Publications by authors named "Shiguo Zhou"

51 Publications

The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes.

Authors:
Yong Zhang He Yang David Turra Shiguo Zhou Dilay Hazal Ayhan Gregory A DeIulio Li Guo Karen Broz Nathan Wiederhold Jeffrey J Coleman Kerry O' Donnell Ilan Youngster Alexander J McAdam Sergey Savinov Terrance Shea Sarah Young Qiandong Zeng Martijn Rep Eric Pearlman David C Schwartz Antonio Di Pietro H Corby Kistler Li-Jun Ma

Commun Biol 2020 01 31;3(1):50. Epub 2020 Jan 31.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA.

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January 2020

Electrostatic confinement and manipulation of DNA molecules for genome analysis.

Authors:
Kristy L Kounovsky-Shafer Juan P Hernandez-Ortiz Konstantinos Potamousis Gene Tsvid Michael Place Prabu Ravindran Kyubong Jo Shiguo Zhou Theo Odijk Juan J de Pablo David C Schwartz

Proc Natl Acad Sci U S A 2017 12 4;114(51):13400-13405. Epub 2017 Dec 4.

Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706-1580;

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December 2017

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.

Authors:
Jean-Félix Dallery Nicolas Lapalu Antonios Zampounis Sandrine Pigné Isabelle Luyten Joëlle Amselem Alexander H J Wittenberg Shiguo Zhou Marisa V de Queiroz Guillaume P Robin Annie Auger Matthieu Hainaut Bernard Henrissat Ki-Tae Kim Yong-Hwan Lee Olivier Lespinet David C Schwartz Michael R Thon Richard J O'Connell

BMC Genomics 2017 Aug 29;18(1):667. Epub 2017 Aug 29.

UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.

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August 2017

Genome Sequence and Annotation of Colletotrichum higginsianum, a Causal Agent of Crucifer Anthracnose Disease.

Authors:
Antonios Zampounis Sandrine Pigné Jean-Félix Dallery Alexander H J Wittenberg Shiguo Zhou David C Schwartz Michael R Thon Richard J O'Connell

Genome Announc 2016 Aug 18;4(4). Epub 2016 Aug 18.

UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France

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August 2016

Allele-Specific Quantification of Structural Variations in Cancer Genomes.

Authors:
Yang Li Shiguo Zhou David C Schwartz Jian Ma

Cell Syst 2016 07 21;3(1):21-34. Epub 2016 Jul 21.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA. Electronic address:

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July 2016

Who are the Best Candidates for Decompressive Surgery and Spine Stabilization in Patients With Metastatic Spinal Cord Compression?: A New Scoring System.

Authors:
Mingxing Lei Jianjie Li Yaosheng Liu Weigang Jiang Shubin Liu Shiguo Zhou

Spine (Phila Pa 1976) 2016 Sep;41(18):1469-1476

Statistics Room, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China.

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September 2016

A gapless genome sequence of the fungus Botrytis cinerea.

Authors:
Jan A L Van Kan Joost H M Stassen Andreas Mosbach Theo A J Van Der Lee Luigi Faino Andrew D Farmer Dimitrios G Papasotiriou Shiguo Zhou Michael F Seidl Eleanor Cottam Dominique Edel Matthias Hahn David C Schwartz Robert A Dietrich Stephanie Widdison Gabriel Scalliet

Mol Plant Pathol 2017 01 9;18(1):75-89. Epub 2016 Jun 9.

Syngenta Crop Protection Münchwilen AG, Crop Protection Research, CH-4332, Stein, Switzerland.

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January 2017

Prediction of survival prognosis after surgery in patients with symptomatic metastatic spinal cord compression from non-small cell lung cancer.

Authors:
Mingxing Lei Yaosheng Liu Chuanghao Tang Shaoxing Yang Shubin Liu Shiguo Zhou

BMC Cancer 2015 Nov 5;15:853. Epub 2015 Nov 5.

Statistics Room, Capital Medical University affiliated Beijing Friendship Hospital, No. 95, Xuanwu District Yongan Rd, Beijing, China.

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November 2015

Association between VEGF -634G/C polymorphism and osteonecrosis of the femoral head susceptibility: a meta analysis.

Authors:
Yaosheng Liu Zhicheng Zhang Shubin Liu Xiuyun Su Shiguo Zhou

Int J Clin Exp Med 2015 15;8(7):10979-85. Epub 2015 Jul 15.

Statistics Room, Capital Medical University Affiliated Beijing Friendship Hospital Beijing, People's Republic of China.

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September 2015

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

Authors:
Shiguo Zhou Steve Goldstein Michael Place Michael Bechner Diego Patino Konstantinos Potamousis Prabu Ravindran Louise Pape Gonzalo Rincon Juan Hernandez-Ortiz Juan F Medrano David C Schwartz

BMC Genomics 2015 Aug 28;16:644. Epub 2015 Aug 28.

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.

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August 2015

Tantalum rod implantation for femoral head osteonecrosis: survivorship analysis and determination of prognostic factors for total hip arthroplasty.

Authors:
Yaosheng Liu Liang Yan Shiguo Zhou Xiuyun Su Yuncen Cao Cheng Wang Shubin Liu

Int Orthop 2016 Jul 11;40(7):1397-407. Epub 2015 Aug 11.

Department of Orthopaedic Surgery, PLA 307th Hospital, No.8, Fengtaidongda Road, Beijing, 100071, China.

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July 2016

Single-molecule analysis reveals widespread structural variation in multiple myeloma.

Authors:
Aditya Gupta Michael Place Steven Goldstein Deepayan Sarkar Shiguo Zhou Konstantinos Potamousis Jaehyup Kim Claire Flanagan Yang Li Michael A Newton Natalie S Callander Peiman Hematti Emery H Bresnick Jian Ma Fotis Asimakopoulos David C Schwartz

Proc Natl Acad Sci U S A 2015 Jun 8;112(25):7689-94. Epub 2015 Jun 8.

Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706; Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706; University of Wisconsin Carbone Cancer Center, Madison, WI 53705;

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June 2015

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense.

Authors:
Yingjie Zhu Jiang Xu Chao Sun Shiguo Zhou Haibin Xu David R Nelson Jun Qian Jingyuan Song Hongmei Luo Li Xiang Ying Li Zhichao Xu Aijia Ji Lizhi Wang Shanfa Lu Alice Hayward Wei Sun Xiwen Li David C Schwartz Yitao Wang Shilin Chen

Sci Rep 2015 Jun 5;5:11087. Epub 2015 Jun 5.

1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.

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June 2015

Combined effect of tnf-α polymorphisms and hypoxia on steroid-induced osteonecrosis of femoral head.

Authors:
Yaosheng Liu Weihao Jiang Shubin Liu Xiuyun Su Shiguo Zhou

Int J Clin Exp Pathol 2015 1;8(3):3215-9. Epub 2015 Mar 1.

Statistics Room, Capital Medical University Affiliated Beijing Friendship Hospital 95 Xuanwu District Yongan Road, Beijing, People's Republic of China.

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April 2016

A modified porous tantalum implant technique for osteonecrosis of the femoral head: survivorship analysis and prognostic factors for radiographic progression and conversion to total hip arthroplasty.

Authors:
Yaosheng Liu Xiuyun Su Shiguo Zhou Lei Wang Cheng Wang Shubin Liu

Int J Clin Exp Med 2015 15;8(2):1918-30. Epub 2015 Feb 15.

Department of Orthopaedics, The 307 Hospital, PLA Beijing 100071, People's Republic of China.

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May 2015

[A modified porous tantalum implant technology for osteonecrosis of the femoral head: survival and prognostic evaluations of conversion into total hip arthroplasty].

Authors:
Yaosheng Liu Shubin Liu Shiguo Zhou Xiuyun Su Cheng Wang Yuncen Cao Weihao Jiang Qiu Cui Lei Wang

Zhonghua Yi Xue Za Zhi 2014 Aug;94(31):2429-33

Email:

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August 2014

High-coverage sequencing and annotated assemblies of the budgerigar genome.

Authors:
Ganeshkumar Ganapathy Jason T Howard James M Ward Jianwen Li Bo Li Yingrui Li Yingqi Xiong Yong Zhang Shiguo Zhou David C Schwartz Michael Schatz Robert Aboukhalil Olivier Fedrigo Lisa Bukovnik Ty Wang Greg Wray Isabelle Rasolonjatovo Roger Winer James R Knight Sergey Koren Wesley C Warren Guojie Zhang Adam M Phillippy Erich D Jarvis

Gigascience 2014 8;3:11. Epub 2014 Jul 8.

Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.

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July 2014

An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

Authors:
Haibao Tang Vivek Krishnakumar Shelby Bidwell Benjamin Rosen Agnes Chan Shiguo Zhou Laurent Gentzbittel Kevin L Childs Mark Yandell Heidrun Gundlach Klaus F X Mayer David C Schwartz Christopher D Town

BMC Genomics 2014 Apr 27;15:312. Epub 2014 Apr 27.

J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA.

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April 2014

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

Authors:
Yoshihiro Kawahara Melissa de la Bastide John P Hamilton Hiroyuki Kanamori W Richard McCombie Shu Ouyang David C Schwartz Tsuyoshi Tanaka Jianzhong Wu Shiguo Zhou Kevin L Childs Rebecca M Davidson Haining Lin Lina Quesada-Ocampo Brieanne Vaillancourt Hiroaki Sakai Sung Shin Lee Jungsok Kim Hisataka Numa Takeshi Itoh C Robin Buell Takashi Matsumoto

Rice (N Y) 2013 Feb 6;6(1). Epub 2013 Feb 6.

Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.

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February 2013

Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis.

Authors:
Mohana Ray Steve Goldstein Shiguo Zhou Konstantinos Potamousis Deepayan Sarkar Michael A Newton Elizabeth Esterberg Christina Kendziorski Oliver Bogler David C Schwartz

BMC Genomics 2013 Jul 26;14:505. Epub 2013 Jul 26.

Department of Chemistry, UW Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA.

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July 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Authors:
Keith R Bradnam Joseph N Fass Anton Alexandrov Paul Baranay Michael Bechner Inanç Birol Sébastien Boisvert Jarrod A Chapman Guillaume Chapuis Rayan Chikhi Hamidreza Chitsaz Wen-Chi Chou Jacques Corbeil Cristian Del Fabbro T Roderick Docking Richard Durbin Dent Earl Scott Emrich Pavel Fedotov Nuno A Fonseca Ganeshkumar Ganapathy Richard A Gibbs Sante Gnerre Elénie Godzaridis Steve Goldstein Matthias Haimel Giles Hall David Haussler Joseph B Hiatt Isaac Y Ho Jason Howard Martin Hunt Shaun D Jackman David B Jaffe Erich D Jarvis Huaiyang Jiang Sergey Kazakov Paul J Kersey Jacob O Kitzman James R Knight Sergey Koren Tak-Wah Lam Dominique Lavenier François Laviolette Yingrui Li Zhenyu Li Binghang Liu Yue Liu Ruibang Luo Iain Maccallum Matthew D Macmanes Nicolas Maillet Sergey Melnikov Delphine Naquin Zemin Ning Thomas D Otto Benedict Paten Octávio S Paulo Adam M Phillippy Francisco Pina-Martins Michael Place Dariusz Przybylski Xiang Qin Carson Qu Filipe J Ribeiro Stephen Richards Daniel S Rokhsar J Graham Ruby Simone Scalabrin Michael C Schatz David C Schwartz Alexey Sergushichev Ted Sharpe Timothy I Shaw Jay Shendure Yujian Shi Jared T Simpson Henry Song Fedor Tsarev Francesco Vezzi Riccardo Vicedomini Bruno M Vieira Jun Wang Kim C Worley Shuangye Yin Siu-Ming Yiu Jianying Yuan Guojie Zhang Hao Zhang Shiguo Zhou Ian F Korf

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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July 2013

Comparative genomics of cryptosporidium.

Authors:
Aurélien J Mazurie João M Alves Luiz S Ozaki Shiguo Zhou David C Schwartz Gregory A Buck

Int J Genomics 2013 2;2013:832756. Epub 2013 May 2.

Department of Microbiology, Montana State University, Bozeman, MT 59717, USA ; Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23284-2030, USA.

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June 2013

Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

Authors:
Sebastiaan van Heesch Wigard P Kloosterman Nico Lansu Frans-Paul Ruzius Elizabeth Levandowsky Clarence C Lee Shiguo Zhou Steve Goldstein David C Schwartz Timothy T Harkins Victor Guryev Edwin Cuppen

BMC Genomics 2013 Apr 16;14:257. Epub 2013 Apr 16.

Hubrecht Institute/KNAW and University Medical Center Utrecht, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands.

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April 2013

Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.

Authors:
Viola A Manning Iovanna Pandelova Braham Dhillon Larry J Wilhelm Stephen B Goodwin Aaron M Berlin Melania Figueroa Michael Freitag James K Hane Bernard Henrissat Wade H Holman Chinnappa D Kodira Joel Martin Richard P Oliver Barbara Robbertse Wendy Schackwitz David C Schwartz Joseph W Spatafora B Gillian Turgeon Chandri Yandava Sarah Young Shiguo Zhou Qiandong Zeng Igor V Grigoriev Li-Jun Ma Lynda M Ciuffetti

G3 (Bethesda) 2013 Jan 1;3(1):41-63. Epub 2013 Jan 1.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-8530, USA.

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January 2013

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.

Authors:
Richard J O'Connell Michael R Thon Stéphane Hacquard Stefan G Amyotte Jochen Kleemann Maria F Torres Ulrike Damm Ester A Buiate Lynn Epstein Noam Alkan Janine Altmüller Lucia Alvarado-Balderrama Christopher A Bauser Christian Becker Bruce W Birren Zehua Chen Jaeyoung Choi Jo Anne Crouch Jonathan P Duvick Mark A Farman Pamela Gan David Heiman Bernard Henrissat Richard J Howard Mehdi Kabbage Christian Koch Barbara Kracher Yasuyuki Kubo Audrey D Law Marc-Henri Lebrun Yong-Hwan Lee Itay Miyara Neil Moore Ulla Neumann Karl Nordström Daniel G Panaccione Ralph Panstruga Michael Place Robert H Proctor Dov Prusky Gabriel Rech Richard Reinhardt Jeffrey A Rollins Steve Rounsley Christopher L Schardl David C Schwartz Narmada Shenoy Ken Shirasu Usha R Sikhakolli Kurt Stüber Serenella A Sukno James A Sweigard Yoshitaka Takano Hiroyuki Takahara Frances Trail H Charlotte van der Does Lars M Voll Isa Will Sarah Young Qiandong Zeng Jingze Zhang Shiguo Zhou Martin B Dickman Paul Schulze-Lefert Emiel Ver Loren van Themaat Li-Jun Ma Lisa J Vaillancourt

Nat Genet 2012 Sep 12;44(9):1060-5. Epub 2012 Aug 12.

Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

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September 2012

AGORA: Assembly Guided by Optical Restriction Alignment.

Authors:
Henry C Lin Steve Goldstein Lee Mendelowitz Shiguo Zhou Joshua Wetzel David C Schwartz Mihai Pop

BMC Bioinformatics 2012 Aug 2;13:189. Epub 2012 Aug 2.

Center for Bioinformatics and Computational Biology, University of Maryland-College Park, College Park, MD, USA.

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August 2012

Genome sequence of the model medicinal mushroom Ganoderma lucidum.

Authors:
Shilin Chen Jiang Xu Chang Liu Yingjie Zhu David R Nelson Shiguo Zhou Chunfang Li Lizhi Wang Xu Guo Yongzhen Sun Hongmei Luo Ying Li Jingyuan Song Bernard Henrissat Anthony Levasseur Jun Qian Jianqin Li Xiang Luo Linchun Shi Liu He Li Xiang Xiaolan Xu Yunyun Niu Qiushi Li Mira V Han Haixia Yan Jin Zhang Haimei Chen Aiping Lv Zhen Wang Mingzhu Liu David C Schwartz Chao Sun

Nat Commun 2012 Jun 26;3:913. Epub 2012 Jun 26.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.

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June 2012

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association.

Authors:
John P Bannantine Chia-wei Wu Chungyi Hsu Shiguo Zhou David C Schwartz Darrell O Bayles Michael L Paustian David P Alt Srinand Sreevatsan Vivek Kapur Adel M Talaat

BMC Genomics 2012 Mar 12;13:89. Epub 2012 Mar 12.

National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa, USA.

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March 2012

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Authors:
Nevin D Young Frédéric Debellé Giles E D Oldroyd Rene Geurts Steven B Cannon Michael K Udvardi Vagner A Benedito Klaus F X Mayer Jérôme Gouzy Heiko Schoof Yves Van de Peer Sebastian Proost Douglas R Cook Blake C Meyers Manuel Spannagl Foo Cheung Stéphane De Mita Vivek Krishnakumar Heidrun Gundlach Shiguo Zhou Joann Mudge Arvind K Bharti Jeremy D Murray Marina A Naoumkina Benjamin Rosen Kevin A T Silverstein Haibao Tang Stephane Rombauts Patrick X Zhao Peng Zhou Valérie Barbe Philippe Bardou Michael Bechner Arnaud Bellec Anne Berger Hélène Bergès Shelby Bidwell Ton Bisseling Nathalie Choisne Arnaud Couloux Roxanne Denny Shweta Deshpande Xinbin Dai Jeff J Doyle Anne-Marie Dudez Andrew D Farmer Stéphanie Fouteau Carolien Franken Chrystel Gibelin John Gish Steven Goldstein Alvaro J González Pamela J Green Asis Hallab Marijke Hartog Axin Hua Sean J Humphray Dong-Hoon Jeong Yi Jing Anika Jöcker Steve M Kenton Dong-Jin Kim Kathrin Klee Hongshing Lai Chunting Lang Shaoping Lin Simone L Macmil Ghislaine Magdelenat Lucy Matthews Jamison McCorrison Erin L Monaghan Jeong-Hwan Mun Fares Z Najar Christine Nicholson Céline Noirot Majesta O'Bleness Charles R Paule Julie Poulain Florent Prion Baifang Qin Chunmei Qu Ernest F Retzel Claire Riddle Erika Sallet Sylvie Samain Nicolas Samson Iryna Sanders Olivier Saurat Claude Scarpelli Thomas Schiex Béatrice Segurens Andrew J Severin D Janine Sherrier Ruihua Shi Sarah Sims Susan R Singer Senjuti Sinharoy Lieven Sterck Agnès Viollet Bing-Bing Wang Keqin Wang Mingyi Wang Xiaohong Wang Jens Warfsmann Jean Weissenbach Doug D White Jim D White Graham B Wiley Patrick Wincker Yanbo Xing Limei Yang Ziyun Yao Fu Ying Jixian Zhai Liping Zhou Antoine Zuber Jean Dénarié Richard A Dixon Gregory D May David C Schwartz Jane Rogers Francis Quétier Christopher D Town Bruce A Roe

Nature 2011 Nov 16;480(7378):520-4. Epub 2011 Nov 16.

Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA.

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November 2011

High-resolution human genome structure by single-molecule analysis.

Authors:
Brian Teague Michael S Waterman Steven Goldstein Konstantinos Potamousis Shiguo Zhou Susan Reslewic Deepayan Sarkar Anton Valouev Christopher Churas Jeffrey M Kidd Scott Kohn Rodney Runnheim Casey Lamers Dan Forrest Michael A Newton Evan E Eichler Marijo Kent-First Urvashi Surti Miron Livny David C Schwartz

Proc Natl Acad Sci U S A 2010 Jun 1;107(24):10848-53. Epub 2010 Jun 1.

The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580, USA.

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June 2010