Paul Peluso

Paul Peluso

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Paul Peluso

Paul Peluso

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Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads.

Authors:
Mitchell R Vollger Glennis A Logsdon Peter A Audano Arvis Sulovari David Porubsky Paul Peluso Aaron M Wenger Gregory T Concepcion Zev N Kronenberg Katherine M Munson Carl Baker Ashley D Sanders Diana C J Spierings Peter M Lansdorp Urvashi Surti Michael W Hunkapiller Evan E Eichler

Ann Hum Genet 2019 Nov 11. Epub 2019 Nov 11.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.

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http://dx.doi.org/10.1111/ahg.12364DOI Listing
November 2019

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.

Authors:
Aaron M Wenger Paul Peluso William J Rowell Pi-Chuan Chang Richard J Hall Gregory T Concepcion Jana Ebler Arkarachai Fungtammasan Alexey Kolesnikov Nathan D Olson Armin Töpfer Michael Alonge Medhat Mahmoud Yufeng Qian Chen-Shan Chin Adam M Phillippy Michael C Schatz Gene Myers Mark A DePristo Jue Ruan Tobias Marschall Fritz J Sedlazeck Justin M Zook Heng Li Sergey Koren Andrew Carroll David R Rank Michael W Hunkapiller

Nat Biotechnol 2019 10 12;37(10):1155-1162. Epub 2019 Aug 12.

Pacific Biosciences, Menlo Park, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0217-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776680PMC
October 2019

Therapist and client emotional expression and psychotherapy outcomes: A meta-analysis.

Authors:
Paul R Peluso Robert R Freund

Psychotherapy (Chic) 2018 12;55(4):461-472

Department of Counseling and Psychological Services, State University of New York at Oswego.

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http://doi.apa.org/getdoi.cfm?doi=10.1037/pst0000165
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http://dx.doi.org/10.1037/pst0000165DOI Listing
December 2018

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Authors:
Benjamin J Matthews Olga Dudchenko Sarah B Kingan Sergey Koren Igor Antoshechkin Jacob E Crawford William J Glassford Margaret Herre Seth N Redmond Noah H Rose Gareth D Weedall Yang Wu Sanjit S Batra Carlos A Brito-Sierra Steven D Buckingham Corey L Campbell Saki Chan Eric Cox Benjamin R Evans Thanyalak Fansiri Igor Filipović Albin Fontaine Andrea Gloria-Soria Richard Hall Vinita S Joardar Andrew K Jones Raissa G G Kay Vamsi K Kodali Joyce Lee Gareth J Lycett Sara N Mitchell Jill Muehling Michael R Murphy Arina D Omer Frederick A Partridge Paul Peluso Aviva Presser Aiden Vidya Ramasamy Gordana Rašić Sourav Roy Karla Saavedra-Rodriguez Shruti Sharan Atashi Sharma Melissa Laird Smith Joe Turner Allison M Weakley Zhilei Zhao Omar S Akbari William C Black Han Cao Alistair C Darby Catherine A Hill J Spencer Johnston Terence D Murphy Alexander S Raikhel David B Sattelle Igor V Sharakhov Bradley J White Li Zhao Erez Lieberman Aiden Richard S Mann Louis Lambrechts Jeffrey R Powell Maria V Sharakhova Zhijian Tu Hugh M Robertson Carolyn S McBride Alex R Hastie Jonas Korlach Daniel E Neafsey Adam M Phillippy Leslie B Vosshall

Nature 2018 11 14;563(7732):501-507. Epub 2018 Nov 14.

Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.

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http://www.nature.com/articles/s41586-018-0692-z
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http://dx.doi.org/10.1038/s41586-018-0692-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421076PMC
November 2018

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Authors:
John Huddleston Mark J P Chaisson Karyn Meltz Steinberg Wes Warren Kendra Hoekzema David Gordon Tina A Graves-Lindsay Katherine M Munson Zev N Kronenberg Laura Vives Paul Peluso Matthew Boitano Chen-Shin Chin Jonas Korlach Richard K Wilson Evan E Eichler

Genome Res 2018 01;28(1):144

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http://dx.doi.org/10.1101/gr.233007.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749179PMC
January 2018

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.

Authors:
Lorena Carro Imen Nouioui Vartul Sangal Jan P Meier-Kolthoff Martha E Trujillo Maria Del Carmen Montero-Calasanz Nevzat Sahin Darren Lee Smith Kristi E Kim Paul Peluso Shweta Deshpande Tanja Woyke Nicole Shapiro Nikos C Kyrpides Hans-Peter Klenk Markus Göker Michael Goodfellow

Sci Rep 2018 01 11;8(1):525. Epub 2018 Jan 11.

School of Biology, Newcastle University, Newcastle upon Tyne, UK.

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http://dx.doi.org/10.1038/s41598-017-17392-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765111PMC
January 2018

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Authors:
Xiaohan Yang Rongbin Hu Hengfu Yin Jerry Jenkins Shengqiang Shu Haibao Tang Degao Liu Deborah A Weighill Won Cheol Yim Jungmin Ha Karolina Heyduk David M Goodstein Hao-Bo Guo Robert C Moseley Elisabeth Fitzek Sara Jawdy Zhihao Zhang Meng Xie James Hartwell Jane Grimwood Paul E Abraham Ritesh Mewalal Juan D Beltrán Susanna F Boxall Louisa V Dever Kaitlin J Palla Rebecca Albion Travis Garcia Jesse A Mayer Sung Don Lim Ching Man Wai Paul Peluso Robert Van Buren Henrique Cestari De Paoli Anne M Borland Hong Guo Jin-Gui Chen Wellington Muchero Yanbin Yin Daniel A Jacobson Timothy J Tschaplinski Robert L Hettich Ray Ming Klaus Winter James H Leebens-Mack J Andrew C Smith John C Cushman Jeremy Schmutz Gerald A Tuskan

Nat Commun 2017 12 1;8(1):1899. Epub 2017 Dec 1.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.

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http://dx.doi.org/10.1038/s41467-017-01491-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711932PMC
December 2017

Improved maize reference genome with single-molecule technologies.

Authors:
Yinping Jiao Paul Peluso Jinghua Shi Tiffany Liang Michelle C Stitzer Bo Wang Michael S Campbell Joshua C Stein Xuehong Wei Chen-Shan Chin Katherine Guill Michael Regulski Sunita Kumari Andrew Olson Jonathan Gent Kevin L Schneider Thomas K Wolfgruber Michael R May Nathan M Springer Eric Antoniou W Richard McCombie Gernot G Presting Michael McMullen Jeffrey Ross-Ibarra R Kelly Dawe Alex Hastie David R Rank Doreen Ware

Nature 2017 06 12;546(7659):524-527. Epub 2017 Jun 12.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature22971DOI Listing
June 2017

Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Authors:
John Huddleston Mark J P Chaisson Karyn Meltz Steinberg Wes Warren Kendra Hoekzema David Gordon Tina A Graves-Lindsay Katherine M Munson Zev N Kronenberg Laura Vives Paul Peluso Matthew Boitano Chen-Shin Chin Jonas Korlach Richard K Wilson Evan E Eichler

Genome Res 2017 05 28;27(5):677-685. Epub 2016 Nov 28.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.

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http://genome.cshlp.org/content/early/2016/11/25/gr.214007.1
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http://dx.doi.org/10.1101/gr.214007.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411763PMC
May 2017

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

Authors:
Valerie A Schneider Tina Graves-Lindsay Kerstin Howe Nathan Bouk Hsiu-Chuan Chen Paul A Kitts Terence D Murphy Kim D Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T Simpson Glen Threadgold James Torrance Jonathan M Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M Phillippy Richard Durbin Richard K Wilson Paul Flicek Evan E Eichler Deanna M Church

Genome Res 2017 05 10;27(5):849-864. Epub 2017 Apr 10.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1101/gr.213611.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411779PMC
May 2017

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.

Authors:
Ole K Tørresen Bastiaan Star Sissel Jentoft William B Reinar Harald Grove Jason R Miller Brian P Walenz James Knight Jenny M Ekholm Paul Peluso Rolf B Edvardsen Ave Tooming-Klunderud Morten Skage Sigbjørn Lien Kjetill S Jakobsen Alexander J Nederbragt

BMC Genomics 2017 01 18;18(1):95. Epub 2017 Jan 18.

Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316, Norway.

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http://dx.doi.org/10.1186/s12864-016-3448-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241972PMC
January 2017

Phased diploid genome assembly with single-molecule real-time sequencing.

Authors:
Chen-Shan Chin Paul Peluso Fritz J Sedlazeck Maria Nattestad Gregory T Concepcion Alicia Clum Christopher Dunn Ronan O'Malley Rosa Figueroa-Balderas Abraham Morales-Cruz Grant R Cramer Massimo Delledonne Chongyuan Luo Joseph R Ecker Dario Cantu David R Rank Michael C Schatz

Nat Methods 2016 Dec 17;13(12):1050-1054. Epub 2016 Oct 17.

Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nmeth.4035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503144PMC
December 2016

Long-read, whole-genome shotgun sequence data for five model organisms.

Authors:
Kristi E Kim Paul Peluso Primo Babayan P Jane Yeadon Charles Yu William W Fisher Chen-Shan Chin Nicole A Rapicavoli David R Rank Joachim Li David E A Catcheside Susan E Celniker Adam M Phillippy Casey M Bergman Jane M Landolin

Sci Data 2014 25;1:140045. Epub 2014 Nov 25.

Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.

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http://dx.doi.org/10.1038/sdata.2014.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365909PMC
December 2015

Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene.

Authors:
Erick W Loomis John S Eid Paul Peluso Jun Yin Luke Hickey David Rank Sarah McCalmon Randi J Hagerman Flora Tassone Paul J Hagerman

Genome Res 2013 Jan 11;23(1):121-8. Epub 2012 Oct 11.

Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California 95616, USA.

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http://dx.doi.org/10.1101/gr.141705.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530672PMC
January 2013

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

Authors:
Daniël P Melters Keith R Bradnam Hugh A Young Natalie Telis Michael R May J Graham Ruby Robert Sebra Paul Peluso John Eid David Rank José Fernando Garcia Joseph L DeRisi Timothy Smith Christian Tobias Jeffrey Ross-Ibarra Ian Korf Simon W L Chan

Genome Biol 2013 Jan 30;14(1):R10. Epub 2013 Jan 30.

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http://dx.doi.org/10.1186/gb-2013-14-1-r10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053949PMC
January 2013

A hybrid approach for the automated finishing of bacterial genomes.

Authors:
Ali Bashir Aaron Klammer William P Robins Chen-Shan Chin Dale Webster Ellen Paxinos David Hsu Meredith Ashby Susana Wang Paul Peluso Robert Sebra Jon Sorenson James Bullard Jackie Yen Marie Valdovino Emilia Mollova Khai Luong Steven Lin Brianna LaMay Amruta Joshi Lori Rowe Michael Frace Cheryl L Tarr Maryann Turnsek Brigid M Davis Andrew Kasarskis John J Mekalanos Matthew K Waldor Eric E Schadt

Nat Biotechnol 2012 Jul 1;30(7):701-707. Epub 2012 Jul 1.

Pacific Biosciences, Menlo Park, CA.

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http://dx.doi.org/10.1038/nbt.2288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731737PMC
July 2012

A mathematical model of psychotherapy: an investigation using dynamic non-linear equations to model the therapeutic relationship.

Authors:
Paul R Peluso Larry S Liebovitch John M Gottman Michael D Norman Jessica Su

Psychother Res 2012 17;22(1):40-55. Epub 2011 Nov 17.

Florida Atlantic University, Counselor Education, Boca Raton, FL 33431, USA.

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http://dx.doi.org/10.1080/10503307.2011.622314DOI Listing
April 2012

Mathematical model of the dynamics of psychotherapy.

Authors:
Larry S Liebovitch Paul R Peluso Michael D Norman Jessica Su John M Gottman

Cogn Neurodyn 2011 Sep 22;5(3):265-75. Epub 2011 May 22.

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http://link.springer.com/10.1007/s11571-011-9157-x
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http://dx.doi.org/10.1007/s11571-011-9157-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179545PMC
September 2011

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.

Authors:
David A Rasko Dale R Webster Jason W Sahl Ali Bashir Nadia Boisen Flemming Scheutz Ellen E Paxinos Robert Sebra Chen-Shan Chin Dimitris Iliopoulos Aaron Klammer Paul Peluso Lawrence Lee Andrey O Kislyuk James Bullard Andrew Kasarskis Susanna Wang John Eid David Rank Julia C Redman Susan R Steyert Jakob Frimodt-Møller Carsten Struve Andreas M Petersen Karen A Krogfelt James P Nataro Eric E Schadt Matthew K Waldor

N Engl J Med 2011 Aug 27;365(8):709-17. Epub 2011 Jul 27.

University of Maryland School of Medicine, Institute for Genome Sciences and Department of Microbiology, Baltimore, USA.

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http://dx.doi.org/10.1056/NEJMoa1106920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168948PMC
August 2011

DHS working toward multi-band radios. Agencies will be able to communicate seamlessly across bands.

Authors:
Paul Peluso

EMS World 2011 Aug;40(8):54-5

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August 2011

The origin of the Haitian cholera outbreak strain.

Authors:
Chen-Shan Chin Jon Sorenson Jason B Harris William P Robins Richelle C Charles Roger R Jean-Charles James Bullard Dale R Webster Andrew Kasarskis Paul Peluso Ellen E Paxinos Yoshiharu Yamaichi Stephen B Calderwood John J Mekalanos Eric E Schadt Matthew K Waldor

N Engl J Med 2011 Jan 9;364(1):33-42. Epub 2010 Dec 9.

Pacific Biosciences, Menlo Park, CA, USA.

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http://dx.doi.org/10.1056/NEJMoa1012928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030187PMC
January 2011

Real-time DNA sequencing from single polymerase molecules.

Authors:
John Eid Adrian Fehr Jeremy Gray Khai Luong John Lyle Geoff Otto Paul Peluso David Rank Primo Baybayan Brad Bettman Arkadiusz Bibillo Keith Bjornson Bidhan Chaudhuri Frederick Christians Ronald Cicero Sonya Clark Ravindra Dalal Alex Dewinter John Dixon Mathieu Foquet Alfred Gaertner Paul Hardenbol Cheryl Heiner Kevin Hester David Holden Gregory 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 Sorenson Austin Tomaney Kevin Travers Mark Trulson John Vieceli Jeffrey Wegener Dawn Wu Alicia Yang Denis Zaccarin Peter Zhao Frank Zhong Jonas Korlach Stephen Turner

Science 2009 Jan 20;323(5910):133-8. Epub 2008 Nov 20.

Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA.

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http://dx.doi.org/10.1126/science.1162986DOI Listing
January 2009

Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotides.

Authors:
Jonas Korlach Arek Bibillo Jeffrey Wegener Paul Peluso Thang T Pham Insil Park Sonya Clark Geoff A Otto Stephen W Turner

Nucleosides Nucleotides Nucleic Acids 2008 Sep;27(9):1072-83

Pacific Biosciences Inc., Menlo Park, California 94025, USA.

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http://dx.doi.org/10.1080/15257770802260741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582155PMC
September 2008

Parallel confocal detection of single molecules in real time.

Authors:
Paul M Lundquist Cheng F Zhong Peiqian Zhao Austin B Tomaney Paul S Peluso John Dixon Brad Bettman Yves Lacroix Deborah P Kwo Etienne McCullough Mark Maxham Kevin Hester Paul McNitt Donald M Grey Carlos Henriquez Mathieu Foquet Stephen W Turner Denis Zaccarin

Opt Lett 2008 May;33(9):1026-8

Pacific Biosciences Inc., 1505 Adams Drive, Menlo Park, California 94025, USA.

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http://dx.doi.org/10.1364/ol.33.001026DOI Listing
May 2008

Optimizing antibody immobilization strategies for the construction of protein microarrays.

Authors:
Paul Peluso David S Wilson Duc Do Huu Tran Maanasa Venkatasubbaiah David Quincy Bettina Heidecker Kelli Poindexter Neil Tolani Michael Phelan Krista Witte Linda S Jung Peter Wagner Steffen Nock

Anal Biochem 2003 Jan;312(2):113-24

Zyomyx, Inc., 26101 Research Road, Hayward, CA 94544, USA.

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http://dx.doi.org/10.1016/s0003-2697(02)00442-6DOI Listing
January 2003

Improved method for pepsinolysis of mouse IgG(1) molecules to F(ab')(2) fragments.

Authors:
David S Wilson Jiangchun Wu Paul Peluso Steffen Nock

J Immunol Methods 2002 Feb;260(1-2):29-36

Department of Biochemistry, Zyomyx, Inc., 26101 Research Road, Hayward, CA 94545, USA.

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http://dx.doi.org/10.1016/s0022-1759(01)00514-2DOI Listing
February 2002