Selected Publications: Kim Worley, Ph.D.

Kim Worley, Ph.D.

International Aphid Genomics Consortium, Genome sequence of the pea aphid Acyrthosiphon pisum.  PLoS Biol.  2010 Feb; 8(2):e1000313. [PubMed]

Nasonia Genome Working Group, Werren, JH, Richards, S, Desjardins, CA, Niehuis, O, Gadau, J, Colbourne, JK, Beukeboom, LW, Desplan, C et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.  Science  2010 Jan 15; 327(5963):343-8. [PubMed]

Liu, Y, Qin, X, Song, XZ, Jiang, H, Shen, Y, Durbin, KJ, Lien, S, Kent, MP, Sodeland, M et al. Bos taurus genome assembly.  BMC Genomics  2009; 10():180. [PubMed]

Bovine Genome Sequencing and Analysis Consortium, Elsik, CG, Tellam, RL, Worley, KC, Gibbs, RA, Muzny, DM, Weinstock, GM, Adelson, DL, Eichler, EE et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution.  Science  2009 Apr 24; 324(5926):522-8. [PubMed]

Bovine HapMap Consortium, Gibbs, RA, Taylor, JF, Van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.  Science  2009 Apr 24; 324(5926):528-32. [PubMed]

Twigger, SN, Pruitt, KD, Fernandez-Suarez, XM, Karolchik, D, Worley, KC, Maglott, DR, Brown, G, Weinstock, G, Gibbs, RA et al. What everybody should know about the rat genome and its online resources.  Nat. Genet.  2008 May; 40(5):523-7. [PubMed]

Tribolium Genome Sequencing Consortium, Richards, S, Gibbs, RA, Weinstock, GM, Brown, SJ, Denell, R, Beeman, RW, Gibbs, R, Beeman, RW et al. The genome of the model beetle and pest Tribolium castaneum.  Nature  2008 Apr 24; 452(7190):949-55. [PubMed]

Worley, KC, Weinstock, GM, Gibbs, RA. Rats in the genomic era.  Physiol. Genomics  2008 Feb 19; 32(3):273-82. [PubMed]

ENCODE Project Consortium, Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigo, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature  2007 Jun 14; 447(7146):799-816. [PubMed]

Margulies, EH, Cooper, GM, Asimenos, G, Thomas, DJ, Dewey, CN, Siepel, A, Birney, E, Keefe, D, Schwartz, AS et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.  Genome Res.  2007 Jun; 17(6):760-74. [PubMed]

Solignac, M, Zhang, L, Mougel, F, Li, B, Vautrin, D, Monnerot, M, Cornuet, JM, Worley, KC, Weinstock, GM et al. The genome of Apis mellifera: dialog between linkage mapping and sequence assembly.  Genome Biol.  2007; 8(3):403. [PubMed]

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs, RA, Rogers, J, Katze, MG, Bumgarner, R, Weinstock, GM, Mardis, ER, Remington, KA, Strausberg, RL et al. Evolutionary and biomedical insights from the rhesus macaque genome.  Science  2007 Apr 13; 316(5822):222-34. [PubMed]

Sea Urchin Genome Sequencing Consortium, Sodergren, E, Weinstock, GM, Davidson, EH, Cameron, RA, Gibbs, RA, Angerer, RC, Angerer, LM, Arnone, MI et al. The genome of the sea urchin Strongylocentrotus purpuratus.  Science  2006 Nov 10; 314(5801):941-52. [PubMed]

Elsik, CG, Worley, KC, Zhang, L, Milshina, NV, Jiang, H, Reese, JT, Childs, KL, Venkatraman, A, Dickens, CM et al. Community annotation: procedures, protocols, and supporting tools.  Genome Res.  2006 Nov; 16(11):1329-33. [PubMed]

Robinson, GE, Evans, JD, Maleszka, R, Robertson, HM, Weaver, DB, Worley, K, Gibbs, RA, Weinstock, GM. Sweetness and light: illuminating the honey bee genome.  Insect Mol. Biol.  2006 Oct; 15(5):535-9. [PubMed]

Honeybee Genome Sequencing Consortium, Insights into social insects from the genome of the honeybee Apis mellifera.  Nature  2006 Oct 26; 443(7114):931-49. [PubMed]

Muzny, DM, Scherer, SE, Kaul, R, Wang, J, Yu, J, Sudbrak, R, Buhay, CJ, Chen, R, Cree, A et al. The DNA sequence, annotation and analysis of human chromosome 3.  Nature  2006 Apr 27; 440(7088):1194-8. [PubMed]

Scherer, SE, Muzny, DM, Buhay, CJ, Chen, R, Cree, A, Ding, Y, Dugan-Rocha, S, Gill, R, Gunaratne, P et al. The finished DNA sequence of human chromosome 12.  Nature  2006 Mar 16; 440(7082):346-51. [PubMed]

Ross, MT, Grafham, DV, Coffey, AJ, Scherer, S, McLay, K, Muzny, D, Platzer, M, Howell, GR, Burrows, C et al. The DNA sequence of the human X chromosome.  Nature  2005 Mar 17; 434(7031):325-37. [PubMed]

Richards, S, Liu, Y, Bettencourt, BR, Hradecky, P, Letovsky, S, Nielsen, R, Thornton, K, Hubisz, MJ, Chen, R et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.  Genome Res.  2005 Jan; 15(1):1-18. [PubMed]

Levenson, JM, Choi, S, Lee, SY, Cao, YA, Ahn, HJ, Worley, KC, Pizzi, M, Liou, HC, Sweatt, JD. A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel.  J. Neurosci.  2004 Apr 21; 24(16):3933-43. [PubMed]

Gibbs, RA, Weinstock, GM, Metzker, ML, Muzny, DM, Sodergren, EJ, Scherer, S, Scott, G, Steffen, D, Worley, KC et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution.  Nature  2004 Apr 1; 428(6982):493-521. [PubMed]

Gunaratne, PH, Wu, JQ, Garcia, AM, Hulyk, S, Worley, KC, Margolin, JF, Gibbs, RA. Concatenation cDNA sequencing for transcriptome analysis.  C. R. Biol.  ; 326(10-11):971-7. [PubMed]

Strausberg, RL, Feingold, EA, Grouse, LH, Derge, JG, Klausner, RD, Collins, FS, Wagner, L, Shenmen, CM, Schuler, GD et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.  Proc. Natl. Acad. Sci. U.S.A.  2002 Dec 24; 99(26):16899-903. [PubMed]

Katsanis, N, Worley, KC, Gonzalez, G, Ansley, SJ, Lupski, JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes.  Proc. Natl. Acad. Sci. U.S.A.  2002 Oct 29; 99(22):14326-31. [PubMed]

Wang, LL, Worley, K, Gannavarapu, A, Chintagumpala, MM, Levy, ML, Plon, SE. Intron-size constraint as a mutational mechanism in Rothmund-Thomson syndrome.  Am. J. Hum. Genet.  2002 Jul; 71(1):165-7. [PubMed]

Katsanis, N, Worley, KC, Lupski, JR. An evaluation of the draft human genome sequence.  Nat. Genet.  2001 Sep; 29(1):88-91. [PubMed]

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M et al. Initial sequencing and analysis of the human genome.  Nature  2001 Feb 15; 409(6822):860-921. [PubMed]

Bouck, J, McLeod, MP, Worley, K, Gibbs, RA. The human transcript database: a catalogue of full length cDNA inserts.  Bioinformatics  2000 Feb; 16(2):176-7. [PubMed]

Zhang, Y, Dipple, KM, Vilain, E, Huang, BL, Finlayson, G, Therrell, BL, Worley, K, Deininger, P, McCabe, ER. AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency.  Hum. Mutat.  2000; 15(4):316-23. [PubMed]

Adams, MD, Celniker, SE, Holt, RA, Evans, CA, Gocayne, JD, Amanatides, PG, Scherer, SE, Li, PW, Hoskins, RA et al. The genome sequence of Drosophila melanogaster.  Science  2000 Mar 24; 287(5461):2185-95. [PubMed]

Bouck, J, Yu, W, Gibbs, R, Worley, K. Comparison of gene indexing databases.  Trends Genet.  1999 Apr; 15(4):159-62. [PubMed]

Worley, KC, Culpepper, P, Wiese, BA, Smith, RF. BEAUTY-X: enhanced BLAST searches for DNA queries.  Bioinformatics  1998; 14(10):890-1. [PubMed]

Yu, W, Andersson, B, Worley, KC, Muzny, DM, Ding, Y, Liu, W, Ricafrente, JY, Wentland, MA, Lennon, G et al. Large-scale concatenation cDNA sequencing.  Genome Res.  1997 Apr; 7(4):353-8. [PubMed]

Worley, KC, Wiese, BA, Smith, RF. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.  Genome Res.  1995 Sep; 5(2):173-84. [PubMed]

Levin, ML, Chatterjee, A, Pragliola, A, Worley, KC, Wehnert, M, Zhuchenko, O, Smith, RF, Lee, CC, Herman, GE. A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28.  Genome Res.  1996 Jun; 6(6):465-77. [PubMed]

Smith, RF, Wiese, BA, Wojzynski, MK, Davison, DB, Worley, KC. BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.  Genome Res.  1996 May; 6(5):454-62. [PubMed]

Worley, KC, King, KY, Chua, S, McCabe, ER, Smith, RF. Identification of new members of a carbohydrate kinase-encoding gene family.  J. Comput. Biol.  1995; 2(3):451-8. [PubMed]

Worley, KC, Lindsay, EA, Bailey, W, Wise, J, McCabe, ER, Baldini, A. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency.  Am. J. Med. Genet.  1995 Jul 17; 57(4):615-9. [PubMed]

Bardoni, B, Zanaria, E, Guioli, S, Floridia, G, Worley, KC, Tonini, G, Ferrante, E, Chiumello, G, McCabe, ER et al. A dosage sensitive locus at chromosome Xp21 is involved in male to female sex reversal.  Nat. Genet.  1994 Aug; 7(4):497-501. [PubMed]

Guo, W, Worley, K, Adams, V, Mason, J, Sylvester-Jackson, D, Zhang, YH, Towbin, JA, Fogt, DD, Madu, S et al. Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene.  Nat. Genet.  1993 Aug; 4(4):367-72. [PubMed]

Worley, KC, Ellison, KA, Zhang, YH, Wang, DF, Mason, J, Roth, EJ, Adams, V, Fogt, DD, Zhu, XM et al. Yeast artificial chromosome cloning in the glycerol kinase and adrenal hypoplasia congenita region of Xp21.  Genomics  1993 May; 16(2):407-16. [PubMed]

Worley, KC, Towbin, JA, Zhu, XM, Barker, DF, Ballabio, A, Chamberlain, J, Biesecker, LG, Blethen, SL, Brosnan, P et al. Identification of new markers in Xp21 between DXS28 (C7) and DMD.  Genomics  1992 Aug; 13(4):957-61. [PubMed]

Gelb, BD, Worley, KC, Griffin, LD, Adams, V, Chinault, AC, McCabe, ER. Characterization of human genomic yeast artificial chromosome inserts containing hexokinase 1 coding information on chromosome 10.  Biochem. Med. Metab. Biol.  1992 Jun; 47(3):265-9. [PubMed]

Adams, V, Griffin, L, Towbin, J, Gelb, B, Worley, K, McCabe, ER. Porin interaction with hexokinase and glycerol kinase: metabolic microcompartmentation at the outer mitochondrial membrane.  Biochem. Med. Metab. Biol.  1991 Jun; 45(3):271-91. [PubMed]