Dan Graur

Dan Graur

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: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements.

Genes (Basel) 2019 02 26;10(3). Epub 2019 Feb 26.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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http://dx.doi.org/10.3390/genes10030181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471834PMC
February 2019

Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.

J Mol Evol 2018 07 28;86(6):365-378. Epub 2018 Jun 28.

Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.

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http://dx.doi.org/10.1007/s00239-018-9853-9DOI Listing
July 2018

An Upper Limit on the Functional Fraction of the Human Genome.

Authors:
Dan Graur

Genome Biol Evol 2017 07;9(7):1880-1885

Department of Biology and Biochemistry, University of Houston, TX.

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http://dx.doi.org/10.1093/gbe/evx121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035PMC
July 2017

Are Synonymous Sites in Primates and Rodents Functionally Constrained?

J Mol Evol 2016 Jan 12;82(1):51-64. Epub 2015 Nov 12.

Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.

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http://link.springer.com/content/pdf/10.1007%2Fs00239-015-97
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http://link.springer.com/10.1007/s00239-015-9719-3
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http://dx.doi.org/10.1007/s00239-015-9719-3DOI Listing
January 2016

IsoPlotter(+): A Tool for Studying the Compositional Architecture of Genomes.

ISRN Bioinform 2013 18;2013:725434. Epub 2013 Apr 18.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1155/2013/725434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393066PMC
May 2015

Reply to Mendez et al: the 'extremely ancient' chromosome that still isn't.

Eur J Hum Genet 2015 May 15;23(5):567-8. Epub 2014 Oct 15.

Department of Biology & Biochemistry, University of Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/ejhg.2014.227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402642PMC
May 2015

An evolutionary classification of genomic function.

Genome Biol Evol 2015 Jan 28;7(3):642-5. Epub 2015 Jan 28.

Department of Biology and Biochemistry, University of Houston.

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http://dx.doi.org/10.1093/gbe/evv021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322545PMC
January 2015

A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.

PLoS Comput Biol 2014 Nov 6;10(11):e1003925. Epub 2014 Nov 6.

Department of Biology & Biochemistry, University of Houston, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222635PMC
November 2014

The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes.

BMC Genomics 2014 Oct 17;15:906. Epub 2014 Oct 17.

Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1186/1471-2164-15-906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223856PMC
October 2014

The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome.

Eur J Hum Genet 2014 Sep 22;22(9):1111-6. Epub 2014 Jan 22.

Department of Biology & Biochemistry, University of Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/ejhg.2013.303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135414PMC
September 2014

Peer review: Payback time for referee refusal.

Authors:
Dan Graur

Nature 2014 Jan;505(7484):483

University of Houston, Texas, USA.

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http://dx.doi.org/10.1038/505483aDOI Listing
January 2014

Detecting negative selection on recurrent mutations using gene genealogy.

BMC Genet 2013 May 7;14:37. Epub 2013 May 7.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1186/1471-2156-14-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661350PMC
May 2013

Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences.

J Mol Evol 2011 Dec 21;73(5-6):305-15. Epub 2011 Dec 21.

Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland.

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http://link.springer.com/10.1007/s00239-011-9477-9
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http://dx.doi.org/10.1007/s00239-011-9477-9DOI Listing
December 2011

Neutral evolution of robustness in Drosophila microRNA precursors.

Mol Biol Evol 2011 Jul 31;28(7):2115-23. Epub 2011 Jan 31.

Department of Biology and Biochemistry, University of Houston, USA.

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http://dx.doi.org/10.1093/molbev/msr029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167684PMC
July 2011

The multiple personalities of Watson and Crick strands.

Biol Direct 2011 Feb 8;6. Epub 2011 Feb 8.

Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.

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http://dx.doi.org/10.1186/1745-6150-6-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055211PMC
February 2011

Detection of functional overlapping genes: simulation and case studies.

J Mol Evol 2010 Oct 4;71(4):308-16. Epub 2010 Sep 4.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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http://dx.doi.org/10.1007/s00239-010-9386-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972474PMC
October 2010

An alignment confidence score capturing robustness to guide tree uncertainty.

Mol Biol Evol 2010 Aug 5;27(8):1759-67. Epub 2010 Mar 5.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

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http://www.tau.ac.il/~talp/publications/GuidanceAlgorithm.pd
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http://guidance.tau.ac.il/An_alignment_confidence_score_capt
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msq066
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http://dx.doi.org/10.1093/molbev/msq066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908709PMC
August 2010

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.

Nucleic Acids Res 2010 Aug 22;38(15):e158. Epub 2010 Jun 22.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkq532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926622PMC
August 2010

GUIDANCE: a web server for assessing alignment confidence scores.

Nucleic Acids Res 2010 Jul 23;38(Web Server issue):W23-8. Epub 2010 May 23.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkq443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896199PMC
July 2010

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Proc Natl Acad Sci U S A 2010 Jul 21;107(27):12168-73. Epub 2010 Jun 21.

J Craig Venter Institute, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1073/pnas.1003379107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901460PMC
July 2010

Comparative testing of DNA segmentation algorithms using benchmark simulations.

Mol Biol Evol 2010 May 16;27(5):1015-24. Epub 2009 Dec 16.

Department of Biology & Biochemistry, University of Houston, TX, USA.

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http://nsmn1.uh.edu/dgraur/pdf/2010_elhaik_josic_graur_mbe.p
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msp307
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http://dx.doi.org/10.1093/molbev/msp307DOI Listing
May 2010

'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve.

Biol Direct 2010 Feb 17;5:10. Epub 2010 Feb 17.

McKusick - Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1186/1745-6150-5-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841071PMC
February 2010

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.

RNA 2010 Jan 1;16(1):141-53. Epub 2009 Dec 1.

Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1261/rna.1745910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802024PMC
January 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives.

Virol J 2009 Sep 17;6:144. Epub 2009 Sep 17.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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http://virologyj.biomedcentral.com/articles/10.1186/1743-422
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http://dx.doi.org/10.1186/1743-422X-6-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754452PMC
September 2009

Can GC content at third-codon positions be used as a proxy for isochore composition?

Mol Biol Evol 2009 Aug 14;26(8):1829-33. Epub 2009 May 14.

Department of Biology and Biochemistry, University of Houston, TX, USA.

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http://dx.doi.org/10.1093/molbev/msp100DOI Listing
August 2009

Characterization of pairwise and multiple sequence alignment errors.

Gene 2009 Jul 3;441(1-2):141-7. Epub 2008 Jun 3.

Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1016/j.gene.2008.05.016DOI Listing
July 2009

A method for the simultaneous estimation of selection intensities in overlapping genes.

PLoS One 2008 22;3(12):e3996. Epub 2008 Dec 22.

Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003996PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2601044PMC
June 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Same-strand overlapping genes in bacteria: compositional determinants of phase bias.

Biol Direct 2008 Aug 21;3:36. Epub 2008 Aug 21.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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http://dx.doi.org/10.1186/1745-6150-3-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542354PMC
August 2008

'Genome order index' should not be used for defining compositional constraints in nucleotide sequences.

Comput Biol Chem 2008 Apr 15;32(2):147. Epub 2007 Dec 15.

Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2007.11.003DOI Listing
April 2008

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Local reliability measures from sets of co-optimal multiple sequence alignments.

Pac Symp Biocomput 2008 :15-24

Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA.

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March 2008

Public control could be a nightmare for researchers.

Authors:
Dan Graur

Nature 2007 Dec;450(7173):1156

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http://dx.doi.org/10.1038/4501156bDOI Listing
December 2007

Heads or tails: a simple reliability check for multiple sequence alignments.

Mol Biol Evol 2007 Jun 25;24(6):1380-3. Epub 2007 Mar 25.

Department of Biology & Biochemistry, University of Houston, TX, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msm060DOI Listing
June 2007

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
Erica Sodergren George M Weinstock Eric H Davidson R Andrew Cameron Richard A Gibbs Robert C Angerer Lynne M Angerer Maria Ina Arnone David R Burgess Robert D Burke James A Coffman Michael Dean Maurice R Elphick Charles A Ettensohn Kathy R Foltz Amro Hamdoun Richard O Hynes William H Klein William Marzluff David R McClay Robert L Morris Arcady Mushegian Jonathan P Rast L Courtney Smith Michael C Thorndyke Victor D Vacquier Gary M Wessel Greg Wray Lan Zhang Christine G Elsik Olga Ermolaeva Wratko Hlavina Gretchen Hofmann Paul Kitts Melissa J Landrum Aaron J Mackey Donna Maglott Georgia Panopoulou Albert J Poustka Kim Pruitt Victor Sapojnikov Xingzhi Song Alexandre Souvorov Victor Solovyev Zheng Wei Charles A Whittaker Kim Worley K James Durbin Yufeng Shen Olivier Fedrigo David Garfield Ralph Haygood Alexander Primus Rahul Satija Tonya Severson Manuel L Gonzalez-Garay Andrew R Jackson Aleksandar Milosavljevic Mark Tong Christopher E Killian Brian T Livingston Fred H Wilt Nikki Adams Robert Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière Manisha Goel Hemant Kelkar Julia Morales Odile Mulner-Lorillon Anthony J Robertson Jared V Goldstone Bryan Cole David Epel Bert Gold Mark E Hahn Meredith Howard-Ashby Mark Scally John J Stegeman Erin L Allgood Jonah Cool Kyle M Judkins Shawn S McCafferty Ashlan M Musante Robert A Obar Amanda P Rawson Blair J Rossetti Ian R Gibbons Matthew P Hoffman Andrew Leone Sorin Istrail Stefan C Materna Manoj P Samanta Viktor Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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http://dx.doi.org/10.1126/science.1133609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423PMC
November 2006

The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.

Mol Biol Evol 2006 Feb 19;23(2):310-6. Epub 2005 Oct 19.

Institüt für Botanik III, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1093/molbev/msj036DOI Listing
February 2006

Inferring the pattern of spontaneous mutation from the pattern of substitution in unitary pseudogenes of Mycobacterium leprae and a comparison of mutation patterns among distantly related organisms.

J Mol Evol 2005 Dec 2;61(6):795-803. Epub 2005 Nov 2.

Department fo Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv, 69978, Israel.

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http://link.springer.com/10.1007/s00239-004-0235-0
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December 2005

Evolutionary conservation of bacterial operons: does transcriptional connectivity matter?

Genetica 2005 Jul;124(2-3):145-66

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1007/s10709-005-0950-5DOI Listing
July 2005

GC composition of the human genome: in search of isochores.

Mol Biol Evol 2005 May 23;22(5):1260-72. Epub 2005 Feb 23.

School of Computing, University of Leeds, Leeds, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msi115DOI Listing
May 2005

Solidarity with the oppressed flat-Earthers.

Authors:
Dan Graur

Nature 2005 May;435(7040):276

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http://dx.doi.org/10.1038/435276cDOI Listing
May 2005

The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence.

Authors:
Tal Dagan Dan Graur

Mol Biol Evol 2005 Mar 3;22(3):496-500. Epub 2004 Nov 3.

Department of Zoology, George S. Wise Faculty of Life Science, Tel Aviv University, Ramat Aviv, Israel.

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March 2005

In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law.

J Exp Zool B Mol Dev Evol 2005 Mar;304(2):150-8

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1002/jez.b.21033DOI Listing
March 2005

Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control.

OMICS 2004 ;8(1):15-24

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel and Bioinformatics Unit, Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel.

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November 2004

Evolution of multicellularity in Metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis.

Cell Biol Int 2004 ;28(3):171-8

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1016/j.cellbi.2003.11.016DOI Listing
October 2004

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

Mol Biol Evol 2004 Sep 16;21(9):1781-91. Epub 2004 Jun 16.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.

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http://dx.doi.org/10.1093/molbev/msh194DOI Listing
September 2004

Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.

Mol Cell 2004 Apr;14(2):221-31

Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1016/s1097-2765(04)00181-9DOI Listing
April 2004

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.

Trends Genet 2004 Feb;20(2):80-6

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1016/j.tig.2003.12.003DOI Listing
February 2004

AluGene: a database of Alu elements incorporated within protein-coding genes.

Nucleic Acids Res 2004 Jan;32(Database issue):D489-92

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkh132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308866PMC
January 2004

pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes.

Mol Biol Evol 2003 Nov 28;20(11):1876-80. Epub 2003 Jul 28.

Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel.

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http://dx.doi.org/10.1093/molbev/msg202DOI Listing
November 2003

Detecting excess radical replacements in phylogenetic trees.

Gene 2003 Nov;319:127-35

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel.

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http://dx.doi.org/10.1016/s0378-1119(03)00802-3DOI Listing
November 2003

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.

Gene 2003 Jul;312:151-63

Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel 69978.

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http://dx.doi.org/10.1016/s0378-1119(03)00612-7DOI Listing
July 2003

Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications.

J Mol Evol 2003 Feb;56(2):169-74

Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, 69978, Ramat Aviv, Israel.

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http://link.springer.com/10.1007/s00239-002-2390-5
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February 2003

Playing chicken (Gallus gallus): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points.

Gene 2002 Oct;300(1-2):59-61

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.

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http://dx.doi.org/10.1016/s0378-1119(02)00851-xDOI Listing
October 2002

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.

Bioinformatics 2002 Aug;18(8):1116-23

The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan.

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http://dx.doi.org/10.1093/bioinformatics/18.8.1116DOI Listing
August 2002

Alu-containing exons are alternatively spliced.

Genome Res 2002 Jul;12(7):1060-7

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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http://dx.doi.org/10.1101/gr.229302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186627PMC
July 2002

The evolutionary history of prosaposin: two successive tandem-duplication events gave rise to the four saposin domains in vertebrates.

J Mol Evol 2002 Jan;54(1):30-4

Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

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January 2002

GENE DIVERSITY IN HYMENOPTERA.

Authors:
Dan Graur

Evolution 1985 Jan;39(1):190-199

Center for Demographic and Population Genetics, The University of Texas Health Science Center at Houston, P.O. Box 20334, Houston, TX, 77225.

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January 1985