiotopoulou,Donald A. Masquelier,Landon Merrill,Jessica M. Terry,Patrice A Mudivarti,Paul Wyatt,Rajiv Bharadwaj,Anthony J. Makarewicz,Yuan Li,Phillip Belgrader,Andrew D. Price,Adam Lowe,Patrick Marks,Gerard M Vurens,Paul Hardenbol,Luz Montesclaros,Melissa Luo,Lawrence Greenfield,Alexander Wong,David E Birch,Steven W Short,Keith Bjornson,Pranav Patel,Erik S. Hopmans,Christina Wood,Sukhvinder Kaur,Glenn K. Lockwood,David Stafford,Joshua Delaney,Indira Wu,Heather Ordonez,Susan M. Grimes,Stephanie Greer,Josephine Y Lee,Kamila Belhocine,Kristina Giorda,William Haynes Heaton,Geoffrey P. McDermott,Zachary Bent,Francesca Meschi,Nikola O Kondov,Ryan Wilson,Jorge Bernate,Shawn Gauby,Alex Kindwall,Clara Bermejo,Adrian Fehr,Adrian Chan,Serge Saxonov,Kevin D. Ness,Benjamin J. Hindson,Hanlee P. Ji +57 more
TL;DR: A microfluidics-based, linked-read sequencing technology that can phase and haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma and cancer genomes using nanograms of input DNA is presented.
Journal ArticleDOI
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Mark Chaisson,Mark Chaisson,Ashley D. Sanders,Xuefang Zhao,Xuefang Zhao,Ankit Malhotra,David Porubsky,David Porubsky,Tobias Rausch,Eugene J. Gardner,Oscar L. Rodriguez,Li Guo,Ryan L. Collins,Xian Fan,Jia Wen,Robert E. Handsaker,Robert E. Handsaker,Susan Fairley,Zev N. Kronenberg,Xiangmeng Kong,Fereydoun Hormozdiari,Dillon Lee,Aaron M. Wenger,Alex Hastie,Danny Antaki,Thomas Anantharaman,Peter A. Audano,Harrison Brand,Stuart Cantsilieris,Han Cao,Eliza Cerveira,Chong Chen,Xintong Chen,Chen-Shan Chin,Zechen Chong,Nelson T. Chuang,Christine C. Lambert,Deanna M. Church,Laura Clarke,Andrew Farrell,Joey Flores,Timur R. Galeev,David U. Gorkin,David U. Gorkin,Madhusudan Gujral,Victor Guryev,William Haynes Heaton,Jonas Korlach,Sushant Kumar,Jee Young Kwon,Ernest T. Lam,Jong Eun Lee,Joyce V. Lee,Wan-Ping Lee,Sau Peng Lee,Shantao Li,Patrick Marks,Karine A. Viaud-Martinez,Sascha Meiers,Katherine M. Munson,Fabio C. P. Navarro,Bradley J. Nelson,Conor Nodzak,Amina Noor,Sofia Kyriazopoulou-Panagiotopoulou,Andy Wing Chun Pang,Yunjiang Qiu,Yunjiang Qiu,Gabriel Rosanio,Mallory Ryan,Adrian M. Stütz,Diana C.J. Spierings,Alistair Ward,Anne Marie E. Welch,Ming Xiao,Wei Xu,Chengsheng Zhang,Qihui Zhu,Xiangqun Zheng-Bradley,Ernesto Lowy,Sergei Yakneen,Steven A. McCarroll,Steven A. McCarroll,Goo Jun,Li Ding,Chong-Lek Koh,Bing Ren,Bing Ren,Paul Flicek,Ken Chen,Mark Gerstein,Pui-Yan Kwok,Peter M. Lansdorp,Peter M. Lansdorp,Peter M. Lansdorp,Gabor T. Marth,Jonathan Sebat,Xinghua Shi,Ali Bashir,Kai Ye,Scott E. Devine,Michael E. Talkowski,Michael E. Talkowski,Ryan E. Mills,Tobias Marschall,Jan O. Korbel,Evan E. Eichler,Charles Lee +107 more
TL;DR: A suite of long-read, short- read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms are applied to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner.
Journal ArticleDOI
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Justin M. Zook,David Catoe,Jennifer McDaniel,Lindsay K. Vang,Noah Spies,Noah Spies,Arend Sidow,Ziming Weng,Yuling Liu,Christopher E. Mason,Noah Alexander,Elizabeth Henaff,Alexa B. R. McIntyre,Dhruva Chandramohan,Feng Chen,Erich Jaeger,Ali Moshrefi,Khoa Pham,William Stedman,Tiffany Y. Liang,Michael Saghbini,Zeljko Dzakula,Alex Hastie,Han Cao,Gintaras Deikus,Eric E. Schadt,Robert Sebra,Ali Bashir,R Truty,Christopher C. Chang,Natali Gulbahce,Keyan Zhao,Srinka Ghosh,Fiona Hyland,Yutao Fu,Mark Chaisson,Chunlin Xiao,Jonathan Trow,Stephen T. Sherry,Alexander Wait Zaranek,Madeleine Ball,Jason Bobe,Preston W. Estep,George M. Church,Patrick Marks,Sofia Kyriazopoulou-Panagiotopoulou,Grace X.Y. Zheng,Michael Schnall-Levin,Heather Ordonez,Patrice A Mudivarti,Kristina Giorda,Ying Sheng,Karoline Bjarnesdatter Rypdal,Marc L. Salit,Marc L. Salit +54 more
TL;DR: A large, diverse set of sequencing data for seven human genomes is described; five are current or candidate NIST Reference Materials and two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry are described.