Terrence S. Furey, Ph.D. - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. Plos Genetics. 16: e1008537. PMID 31961859 DOI: 10.1371/journal.pgen.1008537  0.48
2018 Israel JW, Chappell GA, Simon JM, Pott S, Safi A, Lewis L, Cotney P, Boulos HS, Bodnar W, Lieb JD, Crawford GE, Furey TS, Rusyn I. Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 29429127 DOI: 10.1007/s00335-018-9739-6  0.48
2017 Lewis L, Crawford GE, Furey TS, Rusyn I. Genetic and epigenetic determinants of inter-individual variability in responses to toxicants. Current Opinion in Toxicology. 6: 50-59. PMID 29276797 DOI: 10.1016/j.cotox.2017.08.006  0.48
2017 Chappell GA, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton KG, Bodnar W, Lieb JD, Crawford GE, Rusyn I, Furey TS. Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice. Environmental Health Perspectives. 125: 107006. PMID 29038090 DOI: 10.1289/EHP1937  0.48
2016 Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, et al. Molecular classification of Crohn's disease reveals two clinically relevant subtypes. Gut. PMID 27742763 DOI: 10.1136/gutjnl-2016-312518  0.48
2016 Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, et al. Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses. European Journal of Immunology. PMID 27159132 DOI: 10.1002/eji.201546237  0.84
2015 Buchkovich ML, Eklund K, Duan Q, Li Y, Mohlke KL, Furey TS. Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci. Bmc Medical Genomics. 8: 43. PMID 26210163 DOI: 10.1186/s12920-015-0117-x  0.84
2015 Peck BC, Weiser M, Lee SE, Gipson GR, Iyer VB, Sartor RB, Herfarth HH, Long MD, Hansen JJ, Isaacs KL, Trembath DG, Rahbar R, Sadiq TS, Furey TS, Sethupathy P, et al. MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility. Inflammatory Bowel Diseases. PMID 26164662 DOI: 10.1097/MIB.0000000000000478  0.84
2014 Weiser M, Mukherjee S, Furey TS. Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics. 198: 879-93. PMID 25230953 DOI: 10.1534/genetics.114.167791  0.84
2014 Xiong Q, Mukherjee S, Furey TS. GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data. Scientific Reports. 4: 6347. PMID 25213199 DOI: 10.1038/srep06347  0.84
2014 Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. Plos One. 9: e107156. PMID 25198066 DOI: 10.1371/journal.pone.0107156  0.84
2014 Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Research. 24: 241-50. PMID 24158655 DOI: 10.1101/gr.158253.113  0.84
2013 Furey TS, Sethupathy P. Genetics. Genetics driving epigenetics. Science (New York, N.Y.). 342: 705-6. PMID 24202168 DOI: 10.1126/science.1246755  0.84
2013 Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biology of Reproduction. 89: 104. PMID 24006278 DOI: 10.1095/biolreprod.113.110403  0.84
2013 Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE. DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Research. 23: 1118-29. PMID 23657885 DOI: 10.1101/gr.150482.112  0.84
2013 Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Research. 23: 777-88. PMID 23482648 DOI: 10.1101/gr.152140.112  0.84
2012 Sheffield NC, Furey TS. Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. Genes. 3: 651-70. PMID 24705081 DOI: 10.3390/genes3040651  0.84
2012 Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nature Reviews. Genetics. 13: 840-52. PMID 23090257 DOI: 10.1038/nrg3306  0.84
2012 Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG. Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biology. 13: R88. PMID 23034120 DOI: 10.1186/gb-2012-13-10-r88  0.84
2012 Bennett BD, Xiong Q, Mukherjee S, Furey TS. A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning. Plos One. 7: e44635. PMID 23028573 DOI: 10.1371/journal.pone.0044635  0.84
2012 Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, ... ... Furey TS, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/nature11232  0.84
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  0.36
2012 Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, et al. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. Plos Genetics. 8: e1002871. PMID 22912592 DOI: 10.1371/journal.pgen.1002871  0.84
2012 Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. Plos Genetics. 8: e1002789. PMID 22761590 DOI: 10.1371/journal.pgen.1002789  0.84
2012 Bischof JM, Ott CJ, Leir SH, Gosalia N, Song L, London D, Furey TS, Cotton CU, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax. 67: 385-91. PMID 22169360 DOI: 10.1136/thoraxjnl-2011-200880  0.84
2012 Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research. 22: 9-24. PMID 22090374 DOI: 10.1101/gr.127597.111  0.84
2012 Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Research. 22: 386-97. PMID 21940837 DOI: 10.1101/gr.124370.111  0.84
2011 Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, ... Furey TS, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/gr.125088.111  0.84
2011 Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, ... ... Furey TS, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/gr.121541.111  0.84
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  0.84
2011 Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research. 21: 456-64. PMID 21106903 DOI: 10.1101/gr.112656.110  0.84
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metabolism. 12: 443-55. PMID 21035756 DOI: 10.1016/j.cmet.2010.09.012  0.84
2010 Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Human Molecular Genetics. 19: R204-9. PMID 20846943 DOI: 10.1093/hmg/ddq404  0.84
2010 Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA. Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biology and Evolution. 2: 67-79. PMID 20333225 DOI: 10.1093/gbe/evq002  0.84
2010 McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/science.1184655  0.84
2010 Ensterö M, Akerborg O, Lundin D, Wang B, Furey TS, Ohman M, Lagergren J. A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. Bmc Bioinformatics. 11: 6. PMID 20047656 DOI: 10.1186/1471-2105-11-6  0.84
2009 Boyle AP, Furey TS. High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 1: 319-329. PMID 20514362 DOI: 10.2217/epi.09.29  0.84
2009 Wang T, Furey TS. Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. Circulation. Cardiovascular Genetics. 2: 199-204. PMID 20031585 DOI: 10.1161/CIRCGENETICS.108.843946  0.84
2009 Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M. DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Research. 37: 7381-93. PMID 19820107 DOI: 10.1093/nar/gkp833  0.84
2009 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. Human Genomics. 3: 221-35. PMID 19403457  0.84
2008 Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (Oxford, England). 24: 2537-8. PMID 18784119 DOI: 10.1093/bioinformatics/btn480  0.84
2008 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. 132: 311-22. PMID 18243105 DOI: 10.1016/j.cell.2007.12.014  0.84
2007 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 Genetics. 3: e136. PMID 17708682 DOI: 10.1371/journal.pgen.0030136  0.84
2007 Goh L, Murphy SK, Muhkerjee S, Furey TS. Genomic sweeping for hypermethylated genes. Bioinformatics (Oxford, England). 23: 281-8. PMID 17148511 DOI: 10.1093/bioinformatics/btl620  0.84
2006 Cohen SM, Furey TS, Doggett NA, Kaufman DG. Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts. Bmc Genomics. 7: 301. PMID 17134498 DOI: 10.1186/1471-2164-7-301  0.84
2006 Wang Z, Willard HF, Mukherjee S, Furey TS. Evidence of influence of genomic DNA sequence on human X chromosome inactivation Plos Computational Biology. 2: 0979-0988. PMID 16948528 DOI: 10.1371/journal.pcbi.0020113  0.84
2006 Furey TS. Comparison of human (and other) genome browsers. Human Genomics. 2: 266-70. PMID 16460652  0.84
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/nar/gkj144  0.84
2004 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, ... ... Furey T, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 14: 2121-7. PMID 15489334 DOI: 10.1101/gr.2596504  0.84
2004 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 Research. 14: 2034-40. PMID 15489323 DOI: 10.1101/gr.2467904  0.84
2004 She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 430: 857-64. PMID 15318213 DOI: 10.1038/nature02806  0.84
2004 Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Research. 14: 528-38. PMID 15059993 DOI: 10.1101/gr.1970304  0.84
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Furey TS, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/nature02426  0.36
2004 Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Research. 32: D493-6. PMID 14681465 DOI: 10.1093/nar/gkh103  0.84
2003 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, ... ... Furey TS, et al. The DNA sequence of human chromosome 7. Nature. 424: 157-64. PMID 12853948 DOI: 10.1038/nature01782  0.84
2003 Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Human Molecular Genetics. 12: 1037-44. PMID 12700172 DOI: 10.1093/hmg/ddg113  0.84
2003 Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/gr.844103  0.84
2003 Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Research. 31: 51-4. PMID 12519945 DOI: 10.1093/nar/gkg129  0.84
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Furey TS, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  0.84
2002 Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Research. 12: 996-1006. PMID 12045153 DOI: 10.1101/gr.229102. Article published online before print in May 2002  0.84
2001 Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 151-63. PMID 11262936  0.84
2001 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, et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 409: 953-8. PMID 11237021 DOI: 10.1038/35057192  0.84
2001 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, ... ... Furey T, et al. A physical map of the human genome. Nature. 409: 934-41. PMID 11237014 DOI: 10.1038/35057157  0.84
2001 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, ... ... Furey TS, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.36
2000 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 (Oxford, England). 16: 906-14. PMID 11120680  0.84
2000 Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D. 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. 97: 262-7. PMID 10618406 DOI: 10.1073/pnas.97.1.262  0.84
Show low-probability matches.