Publications by authors named "David H Ardell"

32Publications

Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens.

PLoS Negl Trop Dis 2020 02 27;14(2):e0007983. Epub 2020 Feb 27.

Quantitative and Systems Biology Program, University of California, Merced, California, United States of America.

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February 2020

tRNA functional signatures classify plastids as late-branching cyanobacteria.

BMC Evol Biol 2019 12 9;19(1):224. Epub 2019 Dec 9.

Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343, USA.

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December 2019

Match fitness landscapes for macromolecular interaction networks: Selection for translational accuracy and rate can displace tRNA-binding interfaces of non-cognate aminoacyl-tRNA synthetases.

Theor Popul Biol 2019 10 28;129:68-80. Epub 2019 Apr 28.

Quantitative and Systems Biology Program, University of California, Merced, CA, 95306, United States; Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, CA, 95306, United States. Electronic address:

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October 2019

Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria.

BMC Genomics 2016 12 8;17(1):1003. Epub 2016 Dec 8.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, BLSB 220, Philadelphia, PA, 19107, USA.

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December 2016

FAST: FAST Analysis of Sequences Toolbox.

Front Genet 2015 19;6:172. Epub 2015 May 19.

Quantitative and Systems Biology Program, University of California, Merced Merced, CA, USA ; Molecular Cell Biology Unit, School of Natural Sciences, University of California, Merced Merced, CA, USA.

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June 2015

Dynamic regulation of mRNA decay during neural development.

Neural Dev 2015 Apr 21;10:11. Epub 2015 Apr 21.

Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.

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April 2015

Eye movements during listening reveal spontaneous grammatical processing.

Front Psychol 2014 21;5:410. Epub 2014 May 21.

Cognitive and Information Sciences, University of California Merced, CA, USA.

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June 2014

tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria.

PLoS Comput Biol 2014 Feb 27;10(2):e1003454. Epub 2014 Feb 27.

Program in Quantitative and Systems Biology, University of California, Merced, Merced, California, United States of America.

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February 2014

CMCpy: Genetic Code-Message Coevolution Models in Python.

Evol Bioinform Online 2013 27;9:111-25. Epub 2013 Feb 27.

Center for Computational Biology, University of California, Merced, CA.

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March 2013

Computational analysis of tRNA identity.

Authors:
David H Ardell

FEBS Lett 2010 Jan;584(2):325-33

School of Natural Sciences and UC Merced Center for Computational Biology, University of California, Merced, CA 95343, USA.

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January 2010

An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters.

BMC Bioinformatics 2009 Aug 28;10:271. Epub 2009 Aug 28.

School of Natural Sciences, University of California, Merced, CA 95344, USA.

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August 2009

Structure is three to ten times more conserved than sequence--a study of structural response in protein cores.

Proteins 2009 Nov;77(3):499-508

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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November 2009

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring.

Genome Res 2008 Jun 17;18(6):888-99. Epub 2008 Mar 17.

Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.

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June 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 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Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu 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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November 2007

Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons.

J Bacteriol 2007 Dec 19;189(24):8993-9000. Epub 2007 Oct 19.

Department of Genetics, Microbiology and Toxicology, Stockholm University, Svante Arrhenius väg 16F, 106 91 Stockholm, Sweden.

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December 2007

New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria.

Biochimie 2007 Oct 31;89(10):1276-88. Epub 2007 Jul 31.

The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, 751 24 Uppsala, Sweden.

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October 2007

TFAM 1.0: an online tRNA function classifier.

Nucleic Acids Res 2007 Jul 25;35(Web Server issue):W350-3. Epub 2007 Jun 25.

Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-751 24 Uppsala, Sweden.

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July 2007

The coevolution of genes and genetic codes: Crick's frozen accident revisited.

J Mol Evol 2006 Sep 12;63(3):297-313. Epub 2006 Jul 12.

Center for the Study of Rationality, The Hebrew University, Givat Ram, 91904, Jerusalem, Israel.

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September 2006

Influences on gene expression in vivo by a Shine-Dalgarno sequence.

Mol Microbiol 2006 Apr;60(2):480-92

Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden.

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April 2006

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Nucleic Acids Res 2006 9;34(3):905-16. Epub 2006 Feb 9.

Linnaeus Centre for Bioinformatics, Uppsala University Uppsala, Sweden.

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March 2006

TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase.

Nucleic Acids Res 2006 9;34(3):893-904. Epub 2006 Feb 9.

Department of Molecular Evolution, Evolutionary Biology Center Norbyvägen 18C Uppsala University SE-752 36 Uppsala Sweden.

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March 2006

The genomic pattern of tDNA operon expression in E. coli.

PLoS Comput Biol 2005 Jun 24;1(1):e12. Epub 2005 Jun 24.

Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.

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June 2005

The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth.

J Mol Biol 2005 Aug;351(1):9-15

Department of Cell and Molecular Biology, Box 596, Biomedical Center, SE-751 24 Uppsala, Sweden.

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August 2005

The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae.

Proc Natl Acad Sci U S A 2004 Jun 21;101(26):9716-21. Epub 2004 Jun 21.

Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, and Department of Medical Sciences, Uppsala University Hospital, Sweden.

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June 2004

SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.

Authors:
David H Ardell

Bioinformatics 2004 Aug 1;20(12):1986-8. Epub 2004 Apr 1.

Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.

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August 2004

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

Genetics 2003 Dec;165(4):1761-77

Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden.

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December 2003

Three neuropeptide Y receptor genes in the spiny dogfish, Squalus acanthias, support en bloc duplications in early vertebrate evolution.

Mol Biol Evol 2003 Aug 30;20(8):1271-80. Epub 2003 May 30.

Department of Neuroscience, Unit of Pharmacology, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden.

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August 2003

No accident: genetic codes freeze in error-correcting patterns of the standard genetic code.

Philos Trans R Soc Lond B Biol Sci 2002 Nov;357(1427):1625-42

Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA.

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November 2002

The impact of message mutation on the fitness of a genetic code.

J Mol Evol 2002 May;54(5):638-51

Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA.

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May 2002