Epernicus: Keith R Bradnam, Ph.D.

Keith R Bradnam, Ph.D.

Position:
Post Doctoral Fellow

Genome Center

University of California, Davis (Davis, CA)
Advisor:
Ian Korf
Degrees:

Ph.D., Molecular Evolution, University of Nottingham (Nottingham, UK)

M.Sc., Bioinformatics, The University of Manchester (Manchester, UK)

B.Sc., Ecology, University of Leeds (Leeds, UK)
Past Advisors:

Richard Durbin (as Senior Scientist)

Sean May (as Senior Scientist)

Paul M Sharp (as Graduate Student - Ph.D.)
Research:
Finding interesting patterns in gene and genome sequence data

Our lab works on a diverse set of problems, that mostly involve analysis of gene and genome data using bioinformatics and (through collaborations) wet lab techniques. The main project with which I am currently involved is exploring the signals and mechanisms involved in intron-mediated enhancement (IME) of gene expression in plants.

Our group has found a motif in the early introns of several plant species which we believe might be responsible for the IME effect. We are further elucidating the extent and significance of this motif in several different species.
Other Experience:
1994 Technical support position for educational software company

Communities:

Keith Bradnam's Genealogy

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Keith Bradnam's Publications (12)

Assemblathon 1: A competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, Maclean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, Derisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B

Genome research. 2011 Dec;21(12):2224-41
Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants.
Parra G, Bradnam K, Rose AB, Korf I

Nucleic acids research. 2011 Jul;39(13):5328-37
Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells.
Varlakhanova N, Cotterman R, Bradnam K, Korf I, Knoepfler PS

Epigenetics & chromatin. 2011;4:20
Assessing the gene space in draft genomes.
Parra G, Bradnam K, Ning Z, Keane T, Korf I

Nucleic acids research. 2009 Jan;37(1):289-97
Longer first introns are a general property of eukaryotic gene structure.
Bradnam KR, Korf I

PloS one. 2008;3(8):e3093
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Parra G, Bradnam K, Korf I

Bioinformatics (Oxford, England). 2007 May 1;23(9):1061-7
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD

Nucleic acids research. 2005 Jan 1;33(Database issue):D383-9
WormBase as an integrated platform for the C. elegans ORFeome.
Chen N, Lawson D, Bradnam K, Harris TW, Stein LD

Genome research. 2004 Oct;14(10B):2155-61
WormBase: a multi-species resource for nematode biology and genomics.
Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD

Nucleic acids research. 2004 Jan 1;32(Database issue):D411-7
WormBase: a cross-species database for comparative genomics.
Harris TW, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W, Blasier D, Kenny E, Cunningham F, Kishore R, Chan J, Muller HM, Petcherski A, Thorisson G, Day A, Bieri T, Rogers A, Chen CK, Spieth J, Sternberg P, Durbin R, Stein LD

Nucleic acids research. 2003 Jan 1;31(1):133-7
Website update: The UK Crop Plant Bioinformatics Network (UK CropNet).
Bradnam K, May S

Yeast (Chichester, England). 2000 Dec;17(4):335-8
G+C content variation along and among Saccharomyces cerevisiae chromosomes.
Bradnam KR, Seoighe C, Sharp PM, Wolfe KH

Molecular biology and evolution. 1999 May;16(5):666-75

Keith Bradnam's Posters and Presentations (4)

What can WormBase do for you? (presentation)
Keith R Bradnam

European Worm Meeting, Interlaken, Switzerland; 06/2004
Onwards and upwards: enhancements and improvements to WormBase (presentation)
Keith R Bradnam

International Worm Meeting, At UCLA; 06/2003
Recent changes and improvements to the WormBase database (presentation)
Keith R Bradnam

European Worm Meeting, Paestum, Italy; 06/2002
UK CropNet – a consortium of crop plant databases (presentation)
Keith R Bradnam

Plant and Animal Genomes (PAG) VIII; 01/1999

One Figure

On average, first introns are longer in the majority of eukaryotic species

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