Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J.

Galaxy: a web-based genome analysis tool for experimentalists.

Current Protocols in Molecular Biology. January 2010; Chapter 19:Unit 19.10.1-21

Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC.

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

Nucleic Acids Research. September 2009;

Yang MQ, Taylor J, Elnitski L.

Comparative analyses of bidirectional promoters in vertebrates.

BMC Bioinformatics. May 2008; 9 Suppl 6:S9

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, et al..

Genome analysis of the platypus reveals unique signatures of evolution.

Nature. May 2008; 453(7192):175-83

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W.

Phylogenomic resources at the UCSC Genome Browser.

Methods in Molecular Biology. December 2007; 422:133-144

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, et al.

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser.

Genome Research. December 2007; 17(12):1797-808

Taylor J, Schenk I, Blankenberg D, and Nekrutenko, A.

Using Galaxy to Perform Large-Scale Interactive Data Analysis.

Current Protocols in Bioinformatics. September 2007; 19:10.5.1-10.5.25

The ENCODE Project Consortium.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Nature. June 2007; 447(7146):799-816

King DC*, Taylor J*, Zhang Y, Cheng Y, Lawson HA, Martin J, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Chiaromonte F, Miller W, Hardison RC.

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

Genome Research. June 2007; 17(6):775-786

Margulies EH et al..

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Research. June 2007; 17(6):760-774

Blankenberg D, Taylor J, Schenk I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova K, Hardison RC, Nekrutenko A..

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly.

Genome Research. June 2007; 17(6):775-786

Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC.

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Genome Research. December 2006; 16(12):1480-1492

Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, and Chiaromonte F. <

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements.

Genome Research. December 2006; 16(12):1596-1604

Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD.

Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison.

Molecular Biology and Evolution. March 2006; 23(3):565-573

Chimpanzee Sequencing and Analysis Consortium.

Initial sequence of the chimpanzee genome and comparison with the human genome.

Nature. September 2005; 437(7055):69-87

Giardine B, Riemer C, Hardison
RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ,
Nekrutenko A.

Galaxy: a platform for interactive large-scale genome analysis.

Genome Research. September 2005;

King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC.

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

Genome Research. August 2005; 15(8):1051-1060

Taylor J.

Clues to function in gene deserts.

Trends in Biotechnology. June 2005; 23(6):269-271

Hillier LW et al.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Nature. April 2005; 434(7034):724-731

International Chicken Genome Sequencing Consortium.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

Nature. December 2004; 432(7018):695-716

Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison R, Chiaromonte F.

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

Genome Research. April 2004; 14(4):700-707

Rat Genome Sequencing Project Consortium.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Nature. April 2004; 428(6982):493-521

Nekrutenko A and Taylor J.

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Nature Reviews Genetics. September 2012; 13:667-672

Goecks, J., Nekrutenko, A., Taylor, J., and The Galaxy Team.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Genome Biology. August 2010; 11(8)

Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J.

Harnessing cloud computing with Galaxy Cloud.

Nature Biotechnology. November 2011; 29:972–974

Goecks J, Eberhard C, Too T, The Galaxy Team, Nekrutenko A, Taylor J.

Web-based Visual Analysis for High-throughput Genomics.

BMC Genomics. June 2013; 14(1):397

Phillips-Cremins JE, Sauria MEG, Sanyal A, Gerasimova TI, Lajoie BR, Bell JK, Ong C, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG.

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment.

Cell. May 2013; 153(6):1281–1295

Hardison RC and Taylor J.

Genomic approaches towards finding cis-regulatory modules in animals.

Nature Reviews Genetics. June 2012; 13(7):469-483