Publications by authors named "David C Schwartz"

85Publications

Biophysics and the Genomic Sciences.

Authors:
David C Schwartz

Biophys J 2019 12 30;117(11):2047-2053. Epub 2019 Jul 30.

Department of Chemistry, Laboratory of Genetics, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison Wisconsin. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.07.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895736PMC
December 2019

A simple dialysis device for large DNA molecules.

Biotechniques 2019 02;66(2):93-95

Laboratory for Molecular & Computational Genomics, UW Biotechnology Center, University of Wisconsin-Madison, USA.

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http://dx.doi.org/10.2144/btn-2018-0133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494463PMC
February 2019

Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules.

ACS Appl Mater Interfaces 2018 Dec 19;10(48):41215-41223. Epub 2018 Nov 19.

Colombia/Wisconsin One-Health Consortium , Universidad Nacional de Colombia-Medellín , Medellín 050034 , Colombia.

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http://pubs.acs.org/doi/10.1021/acsami.8b18157
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http://dx.doi.org/10.1021/acsami.8b18157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453721PMC
December 2018

Discrete and Continuum Models for the Salt in Crowded Environments of Suspended Charged Particles.

J Chem Theory Comput 2018 Sep 15;14(9):4901-4913. Epub 2018 Aug 15.

Departamento de Materiales y Nanotecnología , Universidad Nacional de Colombia-Medellín , Medellín 050034 , Colombia.

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http://dx.doi.org/10.1021/acs.jctc.8b00221DOI Listing
September 2018

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

In silico evidence for sequence-dependent nucleosome sliding.

Proc Natl Acad Sci U S A 2017 10 18;114(44):E9197-E9205. Epub 2017 Oct 18.

Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637;

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http://dx.doi.org/10.1073/pnas.1705685114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676884PMC
October 2017

Tension-Dependent Free Energies of Nucleosome Unwrapping.

ACS Cent Sci 2016 Sep 23;2(9):660-666. Epub 2016 Aug 23.

Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States; Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043429PMC
http://dx.doi.org/10.1021/acscentsci.6b00201DOI Listing
September 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

Maligner: a fast ordered restriction map aligner.

Bioinformatics 2016 04 3;32(7):1016-22. Epub 2015 Dec 3.

Center for Bioinformatics and Computational Biology, Applied Math & Statistics, and Scientific Computation, Department of Computer Science, University of Maryland, College Park, MD 20742, USA and.

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http://dx.doi.org/10.1093/bioinformatics/btv711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907389PMC
April 2016

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

DNA binding fluorescent proteins for the direct visualization of large DNA molecules.

Nucleic Acids Res 2016 Jan 11;44(1):e6. Epub 2015 Aug 11.

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA.

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http://dx.doi.org/10.1093/nar/gkv834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705684PMC
January 2016

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

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

Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

Macromolecules 2013 Oct;46(20):8356-8368

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706-1580.

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http://dx.doi.org/10.1021/ma400926hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964590PMC
October 2013

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

Using latent class analysis to model prescription medications in the measurement of falling among a community elderly population.

BMC Med Inform Decis Mak 2013 May 25;13:60. Epub 2013 May 25.

Department of Public Health, Nova Southeastern University, Health Professions Division, Ft. Lauderdale, FL 33328, USA.

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http://dx.doi.org/10.1186/1472-6947-13-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673854PMC
May 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

Statistical significance of optical map alignments.

J Comput Biol 2012 May 16;19(5):478-92. Epub 2012 Apr 16.

Theoretical Statistics and Mathematics Unit, Indian Statistical Institute, New Delhi, India.

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http://www.liebertpub.com/doi/10.1089/cmb.2011.0221
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http://dx.doi.org/10.1089/cmb.2011.0221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342520PMC
May 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

Nanochannel confinement: DNA stretch approaching full contour length.

Lab Chip 2011 May 23;11(10):1721-9. Epub 2011 Mar 23.

Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.

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http://xlink.rsc.org/?DOI=c0lc00680g
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http://dx.doi.org/10.1039/c0lc00680gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222331PMC
May 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

New Generations: Sequencing Machines and Their Computational Challenges.

J Comput Sci Technol 2010 Jan;25(1):3-9

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

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http://dx.doi.org/10.1007/s11390-010-9300-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222932PMC
January 2010

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

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 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

The challenges of sequencing by synthesis.

Nat Biotechnol 2009 Nov 6;27(11):1013-23. Epub 2009 Nov 6.

GE Healthcare Life Sciences, Piscataway, New Jersey, USA.

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http://dx.doi.org/10.1038/nbt.1585DOI 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

Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows.

Lab Chip 2009 Aug 10;9(16):2348-55. Epub 2009 Jun 10.

Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.

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http://dx.doi.org/10.1039/b902292aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768593PMC
August 2009

A single-molecule barcoding system using nanoslits for DNA analysis : nanocoding.

Methods Mol Biol 2009 ;544:29-42

Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1007/978-1-59745-483-4_3DOI Listing
November 2009

Microfluidic-assisted analysis of replicating DNA molecules.

Nat Protoc 2009 14;4(6):849-61. Epub 2009 May 14.

Department of Pathology, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nprot.2009.54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762429PMC
September 2009

Molecular propulsion: chemical sensing and chemotaxis of DNA driven by RNA polymerase.

J Am Chem Soc 2009 Apr;131(16):5722-3

Department of Chemistry, University of Wisconsin, 425 Henry Mall, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1021/ja900372mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770815PMC
April 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

Imaging and analysis of transcription on large, surface-mounted single template DNA molecules.

Anal Biochem 2008 Sep 24;380(1):111-21. Epub 2008 May 24.

Department of Chemistry, 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/10.1016/j.ab.2008.05.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561992PMC
September 2008

The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores.

J Chem Phys 2008 Feb;128(8):085102

Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA.

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http://dx.doi.org/10.1063/1.2831777DOI Listing
February 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

The Ulp2 SUMO protease is required for cell division following termination of the DNA damage checkpoint.

Mol Cell Biol 2007 Oct 30;27(19):6948-61. Epub 2007 Jul 30.

Department of Molecular Biophysics, Yale University, New Haven, CT 06520-8114, USA.

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http://dx.doi.org/10.1128/MCB.00774-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099214PMC
October 2007

A quantile method for sizing optical maps.

J Comput Biol 2007 Apr;14(3):255-66

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1089/cmb.2006.0006DOI Listing
April 2007

Pulsed-field gel electrophoresis.

Nat Protoc 2007 ;2(3):677-84

Department of Chemistry, UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1038/nprot.2007.94DOI Listing
June 2007

A coarse grain model for DNA.

J Chem Phys 2007 Feb;126(8):084901

Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA.

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http://aip.scitation.org/doi/10.1063/1.2431804
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http://dx.doi.org/10.1063/1.2431804DOI Listing
February 2007

A single-molecule barcoding system using nanoslits for DNA analysis.

Proc Natl Acad Sci U S A 2007 Feb 12;104(8):2673-8. Epub 2007 Feb 12.

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

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http://dx.doi.org/10.1073/pnas.0611151104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815240PMC
February 2007

Transchip: single-molecule detection of transcriptional elongation complexes.

Anal Biochem 2007 Feb 16;361(1):31-46. Epub 2006 Nov 16.

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

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http://dx.doi.org/10.1016/j.ab.2006.10.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1945215PMC
February 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

Alignment of optical maps.

J Comput Biol 2006 Mar;13(2):442-62

Department of Mathematics, University of Southern California, Los Angeles, 90089-1113, USA.

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http://dx.doi.org/10.1089/cmb.2006.13.442DOI Listing
March 2006

Refinement of optical map assemblies.

Bioinformatics 2006 May 24;22(10):1217-24. Epub 2006 Feb 24.

MCB 1050 Childs Way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl063DOI Listing
May 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

High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides.

Anal Biochem 2005 Feb;337(1):1-11

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

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http://dx.doi.org/10.1016/j.ab.2004.09.043DOI Listing
February 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

A microfluidic system for large DNA molecule arrays.

Anal Chem 2004 Sep;76(18):5293-301

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

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http://dx.doi.org/10.1021/ac0496401DOI Listing
September 2004

Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels [corrected].

J Chem Phys 2004 Feb;120(5):2513-29

Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1063/1.1637331DOI Listing
February 2004

An integrative approach for the optical sequencing of single DNA molecules.

Anal Biochem 2004 Jul;330(2):227-41

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

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http://dx.doi.org/10.1016/j.ab.2004.03.029DOI Listing
July 2004

DNA dynamics in a microchannel.

Phys Rev Lett 2003 Jul 15;91(3):038102. Epub 2003 Jul 15.

Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1103/PhysRevLett.91.038102DOI Listing
July 2003

A superfamily of protein tags: ubiquitin, SUMO and related modifiers.

Trends Biochem Sci 2003 Jun;28(6):321-8

Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.

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http://dx.doi.org/10.1016/S0968-0004(03)00113-0DOI Listing
June 2003

Analysis of recombinant yeast decapping enzyme.

RNA 2003 Feb;9(2):231-8

Department of Molecular and Cellular Biology & Howard Hughes Medical Institute, University of Arizona, 1007 E. Lowell Street, Tucson, AZ 85704, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370389PMC
http://dx.doi.org/10.1261/rna.2151403DOI Listing
February 2003

Serial intracoronary ultrasound in children: feasibility, reproducibility, limitations, and safety.

J Am Soc Echocardiogr 2002 Aug;15(8):782-90

Division of Pediatric Cardiology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1067/mje.2002.119911DOI Listing
August 2002