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Dan Graur

TitleProfessor
InstitutionUniversity of Houston
DepartmentBiology
Address4800 Calhoun Rd
Houston TX 77004
Phone713-743-7236
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    Collapse Research 
    Collapse research activities and funding
    R01LM010009     (GRAUR, DAN)Jul 1, 2009 - Jun 30, 2012
    NIH/NLM
    Error Correction in Multiple Sequence Alignments
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Graur D. An Upper Limit on the Functional Fraction of the Human Genome. Genome Biol Evol. 2017 Jul 01; 9(7):1880-1885. PMID: 28854598.
      View in: PubMed
    2. Price N, Graur D. Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol. 2016 Jan; 82(1):51-64. PMID: 26563252.
      View in: PubMed
    3. Graur D, Zheng Y, Azevedo RB. An evolutionary classification of genomic function. Genome Biol Evol. 2015 Jan 28; 7(3):642-5. PMID: 25635041.
      View in: PubMed
    4. Elhaik E, Graur D. A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes. PLoS Comput Biol. 2014 Nov; 10(11):e1003925. PMID: 25375262; PMCID: PMC4222635.
      View in: PubMed, PubMed Central
    5. Woehle C, Kusdian G, Radine C, Graur D, Landan G, Gould SB. 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. PMID: 25326207; PMCID: PMC4223856.
      View in: PubMed, PubMed Central
    6. Elhaik E, Tatarinova TV, Klyosov AA, Graur D. Reply to Mendez et al: the 'extremely ancient' chromosome that still isn't. Eur J Hum Genet. 2015 May; 23(5):567-8. PMID: 25315661; PMCID: PMC4402642.
      View in: PubMed, PubMed Central
    7. Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RF, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Vaerenbergh MV, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, Gibbs RA. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics. 2014 Jan 30; 15:86. PMID: 24479613; PMCID: PMC4028053.
      View in: PubMed, PubMed Central
    8. Graur D. Peer review: Payback time for referee refusal. Nature. 2014 Jan 23; 505(7484):483. PMID: 24451533.
      View in: PubMed
    9. Elhaik E, Tatarinova TV, Klyosov AA, Graur D. 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(9):1111-6. PMID: 24448544; PMCID: PMC4135414.
      View in: PubMed, PubMed Central
    10. Ezawa K, Landan G, Graur D. Detecting negative selection on recurrent mutations using gene genealogy. BMC Genet. 2013 May 07; 14:37. PMID: 23651527; PMCID: PMC3661350.
      View in: PubMed, PubMed Central
    11. Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Muñoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res. 2013 Aug; 23(8):1235-47. PMID: 23636946; PMCID: PMC3730098.
      View in: PubMed, PubMed Central
    12. Elhaik E, Graur D. IsoPlotter(+): A Tool for Studying the Compositional Architecture of Genomes. ISRN Bioinform. 2013; 2013:725434. PMID: 25937951; PMCID: PMC4393066.
      View in: PubMed, PubMed Central
    13. Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 2013; 5(3):578-90. PMID: 23431001; PMCID: PMC3622293.
      View in: PubMed, PubMed Central
    14. Sabath N, Morris JS, Graur D. 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; 73(5-6):305-15. PMID: 22187135.
      View in: PubMed
    15. Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 2011 Feb 10; 7(2):e1002007. PMID: 21347285; PMCID: PMC3037820.
      View in: PubMed, PubMed Central
    16. Cartwright RA, Graur D. The multiple personalities of Watson and Crick strands. Biol Direct. 2011 Feb 08; 6:7. PMID: 21303550; PMCID: PMC3055211.
      View in: PubMed, PubMed Central
    17. Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A. 2011 Apr 05; 108(14):5673-8. PMID: 21282631; PMCID: PMC3078359.
      View in: PubMed, PubMed Central
    18. Price N, Cartwright RA, Sabath N, Graur D, Azevedo RB. Neutral evolution of robustness in Drosophila microRNA precursors. Mol Biol Evol. 2011 Jul; 28(7):2115-23. PMID: 21285032; PMCID: PMC3167684.
      View in: PubMed, PubMed Central
    19. Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A. 2011 Apr 05; 108(14):5667-72. PMID: 21282651; PMCID: PMC3078412.
      View in: PubMed, PubMed Central
    20. Sabath N, Graur D. Detection of functional overlapping genes: simulation and case studies. J Mol Evol. 2010 Oct; 71(4):308-16. PMID: 20820768; PMCID: PMC2972474.
      View in: PubMed, PubMed Central
    21. Elhaik E, Graur D, Josic K, Landan G. Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm. Nucleic Acids Res. 2010 Aug; 38(15):e158. PMID: 20571085; PMCID: PMC2926622.
      View in: PubMed, PubMed Central
    22. Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Krause E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR. 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 06; 107(27):12168-73. PMID: 20566863; PMCID: PMC2901460.
      View in: PubMed, PubMed Central
    23. Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W23-8. PMID: 20497997; PMCID: PMC2896199.
      View in: PubMed, PubMed Central
    24. Penn O, Privman E, Landan G, Graur D, Pupko T. An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol. 2010 Aug; 27(8):1759-67. PMID: 20207713; PMCID: PMC2908709.
      View in: PubMed, PubMed Central
    25. Elhaik E, Graur D, Josic K. '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. PMID: 20158921; PMCID: PMC2841071.
      View in: PubMed, PubMed Central
    26. Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010 Jan 15; 327(5963):343-8. PMID: 20075255; PMCID: PMC2849982.
      View in: PubMed, PubMed Central
    27. Elhaik E, Graur D, Josic K. Comparative testing of DNA segmentation algorithms using benchmark simulations. Mol Biol Evol. 2010 May; 27(5):1015-24. PMID: 20018981.
      View in: PubMed
    28. Shaul S, Berel D, Benjamini Y, Graur D. Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications. RNA. 2010 Jan; 16(1):141-53. PMID: 19952117; PMCID: PMC2802024.
      View in: PubMed, PubMed Central
    29. Sabath N, Price N, Graur D. A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. Virol J. 2009 Sep 17; 6:144. PMID: 19761605; PMCID: PMC2754452.
      View in: PubMed, PubMed Central
    30. Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol. 2009 Jun 05; 1:114-8. PMID: 20333182; PMCID: PMC2817407.
      View in: PubMed, PubMed Central
    31. Elhaik E, Landan G, Graur D. Can GC content at third-codon positions be used as a proxy for isochore composition? Mol Biol Evol. 2009 Aug; 26(8):1829-33. PMID: 19443854.
      View in: PubMed
    32. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24; 324(5926):522-8. PMID: 19390049; PMCID: PMC2943200.
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    33. Sabath N, Landan G, Graur D. A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS One. 2008; 3(12):e3996. PMID: 19098983; PMCID: PMC2601044.
      View in: PubMed, PubMed Central
    34. Sabath N, Graur D, Landan G. Same-strand overlapping genes in bacteria: compositional determinants of phase bias. Biol Direct. 2008 Aug 21; 3:36. PMID: 18717987; PMCID: PMC2542354.
      View in: PubMed, PubMed Central
    35. Landan G, Graur D. Characterization of pairwise and multiple sequence alignment errors. Gene. 2009 Jul 15; 441(1-2):141-7. PMID: 18614299.
      View in: PubMed
    36. Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G. The genome of the model beetle and pest Tribolium castaneum. Nature. 2008 Apr 24; 452(7190):949-55. PMID: 18362917.
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    37. Landan G, Graur D. Local reliability measures from sets of co-optimal multiple sequence alignments. Pac Symp Biocomput. 2008; 15-24. PMID: 18229673.
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    38. Graur D. Public control could be a nightmare for researchers. Nature. 2007 Dec 20; 450(7173):1156. PMID: 18097376.
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    39. Elhaik E, Graur D, Josic K. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. Comput Biol Chem. 2008 Apr; 32(2):147. PMID: 18243804.
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    40. Landan G, Graur D. Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol. 2007 Jun; 24(6):1380-3. PMID: 17387100.
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    41. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10; 314(5801):941-52. PMID: 17095691; PMCID: PMC3159423.
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    42. Hazkani-Covo E, Graur D. A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol. 2007 Jan; 24(1):13-8. PMID: 17056643.
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    43. Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol. 2006 Oct; 23(10):1863-8. PMID: 16829541.
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    44. Mitchell A, Graur D. 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; 61(6):795-803. PMID: 16315108.
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    45. Dagan T, Blekhman R, Graur D. 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; 23(2):310-6. PMID: 16237210.
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    46. Elhaik E, Sabath N, Graur D. The "inverse relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence. Mol Biol Evol. 2006 Jan; 23(1):1-3. PMID: 16151190.
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    47. Hazkani-Covo E, Graur D. Evolutionary conservation of bacterial operons: does transcriptional connectivity matter? Genetica. 2005 Jul; 124(2-3):145-66. PMID: 16134329.
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    48. Graur D. Solidarity with the oppressed flat-Earthers. Nature. 2005 May 19; 435(7040):276. PMID: 15902231.
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    49. Hazkani-Covo E, Wool D, Graur D. 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 15; 304(2):150-8. PMID: 15779077.
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    50. Cohen N, Dagan T, Stone L, Graur D. GC composition of the human genome: in search of isochores. Mol Biol Evol. 2005 May; 22(5):1260-72. PMID: 15728737.
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    51. Dagan T, Graur D. The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence. Mol Biol Evol. 2005 Mar; 22(3):496-500. PMID: 15525696.
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    52. Mayrose I, Graur D, Ben-Tal N, Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol. 2004 Sep; 21(9):1781-91. PMID: 15201400.
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    53. Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, Graur D, Ast G. Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell. 2004 Apr 23; 14(2):221-31. PMID: 15099521.
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    54. Graur D, Martin W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 2004 Feb; 20(2):80-6. PMID: 14746989.
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    55. Dagan T, Sorek R, Sharon E, Ast G, Graur D. AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D489-92. PMID: 14681464; PMCID: PMC308866.
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    56. Hazkani-Covo E, Levanon EY, Rotman G, Graur D, Novik A. 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. PMID: 14984742.
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    57. Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS. 2004; 8(1):15-24. PMID: 15107234.
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    58. Pupko T, Sharan R, Hasegawa M, Shamir R, Graur D. Detecting excess radical replacements in phylogenetic trees. Gene. 2003 Nov 13; 319:127-35. PMID: 14597178.
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    59. Fleishman SJ, Dagan T, Graur D. pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes. Mol Biol Evol. 2003 Nov; 20(11):1876-80. PMID: 12885960.
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    60. Gophna U, Ron EZ, Graur D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene. 2003 Jul 17; 312:151-63. PMID: 12909351.
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    61. Hazkani-Covo E, Sorek R, Graur D. 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. PMID: 12574863.
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    62. Shaul S, Graur D. Playing chicken (Gallus gallus): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points. Gene. 2002 Oct 30; 300(1-2):59-61. PMID: 12468086.
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    63. Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N. 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. PMID: 12176835.
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    64. Dagan T, Talmor Y, Graur D. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol. 2002 Jul; 19(7):1022-5. PMID: 12082122.
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    65. Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res. 2002 Jul; 12(7):1060-7. PMID: 12097342; PMCID: PMC186627.
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    66. Hazkani-Covo E, Altman N, Horowitz M, Graur D. 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. PMID: 11734895.
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    67. Graur D, Pupko T. The Permian bacterium that isn't. Mol Biol Evol. 2001 Jun; 18(6):1143-6. PMID: 11371604.
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    68. Armon A, Graur D, Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol. 2001 Mar 16; 307(1):447-63. PMID: 11243830.
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    69. Pupko T, Pe'er I, Shamir R, Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol. 2000 Jun; 17(6):890-6. PMID: 10833195.
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    70. Mokady O, Loya Y, Achituv Y, Geffen E, Graur D, Rozenblatt S, Brickner I. Speciation versus phenotypic plasticity in coral inhabiting barnacles: Darwin's observations in an ecological context. J Mol Evol. 1999 Sep; 49(3):367-75. PMID: 10473778.
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    71. Pupko T, Graur D. Evolution of microsatellites in the yeast Saccharomyces cerevisiae: role of length and number of repeated units. J Mol Evol. 1999 Mar; 48(3):313-6. PMID: 10093220.
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    72. Ophir R, Itoh T, Graur D, Gojobori T. A simple method for estimating the intensity of purifying selection in protein-coding genes. Mol Biol Evol. 1999 Jan; 16(1):49-53. PMID: 10331251.
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    73. Ben-Dor A, Chor B, Graur D, Ophir R, Pelleg D. Constructing phylogenies from quartets: elucidation of eutherian superordinal relationships. J Comput Biol. 1998; 5(3):377-90. PMID: 9773339.
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    74. Ophir R, Graur D. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene. 1997 Dec 31; 205(1-2):191-202. PMID: 9461394.
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    75. Graur D, Gouy M, Duret L. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata. Mol Phylogenet Evol. 1997 Apr; 7(2):195-200. PMID: 9126561.
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    76. Arnason U, Xu X, Gullberg A, Graur D. The "Phoca standard": an external molecular reference for calibrating recent evolutionary divergences. J Mol Evol. 1996 Jul; 43(1):41-5. PMID: 8660422.
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    77. Jermiin LS, Foster PG, Graur D, Lowe RM, Crozier RH. Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA. J Mol Evol. 1996 Apr; 42(4):476-80. PMID: 8642618.
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    78. Graur D, Duret L, Gouy M. Phylogenetic position of the order Lagomorpha (rabbits, hares and allies) Nature. 1996 Jan 25; 379(6563):333-5. PMID: 8552186.
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    79. Elkeles A, Devos KM, Graur D, Zizi M, Breiman A. Multiple cDNAs of wheat voltage-dependent anion channels (VDAC): isolation, differential expression, mapping and evolution. Plant Mol Biol. 1995 Oct; 29(1):109-24. PMID: 7579156.
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    80. Crozier RH, Dobric N, Imai HT, Graur D, Cornuet JM, Taylor RW. Mitochondrial-DNA sequence evidence on the phylogeny of Australian jack-jumper ants of the Myrmecia pilosula complex. Mol Phylogenet Evol. 1995 Mar; 4(1):20-30. PMID: 7620633.
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    81. Jermiin LS, Graur D, Lowe RM, Crozier RH. Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. J Mol Evol. 1994 Aug; 39(2):160-73. PMID: 7932780.
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    82. Mokady O, Rozenblatt S, Graur D, Loya Y. Coral-host specificity of Red Sea Lithophaga bivalves: interspecific and intraspecific variation in 12S mitochondrial ribosomal RNA. Mol Mar Biol Biotechnol. 1994 Jun; 3(3):158-64. PMID: 7522832.
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    83. Graur D, Higgins DG. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Mol Biol Evol. 1994 May; 11(3):357-64. PMID: 8015431.
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    84. Graur D. Reply from d. Graur. Trends Ecol Evol. 1993 Sep; 8(9):341-2. PMID: 21236189.
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    85. Graur D. Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals. FEBS Lett. 1993 Jun 28; 325(1-2):152-9. PMID: 8513886.
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    86. Graur D. Molecular deconstructivism. Nature. 1993 Jun 10; 363(6429):490. PMID: 8505972.
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    87. Graur D. Molecular phylogeny and the higher classification of eutherian mammals. Trends Ecol Evol. 1993 Apr; 8(4):141-7. PMID: 21236131.
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    88. Ma DP, Zharkikh A, Graur D, VandeBerg JL, Li WH. Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes. J Mol Evol. 1993 Apr; 36(4):327-34. PMID: 8315653.
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    89. Li WH, Hide WA, Graur D. Origin of rodents and guinea-pigs. Nature. 1992 Sep 24; 359(6393):277-8. PMID: 1406931.
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    90. Li WH, Hide WA, Zharkikh A, Ma DP, Graur D. The molecular taxonomy and evolution of the guinea pig. J Hered. 1992 May-Jun; 83(3):174-81. PMID: 1624762.
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    91. Graur D, Hide WA, Zharkikh A, Li WH. The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order rodentia. Comp Biochem Physiol B. 1992 Apr; 101(4):495-8. PMID: 1611868.
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    92. Breiman A, Bogher M, Sternberg H, Graur D. Variability and uniformity of mitochondrial DNA in populations of putative diploid ancestors of common wheat. Theor Appl Genet. 1991 Aug; 82(2):201-8. PMID: 24213067.
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    93. Graur D, Hide WA, Li WH. Is the guinea-pig a rodent? Nature. 1991 Jun 20; 351(6328):649-52. PMID: 2052090.
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    94. Landan G, Bdolah A, Wollberg Z, Kochva E, Graur D. The evolutionary history of the sarafotoxin/endothelin/endothelin-like superfamily. J Cardiovasc Pharmacol. 1991; 17 Suppl 7:S517-9. PMID: 1725430.
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    95. Landan G, Bdolah A, Wollberg Z, Kochva E, Graur D. Evolution of the sarafotoxin/endothelin superfamily of proteins. Toxicon. 1991; 29(2):237-44. PMID: 2048141.
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    96. Landan G, Cohen G, Aharonowitz Y, Shuali Y, Graur D, Shiffman D. Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer. Mol Biol Evol. 1990 Sep; 7(5):399-406. PMID: 2263192.
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    97. Graur D, Shuali Y, Li WH. Deletions in processed pseudogenes accumulate faster in rodents than in humans. J Mol Evol. 1989 Apr; 28(4):279-85. PMID: 2499684.
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    98. Ticher A, Graur D. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J Mol Evol. 1989 Apr; 28(4):286-98. PMID: 2499685.
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    99. Graur D, Li WH. Evolution of protein inhibitors of serine proteinases: positive Darwinian selection or compositional effects? J Mol Evol. 1988 Dec-1989 Feb; 28(1-2):131-5. PMID: 3148733.
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    100. Graur D. The evolution of electrophoretic mobility of proteins. J Theor Biol. 1986 Feb 21; 118(4):443-69. PMID: 3713219.
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    101. Graur D. Amino acid composition and the evolutionary rates of protein-coding genes. J Mol Evol. 1985; 22(1):53-62. PMID: 3932664.
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    102. Graur D. GENE DIVERSITY IN HYMENOPTERA. Evolution. 1985 Jan; 39(1):190-199. PMID: 28563652.
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    103. Graur D. Pattern of nucleotide substitution and the extent of purifying selection in retroviruses. J Mol Evol. 1984-1985; 21(3):221-31. PMID: 6443129.
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    104. Graur D, Wool D. Dynamics and genetics of mating behavior in Tribolium castaneum (Coleoptera: Tenebrionidae). Behav Genet. 1982 Mar; 12(2):161-9. PMID: 6957191.
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    105. Gojobori T, Li WH, Graur D. Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol. 1982; 18(5):360-9. PMID: 7120431.
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