Selected Publications: Donna Muzny, M.S.

Donna Muzny, M.S.

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]

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]

Hampton, OA, Den Hollander, P, Miller, CA, Delgado, DA, Li, J, Coarfa, C, Harris, RA, Richards, S, Scherer, SE et al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.  Genome Res.  2008 Dec 3; . [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]

Wheeler, DA, Srinivasan, M, Egholm, M, Shen, Y, Chen, L, McGuire, A, He, W, Chen, YJ, Makhijani, V et al. The complete genome of an individual by massively parallel DNA sequencing.  Nature  2008 Apr 17; 452(7189):872-6. [PubMed]

Durfee, T, Nelson, R, Baldwin, S, Plunkett, G, Burland, V, Mau, B, Petrosino, JF, Qin, X, Muzny, DM et al. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.  J. Bacteriol.  2008 Apr; 190(7):2597-606. [PubMed]

Highlander, SK, Hulten, KG, Qin, X, Jiang, H, Yerrapragada, S, Mason, EO, Shang, Y, Williams, TM, Fortunov, RM et al. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus.  BMC Microbiol.  2007; 7():99. [PubMed]

Albert, TJ, Molla, MN, Muzny, DM, Nazareth, L, Wheeler, D, Song, X, Richmond, TA, Middle, CM, Rodesch, MJ et al. Direct selection of human genomic loci by microarray hybridization.  Nat. Methods  2007 Nov; 4(11):903-5. [PubMed]

International HapMap Consortium, Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A et al. A second generation human haplotype map of over 3.1 million SNPs.  Nature  2007 Oct 18; 449(7164):851-61. [PubMed]

Sabeti, PC, Varilly, P, Fry, B, Lohmueller, J, Hostetter, E, Cotsapas, C, Xie, X, Byrne, EH, McCarroll, SA et al. Genome-wide detection and characterization of positive selection in human populations.  Nature  2007 Oct 18; 449(7164):913-8. [PubMed]

Gioia, J, Yerrapragada, S, Qin, X, Jiang, H, Igboeli, OC, Muzny, D, Dugan-Rocha, S, Ding, Y, Hawes, A et al. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032.  PLoS ONE  2007; 2(9):e928. [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]

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]

Hernandez, RD, Hubisz, MJ, Wheeler, DA, Smith, DG, Ferguson, B, Rogers, J, Nazareth, L, Indap, A, Bourquin, T et al. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.  Science  2007 Apr 13; 316(5822):240-3. [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]

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]

Gioia, J, Qin, X, Jiang, H, Clinkenbeard, K, Lo, R, Liu, Y, Fox, GE, Yerrapragada, S, McLeod, MP et al. The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny.  J. Bacteriol.  2006 Oct; 188(20):7257-66. [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]

Eichinger, L, Pachebat, JA, Glockner, G, Rajandream, MA, Sucgang, R, Berriman, M, Song, J, Olsen, R, Szafranski, K et al. The genome of the social amoeba Dictyostelium discoideum.  Nature  2005 May 5; 435(7038):43-57. [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]

Gerhard, DS, Wagner, L, Feingold, EA, Shenmen, CM, Grouse, LH, Schuler, G, Klein, SL, Old, S, Rasooly, R et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).  Genome Res.  2004 Oct; 14(10B):2121-7. [PubMed]

McLeod, MP, Qin, X, Karpathy, SE, Gioia, J, Highlander, SK, Fox, GE, McNeill, TZ, Jiang, H, Muzny, D et al. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.  J. Bacteriol.  2004 Sep; 186(17):5842-55. [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]

Sucgang, R, Chen, G, Liu, W, Lindsay, R, Lu, J, Muzny, D, Shaulsky, G, Loomis, W, Gibbs, R et al. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium.  Nucleic Acids Res.  2003 May 1; 31(9):2361-8. [PubMed]

Celniker, SE, Wheeler, DA, Kronmiller, B, Carlson, JW, Halpern, A, Patel, S, Adams, M, Champe, M, Dugan, SP et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.  Genome Biol.  2002; 3(12):RESEARCH0079. [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]

Mouse Genome Sequencing Consortium, Waterston, RH, Lindblad-Toh, K, Birney, E, Rogers, J, Abril, JF, Agarwal, P, Agarwala, R, Ainscough, R et al. Initial sequencing and comparative analysis of the mouse genome.  Nature  2002 Dec 5; 420(6915):520-62. [PubMed]

Dederich, DA, Okwuonu, G, Garner, T, Denn, A, Sutton, A, Escotto, M, Martindale, A, Delgado, O, Muzny, DM et al. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes.  Nucleic Acids Res.  2002 Apr 1; 30(7):e32. [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]

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]

Muzny, DM, Metzker, ML, Bouck, J, Gorrell, JH, Ding, Y, Maxim, E, Gibbs, RA. Using BODIPY dye-primer chemistry in large-scale sequencing.  IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society  ; 17(6):88-93. [PubMed]

Bouck, J, Miller, W, Gorrell, JH, Muzny, D, Gibbs, RA. Analysis of the quality and utility of random shotgun sequencing at low redundancies.  Genome Res.  1998 Oct; 8(10):1074-84. [PubMed]

Ansari-Lari, MA, Oeltjen, JC, Schwartz, S, Zhang, Z, Muzny, DM, Lu, J, Gorrell, JH, Chinault, AC, Belmont, JW et al. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.  Genome Res.  1998 Jan; 8(1):29-40. [PubMed]

Oeltjen, JC, Malley, TM, Muzny, DM, Miller, W, Gibbs, RA, Belmont, JW. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.  Genome Res.  1997 Apr; 7(4):315-29. [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]

Ansari-Lari, MA, Shen, Y, Muzny, DM, Lee, W, Gibbs, RA. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.  Genome Res.  1997 Mar; 7(3):268-80. [PubMed]

Timms, KM, Bondeson, ML, Ansari-Lari, MA, Lagerstedt, K, Muzny, DM, Dugan-Rocha, SP, Nelson, DL, Pettersson, U, Gibbs, RA. Molecular and phenotypic variation in patients with severe Hunter syndrome.  Hum. Mol. Genet.  1997 Mar; 6(3):479-86. [PubMed]

Andersson, B, Lu, J, Edwards, KE, Muzny, DM, Gibbs, RA. Method for 96-well M13 DNA template preparations for large-scale sequencing.  BioTechniques  1996 Jun; 20(6):1022-7. [PubMed]

Timms, KM, Lu, F, Shen, Y, Pierson, CA, Muzny, DM, Gu, Y, Nelson, DL, Gibbs, RA. 130 kb of DNA sequence reveals two new genes and a regional duplication distal to the human iduronate-2-sulfate sulfatase locus.  Genome Res.  1995 Aug; 5(1):71-8. [PubMed]

Ansari-Lari, MA, Muzny, DM, Lu, J, Lu, F, Lilley, CE, Spanos, S, Malley, T, Gibbs, RA. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.  Genome Res.  1996 Apr; 6(4):314-26. [PubMed]

Reiter, LT, Murakami, T, Koeuth, T, Pentao, L, Muzny, DM, Gibbs, RA, Lupski, JR. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element.  Nat. Genet.  1996 Mar; 12(3):288-97. [PubMed]

Andersson, B, Lu, F, Muzny, DM, Warren, ST, Gibbs, RA. Complete sequence of a 38.4-kb human cosmid insert containing the polymorphic marker DXS455 from Xq28.  DNA Seq.  1995; 5(4):219-23. [PubMed]

Oeltjen, JC, Liu, X, Lu, J, Allen, RC, Muzny, D, Belmont, JW, Gibbs, RA. Sixty-nine kilobases of contiguous human genomic sequence containing the alpha-galactosidase A and Bruton's tyrosine kinase loci.  Mamm. Genome  1995 May; 6(5):334-8. [PubMed]

Andersson, B, Povinelli, CM, Wentland, MA, Shen, Y, Muzny, DM, Gibbs, RA. Adaptor-based uracil DNA glycosylase cloning simplifies shotgun library construction for large-scale sequencing.  Anal. Biochem.  1994 May 1; 218(2):300-8. [PubMed]

Chamberlain, JS, Pearlman, JA, Muzny, DM, Gibbs, RA, Ranier, JE, Caskey, CT, Reeves, AA. Expression of the murine Duchenne muscular dystrophy gene in muscle and brain.  Science  1988 Mar 18; 239(4846):1416-8. [PubMed]

Lee, CC, Wu, XW, Gibbs, RA, Cook, RG, Muzny, DM, Caskey, CT. Generation of cDNA probes directed by amino acid sequence: cloning of urate oxidase.  Science  1988 Mar 11; 239(4845):1288-91. [PubMed]