Turaga N, Freeberg MA, Baker D, Chilton J, Galaxy Team, Nekrutenko A, Taylor J. A guide and best practices for R/Bioconductor tool integration in Galaxy. F1000Research. November 2016; 5:2757
Goonasekera N, Lonie A, Taylor J, Afgan E. CloudBridge – a Simple Cross-Cloud Python Library. XSEDE16. July 2016; :1-6
Forer L, Afgan E, Weissensteiner H, Davidovic D, Specht G, Kronenberg F, Schoenherr S. Cloudflow - enabling faster biomedical pipelines with MapReduce and Spark. Scalable Computing: Practice and Experience (SCPE). June 2016; 17(2):103-114
Afgan E, Baker D, Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. May 2016; 44(W1):W3-W10
Skala K, Davidović D, Afgan E, Sović I, Šojat Z. Scalable Distributed Computing Hierarchy: Cloud, Fog and Dew Computing. Open Journal of Cloud Computing (OJCC). December 2015; 2(1):16-24
Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. PLoS ONE. October 2015; 10(10):1-20
Sauria MEG, Phillips-Cremins JE, Corces VG, Taylor J. HiFive: a tool suite for easy and efficient HiC and 5C data analysis. Genome Biology. October 2015; 16:237
Stewart CA, Cockerill TM, Foster I, Hancock D, Merchant N, Skidmore E, Stanzione D, Taylor J, Tuecke S, Turner G, Vaughn M, Gaffney, NI. Jetstream: A Self-provisioned, Scalable Science and Engineering Cloud Environment. Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. July 2015; :29:1--29:8
Afgan E, Coraor N, Chilton J, Baker D, Taylor J. Enabling cloud bursting for life sciences within Galaxy. Concurrency and Computation: Practice and Experience (CCPE). June 2015; 27(16):4330-4343
Martens AT, Taylor J, Hilser VJ. Ribosome A and P sites revealed by length analysis of ribosome profiling data. Nucleic Acids Research. April 2015; 43(7):3680-3687
Blankenberg D, Taylor J, Nekrutenko A. Online Resources for Genomic Analysis Using High-Throughput Sequencing. Cold Spring Harbor Protocols. April 2015; 2015(4)
Goecks J, El-Rayes BF, Maithel SK, Khoury HJ, Taylor J, Rossi MR. Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. Cancer Medicine. March 2015; 4(3):392-403
Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. BMC Genomics. February 2015; 16:87
Möller S, Afgan E, Banck M, Bonnal R, Booth T, Chilton J, Cock P, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel D, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis A, Guimera R, Katayama T, Chapman B. Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics. November 2014; 15(S14):16-24
Pope BD, Ryba T, Dileep V, Yue F, Wu Q, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Topologically associating domains are stable units of replication-timing regulation. Nature. November 2014; 515:402–405
The Mouse ENCODE Consortium. A comparative encyclopedia of DNA elements in the mouse genome. Nature. November 2014; 515:355–364
Afgan E, Baker D, Coraor N, Taylor J. Galaxy cluster to cloud - genomics at scale. GCE '14 Proceedings of the 9th Gateway Computing Environments Workshop. November 2014; :47-50
Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G. BioBlend.objects: metacomputing with Galaxy. Bioinformatics. June 2014; 30(19):2816-2817
Blankenberg D, Johnson JE, The Galaxy Team, Taylor J, Nekrutenko A. Wrangling Galaxy's Reference Data. Bioinformatics. March 2014;
Blankenberg, D, von Kuster, G, Bouvier E, Baker, B, Afgan, E, Stoler N, Rebolledo-Jaramillo B, The Galaxy Team, Taylor J, Nekrutenko A. Dissemination of scientific software with Galaxy ToolShed. Genome Biology. February 2014; 15:403
Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. PLoS Computational Biology. October 2013; 9(10):e1003285
LeDuc R, Vaughn M, Fonner JM, Sullivan M, Williams J, Blood PD, Taylor J, Barnett W. Leveraging the National Cyberinfrastructure for Biomedical Research. Journal of the American Medical Informatics Association. August 2013;
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
Goecks J, Mortimer NT, Mobley JA, Bowersock GJ, Taylor J, Schlenke, TA. Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms. PLoS ONE. May 2013; 8(5):e64125
Mortimer NT, Goecks J, Kacsoh BZ, Mobley JA, Bowersock GJ, Taylor J, Schlenke, TA. Parasitoid Wasp Venom SERCA Regulates Drosophila Calcium Levels and Inhibits Cellular Immunity. Proceedings of the National Academy of Science USA. May 2013; 110(23):9427–9432
Nekrutenko A and Taylor J. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nature Reviews Genetics. September 2012; 13:667-672
Mouse ENCODE Project Consortium. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. August 2012; 13:418
Hardison RC and Taylor J. Genomic approaches towards finding cis-regulatory modules in animals. Nature Reviews Genetics. June 2012; 13(7):469-483
Hillman‐Jackson J, Clements D, Blankenberg D, Taylor J, Anton Nekrutenko. Using Galaxy to Perform Large‐Scale Interactive Data Analyses. Current Protocols in Bioinformatics. June 2012; 38:10.5.1-10.5.25
Afgan E, Chapman B, Jadan M, Franke B, Taylor J. Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy. Current Protocols in Bioinformatics. June 2012; 38:11.9.1-11.9.20
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, Li K, Clements D, The Galaxy Team, and Taylor J. The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool. 2011 IEEE Symposium on Biological Data Visualization. October 2011;
Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. September 2011; 27(17):2426-2428
Afgan E, Baker D, Galaxy Team, Nekrutenko A, Taylor J. A reference model for deploying applications in virtualized environments. Concurrency and Computation: Practice & Experience. August 2011;
Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, and Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biology. June 2011; 12:R59
Afgan E, Goecks J, Baker D, Coraor N, The Galaxy Team, Nekrutenko A, and Taylor J. Galaxy - a Gateway to Tools in e-Science. Guide to e-Science: Next Generation Scientific Research and Discovery. May 2011;
Blankenberg D, Coraor N, Von Kuster G, Taylor J and Nekrutenko A. Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database. March 2011; 2011:bar011
Suen G, ..., Denas O, ..., Taylor J, ..., Gerardo NM, Currie CR [49 authors]. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genetics. February 2011; 7(2):e1002007
Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics. December 2010; 11(Suppl 12):S4
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)
Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A. Manipulation of FASTQ data with Galaxy. Bioinformatics. July 2010; 26(14):1783-5
Chiaromonte F and Taylor J. Information Based Agglomerative Segmentation in Metric Spaces. Journal of the Indian Society of Agricultural Statistics. May 2010; 64(1):33-44
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
Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, and Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. October 2009; 19(11):2144-53
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
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
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
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; 15(10):1451-1455
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