Publications

 

2013

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

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 (online before print) (2013). PMID:24158655

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