Bouffard Publications

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services


Gerard Bouffard, Ph.D.

Director, Bioinformatics Group, NIH Intramural Sequencing Center [nisc.nih.gov]
Associate Investigator, NIH Intramural Sequencing Center [nisc.nih.gov]
 

Selected Publications

Bouffard, G., J. Ostell, and K. E. Rudd. GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers. Comput Appl Biosci, 8:563-7. 1992. [PubMed]

Bouffard G.G., Rudd K.E., Adhya S.L. Dependence of lactose metabolism upon mutarotase encoded in the gal operon in Escherichia coli. J Mol Biol, 244(3):269-78. 1994. [PubMed]

Bouffard G.G., Idol J.I., Braden V.V., Iyer L.M., Cunningham A.F., Weintraub L.A., Touchman J.W., Mohr-Tidwell R.M., Peluso D.C., Fulton R.S., Ueltzen M.S., Weissenbach J., Magness C.L., Green E.D. A physical map of human chromosome 7: an integrated YAC contig map with average STS spacing of 79 kb. Genome Res, 7:673-692. 1997. [PubMed]

Gubin A.N., Njoroge J.M., Bouffard G.G., Miller J.L. Gene expression in proliferating human erythroid cells. Genomics, 59(2):168-77. 1999. [PubMed]

Blackshear PJ, Lai WS, Thorn JM, Kennington EA, Staffa NG, Moore DT, Bouffard GG, Beckstrom-Sternberg SM, Touchman JW, Bonaldo MF, Soares MB.  The NIEHS Xenopus maternal EST project: interim analysis of the first 13,879 ESTs from unfertilized eggs. Gene, 267(1):71-87. 2001. [PubMed]

Shevchenko Y, Bouffard GG, Butterfield YS, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJ, Touchman JW, Green ED.  Systematic sequencing of cDNA clones using the transposon Tn5.  Nucleic Acids Res, 30(11):2469-77. 2002. [PubMed]

Wistow G, Bernstein SL, Wyatt MK, Fariss RN, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K.  Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants.  Mol Vis, 8:205-20. 2002. [PubMed]

Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B.  Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science, 299(5607):697-700. 2003. [PubMed]

Thomas J.W., Touchman J.W., Blakesley R.W., Bouffard G.G., Beckstrom-Sternberg S.M., Margulies E.H., Blanchette M., Siepel A.C., Thomas P.J., McDowell J.C., Maskeri B., Hansen N.F., Schwartz M.S., Weber R.J., Kent W.J., Karolchik D., Bruen T.C., Bevan R., Cutler D.J., Schwartz S., Elnitski L., Idol J.R., Prasad A.B., Lee-Lin S.Q., Maduro V.V., Summers T.J., Portnoy M.E., Dietrich N.L., Akhter N., Ayele K., Benjamin B., Cariaga K., Brinkley C.P., Brooks S.Y., Granite S., Guan X., Gupta J., Haghighi P., Ho S.L., Huang M.C., Karlins E., Laric P.L., Legaspi R., Lim M.J., Maduro Q.L., Masiello C.A., Mastrian S.D., McCloskey J.C., Pearson R., Stantripop S., Tiongson E.E., Tran J.T., Tsurgeon C., Vogt J.L., Walker M.A., Wetherby K.D., Wiggins L.S., Young A.C., Zhang L.H., Osoegawa K., Zhu B., Zhao B., Shu C.L., De Jong P.J., Lawrence C.E., Smit A.F., Chakravarti A., Haussler D., Green P., Miller W., Green E.D. Comparative analyses of multi-species sequences from targeted genomic regions. Nature, 424(6950):788-93. 2003. [PubMed]

Crawford GE, Holt IE, Mullikin JC, Tai D, Blakesley R, Bouffard G, Young A, Masiello C, Green ED, Wolfsberg TG, Collins FS. Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc Natl Acad Sci U S A, 101(4):992-7. 2004. [PubMed]

Goh SH, Lee YT, Bouffard GG, Miller JL. Hembase: browser and genome portal for hematology and erythroid biology. Nucleic Acids Res, 1;32(Database issue):D572-4. 2004. [PubMed]

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature, 447(7146):799-816. 2007. [PubMed]

Zhang W, Bouffard GG, Wallace SS, Bond JP; NISC Comparative Sequencing Program.  Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences.  J Mol Evol, 65(3):207-14. 2007. [PubMed]

Grice EA, Kong HH, Conlan, S, Deming, CB, Davis, J, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Segre JA. Topographical and temporal diversity of the human skin microbiome. Science, 324:1190-1192. 2009. [PubMed]

MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Bouffard GG, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res , 19:2324-2333. 2009. [PubMed]

Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, Bouffard GG, Chines PS, Cruz P, Green ED. The ClinSeq project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res, 19:1665-1674. 2009. [PubMed]

Blakesley RW, Hansen NF, Gupta J, McDowell JC, Maskeri B, Barnabas BB, Brooks SY, Coleman H, Bouffard GG, Green ED. Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates. BMC Genomics, 11:21. 2010. [PubMed]

Stephen C. J. Parker, Michael L. Stitzel, D. Leland Taylor, Jose Miguel Orozco, Michael R. Erdos, Jennifer A. Akiyama, Kelly Lammerts van Bueren, Peter S. Chines, Narisu Narisu, NISC Comparative Sequencing Program, Brian L. Black, Axel Visel, Len A. Pennacchio, Francis S. Collins, National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors, NISC Comparative Sequencing Program Authors., Jesse Becker, Betty Benjamin, Robert Blakesley, Gerry Bouffard, Shelise Brooks, Holly Coleman, Mila Dekhtyar, Michael Gregory, Xiaobin Guan, Jyoti Gupta, Joel Han, April Hargrove, Shi-ling Ho, Taccara Johnson, Richelle Legaspi, Sean Lovett, Quino Maduro, Cathy Masiello, Baishali Maskeri, Jenny McDowell, Casandra Montemayor, James Mullikin, Morgan Park, Nancy Riebow, Karen Schandler, Brian Schmidt, Christina Sison, Mal Stantripop, James Thomas, Pam Thomas, Meg Vemulapalli, Alice Young. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A, 110(44): 17921-17926. [PubMed]
Book Chapters
Rudd, K. E., G. G. Bouffard, and W. Miller. Computer Analysis of Escherichia coli Restriction Maps, p. 1-38. In Genome Analysis: Strategies of Physical Mapping. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.1992.

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Last Updated: June 20, 2014