National Human Genome Research Institute Publications ( 63 ) Bauchet M. McEvoy B. Pearson LN. Quillen EE. Sarkisian T. Hovhannesyan K. Deka R. Bradley DG. Shriver MD. Measuring European population stratification with microarray genotype data. 2007 May. Am J Hum Genet. 80(5):948-56. National Human Genome Research Institute Norton HL. Kittles RA. Parra E. McKeigue P. Mao X. Cheng K. Canfield VA. Bradley DG. McEvoy B. Shriver MD. Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. 2007 Mar. Mol Biol Evol. 24(3):710-22. National Human Genome Research Institute Giardine B. Riemer C. Hefferon T. Thomas D. Hsu F. Zielenski J. Sang Y. Elnitski L. Cutting G. Trumbower H. Kern A. Kuhn R. Patrinos GP. Hughes J. Higgs D. Chui D. Scriver C. Phommarinh M. Patnaik SK. Blumenfeld O. Gottlieb B. Vihinen M. Väliaho J. Kent J. Miller W. Hardison RC. PhenCode: connecting ENCODE data with mutations and phenotype. 2007 Jun. Hum Mutat. 28(6):554-62. National Center for Research Resources National Institute for Biomedical Imaging and Bioengineering National Human Genome Research Institute National Institute of Diabetes and Digestive and Kidney Diseases Mao X. Bigham AW. Mei R. Gutierrez G. Weiss KM. Brutsaert TD. Leon-Velarde F. Moore LG. Vargas E. McKeigue PM. Shriver MD. Parra EJ. A genomewide admixture mapping panel for Hispanic/Latino populations. 2007 Jun. Am J Hum Genet. 80(6):1171-8. National Human Genome Research Institute National Heart, Lung, and Blood Institute Public Health Service Blankenberg D. Taylor J. Schenck I. He J. Zhang Y. Ghent M. Veeraraghavan N. Albert I. Miller W. Makova KD. Hardison RC. Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. 2007 Jun. Genome Res. 17(6):960-4. National Institute of General Medical Sciences National Human Genome Research Institute King DC. Taylor J. Zhang Y. Cheng Y. Lawson HA. Martin J. ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis. Chiaromonte F. Miller W. Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. 2007 Jun. Genome Res. 17(6):775-86. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Karro JE. Yan Y. Zheng D. Zhang Z. Carriero N. Cayting P. Harrrison P. Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. 2007 Jan. Nucleic Acids Res. 35(Database issue):D55-60. National Human Genome Research Institute Hou M. Berman P. Hsu CH. Harris RS. HomologMiner: looking for homologous genomic groups in whole genomes. 2007 Apr 15. Bioinformatics. 23(8):917-25. National Human Genome Research Institute Carrel L. Park C. Tyekucheva S. Dunn J. Chiaromonte F. Makova KD. Genomic environment predicts expression patterns on the human inactive X chromosome. 2006 Sep 29. PLoS Genet. 2(9):e151. National Institute of General Medical Sciences National Human Genome Research Institute Chi A. Valencia JC. Hu ZZ. Watabe H. Yamaguchi H. Mangini NJ. Huang H. Canfield VA. Cheng KC. Yang F. Abe R. Yamagishi S. Shabanowitz J. Hearing VJ. Wu C. Appella E. Hunt DF. Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. 2006 Nov. J Proteome Res. 5(11):3135-44. National Institute of General Medical Sciences National Institute of Child Health and Human Development National Center for Research Resources National Human Genome Research Institute Ma J. Zhang L. Suh BB. Raney BJ. Burhans RC. Kent WJ. Blanchette M. Haussler D. Miller W. Reconstructing contiguous regions of an ancestral genome. 2006 Dec. Genome Res. 16(12):1557-65. Public Health Service National Human Genome Research Institute Taylor J. Tyekucheva S. King DC. Hardison RC. Miller W. Chiaromonte F. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. 2006 Dec. Genome Res. 16(12):1596-604. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Wang H. Zhang Y. Cheng Y. Zhou Y. King DC. Taylor J. Chiaromonte F. Kasturi J. Petrykowska H. Gibb B. Dorman C. Miller W. Dore LC. Welch J. Weiss MJ. Hardison RC. Experimental validation of predicted mammalian erythroid cis-regulatory modules. 2006 Dec. Genome Res. 16(12):1480-92. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Jeong J. Berman P. Przytycka T. Fold classification based on secondary structure--how much is gained by including loop topology? 2006. BMC Struct Biol. 6:3. National Human Genome Research Institute Giardine B. Riemer C. Hardison RC. Burhans R. Elnitski L. Shah P. Zhang Y. Blankenberg D. Albert I. Taylor J. Miller W. Kent WJ. Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. 2005 Oct. Genome Res. 15(10):1451-5. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Parrott RL. Silk KJ. Dillow MR. Krieger JL. Harris TM. Condit CM. Development and validation of tools to assess genetic discrimination and genetically based racism. 2005 Jul. J Natl Med Assoc. 97(7):980-90. National Human Genome Research Institute Lamason RL. Mohideen MA. Mest JR. Wong AC. Norton HL. Aros MC. Jurynec MJ. Mao X. Humphreville VR. Humbert JE. Sinha S. Moore JL. Jagadeeswaran P. Zhao W. Ning G. Makalowska I. McKeigue PM. O'donnell D. Kittles R. Parra EJ. Mangini NJ. Grunwald DJ. Shriver MD. Canfield VA. Cheng KC. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. 2005 Dec 16. Science. 310(5755):1782-6. National Cancer Institute National Eye Institute National Institute of Child Health and Human Development National Human Genome Research Institute National Heart, Lung, and Blood Institute National Center for Research Resources Bonilla C. Gutiérrez G. Parra EJ. Kline C. Shriver MD. Admixture analysis of a rural population of the state of Guerrero, Mexico. 2005 Dec. Am J Phys Anthropol. 128(4):861-9. National Human Genome Research Institute King DC. Taylor J. Elnitski L. Chiaromonte F. Miller W. Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. 2005 Aug. Genome Res. 15(8):1051-60. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Klein RJ. Zeiss C. Chew EY. Tsai JY. Sackler RS. Haynes C. Henning AK. SanGiovanni JP. Mane SM. Mayne ST. Bracken MB. Ferris FL. Ott J. Barnstable C. Hoh J. Complement factor H polymorphism in age-related macular degeneration. 2005 Apr 15. Science. 308(5720):385-9. National Center for Research Resources National Human Genome Research Institute National Eye Institute National Institute of Mental Health Shashikant C. Bolanowski SA. Danke J. Amemiya CT. Hoxc8 early enhancer of the Indonesian coelacanth, Latimeria menadoensis. 2004 Nov 15. J Exp Zoolog B Mol Dev Evol. 302(6):557-63. National Human Genome Research Institute Piontkivska H. Zhang Y. Green ED. Elnitski L. NISC Comparative Sequencing Program. Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions. 2004 May 18. BMC Genomics. 5(1):31. National Institute of General Medical Sciences National Human Genome Research Institute Kolbe D. Taylor J. Elnitski L. Eswara P. Li J. Miller W. Hardison R. Chiaromonte F. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. 2004 Apr. Genome Res. 14(4):700-7. National Human Genome Research Institute Yang S. Smit AF. Schwartz S. Chiaromonte F. Roskin KM. Haussler D. Miller W. Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. 2004 Apr. Genome Res. 14(4):517-27. National Human Genome Research Institute Berman P. Bertone P. Dasgupta B. Gerstein M. Kao MY. Snyder M. Fast optimal genome tiling with applications to microarray design and homology search. 2004. J Comput Biol. 11(4):766-85. National Library of Medicine National Human Genome Research Institute National Cancer Institute Halder I. Shriver MD. Measuring and using admixture to study the genetics of complex diseases. 2003 Nov. Hum Genomics. 1(1):52-62. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Schwartz S. Elnitski L. Li M. Weirauch M. Riemer C. Smit A. Green ED. Hardison RC. Miller W. NISC Comparative Sequencing Program. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. 2003 Jul 1. Nucleic Acids Res. 31(13):3518-24. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Schwartz S. Kent WJ. Smit A. Zhang Z. Baertsch R. Hardison RC. Haussler D. Miller W. Human-mouse alignments with BLASTZ. 2003 Jan. Genome Res. 13(1):103-7. National Human Genome Research Institute National Institute of Diabetes and Digestive and Kidney Diseases Elnitski L. Hardison RC. Li J. Yang S. Kolbe D. Eswara P. O'Connor MJ. Schwartz S. Miller W. Chiaromonte F. Distinguishing regulatory DNA from neutral sites. 2003 Jan. Genome Res. 13(1):64-72. National Human Genome Research Institute Hardison RC. Roskin KM. Yang S. Diekhans M. Kent WJ. Weber R. Elnitski L. Li J. O'Connor M. Kolbe D. Schwartz S. Furey TS. Whelan S. Goldman N. Smit A. Miller W. Chiaromonte F. Haussler D. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. 2003 Jan. Genome Res. 13(1):13-26. National Human Genome Research Institute National Institute of Diabetes and Digestive and Kidney Diseases Chiaromonte F. Miller W. Bouhassira EE. Gene length and proximity to neighbors affect genome-wide expression levels. 2003 Dec. Genome Res. 13(12):2602-8. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute National Heart, Lung, and Blood Institute Giardine B. Elnitski L. Riemer C. Makalowska I. Schwartz S. Miller W. Hardison RC. GALA, a database for genomic sequence alignments and annotations. 2003 Apr. Genome Res. 13(4):732-41. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Shriver MD. Parra EJ. Dios S. Bonilla C. Norton H. Jovel C. Pfaff C. Jones C. Massac A. Cameron N. Baron A. Jackson T. Argyropoulos G. Jin L. Hoggart CJ. McKeigue PM. Kittles RA. Skin pigmentation, biogeographical ancestry and admixture mapping. 2003 Apr. Hum Genet. 112(4):387-99. National Human Genome Research Institute National Center for Research Resources National Institute of Mental Health Hardison RC. Chiaromonte F. Kolbe D. Wang H. Petrykowska H. Elnitski L. Yang S. Giardine B. Zhang Y. Riemer C. Schwartz S. Haussler D. Roskin KM. Weber RJ. Diekhans M. Kent WJ. Weiss MJ. Welch J. Miller W. Global predictions and tests of erythroid regulatory regions. 2003. Cold Spring Harb Symp Quant Biol. 68:335-44. National Human Genome Research Institute National Institute of Diabetes and Digestive and Kidney Diseases Chiaromonte F. Weber RJ. Roskin KM. Diekhans M. Kent WJ. Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. 2003. Cold Spring Harb Symp Quant Biol. 68:245-54. National Human Genome Research Institute Wagner JK. Parra EJ. L Norton H. Jovel C. Shriver MD. Skin responses to ultraviolet radiation: effects of constitutive pigmentation, sex, and ancestry. 2002 Oct. Pigment Cell Res. 15(5):385-90. National Human Genome Research Institute National Center for Research Resources Wagner JK. Jovel C. Norton HL. Parra EJ. Shriver MD. Comparing quantitative measures of erythema, pigmentation and skin response using reflectometry. 2002 Oct. Pigment Cell Res. 15(5):379-84. National Human Genome Research Institute National Center for Research Resources Ye J. Parra EJ. Sosnoski DM. Hiester K. Underhill PA. Shriver MD. Melting curve SNP (McSNP) genotyping: a useful approach for diallelic genotyping in forensic science. 2002 May. J Forensic Sci. 47(3):593-600. National Human Genome Research Institute Chase GA. Geller G. Havstad SL. Holtzman NA. Bassett SS. Physicians' propensity to offer genetic testing for Alzheimer's disease: results from a survey. 2002 Jul-Aug. Genet Med. 4(4):297-303. National Human Genome Research Institute Molete JM. Petrykowska H. Sigg M. Miller W. Hardison R. Functional and binding studies of HS3.2 of the beta-globin locus control region. 2002 Jan 23. Gene. 283(1-2):185-97. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Elnitski L. Riemer C. Petrykowska H. Florea L. Schwartz S. Miller W. Hardison R. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. 2002 Dec. Genomics. 80(6):681-90. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Chiaromonte F. Yap VB. Miller W. Scoring pairwise genomic sequence alignments. 2002. Pac Symp Biocomput. 115-26. National Human Genome Research Institute Nicewarner-Pena SR. Freeman RG. Reiss BD. He L. Pena DJ. Walton ID. Cromer R. Keating CD. Natan MJ. Submicrometer metallic barcodes. 2001 Oct 5. Science. 294(5540):137-41. National Human Genome Research Institute Miller W. Comparison of genomic DNA sequences: solved and unsolved problems. 2001 May. Bioinformatics. 17(5):391-7. National Human Genome Research Institute Molete JM. Petrykowska H. Bouhassira EE. Feng YQ. Miller W. Hardison RC. Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement. 2001 May. Mol Cell Biol. 21(9):2969-80. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute National Heart, Lung, and Blood Institute National Library of Medicine Parra EJ. Kittles RA. Argyropoulos G. Pfaff CL. Hiester K. Bonilla C. Sylvester N. Parrish-Gause D. Garvey WT. Jin L. McKeigue PM. Kamboh MI. Ferrell RE. Pollitzer WS. Shriver MD. Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. 2001 Jan. Am J Phys Anthropol. 114(1):18-29. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Pfaff CL. Parra EJ. Bonilla C. Hiester K. McKeigue PM. Kamboh MI. Hutchinson RG. Ferrell RE. Boerwinkle E. Shriver MD. Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. 2001 Jan. Am J Hum Genet. 68(1):198-207. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute National Heart, Lung, and Blood Institute Hardison RC. New views of evolution and regulation of vertebrate beta-like globin gene clusters from an orphaned gene in marsupials. 2001 Feb 13. Proc Natl Acad Sci U S A. 98(4):1327-9. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Chiaromonte F. Yang S. Elnitski L. Yap VB. Miller W. Hardison RC. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. 2001 Dec 4. Proc Natl Acad Sci U S A. 98(25):14503-8. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Bailey JA. Carrel L. Chakravarti A. Eichler EE. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. 2000 Jun 6. Proc Natl Acad Sci U S A. 97(12):6634-9. National Institute of General Medical Sciences National Human Genome Research Institute Stoneking M. Fontius JJ. Clifford SL. Soodyall H. Arcot SS. Saha N. Jenkins T. Tahir MA. Deininger PL. Batzer MA. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. 1997 Nov. Genome Res. 7(11):1061-71. National Human Genome Research Institute Hannenhalli S. Feldman W. Lewis HF. Skiena SS. Pevzner PA. Positional sequencing by hybridization. 1996 Feb. Comput Appl Biosci. 12(1):19-24. National Human Genome Research Institute Rogan PK. Close P. Blouin JL. Seip JR. Gannutz L. Ladda RL. Antonarakis SE. Duplication and loss of chromosome 21 in two children with Down syndrome and acute leukemia. 1995 Nov 6. Am J Med Genet. 59(2):174-81. National Human Genome Research Institute National Institute of Child Health and Human Development Hannenhalli S. Chappey C. Koonin EV. Pevzner PA. Genome sequence comparison and scenarios for gene rearrangements: a test case. 1995 Nov 20. Genomics. 30(2):299-311. National Human Genome Research Institute Jiang W. Dewald G. Brundage E. Mücher G. Schildhaus HU. Zerres K. Bond JS. Fine mapping of MEP1A, the gene encoding the alpha subunit of the metalloendopeptidase meprin, to human chromosome 6P21. 1995 Nov 13. Biochem Biophys Res Commun. 216(2):630-5. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute Bond JS. Rojas K. Overhauser J. Zoghbi HY. Jiang W. The structural genes, MEP1A and MEP1B, for the alpha and beta subunits of the metalloendopeptidase meprin map to human chromosomes 6p and 18q, respectively. 1995 Jan 1. Genomics. 25(1):300-3. National Institute of Diabetes and Digestive and Kidney Diseases National Human Genome Research Institute National Institute of Neurological Disorders and Stroke Feldman W. Pevzner P. Gray code masks for sequencing by hybridization. 1994 Sep 1. Genomics. 23(1):233-5. National Human Genome Research Institute Pevzner PA. Rearrangements of DNA sequences and SBH. 1994 Sep. Comput Chem. 18(3):221-3. National Human Genome Research Institute Lafrenière RG. Carrel L. Willard HF. A novel transmembrane transporter encoded by the XPCT gene in Xq13.2. 1994 Jul. Hum Mol Genet. 3(7):1133-9. National Institute of General Medical Sciences National Human Genome Research Institute Malo D. Gros P. Bergmann A. Trask B. Mohrenweiser HW. Canfield VA. Levenson R. Genes encoding the H,K-ATPase alpha and Na,K-ATPase alpha 3 subunits are linked on mouse chromosome 7 and human chromosome 19. 1993 Nov. Mamm Genome. 4(11):644-9. National Cancer Institute National Human Genome Research Institute National Heart, Lung, and Blood Institute Perna NT. Batzer MA. Deininger PL. Stoneking M. Alu insertion polymorphism: a new type of marker for human population studies. 1992 Oct. Hum Biol. 64(5):641-8. National Human Genome Research Institute Lafrenière RG. Brown CJ. Powers VE. Carrel L. Davies KE. Barker DF. Willard HF. Physical mapping of 60 DNA markers in the p21.1----q21.3 region of the human X chromosome. 1991 Oct. Genomics. 11(2):352-63. National Human Genome Research Institute Kozono H. Bronson SK. Taillon-Miller P. Moorti MK. Jamry I. Chaplin DD. Molecular linkage of the HLA-DR, HLA-DQ, and HLA-DO genes in yeast artificial chromosomes. 1991 Nov. Genomics. 11(3):577-86. 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