Terrence Furey, PhD

Department:
Biostatistics and Bioinformatics

Email Address:
terry.furey@duke.edu

Website:
http://www.genome.duke.edu/people/faculty/furey
http://www.genome.duke.edu/labs/furey/

Address:
Box 3382
DUMC
Durham, NC 27708

Telephone:
9196684728

Fax Telephone:
9196690795

Research Interests:
Chromatin Structure and Relationship to Gene Expression

Chromosomes are compacted into increasingly complex chromatin structures within eukaryotic nuclei.  In collaboration with Dr. Greg Crawford and his lab, we analyze data from genome-wide DNaseI hypersensitivity experiments using high-throughput Illumina sequencing and whole-genome microarrays to identify regions of open chromatin as described in our recent publication in
Cell. The computational integration of these data with related gene expression, transcription factor binding, and epigenetic data will provide a more complete picture of the complex process of gene transcription.

We are members of the International ENCODE Consortium whose goal is to identify all functional elements in the human genome.  Along with the Crawford, our group includes Jason Lieb's lab at UNC-Chapel Hill, Vishy Iyer's lab at Univ Texas-Austin, and Ewan Birney's lab at the EBI.  The goal of our group is to create an open chromatin map of the human genome in several diverse cell types, and to provide an initial functional annotation of these regions. The Furey lab is developing computational methods to integrate substantial sequence and microarray data from DNase I hypersensitivity, FAIRE, and ChIP experiments to create these maps.        
To promote these analyses, We maintain a full mirror of the UCSC Genome Browser at http://genome-mirror.duhs.duke.edu. This not only provides direct access to the extensive database of annotations of the human and other genomes compiled at UCSC, but also allows us to develop new annotations related to ongoing research based on analyses performed within the lab.

Cancer Genomics

Cancer is a complex disease with many histological subtypes and probably thousands of molecular subtypes that differ substantially with respect to their onset, progression, and response to treatment. High-throughput microarray and sequence-based assays are now capable of assessing genome-wide changes andvariation in gene expression, genome copy number, allele expression, and DNA methylation status throughout cancer initiation and progression. These experiments reveal different yet complementary information regarding the current state of a population of cancer cells.  This ability to molecularly characterize cancer has already resulted in novel diagnostic tests and treatments. Current computational models designed to distinguish between phenotypically disparate samples are generally accurate but are difficult to interpret biologically and primarily rely on data from a single molecular assay.  The careful and accurate integration of complementary data in biologically interpretable models will provide a more complete and interpretable portrait of cancer, for example providing new and stronger evidence of genetic changes associated with the root causes of observed differential gene expression.                                                                                                                           
The goal of our lab is to develop statistical methods and computational software that integrate high-dimensional heterogeneous but complementary data from cancer samples to identify fundamental genomic alterations with clinical and biological relevance. These methods are being developed in collaboration with Dr. Sayan Mukherjee and Dr. Phil Febbo.

Publications:
2009 -- Pubmed # 19403457 -- Wang T, Furey TS, Connelly JJ, Ji S, Nelson S, Heber S, Gregory SG, Hauser ER. A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. Hum Genomics. 2009 Apr;3(3):221-35.

2008 -- Pubmed # 18243105 -- Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22.

2008 -- Pubmed # 18784119 -- Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8.

2007 -- Pubmed # 17148511 -- Goh L, Murphy SK, Muhkerjee S, Furey TS. Genomic sweeping for hypermethylated genes. Bioinformatics. 2007 Feb 1;23(3):281-8.

2007 -- Pubmed # 17708682 -- Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 2007 Aug;3(8):e136.

2006 -- Pubmed # 16948528 -- Wang Z, Willard HF, Mukherjee S, Furey TS. Evidence of influence of genomic DNA sequence on human X chromosome inactivation. PLoS Comput Biol. 2006 Sep 1;2(9):e113.

2004 -- Pubmed # 15489323 -- Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res. 2004 Oct;14(10B):2034-40.

2004 -- International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45.

2003 -- Pubmed # 12700172 -- Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-44.

2002 -- Pubmed # 12045153 -- Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

2001 -- Pubmed # 11237021 -- Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ, . Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8.

2001 -- Pubmed # 11237011 -- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, BorkP, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, . Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.

2001 -- Pubmed # 11237014 -- McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati , Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H, . A physical map of the human genome. Nature. 2001 Feb 15;409(6822):934-41.

2000 -- Pubmed # 11120680 -- Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000 Oct;16(10):906-14.