David H Ardell

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

Whole RNA-Sequencing and Transcriptome Assembly of Candida albicans and Candida africana under Chlamydospore-Inducing Conditions.

Authors:

Domenico Giosa Maria Rosa Felice Travis J Lawrence Megha Gulati Fabio Scordino Letterio Giuffrè Carla Lo Passo Enrico D'Alessandro Giuseppe Criseo David H Ardell Aaron D Hernday Clarissa J Nobile Orazio Romeo

Genome Biol Evol 2017 07;9(7):1971-1977

IRCCS Centro Neurolesi "Bonino-Pulejo," Messina, Italy.

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July 2017

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

Authors:

David H Ardell Ya-Ming Hou

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.

Authors:

Travis J Lawrence Kyle T Kauffman Katherine C H Amrine Dana L Carper Raymond S Lee Peter J Becich Claudia J Canales David H Ardell

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.

Authors:

Dana A Burow Maxine C Umeh-Garcia Marie B True Crystal D Bakhaj David H Ardell Michael D Cleary

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.

Authors:

Stephanie Huette Bodo Winter Teenie Matlock David H Ardell Michael Spivey

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.

Authors:

Katherine C H Amrine Wesley D Swingley David H Ardell

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.

Authors:

Peter J Becich Brian P Stark Harish S Bhat David H Ardell

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.

Authors:

Ronna R Mallios David M Ojcius David H Ardell

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.

Authors:

Kristoffer Illergård David H Ardell Arne Elofsson

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.

Authors:

Pontus Larsson Andrea Hinas David H Ardell Leif A Kirsebom Anders Virtanen Fredrik Söderbom

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 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 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.

Authors:

Mirjana Macvanin Ernesto I Gonzalez de Valdivia David H Ardell Leif A Isaksson

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.

Authors:

Eva Freyhult Yuanyuan Cui Olle Nilsson David H Ardell

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.

Authors:

Helena Tåquist Yuanyuan Cui David H Ardell

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

Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates: a hypothesis for interconversion between DNA and RNA deletion.

Authors:

Wei-Jen Chang Victoria M Addis Anya J Li Elin Axelsson David H Ardell Laura F Landweber

Biol Direct 2007 Feb 1;2. Epub 2007 Feb 1.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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February 2007

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

Authors:

Guy Sella David H Ardell

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.

Authors:

Haining Jin Qing Zhao Ernesto I Gonzalez de Valdivia David H Ardell Magnus Stenström Leif A Isaksson

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.

Authors:

Eva Freyhult Vincent Moulton David H Ardell

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.

Authors:

David H Ardell Siv G E Andersson

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.

Authors:

David H Ardell Leif A Kirsebom

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.

Authors:

B M Fredrik Pettersson David H Ardell Leif A Kirsebom

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.

Authors:

Cecilia M Alsmark A Carolin Frank E Olof Karlberg Boris-Antoine Legault David H Ardell Björn Canbäck Ann-Sofie Eriksson A Kristina Näslund Scott A Handley Maxime Huvet Bernard La Scola Martin Holmberg Siv G E Andersson

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