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Bruce Birren

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Chemicals & Drugs

Anatomy

Bacterial Chromosomes

Genes & Molecular Sequences

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Aleksandar D Kostic; Chen Liu; Monia Michaud; Shuji Ogino; Akinyemi I Ojesina; Chandra Sekhar Pedamallu; Ramesh A Shivdasani; Josep Tabernero; José Baselga; Adam J Bass; Bruce Birren; Fujiko Duke; Ashlee M Earl; Wendy S Garrett; Dirk Gevers; Curtis Huttenhower; Joonil Jung; Matthew Meyerson
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.
Anthony A Fodor; Theresa Hepburn; Ping Hu; Heather Huot-Creasy; Konstantinos Liolios; Erica Sodergren; Kristine M Wylie; Yuzhen Ye; Jonathan H Badger; Bruce Birren; Todd Z DeSantis; Ashlee M Earl
The "most wanted" taxa from the human microbiome for whole genome sequencing.
Veronica N Kos; Trevor Lawley; Emmanuel F Mongodin; Kelli L Palmer; Andries Van Tonder; Jennifer Wortman; Bruce Birren; Kip Bodi; Gustavo Cerqueira; Christopher A Desjardins; Michael Feldgarden; Steven R Gill; Paul Godfrey; Allison Griggs; Brian J Haas; Matthew T G Holden; Michael S Gilmore
Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.

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All Publications

2012: Aleksandar D Kostic; Chen Liu; Monia Michaud; Shuji Ogino; Akinyemi I Ojesina; Chandra Sekhar Pedamallu; Ramesh A Shivdasani; Josep Tabernero; José Baselga; Adam J Bass; Bruce Birren; Fujiko Duke; Ashlee M Earl; Wendy S Garrett; Dirk Gevers; Curtis Huttenhower; Joonil Jung; Matthew Meyerson
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.
Genome research 2012;22(2):292-8.
2012: Anthony A Fodor; Theresa Hepburn; Ping Hu; Heather Huot-Creasy; Konstantinos Liolios; Erica Sodergren; Kristine M Wylie; Yuzhen Ye; Jonathan H Badger; Bruce Birren; Todd Z DeSantis; Ashlee M Earl
The "most wanted" taxa from the human microbiome for whole genome sequencing.
PloS one 2012;7(7):e41294.
2012: Veronica N Kos; Trevor Lawley; Emmanuel F Mongodin; Kelli L Palmer; Andries Van Tonder; Jennifer Wortman; Bruce Birren; Kip Bodi; Gustavo Cerqueira; Christopher A Desjardins; Michael Feldgarden; Steven R Gill; Paul Godfrey; Allison Griggs; Brian J Haas; Matthew T G Holden; Michael S Gilmore
Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.
mBio 2012;3(3):.
2012: Georgia Giannoukos; Bruce Birren; Dawn M Ciulla; Ashlee M Earl; Dirk Gevers; Brian J Haas; Katherine Huang; Jacques Izard; Joshua Z Levin; Jonathan Livny; Chad Nusbaum; Doyle V Ward; Andreas Gnirke
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
Genome biology 2012;13(3):R23.
2012: Kelli L Palmer; Suzanne Walker; Jennifer Wortman; Jeremy Zucker; Bruce Birren; Gustavo Cerqueira; Christopher Desjardins; Michael Feldgarden; Dirk Gevers; Paul Godfrey; Allison Griggs; Brian Haas; Veronica N Kos; Michael S Gilmore
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.
mBio 2012;3(1):e00318-11.
2012: Brian Weiner; Jared White; Bruce Birren; Sebastien Gagneux; Nicolass C Gey van Pittius; James Gomez; Deborah Hung; Michael Koehrsen; Megan Murray; Bonnie B Plikaytis; James E Posey; Peter Sisk; Alexander Sloutsky; Christian Stolte; Paul D van Helden; Thomas C Victor; Robert M Warren; James E Galagan
Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region.
PloS one 2012;7(2):e26038.
2011: Brian J Haas; Dirk Gevers; Ashlee M Earl; Mike Feldgarden; Doyle V Ward; Georgia Giannoukos; Dawn Ciulla; Diana Tabbaa; Sarah Katherine Highlander; Erica Sodergren; Barbara Methé; Todd Z DeSantis; Joseph F Petrosino; Rob Knight; Bruce Birren
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Genome research 2011;21(3):494-504.
2011: Alexandre Melnikov; Daouda Ndiaye; Kayla G Barnes; Bruce Birren; James Bochicchio; Rachel Daniels; Timothy Fennell; Kevin Galinsky; Andreas Gnirke; Chad Nusbaum; Peter Rogov; Carsten Russ; Papa D Sene; Daria Van Tyne; Sarah K Volkman; Dyann F Wirth; Daniel E Neafsey
Hybrid selection for sequencing pathogen genomes from clinical samples.
Genome biology 2011;12(8):R73.
2010: Kelli L Palmer; Karen Carniol; Janet Manson; David Heiman; Terry Shea; Sarah Young; Qiandong Zeng; Dirk Gevers; Michael Feldgarden; Bruce Birren; Michael S Gilmore
High-quality draft genome sequences of 28 Enterococcus sp. isolates.
Journal of bacteriology 2010;192(9):2469-70.
2010: Christina A Cuomo; Bruce Birren
The fungal genome initiative and lessons learned from genome sequencing.
Methods in enzymology 2010;470():833-55.
2009: Mia D Champion; Qiandong Zeng; Eli B Nix; Francis E Nano; Paul Keim; Chinnappa D Kodira; Mark Borowsky; Sarah Young; Michael Koehrsen; Reinhard Engels; Matthew Pearson; Clint Howarth; Lisa Larson; Jared White; Lucia Alvarado; Mats Forsman; Scott W Bearden; Anders Sjöstedt; Richard Titball; Stephen L Michell; Bruce Birren; James E Galagan
Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.
PLoS pathogens 2009;5(5):e1000459.
2008: Kalai Mathee; Giri Narasimhan; Camilo Valdes; Xiaoyun Qiu; Jody M Matewish; Michael Koehrsen; Antonis Rokas; Chandri N Yandava; Reinhard Engels; Erliang Zeng; Raquel Olavarietta; Melissa Doud; Roger S Smith; Philip Montgomery; Jared R White; Paul A Godfrey; Chinnappa Kodira; Bruce Birren; James E Galagan; Stephen Lory
Dynamics of Pseudomonas aeruginosa genome evolution.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(8):3100-5.
2007: James K Hane; Rohan G T Lowe; Peter Solomon; Kar-Chun Tan; Conrad Schoch; Joseph W Spatafora; Pedro W Crous; Chinappa Kodira; Bruce Birren; James E Galagan; Stefano F F Torriani; Bruce A McDonald; Richard Oliver
Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum.
The Plant cell 2007;19(11):3347-68.
2007: Sarah K Volkman; Pardis C Sabeti; David DeCaprio; Daniel E Neafsey; Stephen F Schaffner; Danny A Milner; Johanna Daily; Ousmane Sarr; Daouda Ndiaye; Omar Ndir; Souleymane MBoup; Manoj T Duraisingh; Amanda Lukens; Alan Derr; Nicole Stange-Thomann; Skye Waggoner; Robert Onofrio; Liuda Ziaugra; Evan Mauceli; Sante Gnerre; David B Jaffe; Joanne Zainoun; Roger C Wiegand; Bruce Birren; Daniel L Hartl; James E Galagan; Eric S Lander; Dyann F Wirth
A genome-wide map of diversity in Plasmodium falciparum.
Nature genetics 2007;39(1):113-9.
2006: Rémy Bruggmann; Arvind K Bharti; Heidrun Gundlach; Jinsheng Lai; Sarah Young; Ana C Pontaroli; Fusheng Wei; Georg Haberer; Galina Fuks; Chunguang Du; Christina Raymond; Matt C Estep; Renyi Liu; Jeffrey L Bennetzen; Agnes P Chan; Pablo D Rabinowicz; John Quackenbush; W Brad Barbazuk; Rod A Wing; Bruce Birren; Chad Nusbaum; Steve Rounsley; Klaus F X Mayer; Joachim Messing
Uneven chromosome contraction and expansion in the maize genome.
Genome research 2006;16(10):1241-51.
2006: Yiting Yu; Heenam Stanley Kim; Hui Hoon Chua; Chi Ho Lin; Siew Hoon Sim; Daoxun Lin; Alan Derr; Reinhard Engels; David DeShazer; Bruce Birren; William C Nierman; Patrick Tan
Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis.
BMC microbiology 2006;6():46.
2005: Georg Haberer; Sarah Young; Arvind K Bharti; Heidrun Gundlach; Christina Raymond; Galina Fuks; Ed Butler; Rod A Wing; Steve Rounsley; Bruce Birren; Chad Nusbaum; Klaus F X Mayer; Joachim Messing
Structure and architecture of the maize genome.
Plant physiology 2005;139(4):1612-24.
2005: James E Galagan; Matthew Henn; Li-Jun Ma; Christina A Cuomo; Bruce Birren
Genomics of the fungal kingdom: insights into eukaryotic biology.
Genome research 2005;15(12):1620-31.
2005: Jade P Vinson; David B Jaffe; Keith O'Neill; Elinor K. Karlsson; Nicole Stange-Thomann; Scott Anderson; Jill P Mesirov; Nori Satoh; Yutaka Satou; Chad Nusbaum; Bruce Birren; James E Galagan; Eric S Lander
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.
Genome research 2005;15(8):1127-35.
2004: Cydney B Nielsen; Brad Friedman; Bruce Birren; Christopher B Burge; James E Galagan
Patterns of intron gain and loss in fungi.
PLoS biology 2004;2(12):e422.
2004: Jacob D Jaffe; Nicole Stange-Thomann; Cherylyn Smith; David DeCaprio; Sheila Fisher; Jonathan Butler; Sarah Calvo; Tim Elkins; Michael G FitzGerald; Nabil Hafez; Chinnappa D Kodira; John Major; Shunguang Wang; Jane Wilkinson; Robert Nicol; Chad Nusbaum; Bruce Birren; Howard C Berg; George M Church
The complete genome and proteome of Mycoplasma mobile.
Genome research 2004;14(8):1447-61.
2004: Manolis Kellis; Bruce Birren; Eric S Lander
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.
Nature 2004;428(6983):617-24.
2004: Torstein Tengs; Thomas LaFramboise; Robert B Den; David Hayes; Jianhua Zhang; Saikat DebRoy; Robert Gentleman; Keith O'Neill; Bruce Birren; Matthew Meyerson
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.
Nucleic acids research 2004;32(15):e121.
2004: Manolis Kellis; Nick Patterson; Bruce Birren; Bonnie Berger; Eric S Lander
Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):319-55.
2003: Manolis Kellis; Nick Patterson; Matthew Endrizzi; Bruce Birren; Eric S Lander
Sequencing and comparison of yeast species to identify genes and regulatory elements.
Nature 2003;423(6937):241-54.
2003: Yaohui Xu; Nicole Stange-Thomann; Griffin Weber; Ronghai Bo; Sheila Dodge; Robert G David; Karen Foley; Javad Beheshti; Nancy Lee Harris; Bruce Birren; Eric S Lander; Matthew Meyerson
Pathogen discovery from human tissue by sequence-based computational subtraction.
Genomics 2003;81(3):329-35.
2002: Armand J MacMurray; Daniel H Moralejo; Anne E Kwitek; Elizabeth A Rutledge; Brian Van Yserloo; Paul Gohlke; Sara J Speros; Ben Snyder; Jonathan Schaefer; Sabine Bieg; Jianjie Jiang; Ruth A Ettinger; Jessica Fuller; Terri L Daniels; Anna Pettersson; Kimberly Orlebeke; Bruce Birren; Howard J Jacob; Eric S Lander; Ake Lernmark
Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene.
Genome research 2002;12(7):1029-39.
2002: Sung Sup Park; Pawel Stankiewicz; Weimin Bi; Christine Shaw; Jessica A Lehoczky; Ken Dewar; Bruce Birren; James R Lupski
Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs.
Genome research 2002;12(5):729-38.
2002: Hope Lancero; Jennifer E Brofft; John Downard; Bruce Birren; Chad Nusbaum; Jerome Naylor; Wenyuan Shi; Lawrence J Shimkets
Mapping of Myxococcus xanthus social motility dsp mutations to the dif genes.
Journal of bacteriology 2002;184(5):1462-5.
2001: Yuko S Askew; Stephen C Pak; Cliff J Luke; David J Askew; Sule Cataltepe; David R Mills; H Kato; Jessica A Lehoczky; Ken Dewar; Bruce Birren; Gary A Silverman
SERPINB12 is a novel member of the human ov-serpin family that is widely expressed and inhibits trypsin-like serine proteinases.
The Journal of biological chemistry 2001;276(52):49320-30.
2001: Ken Inoue; Ken Dewar; Nicholas Katsanis; Lawrence Reiter; Eric S Lander; KL Devon; D W Wyman; James R Lupski; Bruce Birren
The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes.
Genome research 2001;11(6):1018-33.
2000: Patrick Onyango; W Miller; Jessica A Lehoczky; Cheuk T. Leung; Bruce Birren; Sarah J Wheelan; Ken Dewar; Andrew P Feinberg
Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain.
Genome research 2000;10(11):1697-710.
1999: Timothy Wiltshire; Mathew Pletcher; Susan Cole; Melissa P Villanueva; Bruce Birren; Jessica A Lehoczky; Ken Dewar; Roger H Reeves
Perfect conserved linkage across the entire mouse chromosome 10 region homologous to human chromosome 21.
Genome research 1999;9(12):1214-22.
1999: James C Engert; Carole Doré; Jocelyne Mercier; Bing Ge; Christine Bétard; John D Rioux; C Owen; P Bérubé; KL Devon; Bruce Birren; SB Melançon; Kenneth Morgan; Thomas J Hudson; Andrea Richter
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS): high-resolution physical and transcript map of the candidate region in chromosome region 13q11.
Genomics 1999;62(2):156-64.
1999: C Sun; Helen Skaletsky; Bruce Birren; KL Devon; Z Tang; Sherman Silber; Robert D Oates; David C Page
An azoospermic man with a de novo point mutation in the Y-chromosomal gene USP9Y.
Nature genetics 1999;23(4):429-32.
1999: Julie R Korenberg; Xiao-Ning Chen; Z Sun; Z Y Shi; S Ma; E Vataru; D Yimlamai; J S Weissenbach; H Shizuya; MI Simon; S S Gerety; H Nguyen; I S Zemsteva; L Hui; J Silva; X Wu; Bruce Birren; T J Hudson
Human genome anatomy: BACs integrating the genetic and cytogenetic maps for bridging genome and biomedicine.
Genome research 1999;9(10):994-1001.
1999: CS Moore; J S Lee; Bruce Birren; Gail Stetten; L L Baxter; Roger H Reeves
Integration of cytogenetic with recombinational and physical maps of mouse chromosome 16.
Genomics 1999;59(1):1-5.
1999: Dietmar Pfeifer; Ralf Kist; Ken Dewar; KL Devon; Eric S Lander; Bruce Birren; L Korniszewski; E Back; Gerd Scherer
Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: evidence for an extended control region.
American journal of human genetics 1999;65(1):111-24.
1999: K Hunter; J Greenwood; Y L Yang; J M Cunningham; Bruce Birren; David E Housman
An integrated somatic cell hybrid, YAC, and BAC map of the Rmc1 region of mouse chromosome 1.
Genomics 1999;58(3):318-22.
1999: Julie R Korenberg; Xiao-Ning Chen; K L Devon; D Noya; M L Oster-Granite; Bruce Birren
Mouse molecular cytogenetic resource: 157 BACs link the chromosomal and genetic maps.
Genome research 1999;9(5):514-23.
1999: M Williams; M S Lyu; Y L Yang; E P Lin; Roland L Dunbrack; Bruce Birren; J Cunningham; K Hunter
Ier5, a novel member of the slow-kinetics immediate-early genes.
Genomics 1999;55(3):327-34.
1998: Ken Dewar; L Sabbagh; G Cardinal; F Veilleux; François Sanschagrin; Bruce Birren; Roger C Levesque
Pseudomonas aeruginosa PAO1 bacterial artificial chromosomes: strategies for mapping, screening, and sequencing 100 kb loci of the 5.9 Mb genome.
Microbial & comparative genomics 1998;3(2):105-17.
1996: UJ Kim; H Shizuya; H L Kang; S S Choi; C L Garrett; L J Smink; Bruce Birren; Julie R Korenberg; Carl Bruder; M I Simon
A bacterial artificial chromosome-based framework contig map of human chromosome 22q.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(13):6297-301.
1996: UJ Kim; Bruce Birren; T Slepak; V Mancino; C Boysen; H L Kang; M I Simon; H Shizuya
Construction and characterization of a human bacterial artificial chromosome library.
Genomics 1996;34(2):213-8.
1996: Bruce Birren; Y Tachi-iri; UJ Kim; M Nguyen; H Shizuya; Julie R Korenberg; M I Simon
A human chromosome 22 fosmid resource: mapping and analysis of 96 clones.
Genomics 1996;34(1):97-106.
1996: B A Hamilton; W N Frankel; AW Kerrebrock; T L Hawkins; W FitzHugh; K Kusumi; L B Russell; K L Mueller; V van Berkel; Bruce Birren; Leonid Kruglyak; Eric S Lander
Disruption of the nuclear hormone receptor RORalpha in staggerer mice.
Nature 1996;379(6567):736-9.
1995: Thomas J Hudson; L D Stein; S S Gerety; J Ma; A B Castle; J Silva; DK Slonim; R Baptista; Leonid Kruglyak; S H Xu; X Hu; A M Colbert; C Rosenberg; Mary Reeve; Steve Rozen; L Hui; X Wu; C Vestergaard; K M Wilson; J S Bae; S Maitra; S Ganiatsas; C A Evans; Margaret DeAngelis; K A Ingalls; R W Nahf; L T Horton; M O Anderson; A J Collymore; W Ye; V Kouyoumjian; I S Zemsteva; J Tam; R Devine; D F Courtney; M T Renaud; H Nguyen; T J O'Connor; C Fizames; S Fauré; Gabor Gyapay; C Dib; J Morissette; J B Orlin; Bruce Birren; N Goodman; Jean Weissenbach; T L Hawkins; S Foote; David C Page; Eric S Lander
An STS-based map of the human genome.
Science (New York, N.Y.) 1995;270(5244):1945-54.
1995: Y Sheng; V Mancino; Bruce Birren
Transformation of Escherichia coli with large DNA molecules by electroporation.
Nucleic acids research 1995;23(11):1990-6.
1994: Bruce Birren; E Lai
Rapid pulsed field separation of DNA molecules up to 250 kb.
Nucleic acids research 1994;22(24):5366-70.
1994: UJ Kim; H Shizuya; Bruce Birren; T Slepak; P de Jong; M I Simon
Selection of chromosome 22-specific clones from human genomic BAC library using a chromosome-specific cosmid library pool.
Genomics 1994;22(2):336-9.
1992: H Shizuya; Bruce Birren; UJ Kim; V Mancino; T Slepak; Y Tachiiri; M Simon
Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(18):8794-7.
1992: UJ Kim; H Shizuya; P J de Jong; Bruce Birren; M I Simon
Stable propagation of cosmid sized human DNA inserts in an F factor based vector.
Nucleic acids research 1992;20(5):1083-5.
1990: Bruce Birren; M I Simon; E Lai
The basis of high resolution separation of small DNAs by asymmetric-voltage field inversion electrophoresis and its application to DNA sequencing gels.
Nucleic acids research 1990;18(6):1481-7.
1989: Bruce Birren; Leroy Hood; E Lai
Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system.
Electrophoresis 1989;10(5-6):302-9.
1989: Bruce Birren; E Lai; Leroy Hood; M I Simon
Pulsed field gel electrophoresis techniques for separating 1- to 50-kilobase DNA fragments.
Analytical biochemistry 1989;177(2):282-6.
1989: E Lai; Bruce Birren; S M Clark; M I Simon; Leroy Hood
Pulsed field gel electrophoresis.
BioTechniques 1989;7(1):34-42.
1988: E Lai; Bruce Birren; S M Clark; Leroy Hood
Relaxation intervals alter the mobility of large DNA molecules in pulsed field gel electrophoresis.
Nucleic acids research 1988;16(21):10376.
1988: S M Clark; E Lai; Bruce Birren; Leroy Hood
A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields.
Science (New York, N.Y.) 1988;241(4870):1203-5.
1988: Bruce Birren; E Lai; S M Clark; Leroy Hood; M I Simon
Optimized conditions for pulsed field gel electrophoretic separations of DNA.
Nucleic acids research 1988;16(15):7563-82.