Shiguo Zhou

Shiguo Zhou

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Shiguo Zhou

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Electrostatic confinement and manipulation of DNA molecules for genome analysis.

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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http://dx.doi.org/10.1073/pnas.1711069114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754773PMC
December 2017

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

Spine (Phila Pa 1976) 2016 Sep;41(18):1469-76

*Department of Orthopedic Surgery, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, China †Department of Pulmonary Neoplasms Internal Medicine, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, China ‡Statistics Room, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China.

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http://dx.doi.org/10.1097/BRS.0000000000001538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001136PMC
September 2016

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

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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http://dx.doi.org/10.1007/s00264-015-2897-1DOI Listing
July 2016

Allele-Specific Quantification of Structural Variations in Cancer Genomes.

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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http://dx.doi.org/10.1016/j.cels.2016.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965314PMC
July 2016

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

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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440152PMC
April 2016

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

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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http://dx.doi.org/10.1186/s12885-015-1852-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635615PMC
November 2015

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

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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565276PMC
September 2015

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

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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http://dx.doi.org/10.1186/s12864-015-1823-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551733PMC
August 2015

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

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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http://dx.doi.org/10.1038/srep11087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457147PMC
June 2015

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

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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http://dx.doi.org/10.1073/pnas.1418577112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485118PMC
June 2015

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

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

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

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

Comparative genomics of cryptosporidium.

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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http://dx.doi.org/10.1155/2013/832756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659464PMC
June 2013

AGORA: Assembly Guided by Optical Restriction Alignment.

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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http://dx.doi.org/10.1186/1471-2105-13-189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431216PMC
August 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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http://dx.doi.org/10.1038/nature10625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272368PMC
November 2011

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

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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http://dx.doi.org/10.1073/pnas.0914638107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890719PMC
June 2010

The physical and genetic framework of the maize B73 genome.

PLoS Genet 2009 Nov 20;5(11):e1000715. Epub 2009 Nov 20.

Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774505PMC
November 2009

A single molecule scaffold for the maize genome.

PLoS Genet 2009 Nov 20;5(11):e1000711. Epub 2009 Nov 20.

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774507PMC
November 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Authors:
Brian J Haas Sophien Kamoun Michael C Zody Rays H Y Jiang Robert E Handsaker Liliana M Cano Manfred Grabherr Chinnappa D Kodira Sylvain Raffaele Trudy Torto-Alalibo Tolga O Bozkurt Audrey M V Ah-Fong Lucia Alvarado Vicky L Anderson Miles R Armstrong Anna Avrova Laura Baxter Jim Beynon Petra C Boevink Stephanie R Bollmann Jorunn I B Bos Vincent Bulone Guohong Cai Cahid Cakir James C Carrington Megan Chawner Lucio Conti Stefano Costanzo Richard Ewan Noah Fahlgren Michael A Fischbach Johanna Fugelstad Eleanor M Gilroy Sante Gnerre Pamela J Green Laura J Grenville-Briggs John Griffith Niklaus J Grünwald Karolyn Horn Neil R Horner Chia-Hui Hu Edgar Huitema Dong-Hoon Jeong Alexandra M E Jones Jonathan D G Jones Richard W Jones Elinor K Karlsson Sridhara G Kunjeti Kurt Lamour Zhenyu Liu Lijun Ma Daniel Maclean Marcus C Chibucos Hayes McDonald Jessica McWalters Harold J G Meijer William Morgan Paul F Morris Carol A Munro Keith O'Neill Manuel Ospina-Giraldo Andrés Pinzón Leighton Pritchard Bernard Ramsahoye Qinghu Ren Silvia Restrepo Sourav Roy Ari Sadanandom Alon Savidor Sebastian Schornack David C Schwartz Ulrike D Schumann Ben Schwessinger Lauren Seyer Ted Sharpe Cristina Silvar Jing Song David J Studholme Sean Sykes Marco Thines Peter J I van de Vondervoort Vipaporn Phuntumart Stephan Wawra Rob Weide Joe Win Carolyn Young Shiguo Zhou William Fry Blake C Meyers Pieter van West Jean Ristaino Francine Govers Paul R J Birch Stephen C Whisson Howard S Judelson Chad Nusbaum

Nature 2009 Sep 9;461(7262):393-8. Epub 2009 Sep 9.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.

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http://dx.doi.org/10.1038/nature08358DOI Listing
September 2009

Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome.

BMC Genomics 2009 Jan 15;10:25. Epub 2009 Jan 15.

The Laboratory of Bacterial Genomics, Department of Pathobiological Sciences, University of Wisconsin-Madison, WI, USA.

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http://dx.doi.org/10.1186/1471-2164-10-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633350PMC
January 2009

Optical mapping discerns genome wide DNA methylation profiles.

BMC Mol Biol 2008 Jul 30;9:68. Epub 2008 Jul 30.

Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1186/1471-2199-9-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516518PMC
July 2008

Validation of rice genome sequence by optical mapping.

BMC Genomics 2007 Aug 15;8:278. Epub 2007 Aug 15.

Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1186/1471-2164-8-278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2048515PMC
August 2007

An algorithm for assembly of ordered restriction maps from single DNA molecules.

Proc Natl Acad Sci U S A 2006 Oct 16;103(43):15770-5. Epub 2006 Oct 16.

Department of Mathematics, University of Southern California, 3620 South Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA.

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http://dx.doi.org/10.1073/pnas.0604040103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635078PMC
October 2006

Whole-genome shotgun optical mapping of Rhodospirillum rubrum.

Appl Environ Microbiol 2005 Sep;71(9):5511-22

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

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http://dx.doi.org/10.1128/AEM.71.9.5511-5522.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1214604PMC
September 2005

The genome of the kinetoplastid parasite, Leishmania major.

Authors:
Alasdair C Ivens Christopher S Peacock Elizabeth A Worthey Lee Murphy Gautam Aggarwal Matthew Berriman Ellen Sisk Marie-Adele Rajandream Ellen Adlem Rita Aert Atashi Anupama Zina Apostolou Philip Attipoe Nathalie Bason Christopher Bauser Alfred Beck Stephen M Beverley Gabriella Bianchettin Katja Borzym Gordana Bothe Carlo V Bruschi Matt Collins Eithon Cadag Laura Ciarloni Christine Clayton Richard M R Coulson Ann Cronin Angela K Cruz Robert M Davies Javier De Gaudenzi Deborah E Dobson Andreas Duesterhoeft Gholam Fazelina Nigel Fosker Alberto Carlos Frasch Audrey Fraser Monika Fuchs Claudia Gabel Arlette Goble André Goffeau David Harris Christiane Hertz-Fowler Helmut Hilbert David Horn Yiting Huang Sven Klages Andrew Knights Michael Kube Natasha Larke Lyudmila Litvin Angela Lord Tin Louie Marco Marra David Masuy Keith Matthews Shulamit Michaeli Jeremy C Mottram Silke Müller-Auer Heather Munden Siri Nelson Halina Norbertczak Karen Oliver Susan O'neil Martin Pentony Thomas M Pohl Claire Price Bénédicte Purnelle Michael A Quail Ester Rabbinowitsch Richard Reinhardt Michael Rieger Joel Rinta Johan Robben Laura Robertson Jeronimo C Ruiz Simon Rutter David Saunders Melanie Schäfer Jacquie Schein David C Schwartz Kathy Seeger Amber Seyler Sarah Sharp Heesun Shin Dhileep Sivam Rob Squares Steve Squares Valentina Tosato Christy Vogt Guido Volckaert Rolf Wambutt Tim Warren Holger Wedler John Woodward Shiguo Zhou Wolfgang Zimmermann Deborah F Smith Jenefer M Blackwell Kenneth D Stuart Bart Barrell Peter J Myler

Science 2005 Jul;309(5733):436-42

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.1112680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470643PMC
July 2005

Shotgun optical mapping of the entire Leishmania major Friedlin genome.

Mol Biochem Parasitol 2004 Nov;138(1):97-106

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

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http://dx.doi.org/10.1016/j.molbiopara.2004.08.002DOI Listing
November 2004