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Terrence Furey

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Genes & Molecular Sequences

Chemicals & Drugs

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Nathan C Sheffield; Lingyun Song; John A Stamatoyannopoulos; Robert E Thurman; Gregory E Crawford; Boris Lenhard; Alexias Safi; Terrence S Furey
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.
Terrence S Furey
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.
Yoichiro Shibata; Lingyun Song; Alok K Tewari; Matthew Wortham; Gregory A Wray; Courtney C Babbitt; Olivier Fedrigo; Terrence S Furey; Vishwanath R Iyer; Bum-Kyu Lee; Darin London; Elliott H Margulies; Stephen C J Parker; Nathan C Sheffield; Gregory E Crawford
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

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All Publications

2013: Nathan C Sheffield; Lingyun Song; John A Stamatoyannopoulos; Robert E Thurman; Gregory E Crawford; Boris Lenhard; Alexias Safi; Terrence S Furey
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.
Genome research 2013;23(5):777-88.
2012: Terrence S Furey
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.
Nature reviews. Genetics 2012;13(12):840-52.
2012: Yoichiro Shibata; Lingyun Song; Alok K Tewari; Matthew Wortham; Gregory A Wray; Courtney C Babbitt; Olivier Fedrigo; Terrence S Furey; Vishwanath R Iyer; Bum-Kyu Lee; Darin London; Elliott H Margulies; Stephen C J Parker; Nathan C Sheffield; Gregory E Crawford
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.
PLoS genetics 2012;8(6):e1002789.
2012: Jared M Bischof; Calvin U Cotton; Gregory E Crawford; Terrence S Furey; Nehal Gosalia; Shih-Hsing Leir; Darin London; Christopher J Ott; Lingyun Song; Ann Harris
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.
Thorax 2012;67(5):385-91.
2012: Qing Xiong; Nicola Ancona; Elizabeth R Hauser; Sayan Mukherjee; Terrence S Furey
Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.
Genome research 2012;22(2):386-97.
2012: Brian D Bennett; Sayan Mukherjee; Qing Xiong; Terrence S Furey
A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning.
PloS one 2012;7(9):e44635.
2012: Stephen C J Parker; STEVEN ROSENBERG; Yardena Samuels; Lingyun Song; Robert L Walker; Xiaomu Wei; Paul S Meltzer; James C Mullikin; Hatice Ozel Abaan; Subramanian S Ajay; Umesh K Bhanot; Isabel Cardenas-Navia; Gregory E Crawford; Terrence S Furey; Jared Gartner; Yevgeniy Gindin; Nancy F Hansen; J Keith Killian; Elliott H Margulies
Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.
PLoS genetics 2012;8(8):e1002871.
2011: Weisheng Wu; Yu Zhang; Gerd A Blobel; Kuan-Bei Chen; Yong Cheng; Francesca Chiaromonte; Gregory E Crawford; Christine M Dorman; Daniela Drautz; Jason Ernst; Terrence S Furey; Belinda Giardine; Cheryl A Keller; Manolis Kellis; Swathi Ashok Kumar; Webb Miller; Tejaswini Mishra; Christapher Morrissey; Max Pimkin; Stephan C Schuster; Yoichiro Shibata; Lingyun Song; James TAYLOR; Mitchell J Weiss; Ross C Hardison
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.
Genome research 2011;21(10):1659-71.
2011: Lingyun Song; Teresa Vales; Tianyuan Wang; Deborah Winter; Zhancheng Zhang; Zhuzhu Zhang; Ewan Birney; Alan P Boyle; Neil D Clarke; Gregory E Crawford; Paul G Giresi; Stefan Gräf; Linda L Grasfeder; Mikael Huss; Vishwanath R Iyer; Damian Keefe; Bum-Kyu Lee; Jason Dillon Lieb; Zheng Liu; Darin London; Ryan M McDaniell; Nathan C Sheffield; Yoichiro Shibata; Kimberly A Showers; Jeremy M Simon; Terrence S Furey
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Genome research 2011;21(10):1757-67.
2011: Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Genome research 2011;21(3):456-64.
2010: Michael L Stitzel; Praveen Sethupathy; Daniel S Pearson; Peter S Chines; Lingyun Song; Michael R Erdos; Ryan Welch; Stephen C J Parker; Alan P Boyle; Laura J Scott; Elliott H Margulies; Michael Boehnke; Terrence S Furey; Gregory E Crawford; Francis S Collins
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.
Cell metabolism 2010;12(5):443-55.
2010: Ewan Birney; Jason Dillon Lieb; Terrence S Furey; Gregory E Crawford; Vishwanath R Iyer
Allele-specific and heritable chromatin signatures in humans.
Human molecular genetics 2010;19(R2):R204-9.
2010: Ryan McDaniell; Bum-Kyu Lee; Lingyun Song; Zheng Liu; Alan P Boyle; Michael R Erdos; Laura J Scott; Mario A Morken; Katerina S Kucera; Anna Battenhouse; Damian Keefe; Francis S Collins; Huntington F Willard; Jason Dillon Lieb; Terrence S Furey; Gregory E Crawford; Vishwanath R Iyer; Ewan Birney
Heritable individual-specific and allele-specific chromatin signatures in humans.
Science (New York, N.Y.) 2010;328(5975):235-9.
2010: Courtney C Babbitt; Olivier Fedrigo; Adam D Pfefferle; Alan P Boyle; Julie E Horvath; Terrence S Furey; Gregory A Wray
Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.
Genome biology and evolution 2010;2():67-79.
2010: Mats Ensterö; Orjan Akerborg; Daniel Lundin; Bei Wang; Terrence S Furey; Marie Ohman; Jens Lagergren
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.
BMC bioinformatics 2010;11():6.
2009: Xueqing Xu; Koji Tsumagari; Janet Sowden; Rabi Tawil; Alan P Boyle; Lingyun Song; Terrence S Furey; Gregory E Crawford; Melanie Ehrlich
DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.
Nucleic acids research 2009;37(22):7381-93.
2009: Tianyuan Wang; Terrence S Furey
Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser.
Circulation. Cardiovascular genetics 2009;2(2):199-204.
2009: Tianyuan Wang; Terrence S Furey; Jessica J Connelly; Shihao Ji; Sarah Nelson; Steffen Heber; Simon G Gregory; Elizabeth R Hauser
A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease.
Human genomics 2009;3(3):221-35.
2008: Alan P Boyle; Justin Guinney; Gregory E Crawford; Terrence S Furey
F-Seq: a feature density estimator for high-throughput sequence tags.
Bioinformatics (Oxford, England) 2008;24(21):2537-8.
2008: Alan P Boyle; Sean Davis; Hennady P Shulha; Paul Meltzer; Elliott H Margulies; Zhiping Weng; Terrence S Furey; Gregory E Crawford
High-resolution mapping and characterization of open chromatin across the genome.
Cell 2008;132(2):311-22.
2007: Hualin Xi; Hennady P Shulha; Jane M Lin; Teresa R Vales; Yutao Fu; David M Bodine; Ronald D G McKay; Josh G Chenoweth; Paul J Tesar; Terrence S Furey; Bing Ren; Zhiping Weng; Gregory E Crawford
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.
PLoS genetics 2007;3(8):e136.
2007: Liang Goh; Susan Murphy; Sayan Muhkerjee; Terrence S Furey
Genomic sweeping for hypermethylated genes.
Bioinformatics (Oxford, England) 2007;23(3):281-8.
2006: Zhong Wang; Huntington F Willard; Sayan Mukherjee; Terrence S Furey
Evidence of influence of genomic DNA sequence on human X chromosome inactivation.
PLoS computational biology 2006;2(9):e113.
2006: Stephanie M Cohen; Terrence S Furey; Norman A Doggett; David G Kaufman
Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts.
BMC genomics 2006;7():301.
2006: Terrence S Furey
Comparison of human (and other) genome browsers.
Human genomics 2006;2(4):266-70.
2006: Angie S Hinrichs; Donna Karolchik; Robert Baertsch; Galt P Barber; Gill Bejerano; Hiram Clawson; Mark Diekhans; Terrence S Furey; Rachel A Harte; Fan Hsu; J Hillman-Jackson; Robert M Kuhn; Jan Skov Pedersen; Andy Pohl; Brian J Raney; Kate Rosenbloom; Adam Siepel; Kayla E Smith; Charles W Sugnet; A Sultan-Qurraie; Daryl J Thomas; Heather Trumbower; RJ Weber; M Weirauch; Ann S Zweig; David Haussler; W James Kent
The UCSC Genome Browser Database: update 2006.
Nucleic acids research 2006;34(Database issue):D590-8.
2004: Terrence S Furey; Mark Diekhans; Yontao Lu; Tina Graves; Lachlan Oddy; Jennifer Randall-Maher; LaDeana W Hillier; Richard K Wilson; David Haussler
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.
Genome research 2004;14(10B):2034-40.
2004: Xinwei She; Julie E Horvath; Zhaoshi Jiang; Ge Liu; Terrence S Furey; Laurie A Christ; Royden Clark; Tina Graves; Cassy L Gulden; Can Alkan; Jeffrey A Bailey; Cenk Sahinalp; Mariano Rocchi; David Haussler; Richard K Wilson; Webb Miller; Stuart Schwartz; Evan E Eichler
The structure and evolution of centromeric transition regions within the human genome.
Nature 2004;430(7002):857-64.
2004: Michael I Jensen-Seaman; Terrence S Furey; Bret Payseur; Yontao Lu; Krishna M Roskin; Chin-Fu Chen; Michael A Thomas; David Haussler; Howard J Jacob
Comparative recombination rates in the rat, mouse, and human genomes.
Genome research 2004;14(4):528-38.
2004: Donna Karolchik; Angie S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
The UCSC Table Browser data retrieval tool.
Nucleic acids research 2004;32(Database issue):D493-6.
2003: Terrence S Furey; David Haussler
Integration of the cytogenetic map with the draft human genome sequence.
Human molecular genetics 2003;12(9):1037-44.
2003: Ross C Hardison; Krishna M Roskin; Shan Yang; Mark Diekhans; W James Kent; Ryan Weber; Laura Elnitski; Jia Li; Michael O'Connor; Diana Kolbe; Scott Schwartz; Terrence S Furey; Simon Whelan; Nick Goldman; Arian Smit; Webb Miller; Francesca Chiaromonte; David Haussler
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Genome research 2003;13(1):13-26.
2003: Donna Karolchik; Robert Baertsch; Mark Diekhans; Terrence S Furey; Angie S Hinrichs; Y T Lu; Krishna M Roskin; M Schwartz; Charles W Sugnet; Daryl J Thomas; RJ Weber; David Haussler; W James Kent
The UCSC Genome Browser Database.
Nucleic acids research 2003;31(1):51-4.
2002: W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
The human genome browser at UCSC.
Genome research 2002;12(6):996-1006.
2001: Paul Pavlidis; Terrence S Furey; M Liberto; David Haussler; WN Grundy
Promoter region-based classification of genes.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():151-63.
2000: Terrence S Furey; N Cristianini; N Duffy; D W Bednarski; Michèl Schummer; David Haussler
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
Bioinformatics (Oxford, England) 2000;16(10):906-14.
2000: M P Brown; WN Grundy; D Lin; N Cristianini; Charles W Sugnet; Terrence S Furey; Manuel Ares; David Haussler
Knowledge-based analysis of microarray gene expression data by using support vector machines.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(1):262-7.