Viets K, Sauria MEG, Chernoff C, Rodriguez Viales R, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ. “Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation”. Developmental Cell. 2019 November; 51(3):341-356.e7. doi:10.1016/j.devcel.2019.09.007
Uritskiy G, Getsin S, Munn A, Gomez-Silva B, Davila A, Glass B, Taylor J, DiRuggiero J. “Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert”. The ISME Journal. 2019 July; 13:2737–2749. doi:10.1038/s41396-019-0468-y
Jalili V, Afgan E and Taylor J and Goecks, J. “Cloud bursting galaxy: federated identity and access management”. Bioinformatics. 2019 June; doi:10.1093/bioinformatics/btz472
Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS. “Measuring the reproducibility and quality of Hi-C data”. Genome Biology. 2019 March; 20:57. doi:10.1186/s13059-019-1658-7
Eldred KC, Hadyniak SE, Hussey KA, Brenerman B, Zhang P, Chamling X, Sluch VM, Welsbie DS, Hattar S, Taylor J, Wahlin K, DJ Zack, Johnston RJ. “Thyroid hormone signaling specifies cone subtypes in human retinal organoids”. Science. 2018 October; 362(6411):eaau6348. doi:10.1126/science.aau6348
Uritskiy GV, DiRuggiero J, Taylor J. “MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis”. Microbiome. 2018 September; 15(6):158. doi:10.1186/s40168-018-0541-1
Zheng X, Hu J, Yue S, Kristiani L, Kim M, Sauria M, Taylor J, Kim Y, Zheng Y. “Lamins organize the global three-dimensional genome from the nuclear periphery”. Molecular cell. 2018 September; 71(5):802-815. doi:10.1016/j.molcel.2018.05.017
Afgan E, Jalili V, Goonasekera N, Taylor J, Goecks J. “Federated Galaxy: Biomedical Computing at the Frontier”. 2018 IEEE 11th International Conference on Cloud Computing (CLOUD). 2018 July;:871-874. doi:http://doi.ieeecomputersociety.org/10.1109/CLOUD.2018.00124
Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J. “Practical computational reproducibility in the life sciences”. Cell Systems. 2018 June; 6(6):631-635. doi:10.1016/j.cels.2018.03.014
Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning B, Guerler A, Hilman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. “The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update”. Nucleic Acids Research. 2018 May;:gky379. doi:10.1093/nar/gky379
Nekrutenko A, The Galaxy Team, Goecks J, Taylor J, Blankenberg D. “Biology Needs Evolutionary Software Tools: Let’s Build Them Right”. Molecular Biology and Evolution. 2018 June; 35(6):1372-1375. doi:10.1093/molbev/msy084
Grüning BA, Rasche E, Rebolledo-Jaramillo B, Eberhard C, Houwaart T, Chilton J, Coraor N, Backofen R, Taylor J, Nekrutenko A. “Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers”. PLOS Computational Biology. 2017 May; 13(5):e1005425. doi:10.1371/journal.pcbi.1005425
Malhotra S, Freeberg MA, Winans SJ, Taylor J, Beemon KL. “A Novel Long Non-Coding RNA in the hTERT Promoter Region Regulates hTERT Expression”. Non-Coding RNA. 2017 December; 2018(4):1. doi:10.3390/ncrna4010001
Anderson C, Reiss I, Zhou C, Cho A, Siddiqi H, Mormann B, Avelis CM, DeFord P, Bergland A, Roberts E, Taylor J, Vasiliauskas D, Johnston Jr RJ. “Natural variation in stochastic photoreceptor specification and color preference in Drosophila”. eLife. 2017 December; 2017(6):e29593. doi:10.7554/eLife.29593
Yoon HJ, Sauria M, Lyu X, Cheema M, Ausio J, Taylor J, Corces V. “Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes”. Cell Reports. 2017 February; 18(6):1366-1382. doi:10.1016/j.celrep.2017.01.034
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. 2016 November; 5:2757. doi:10.12688/f1000research.9821.1
Goonasekera N, Lonie A, Taylor J, Afgan E. “CloudBridge – a Simple Cross-Cloud Python Library”. XSEDE16. 2016 July;: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). 2016 June; 17(2):103-114. doi:10.12694/scpe.v17i2.1159
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. 2016 May; 44(W1):W3-W10. doi:10.1093/nar/gkw343
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. 2015 March; 4(3):392-403. doi:10.1002/cam4.360
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). 2015 December; 2(1):16-24. doi:10.19210/1002.2.1.16
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. 2015 October; 10(10):1-20. doi:10.1371/journal.pone.0140829
Sauria MEG, Phillips-Cremins JE, Corces VG, Taylor J. “HiFive: a tool suite for easy and efficient HiC and 5C data analysis”. Genome Biology. 2015 October; 16:237. doi:10.1186/s13059-015-0806-y
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. 2015 July;:29:1--29:8. doi:10.1145/2792745.2792774
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). 2015 June; 27(16):4330-4343. doi:10.1002/cpe.3536
Martens AT, Taylor J, Hilser VJ. “Ribosome A and P sites revealed by length analysis of ribosome profiling data”. Nucleic Acids Research. 2015 April; 43(7):3680-3687. doi:10.1093/nar/gkv200
Blankenberg D, Taylor J, Nekrutenko A. “Online Resources for Genomic Analysis Using High-Throughput Sequencing”. Cold Spring Harbor Protocols. 2015 April; 2015(4). doi:10.1101/pdb.top083667
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. 2015 February; 16:87. doi:10.1186/s12864-015-1245-6
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. 2014 November; 15(S14):16-24. doi:10.1186/1471-2105-15-S14-S7
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. 2014 November; 515:402–405. doi:10.1038/nature13986
The Mouse ENCODE Consortium. “A comparative encyclopedia of DNA elements in the mouse genome”. Nature. 2014 November; 515:355–364. doi:10.1038/nature13992
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. 2014 November;:47-50. doi:10.1109/GCE.2014.13
Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G. “BioBlend.objects: metacomputing with Galaxy”. Bioinformatics. 2014 June; 30(19):2816-2817. doi:10.1093/bioinformatics/btu386
Blankenberg D, Johnson JE, The Galaxy Team, Taylor J, Nekrutenko A. “Wrangling Galaxy's Reference Data”. Bioinformatics. 2014 March; doi:10.1093/bioinformatics/btu119
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. 2014 February; 15:403. doi:doi:10.1186/gb4161
Sandve GK, Nekrutenko A, Taylor J, Hovig E. “Ten simple rules for reproducible computational research”. PLoS Computational Biology. 2013 October; 9(10):e1003285. doi:10.1371/journal.pcbi.1003285
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. 2013 August; doi:10.1136/amiajnl-2013-002059
Goecks J, Eberhard C, Too T, The Galaxy Team, Nekrutenko A, Taylor J. “Web-based Visual Analysis for High-throughput Genomics”. BMC Genomics. 2013 June; 14(1):397. doi:10.1186/1471-2164-14-397
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. 2013 May; 153(6):1281–1295. doi:10.1016/j.cell.2013.04.053
Goecks J, Mortimer NT, Mobley JA, Bowersock GJ, Taylor J, Schlenke, TA. “Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms”. PLoS ONE. 2013 May; 8(5):e64125. doi:10.1371/journal.pone.0064125
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. 2013 May; 110(23):9427–9432. doi:10.1073/pnas.1222351110
Nekrutenko A, Taylor J. “Next-generation sequencing data interpretation: enhancing reproducibility and accessibility”. Nature Reviews Genetics. 2012 September; 13:667-672. doi:10.1038/nrg3305
Mouse ENCODE Project Consortium. “An encyclopedia of mouse DNA elements (Mouse ENCODE)”. Genome Biology. 2012 August; 13:418. doi:10.1186/gb-2012-13-8-418
Hardison RC, Taylor J. “Genomic approaches towards finding cis-regulatory modules in animals”. Nature Reviews Genetics. 2012 June; 13(7):469-483. doi:10.1038/nrg3242
Hillman‐Jackson J, Clements D, Blankenberg D, Taylor J, Anton Nekrutenko. “Using Galaxy to Perform Large‐Scale Interactive Data Analyses”. Current Protocols in Bioinformatics. 2012 June; 38:10.5.1-10.5.25. doi:10.1002/0471250953.bi1005s38
Afgan E, Chapman B, Jadan M, Franke B, Taylor J. “Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy”. Current Protocols in Bioinformatics. 2012 June; 38:11.9.1-11.9.20. doi:10.1002/0471250953.bi1109s38
Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team. “Making whole genome multiple alignments usable for biologists”. Bioinformatics. 2011 September; 27(17):2426-2428. doi:10.1093/bioinformatics/btr398
Afgan E, Goecks J, Baker D, Coraor N, The Galaxy Team, Nekrutenko A,, Taylor J. “Galaxy - a Gateway to Tools in e-Science”. Guide to e-Science: Next Generation Scientific Research and Discovery. 2011 May; doi:10.1007/978-0-85729-439-5_6
Goecks J, Li K, Clements D, The Galaxy Team,, Taylor J. “The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool”. 2011 IEEE Symposium on Biological Data Visualization. 2011 October; doi:10.1109/BioVis.2011.6094046
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. 2011 February; 7(2):e1002007. doi:10.1371/journal.pgen.1002007
Afgan E, Baker D, Galaxy Team, Nekrutenko A, Taylor J. “A reference model for deploying applications in virtualized environments”. Concurrency and Computation: Practice & Experience. 2011 August; doi:10.1002/cpe.1836
Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD,, Nekrutenko A. “Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study”. Genome Biology. 2011 June; 12:R59. doi:10.1186/gb-2011-12-6-r59
Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A. “Integrating diverse databases into an unified analysis framework: a Galaxy approach”. Database. 2011 March; 2011:bar011. doi:10.1093/database/bar011
Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. “Harnessing cloud computing with Galaxy Cloud”. Nature Biotechnology. 2011 November; 29:972–974. doi:doi:10.1038/nbt.2028
Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A. “Manipulation of FASTQ data with Galaxy”. Bioinformatics. 2010 July; 26(14):1783-5. doi:10.1093/bioinformatics/btq281
Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. “Galaxy CloudMan: delivering cloud compute clusters”. BMC Bioinformatics. 2010 December; 11(Suppl 12):S4. doi:10.1186/1471-2105-11-S12-S4
Goecks, J., Nekrutenko, A., Taylor, J.,, The Galaxy Team. “Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences”. Genome Biology. 2010 August; 11(8). doi:10.1186/gb-2010-11-8-r86
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. 2010 January; Chapter 19:Unit 19.10.1-21. doi:10.1002/0471142727.mb1910s89
Chiaromonte F, Taylor J. “Information Based Agglomerative Segmentation in Metric Spaces”. Journal of the Indian Society of Agricultural Statistics. 2010 May; 64(1):33-44.
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. 2009 September; doi:10.1093/nar/gkp747
Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J,, Nekrutenko A. “Windshield splatter analysis with the Galaxy metagenomic pipeline”. Genome Research. 2009 October; 19(11):2144-53. doi:10.1101/gr.094508.109
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. 2008 May; 453(7192):175-83. doi:10.1038/nature06936
Yang MQ, Taylor J, Elnitski L. “Comparative analyses of bidirectional promoters in vertebrates”. BMC Bioinformatics. 2008 May; 9 Suppl 6:S9. doi:10.1186/1471-2105-9-S6-S9
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. 2007 December; 17(12):1797-808. doi:10.1101/gr.6761107
Margulies EH et al.. “Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome”. Genome Research. 2007 June; 17(6):760-774. doi:10.1101/gr.6034307
Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. “Phylogenomic resources at the UCSC Genome Browser”. Methods in Molecular Biology. 2007 December; 422:133-144. doi:10.1007/978-1-59745-581-7_9
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. 2007 June; 17(6):775-786. doi:10.1101/gr.5578007
Taylor J, Schenk I, Blankenberg D,, Nekrutenko, A. “Using Galaxy to Perform Large-Scale Interactive Data Analysis”. Current Protocols in Bioinformatics. 2007 September; 19:10.5.1-10.5.25. doi:10.1002/0471250953.bi1005s19
The ENCODE Project Consortium. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project”. Nature. 2007 June; 447(7146):799-816. doi:10.1038/nature05874
King DC*, Taylor J*, Zhang Y, Cheng Y, Lawson HA, Martin J, ENCODE groups for Transcriptional Regulation, Multispecies Alignment, Chiaromonte F, Miller W, Hardison RC. “Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data”. Genome Research. 2007 June; 17(6):775-786. doi:10.1101/gr.5592107
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. 2006 March; 23(3):565-573. doi:10.1093/molbev/msj060
Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W,, Chiaromonte F. “ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements”. Genome Research. 2006 December; 16(12):1596-1604. doi:10.1101/gr.4537706
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. 2006 December; 16(12):1480-1492. doi:10.1101/gr.5353806
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. 2005 September; 15(10):1451-1455. doi:10.1101/gr.4086505
Hillier LW et al. “Generation and annotation of the DNA sequences of human chromosomes 2 and 4”. Nature. 2005 April; 434(7034):724-731. doi:10.1038/nature03466
Chimpanzee Sequencing, Analysis Consortium. “Initial sequence of the chimpanzee genome and comparison with the human genome”. Nature. 2005 September; 437(7055):69-87. doi:10.1038/nature04072
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. 2005 August; 15(8):1051-1060. doi:10.1101/gr.3642605
Taylor J. “Clues to function in gene deserts”. Trends in Biotechnology. 2005 June; 23(6):269-271. doi:10.1016/j.tibtech.2005.04.003
International Chicken Genome Sequencing Consortium. “Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution”. Nature. 2004 December; 432(7018):695-716. doi:doi:10.1038/nature03154
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. 2004 April; 14(4):700-707. doi:10.1101/gr.1976004
Rat Genome Sequencing Project Consortium. “Genome sequence of the Brown Norway rat yields insights into mammalian evolution”. Nature. 2004 April; 428(6982):493-521. doi:doi:10.1038/nature02426