Publications

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2012
Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Scheid OMittelsten, von Haeseler A. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One. 2012 ;7(7):e41528.
English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012 ;7(11):e47768.
Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. PLoS One. 2012 ;7(8):e42680.
Wang L, Tsutsumi S, Kawaguchi T, Nagasaki K, Tatsuno K, Yamamoto S, Sang F, Sonoda K, Sugawara M, Saiura A, Hirono S, Yamaue H, Miki Y, Isomura M, Totoki Y, Nagae G, Isagawa T, Ueda H, Murayama-Hosokawa S, Shibata T, Sakamoto H, Kanai Y, Kaneda A, Noda T, Aburatani H. Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. Genome Res. 2012 ;22(2):208-19.
2010
Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 ;337(2):484-95.
Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu Y-Q, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010 ;11(6):R62.
2008
Lin H, Doddapaneni H, Bai X, Yao J, Zhao X, Civerolo EL. Acquisition of uncharacterized sequences from Candidatus liberibacter, an unculturable bacterium, using an improved genomic walking method. Mol Cell Probes. 2008 ;22(1):30-7.
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y-J, Makhijani V, G Roth T, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song X-Z, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 ;452(7189):872-6.
Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM. Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol. 2008 ;8:76.
2007
Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MCatira, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet. 2007 ;80(6):1024-36.
2005
Lewis EK, Haaland WC, Nguyen F, Heller DA, Allen MJ, MacGregor RR, C Berger S, Willingham B, Burns LA, Scott GBI, Kittrell C, Johnson BR, Curl RF, Metzker ML. Color-blind fluorescence detection for four-color DNA sequencing. Proc Natl Acad Sci U S A. 2005 ;102(15):5346-51.
Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 ;1(5):e53.
2004
Yan Y, Wang M, Lemon WJ, You M. Single nucleotide polymorphism (SNP) analysis of mouse quantitative trait loci for identification of candidate genes. J Med Genet. 2004 ;41(9):e111.
2003
Csuros M, Li B, Milosavljevic A. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform. 2003 ;14:186-95.
Heilig R, Eckenberg R, Petit J-L, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Brüls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Ségurens B, Anière F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Ménard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufossé-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guérin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier LD, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quétier F, Waterston R, Hood L, Weissenbach J. The DNA sequence and analysis of human chromosome 14. Nature. 2003 ;421(6923):601-7.
2002
Dederich DA, Okwuonu G, Garner T, Denn A, Sutton A, Escotto M, Martindale A, Delgado O, Muzny DM, Gibbs RA, Metzker ML. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. Nucleic Acids Res. 2002 ;30(7):e32.
1998
Metzker ML, Ansari-Lari MA, Liu XM, Holder DJ, Gibbs RA. Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers. Biotechniques. 1998 ;25(3):446-7, 450-2, 454, passim.
Muzny DM, Metzker ML, Bouck J, Gorrell JH, Ding Y, Maxim E, Gibbs RA. Using BODIPY dye-primer chemistry in large-scale sequencing. IEEE Eng Med Biol Mag. 1998 ;17(6):88-93.
1995
Gingras M-C, Roussel E, Roth JA, Moser RP. Little expression of cytokine mRNA by fresh tumour-infiltrating mononuclear leukocytes from glioma and lung adenocarcinoma. Cytokine. 1995 ;7(6):580-8.