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James Taylor 0001

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affiliation: Johns Hopkins University, Department of Biology, Baltimore, MD, USA
affiliation (2008 - 2013): Emory University, Atlanta, GA, USA

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2020 – today

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2022
[j18]
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Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50(W1): 345-351 (2022)
2020
[j17]
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Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks:
Cloud bursting galaxy: federated identity and access management. Bioinform. 36(1): 1-9 (2020)
[j16]
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Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel J. Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res. 48(Webserver-Issue): W395-W402 (2020)

2010 – 2019

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2019
[j15]
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Enis Afgan, Andrew Lonie, James Taylor, Nuwan Goonasekera:
CloudLaunch: Discover and deploy cloud applications. Future Gener. Comput. Syst. 94: 802-810 (2019)
2018
[j14]
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Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia D. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(Webserver-Issue): W537-W544 (2018)
[c10]
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Enis Afgan, Vahid Jalili, Nuwan Goonasekera, James Taylor, Jeremy Goecks:
Federated Galaxy: Biomedical Computing at the Frontier. IEEE CLOUD 2018: 871-874
[i2]
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  - journals/corr/abs-1805-04005
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Enis Afgan, Andrew Lonie, James Taylor, Nuwan Goonasekera:
CloudLaunch: Discover and Deploy Cloud Applications. CoRR abs/1805.04005 (2018)
2017
[j13]
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Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko:
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS Comput. Biol. 13(5) (2017)
2016
[j12]
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Enis Afgan, Dannon Baker, Marius van den Beek, Daniel J. Blankenberg, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44(Webserver-Issue): W3-W10 (2016)
[c9]
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Enis Afgan, Andrew Lonie, James Taylor, Karolj Skala, Nuwan Goonasekera:
Architectural models for deploying and running virtual laboratories in the cloud. MIPRO 2016: 282-286
[c8]
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  - conf/xsede/StewartHVFCLMML16
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Craig A. Stewart, David Y. Hancock, Matthew Vaughn, Jeremy Fischer, Tim Cockerill, Liming Lee, Nirav C. Merchant, Therese Miller, John Michael Lowe, Daniel C. Stanzione Jr., James Taylor, Edwin Skidmore:
Jetstream: performance, early experiences, and early results. XSEDE 2016: 22:1-22:8
[c7]
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Nuwan Goonasekera, Andrew Lonie, James Taylor, Enis Afgan:
CloudBridge: a Simple Cross-Cloud Python Library. XSEDE 2016: 37:1-37:8
[i1]
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  - journals/f1000research/TuragaFBCTNT16
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Nitesh Turaga, Mallory Ann Freeberg, Dannon Baker, John Chilton, The Galaxy Team, Anton Nekrutenko, James Taylor:
A guide and best practices for R/Bioconductor tool integration in Galaxy. F1000Research 5: 2757 (2016)
2015
[j11]
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Enis Afgan, Nathan Coraor, John Chilton, Dannon Baker, James Taylor, The Galaxy Team:
Enabling cloud bursting for life sciences within Galaxy. Concurr. Comput. Pract. Exp. 27(16): 4330-4343 (2015)
[c6]
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Enis Afgan, Konstantinos Krampis, Nuwan Goonasekera, Karolj Skala, James Taylor:
Building and provisioning bioinformatics environments on public and private Clouds. MIPRO 2015: 223-228
[c5]
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Craig A. Stewart, Timothy M. Cockerill, Ian T. Foster, David Y. Hancock, Nirav C. Merchant, Edwin Skidmore, Daniel Stanzione, James Taylor, Steven Tuecke, George W. Turner, Matthew Vaughn, Niall I. Gaffney:
Jetstream: a self-provisioned, scalable science and engineering cloud environment. XSEDE 2015: 29:1-29:8
2014
[j10]
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Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko:
Wrangling Galaxy's reference data. Bioinform. 30(13): 1917-1919 (2014)
[j9]
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  - journals/jamia/LeDucVFSWBTB14
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Richard D. LeDuc, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D. Blood, James Taylor, William K. Barnett:
Leveraging the national cyberinfrastructure for biomedical research. J. Am. Medical Informatics Assoc. 21(2): 195-199 (2014)
[j8]
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Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Wei-Sheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert:
Topologically associating domains are stable units of replication-timing regulation Open. Nat. 515(7527): 402-405 (2014)
[c4]
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Enis Afgan, Dannon Baker, John Chilton, Nathan Coraor, James Taylor:
Galaxy cluster to cloud - genomics at scale. GCE@SC 2014: 47-50
2013
[j7]
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  - journals/ploscb/SandveNTH13
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Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig:
Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. 9(10) (2013)
[c3]
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James Taylor, Anton Nekrutenko, Nathan Coraor, Philip D. Blood, Alex Ropelewski, Zhihui Zhang, Josephine Palencia, Sergiu Sanielevici, Jared Yanovich, Robert Budden:
A sustainable national gateway for biological computation. XSEDE 2013: 32:1-32:3
2012
[j6]
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  - journals/bmcbi/AfganCT12
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Enis Afgan, Brad Chapman, James Taylor:
CloudMan as a platform for tool, data, and analysis distribution. BMC Bioinform. 13: 315 (2012)
[j5]
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Enis Afgan, Dannon Baker, Anton Nekrutenko, James Taylor:
A reference model for deploying applications in virtualized environments. Concurr. Comput. Pract. Exp. 24(12): 1349-1361 (2012)
[c2]
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  - conf/eScience/GoecksTNT12
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Jeremy Goecks, The Galaxy Team, Anton Nekrutenko, James Taylor:
Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses. eScience 2012: 1-6
2011
[j4]
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  - journals/biodb/BlankenbergCKTN11
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Daniel J. Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko:
Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database J. Biol. Databases Curation 2011 (2011)
[j3]
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Daniel J. Blankenberg, James Taylor, Anton Nekrutenko:
Making whole genome multiple alignments usable for biologists. Bioinform. 27(17): 2426-2428 (2011)
[c1]
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Jeremy Goecks, Kanwei Li, Dave Clements, The Galaxy Team, James Taylor:
The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool. BioVis 2011: 39-46
[p1]
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Enis Afgan, Jeremy Goecks, Dannon Baker, Nate Coraor, Anton Nekrutenko, James Taylor:
Galaxy: A Gateway to Tools in e-Science. Guide to e-Science 2011: 145-177
2010
[j2]
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Daniel J. Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko:
Manipulation of FASTQ data with Galaxy. Bioinform. 26(14): 1783-1785 (2010)
[j1]
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Enis Afgan, Dannon Baker, Nathan Coraor, Brad Chapman, Anton Nekrutenko, James Taylor:
Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinform. 11(S-12): S4 (2010)

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