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Faculty Biography For:

Dan Graur
John and Rebecca Moores Professor
Ph.D., University of Texas at Houston, 1985

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

Office: SR2 352
Phone: (713) 743-7236
dgraur@uh.edu


My research interests consist of several theoretical, statistical, and analytical topics within the broad area of molecular evolution:

Elucidation of the relative roles of mutation and drift versus purifying selection in determining the pattern of nucleotide substitution. A major part of this study involves studies of the methodology of inferring selection from comparative genomic data.

Producing dynamic and static descriptions of the compositional features of genomes. Studying compositionally homogeneous regions within genomes.

Assessment of the efficiency and efficacy limits of alignment and phylogenetic reconstruction methods. Correcting errors in multiple sequence alignments.

Identification of pseudogenes within completely sequenced genomes and determination of nonfunctionalization times.

Assessing mutation rate variation within and between genomes.

Physico-chemical characterization of deleterious and neutral amino-acid replacements.

Determination of the validity and applicability of the "molecular clock" concept to protein-coding genes and pseudogenes at the inter- and intraordinal levels.

Reconstruction of phylogenetic relationships among and within eutherian orders. Such studies are also concerned with questions pertaining to the monophyly or paraphyly of higher taxa.

Cartwright RA and Graur D. 2011. The multiple personalities of Watson and Crick strands. Biology Direct 6:7.

Suen G et al. 2011. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 7:e1002007.

Smith CR et al. 2011.The draft genome of the red harvester ant, Pogonomyrmex barbatus. Proc. Natl. Acad. Sci. USA 108:5667-5672.

Smith C et al. 2011. The draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc. Natl. Acad. Sci. USA 108:5673-5678.

Price N et al. 2011. Neutral evolution of robustness in Drosophila microRNA precursors. Mol. Biol. Evol. 28:2115-2123.

Sabath N et al. 2011. 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. 73:305-315.

Elhaik E et al. 2010. Genome order index should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve. Biology Direct 5:10.

Kirkness EF et al. 2010. Sequences of the human body louse and its primary endosymbiont. Proc. Natl. Acad. Sci. USA 107:1216812173.

Penn O et al. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Mol. Biol. Evol. 27:1759-1767.

Penn O et al. 2010. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38: W23-W28.

Sabath N and Graur D. 2010. Detection of functional overlapping genes: simulation and case studies. J. Mol. Evol. 71:308-316.

Elhaik E et al. 2010. Identifying compositionally homogeneous domains within the human genome using a novel segmentation algorithm. Nucleic Acids Res. 38:e158.

Werren JH et al. 2010. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327:343-348.

Shaul S et al. 2010. Revisiting the operational RNA code for amino acids: ensemble attributes and their implications. RNA 16:141-153.

Elsik CG et al. 2009. The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science 324:522-528.

Schneider A et al. 2009. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol. Evol. 1:114-118.

Sabath N et al. 2009. A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. Virol. J. 6:144.

Elhaik E et al. 2009. Can GC content at third-codon positions be used as proxy for isochore composition? Mol. Biol. Evol. 26: 1829-1833.

Landan G and Graur D. 2009. Characterization of pairwise and multiple sequence alignment errors. Gene 441: 141-147.

Landan G and Graur D. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pacific Symp. Biocomput. 13:15-24.

Sabath N et al. 2008. A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS ONE 3(12): e3996.

Sabath N et al. 2008. Same-strand overlapping genes in bacteria: compositional determinants of phase bias. Biol. Direct 3:36.

Richards S et al. 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452: 949-955.

Elhaik E et al. 2008. "Genome order index" should not be used for defining compositional constraints in nucleotide sequences. Comp. Biol. Chem. 32: 147.

Graur D. (2007). Public control could be a nightmare for researchers. Nature, 450(7173):1156.

Landan G and Graur D. 2007. Heads or tails: A simple reliability check for multiple sequence alignments. Mol. Biol. Evol. 24: 1380-1383.

Hazkani-Covo E and Graur D. 2007. A comparative analysis of numt evolution in human and chimpanzee. Mol. Biol. Evol. 24:13-18.

Sodergren E et al. 2006. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314:941-952.

Weinstock et al. 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443: 931-949.

Putonti C et al. 2006. 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. 23:1863-1868.

Elhaik E et al. 2006. 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. 23: 1-3

Dagan T et al. 2006. The "domino theory" of gene death: Gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens. Mol. Biol. Evol. 23: 310-316.

Yorav A et al. 2005. An exploratory study on the use of a phylogenetic algorithm in the reconstruction of stemmata of Halachic texts. Hebrew Union College Annual 76:273-288.

Mitchell A and Graur D. 2005. The pattern of spontaneous mutation in Mycobacterium leprae and a comparison of mutation patterns across large evolutionary distances. J. Mol. Evol. 61:795-803.

Hazkani-Covo E and Graur D. 2005. Evolutionary conservation of bacterial operons: Does transcriptional connectivity matter? Genetica 124:145-166.

Hazkani-Covo E et al. 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. (Mol. Dev. Evol.) 304B:150-158.

Cohen N et al. 2005. GC Composition of the human genome: In search of isochores. Mol. Biol. Evol. 22:1260-1272.

Dagan T and Graur D. 2005. The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence. Mol. Biol. Evol. 22: 496-500.

Hazkani-Covo E et al. 2004. Evolution of multicellularity in Metazoa: Comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila, and Caenorhabditis. Cell Biol. Int. 28:171-178.

Dagan T et al. 2004. AluGene: A database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res. 32: D489-D492.

Mayrose I et al. 2004. Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Mol. Biol. Evol. 21:1781-1791.

Yanai I et al. 2004. Incongruent expression profiles between human and mouse suggest widespread neutral transcription. OMICS 8:15-24.

Sorek R et al. 2004. Minimal conditions for exonization of intronic sequences: 5' splice site formation in Alu exons. Mol. Cell 14:221-231

Graur D and Martin W. 2004. Reading the entrails of chickens: Molecular timescales of evolution and the illusion of precision. Trends Genet. 20:80-86.

Fleishman SJ et al. 2003. pANT: A method for the pairwise assessment of nonfunctionalization time of processed pseudogenes. Mol. Biol. Evol. 20: 1876-1880.

Pupko T et al. 2003. Detecting excess radical replacements in phylogenetic trees. Gene 319: 127-135.

Gophna U et al. 2003. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312:151-163.

Hazkani-Covo E et al. 2003. Evolutionary dynamics of large numts in the human genome: Rarity of independent insertions and abundance of post-insertion duplications. J. Mol. Evol. 56:169-174.

Shaul S and Graur D. 2002. Playing chicken (Gallus gallus): Methodological inconsistencies of molecular-divergence date estimates due to secondary calibration points. Gene 300: 59-61.

Pupko T et al. 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 18:1116-1123.

Pupko T and Graur D. 2002. Fast computation of maximum likelihood trees by numerical approximation of amino-acid replacement probabilities. Comput. Stat. Data Analysis 40:285-291.

Sorek R, et al. 2002. Alu-containing exons are alternatively spliced. Genome Res. 12:1060-1067.

Dagan T et al. 2002. 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. 19:1022-1025.

Hazkani-Covo E et al. 2002. The evolutionary history of prosaposin: Two successive tandem-duplication events gave rise to the four saposin domains. J. Mol. Evol. 54:30-34.

Barki Y et al. 2002. Soft-coral natural chimerism: A window in ontogeny allows the creation of entities comprised of incongruous parts. Marine Ecol. Prog. Ser. 231:91-99.

Graur, D. and Pupko, T. 2001. The Permian bacterium that isn't. Mol. Biol. Evol. 18:1143-1146.

Armon A et al. 2001. Consurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307:447-463.

Robinson-Rechavi M and Graur D. 2001. Usage optimization of unevenly sampled data through the combination of quartet trees: An eutherian draft phylogeny based on 640 nuclear and mitochondrial proteins. Israel J. Zool. 47: 259-270.

Pupko T et al. 2000. A fast algorithm for joint reconstruction of ancestral amino-acid sequences. Mol. Biol. Evol. 17:890-896.

Barki Y et al. 2000. Polymorphism in soft coral larvae revealed by amplified fragment-length polymorphism (AFLP) markers. Marine Biol. 136:37-41.

Graur D and Li W-H. 2000. Fundamentals of Molecular Evolution. Second Edition, Sinauer Associates, Sunderland, MA (xiv 481 pp.)