Publications

2020

Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ*, Furey TS*. Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis. 2020 May 29:izaa103. doi: 10.1093/ibd/izaa103. (*Co-senior authors) PMID: 32469069

Keele GR, Quach B, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W*, Rusyn IR*, Furey TS*. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genetics 2020 Jan 21;16(1):e1008537. (*Co-senior authors). PMID: 31961859

Toyonaga T, Steinbach EC, Keith BP, Barrow JB, Schaner MR, Wolber EA, Beasley C, Huling J, Wang Y, Allbritton NL, Chaumont N, Sadiq TS, Koruda MJ, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Shanahan MT, Rahbar R, Furey TS, Sethupathy P, Sheikh SZ. Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn’s Disease. Cell Mol Gastroenterol Hepatol. 2020 Jun 16:S2352-345X(20)30094-1. doi: 10.1016/j.jcmgh.2020.06.005. PMID: 32561494

2019

Raulerson CK, Ko A, Kidd JC, Currin KW, Brotman SM, Cannon ME, Wu Y, Spracklen CN, Jackson AU, Stringham HM, Welch RC, Fuchsberger C, Locke AE, Narisu N, Lusis AJ, Civelek M, Furey TS, Kuusisto J, Collins FS, Boehnke M, Scott LJ, Lin D, Love MI, Laakso M, Pajukanta P, Mohlke KL. Adipose tissue gene expression associations reveal hundreds of candidate genes for cardiometabolic traits. Am J Hum Genet. 2019 Oct 3;105(4):773-787. PMID: 31564431

Furey TS, Sethupathy P, Sheikh SZ. Redefining the IBDs using genome-scale molecular phenotyping.Nat Rev Gastroenterol Hepatol.  2019 May;16(5):296-311. PMID: 30787446

2018

Keith B, Barrow J, Toyonaga T, Kazgan N, O’Connor MH, Shah ND, Schaner MS, Wolber EA, Trad OK, Gipson GR, Pitman WA, Kanke M, Saxena SJ, Chaumont N, Sadiq TS, Koruda MJ, Cotney PA, Albritton N, Trembath DG, Sylvester S, Furey TS*, Sethupathy P*, Sheikh S*. Colonic epithelial miR-31 associates with the development of Crohn’s phenotypes. JCI Insight. 2018 Oct 4;3(19). pii: 122788. (*Co-senior authors).  PMID: 30282822

Israel JW, Lewis L, Chappell G, Pott S, Safi A, Cotney P, Sexton K, Bodnar W, Crawford GC*, Furey TS*, Rusyn I*. Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. Mamm Genome. 2018 Feb;29(1-2):153-167. PMID: 29429127

Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robison A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq T, Koruda MJ, Furey TS*, Sheikh SZ*. Molecular classification of Crohn’s disease reveals two clinically relevant subtypes. Gut. 2018 Jan;67(1):36-42. (*Co-senior authors). PMID:27742763

2017

Lewis L, Crawford GE, Furey TS, Rusyn I. Genetic and epigenetic determinants of inter-individual variability in responses to toxicants. Curr Opin Toxicol. 2017 Oct;6:50-59. PMID: 29276797

Chappell G, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton K, Bodnar W, Lieb JD, Crawford GC*, Rusyn I*, Furey TS*. Mouse strain-specific chromatin and transcriptional states modulate the DNA-damage response to an inhalational carcinogen. Environ Health Perspect. 2017 Oct 16;125(10):107006. (*Co-senior authors) PMID: 29038090

Wang JW, Quach BC, Furey TS. Correcting nucleotide-specific biases in high-throughput sequencing data. BMC Bioinformatics. 2017 Aug 1;18(1):357. PMID: 28764645

Lickwar CR, Camp JG, Weiser M, Kingsley DM, Furey TS, Sheikh SZ, Rawls Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biol. 2017 Aug 29;15(8):e2002054. PMID: 28850571

Quach BC, Furey TS. Modeling Heterogeneity in DNase-seq Data to Predict Transcription Factor Binding Sites Using a Discriminative Supervised Learning Framework. Bioinformatics 33(7):956-963 (2017). PMID:27993786

2016

Lu Y, Day FR, Gustafsson S, Buchkovich ML,…,Furey TS,…,Mohlke KL, Hirschhorn JN, Pospisilik JA, Zillikens MC, Lindgren C, Kilpeläinen TO, Loos RJ. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nat Commun. 7:10495 (2016). PMID:26833246.

Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M*, Li Y*. A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C Data. Bioinformatics 32(5):650-6 (2016). PMID:26543175

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 Med Genomics 8(1):43 (2015). PMID:26210163

Peck BCE, 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*, Sheikh SZ*. microRNAS classify different disease behavior phenotypes of Crohn’s disease and may have prognostic utility. Inflamm Bowel Dis Sep;21(9):2178-87 (2015). (*Co-senior authors). PMID:26164662.

2014

Weiser M, Mukherjee S, Furey TS. Novel trans-eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics 198(3):879-93 (2014). PMID:25230953.

Xiong Q, Mukherjee S, Furey TS. GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data. Scientific Reports 4:6347 (2014). PMID:25213199.

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 Res 24(2):241-50 (2014). PMID:24158655.

Wortham M, Guo C, Zhang MM, Song L, Lee B-K, Iyer V, Furey TS, Crawford GE, Yan H. Chromatin accessibility mapping identifies mediators of basal transcription retinoid-induced repression of OTX2 in Medulloblastoma. PLoS ONE 9(9):e107156 (2014). PMID: 25198066.

2013

Furey TS, Sethupathy P. Gentics driving epigenetics. Science 342(6159):705-706 (2013). PMID: 24202168; Summary; PDF; Full Text

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. Biol Reprod 89(4):104(1-8) (2013). PMID:24006278

Winter DR, Song L, Mukherjee S, Furey TS*, Crawford GE*. DNase-seq predicts regions of rotational nucleosome stability and suggests sequence asymmetry around the dyad axis. Genome Res (2013) (*Co-senior authors). PMID: 23657885

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 Res 23(5):777-88 (2012) (*Co-senior authors). PMID: 23482648

2012

Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nature Reviews Genetics 13(12):840-852 (2012). PMID: 23090257

Sheffield NC and Furey TS. Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. Genes 3(4):651-670 (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. Chrmoatin Accessibility Reveals Insights into Androgen Receptor Activation and Transcriptional Specificity. Genome Biology 13(10):R88 (2012). PMID: 23034120

The ENCODE Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74 (2012). PMID: 22955616

Thurman RE, Rynes E, Humbert R, …, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature 489(7414):75-82 (2012). PMID: 22955617

Parker SCJ, Gartner J, Cardenas-Navia I, Wei X, Abaan HO, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Furey TS, Crawford GE, Rosenberg SA, Samuels Y, Margulies EH. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genetics. 8(8):e1002871 (2012). PMID: 22912592 PMCID: PMC3415438

Shibata Y, Sheffield N, Fedrigo O, Babbitt CC, Wortham MJ, London D, Song L, Tewari AK, Parker SC, Margulies EH, Wray GA*, Furey TS*, and Crawford GE*. Extensive evolutionary changes in regulatory element activity during human origins are closely associated with altered gene expression and positive selection.  PLoS Genetics. 8(6):e1002789 (2012) (*-Co-senior authors). PMID: 22761590

Bennett BD, Xiong Q, Mukherjee S, and 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(9):e44635 (2012). PMID: 23028573

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(5):385-91 (2012) PMID: 22169360

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 Res 22(2):386-97 (2012) (*-Co-senior authors). PMID: 21940837

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 Res. 22(1):9-24 (2012). PMID: 22090374

2011

Song L#…, Zhang Z#…, Grasfeder LL#…, Boyle AP#…, Giresi PG#…, Lee B-K…#, Sheffield N#…, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E*, Iyer VR*, Crawford GE*, Lieb JD*, Furey TS*. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21(10):1757-67 (2011) (# …-Equal contributions, *-Co-senior authors). PMID: 21750106

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen K-B, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, and Hardison RC. Dynamics of the Epigenetic Landscape During Erythroid Differentiation after GATA1 Restoration. Genome Res. (Accepted). PMID: 21795386

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 Res. 21(3):456-64 (2011). (*-Co-senior authors). PMID: 21106903

The ENCODE Project Consortium. A user’s guide to the encyclopedia of DNA elements (ENCODE).  PLoS Biol. 9(4):e1001046 (2011). PMID: 21526222

2010

Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Boyle AP, Erdos MR, Welch R, Parker SC, Scott LJ, NISC Comparative Sequencing Program, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins F. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.  Cell Metabolism. 12(5):443-55 (2010). PMID: 21035756

Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Hum Mol Genet. 19(R2):R204-9 (2010). PMID: 20846943

McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Battenhouse A, Kucera KS, Keefe D, Lieb J, Furey TS, Crawford GE, Iyer VR, Birney E. Heritable individual-specific and allele-specific chromatin signatures in humans. Science. 328(5975):235-9 (2010). PMID: 20047656

Babbitt CC, Fedrigo O, Pfefferle AD, HorvathJE, FureyTS, and Wray GA. Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain.  Genome Biology and Evolution 2(1):67-79 (2010). PMID: 20333225

Ensterö M, Åkerborg Ö, Lundin D, Wang B, Furey TS, Öhman M, and Lagergren J. A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.  BMC Bioinformatics 11(1):6 (2010). PMID: 20047656

2009

Boyle AP and Furey TS. High resolution mapping studies of chromatin and gene regulatory elements.  Epigenomics. 1(2):319-329 (2009). PMID: 20514362

Xu X, Tsumagari K, Sowden J, Tawil R, Boyle A, Song L, Furey TS, Crawford G, Ehrlich M. DNaseI Hypersensitivity at Gene-Poor, FSH Dystrophy-Linked 4q35.2.  Nucleic Acids Res.  37(22):7381-93 (2009). PMID: 19820107

Wang T and Furey TS. Analysis of Complex Disease Association and Linkage Studies Using the UCSC Genome Browser.  Circulation:Cardiovascular Genetics.  2: 199-204   (2009). PMID: 20031585

Wang T, Furey TS, Connelly JJ, Ji S, Nelson S, Heber S, Gregory SG, Hauser ER, A novel genome-scale transcription factor binding site prediction method and its application to candidate gene identification in human disease.  Human Genomics. 3(3): 221-235. (2009). PMID: 19403457

2008

Boyle AP, Guinney J, Crawford CE, and Furey TS, F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags.  Bioinformatics. 24(21):2537-8 (2008). PMID: 18784119

Boyle AP, Davis S, Shulha HP, Meltzer P, Weng Z, Furey TS*, and Crawford CE*, High-resolution mapping and characterization of open chromatin across the genome.  Cell. 132(2):311-322 (2008). (* Co-senior authors). PMID: 18243105

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 Genet 3(8): e136 (2007). PMID: 17708682

Goh L, Murphy SK, Mukherjee S, and Furey TS, Genomic sweeping for hypermethylated genes, Bioinformatics, 23(3):281-288 (2007). PMID: 17148511

2006

Cohen SM*, Furey TS*, Doggett NA, and Kaufman DG, Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts, BMC Genomic, 7:301 (2006). (* Equal contributors). PMID: 17134498

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

Furey TS, Comparison of human (and other) genome browsers, Human Genomics, 2(4):266-270 (2006). PMID: 16460652

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, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ, The UCSC Genome Browser database: update2006, Nucleic Acids Res., 34(Database issue):D590-9 (2006). PMID: 16381938

2005

Hillier LW, et. al., Generation and annotation of the DNA sequences of human chromosomes 2 and 4, Nature, 434(7034):724-731 (2005). PMID: 15815621

2004

Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, and Haussler D, Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing, Gen. Res., 14(10B):2034-2040 (2004). PMID: 15489323

Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen C, Thomas MA, Haussler D, and Jacob H, Comparative recombination rates in Rat, Mouse, and Human Genomes, Gen. Res., 14:528-538 (2004). PMID: 15059993

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 R, Miller W, Schwartz S, and Eichler EE, The structure and evolution of centromeric transition regions within the human genome, Nature, 430:857-864 (2004). PMID: 15318213

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ, The UCSC Table Browser data retrieval tool, Nucleic Acids Res., 32:D493-496 (2004). PMID: 14681465

International Human Genome Sequencing Consortium, Finishing the euchromatic sequence of the human genome, Nature, 431(7011):931-945 (2004). PMID: 15496913

Gerhard DS, et. al., The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC), Gen. Res., 14(10B):2121-2127 (2004). PMID: 15489334

International Chicken Genome Sequencing Consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, 432(7018):695-716 (2004). PMID: 15592404

Rat Genome Sequencing Consortium, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, 428(6982):493-521 (2004). PMID: 15057822

Grimwood J, et. al., The DNA sequence and biology of human chromosome 19, Nature, 428(6982):529-535 (2004). PMID: 15057824

2003

Furey TS, and Haussler D, Integration of the Cytogenetic Map with the Draft Human Genome Sequence, Hum. Mol. Gen., 12(9):1037-1044 (2003). PMID: 12700172

Hardison R, 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, Miller W, Chiramonte F, and Haussler D, Co-variation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution, Gen. Res., 13(1): 13-26 (2003). PMID: 12529302

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CS, Thomas DJ, Weber RJ, Haussler D, Kent WJ, The UCSC Genome Browser Database, Nuc. Acids Res., 31(1): 51-4 (2003). PMID: 12519945

Hillier LW, et. al., The DNA sequence of human chromosome 7, Nature, 424:157-164 (2003). PMID: 12853948

2002

Kent WJ, Sugnet CS, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D, The Human Genome Browser at UCSC, Gen. Res., 12(6): 996-1006 (2002). PMID: 12045153

Mouse Genome Sequencing Consortium, Initial Sequencing and Comparative Analysis of the Mouse Genome, Nature, 420(6915): 520-562 (2002). PMID: 12466850

2001

Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN, Promoter Region-Based Classification of Genes, Pacific Symposium on Biocomputing (PSB), 6:151-164 (2001). PMID: 11262936

International Human Genome Sequencing Consortium, Initial Sequencing and Analysis of the Human Genome, Nature, 409(6822): 860-921 (2001). PMID: 11237011

The BAC Resource Consortium, Integration of Cytogenetic Landmarks into the Draft Sequence of the Human Genome, Nature, 409(6822): 953-958 (2001). PMID: 11237021

International Human Genome Mapping Consortium, A Physical Map of the Human Genome, Nature, 409(6822): 934-941 (2001). PMID: 11237014

2000

Furey TS, Duffy N, Cristianini N, Bednarski D, Schummer M, Haussler D, Support Vector Machine Classification and Validation of Cancer Tissue Samples Using Microarray Expression Data, Bioinformatics, 16(10):906-914 (2000). PMID: 11120680

Brown MPS, Grundy WN, Lin D, Cristianini N, Sugnet C, Furey TS, Ares M, Haussler D, Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines, PNAS, 97(1):262-267 (2000). PMID: 10618406