Publications by authors named "James A Yorke"

42Publications

When the Best Pandemic Models are the Simplest.

Biology (Basel) 2020 Oct 23;9(11). Epub 2020 Oct 23.

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.3390/biology9110353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7690679PMC
October 2020

Low-dimensional paradigms for high-dimensional hetero-chaos.

Chaos 2018 Oct;28(10):103110

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1063/1.5045693DOI Listing
October 2018

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Gigascience 2017 01;6(1):1-4

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD.

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http://dx.doi.org/10.1093/gigascience/giw016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437942PMC
January 2017

Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species.

BMC Genomics 2016 11 11;17(Suppl 10):826. Epub 2016 Nov 11.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA.

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http://dx.doi.org/10.1186/s12864-016-3102-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123246PMC
November 2016

Hybrid assembly of the large and highly repetitive genome of , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Genome Res 2017 05 27;27(5):787-792. Epub 2017 Jan 27.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.213405.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411773PMC
May 2017

Partially controlling transient chaos in the Lorenz equations.

Philos Trans A Math Phys Eng Sci 2017 Mar;375(2088)

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1098/rsta.2016.0211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311432PMC
March 2017

Testing for Basins of Wada.

Sci Rep 2015 Nov 10;5:16579. Epub 2015 Nov 10.

University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1038/srep16579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4639726PMC
November 2015

QuorUM: An Error Corrector for Illumina Reads.

PLoS One 2015 17;10(6):e0130821. Epub 2015 Jun 17.

IPST, University of Maryland, College Park, MD, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471408PMC
May 2016

Geometry of the edge of chaos in a low-dimensional turbulent shear flow model.

Phys Rev E Stat Nonlin Soft Matter Phys 2015 May 7;91(5):052903. Epub 2015 May 7.

University of Maryland, College Park, Maryland 20742, USA.

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https://link.aps.org/doi/10.1103/PhysRevE.91.052903
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http://dx.doi.org/10.1103/PhysRevE.91.052903DOI Listing
May 2015

Scaling of chaos versus periodicity: how certain is it that an attractor is chaotic?

Phys Rev Lett 2014 Aug 20;113(8):084101. Epub 2014 Aug 20.

University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1103/PhysRevLett.113.084101DOI Listing
August 2014

A period-doubling cascade precedes chaos for planar maps.

Chaos 2013 Sep;23(3):033113

Department of Mathematical Sciences, George Mason University, 4400 University Dr., Fairfax, Virginia 22030, USA.

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http://dx.doi.org/10.1063/1.4813600DOI Listing
September 2013

The MaSuRCA genome assembler.

Bioinformatics 2013 Nov 29;29(21):2669-77. Epub 2013 Aug 29.

Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742, USA, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Department of Physics, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799473PMC
November 2013

Dynamics of partial control.

Chaos 2012 Dec;22(4):047507

Departamento de Física, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid, Spain.

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http://dx.doi.org/10.1063/1.4754874DOI Listing
December 2012

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

PLoS One 2012 3;7(8):e42680. Epub 2012 Aug 3.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042680PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411808PMC
January 2013

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Duplication count distributions in DNA sequences.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Dec 11;78(6 Pt 1):061912. Epub 2008 Dec 11.

Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121164PMC
http://dx.doi.org/10.1103/PhysRevE.78.061912DOI Listing
December 2008

When Lyapunov exponents fail to exist.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Nov 7;78(5 Pt 2):056203. Epub 2008 Nov 7.

Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA.

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http://dx.doi.org/10.1103/PhysRevE.78.056203DOI Listing
November 2008

Partial control of chaotic systems.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 May 6;77(5 Pt 2):055201. Epub 2008 May 6.

Departamento de Física, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid, Spain.

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http://dx.doi.org/10.1103/PhysRevE.77.055201DOI Listing
May 2008

Figaro: a novel statistical method for vector sequence removal.

Bioinformatics 2008 Feb 17;24(4):462-7. Epub 2008 Jan 17.

Center for Bioinformatics and Computational Biology, University of Maryland - College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm632DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725436PMC
February 2008

Assembly reconciliation.

Bioinformatics 2008 Jan 5;24(1):42-5. Epub 2007 Dec 5.

IPST, University of Maryland, College Park, Agencourt Bioscience Inc., Beverly, MA.

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http://dx.doi.org/10.1093/bioinformatics/btm542DOI Listing
January 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja 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Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Turbulence transition and the edge of chaos in pipe flow.

Phys Rev Lett 2007 Jul 20;99(3):034502. Epub 2007 Jul 20.

Fachbereich Physik, Philipps-Universität Marburg, Renthof 6, D-35032 Marburg, Germany.

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http://dx.doi.org/10.1103/PhysRevLett.99.034502DOI Listing
July 2007

Reconciling different infectivity estimates for HIV-1.

J Acquir Immune Defic Syndr 2006 Nov;43(3):253-6

Natural Sciences and Mathematics, NAMS, Richard Stockton College of New Jersey, Pomona, 08240, USA.

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http://www.who.int/hiv/events/artprevention/rapatski.pdf
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/01.qai.0000243095.19405.5cDOI Listing
November 2006

Edge of chaos in a parallel shear flow.

Phys Rev Lett 2006 May 5;96(17):174101. Epub 2006 May 5.

Department of Mathematics, University of Maryland, College Park, USA.

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http://yorke.umd.edu/Yorke_papers_most_cited_and_post2000/20
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http://link.aps.org/doi/10.1103/PhysRevLett.96.174101
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http://dx.doi.org/10.1103/PhysRevLett.96.174101DOI Listing
May 2006

Making forecasts for chaotic physical processes.

Phys Rev Lett 2006 Apr 14;96(14):144102. Epub 2006 Apr 14.

University of Maryland, College Park, MD 20742-4015, USA.

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http://dx.doi.org/10.1103/PhysRevLett.96.144102DOI Listing
April 2006

Beware of mis-assembled genomes.

Bioinformatics 2005 Dec;21(24):4320-1

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http://dx.doi.org/10.1093/bioinformatics/bti769DOI Listing
December 2005

Convex error growth patterns in a global weather model.

Phys Rev Lett 2005 Jun 10;94(22):228501. Epub 2005 Jun 10.

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.

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http://www.personal.psu.edu/jzh13/paper/PRL2005_HarOczYorKal
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http://www.weatherchaos.umd.edu/papers/Harlim_et_al_2005.pdf
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http://link.aps.org/doi/10.1103/PhysRevLett.94.228501
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http://dx.doi.org/10.1103/PhysRevLett.94.228501DOI Listing
June 2005

HIV epidemics driven by late disease stage transmission.

J Acquir Immune Defic Syndr 2005 Mar;38(3):241-53

Department of Mathematics, University of Maryland, College Park, MD 20742, USA.

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http://www.killi.com/brandy/JAIDS3-05.pdf
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March 2005

A preprocessor for shotgun assembly of large genomes.

J Comput Biol 2004 ;11(4):734-52

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA.

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http://dx.doi.org/10.1089/cmb.2004.11.734DOI Listing
January 2005

Reducing storage requirements for biological sequence comparison.

Bioinformatics 2004 Dec 15;20(18):3363-9. Epub 2004 Jul 15.

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth408DOI Listing
December 2004

Indecomposable continua in dynamical systems with noise: Fluid flow past an array of cylinders.

Chaos 1997 Mar;7(1):125-138

Institute for Physical Science and Technology, University of Maryland at College Park, College Park, Maryland 20742and Departamento de Fisica e Instalaciones Aplicadas, E.T.S. de Arquitectura, Universidad Politecnica de Madrid, 28040 Madrid, Spain.

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http://dx.doi.org/10.1063/1.166244DOI Listing
March 1997