Research
Our research is focused on two broad and complementary areas of research. First, we develop computational infrastructure and machine learning approaches for large-scale biomedical data science. Second, we use data science methods to advance precision cancer treatment by analyzing molecular datasets to predict tumor response to therapy and mechanisms of resistance.
Highlighted
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks
PLOS Computational Biology
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01 Jun 2021
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doi:10.1371/journal.pcbi.1009014
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2023
“Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers”
Allison L. Creason, Jay Egger, Cameron Watson, Shamilene Sivagnanam, Koei Chin, ..., Lisa M. Coussens, Andrew C. Adey, Joe W. Gray, Gordon B. Mills, Jeremy Goecks
Cold Spring Harbor Laboratory
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29 Sep 2023
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doi:10.1101/2023.09.27.557464
2022
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Enis Afgan, Anton Nekrutenko, Bjórn A Grüning, Daniel Blankenberg, Jeremy Goecks, ..., Vijay K Nagampalli, Wendi A Bacon, Willem de Koning, Wolfgang Maier, Peter J Briggs
Nucleic Acids Research
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21 Apr 2022
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doi:10.1093/nar/gkac247
Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma
Katie E. Blise, Shamilene Sivagnanam, Grace L. Banik, Lisa M. Coussens, Jeremy Goecks
npj Precision Oncology
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25 Feb 2022
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doi:10.1038/s41698-022-00253-z
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer
Brett E. Johnson, Allison L. Creason, Jayne M. Stommel, Jamie M. Keck, Swapnil Parmar, ..., Jeremy Goecks, Raymond Bergan, Zahi Mitri, Gordon B. Mills, Joe W. Gray
Cell Reports Medicine
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01 Feb 2022
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doi:10.1016/j.xcrm.2022.100525
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, ..., Radhika Reddy, Eric Torstenson, M. Katie Banasiewicz, Haley J. Abel, Jason Walker
Cell Genomics
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01 Jan 2022
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doi:10.1016/j.xgen.2021.100085
2021
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L. Muhlich, ..., Jeremy Goecks, Robert J. Coffey, Lisa M. Coussens, Sandro Santagata, Peter K. Sorger
Nature Methods
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25 Nov 2021
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doi:10.1038/s41592-021-01308-y
Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies
Marilyne Labrie, Allen Li, Allison Creason, Courtney Betts, Jamie Keck, ..., Christopher L. Corless, Raymond Bergan, Joe W. Gray, Gordon B. Mills, Zahi I. Mitri
npj Precision Oncology
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19 Oct 2021
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doi:10.1038/s41698-021-00232-w
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks
PLOS Computational Biology
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01 Jun 2021
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doi:10.1371/journal.pcbi.1009014
Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome
Shannon M. Liudahl, Courtney B. Betts, Shamilene Sivagnanam, Vicente Morales-Oyarvide, Annacarolina da Silva, ..., Byung S. Park, Motomi Mori, Jonathan A. Nowak, Brian M. Wolpin, Lisa M. Coussens
Cancer Discovery
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16 Mar 2021
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doi:10.1158/2159-8290.CD-20-0841
2020
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin
PLOS Computational Biology
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04 Jun 2020
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doi:10.1371/journal.pcbi.1007863
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko
Nucleic Acids Research
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01 Jun 2020
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doi:10.1093/nar/gkaa434
A long-read RNA-seq approach to identify novel transcripts of very large genes
Prech Uapinyoying, Jeremy Goecks, Susan M. Knoblach, Karuna Panchapakesan, Carsten G. Bonnemann, Terence A. Partridge, Jyoti K. Jaiswal, Eric P. Hoffman
Genome Research
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01 Jun 2020
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doi:10.1101/gr.259903.119
How Machine Learning Will Transform Biomedicine
Jeremy Goecks, Vahid Jalili, Laura M. Heiser, Joe W. Gray
Cell
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01 Apr 2020
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doi:10.1016/j.cell.2020.03.022
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
Alex H. Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, ..., Mark Lawler, Jeremy Goecks, Malachi Griffith, Obi L. Griffith, Adam A. Margolin
Nature Genetics
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01 Apr 2020
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doi:10.1038/s41588-020-0603-8
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, ..., Houxiang Zhu, Qin Zhu, Xiangzhu Zhu, Yuankun Zhu, Xiaowei Zhuang
Cell
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01 Apr 2020
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doi:10.1016/j.cell.2020.03.053
High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers
Grace Banik, Courtney B. Betts, Shannon M. Liudahl, Shamilene Sivagnanam, Rie Kawashima, ..., Jeremy Goecks, Sara I. Pai, Daniel R. Clayburgh, Takahiro Tsujikawa, Lisa M. Coussens
Methods in Enzymology
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01 Jan 2020
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doi:10.1016/bs.mie.2019.05.039
2019
Next Generation Indexing for Genomic Intervals
Vahid Jalili, Matteo Matteucci, Jeremy Goecks, Yashar Deldjoo, Stefano Ceri
IEEE Transactions on Knowledge and Data Engineering
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01 Oct 2019
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doi:10.1109/TKDE.2018.2871031
Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming
Mautin Hundeyin, Emma Kurz, Ankita Mishra, Juan Andres Kochen Rossi, Shannon M. Liudahl, ..., Varshini Vasudevaraja, Deepak Saxena, Kwok-Kin Wong, Lisa M. Coussens, George Miller
Cancer Discovery
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01 Sep 2019
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doi:10.1158/2159-8290.CD-19-0161
Cloud bursting galaxy: federated identity and access management
Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks
Bioinformatics
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14 Jun 2019
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doi:10.1093/bioinformatics/btz472
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes
Yating Liu, Luke Sargent, Wilson Leung, Sarah C R Elgin, Jeremy Goecks
Bioinformatics
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09 May 2019
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doi:10.1093/bioinformatics/btz309
2018
Federated Galaxy: Biomedical Computing at the Frontier
Enis Afgan, Vahid Jalili, Nuwan Goonasekera, James Taylor, Jeremy Goecks
2018 IEEE 11th International Conference on Cloud Computing (CLOUD)
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01 Jul 2018
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doi:10.1109/cloud.2018.00124
Practical Computational Reproducibility in the Life Sciences
Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor
Cell Systems
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01 Jun 2018
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doi:10.1016/j.cels.2018.03.014
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, ..., Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg
Nucleic Acids Research
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22 May 2018
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doi:10.1093/nar/gky379
Biology Needs Evolutionary Software Tools: Let’s Build Them Right
Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg
Molecular Biology and Evolution
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23 Apr 2018
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doi:10.1093/molbev/msy084
2016
Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations
Vahan Simonyan, Jeremy Goecks, Raja Mazumder
PDA Journal of Pharmaceutical Science and Technology
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14 Dec 2016
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doi:10.5731/pdajpst.2016.006734
Impact of germline and somatic missense variations on drug binding sites
C Yan, N Pattabiraman, J Goecks, P Lam, A Nayak, Y Pan, J Torcivia-Rodriguez, A Voskanian, Q Wan, R Mazumder
The Pharmacogenomics Journal
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26 Jan 2016
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doi:10.1038/tpj.2015.97
2015
A Quick Guide for Building a Successful Bioinformatics Community
Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg
PLOS Computational Biology
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05 Feb 2015
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doi:10.1371/journal.pcbi.1003972
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines
Jeremy Goecks, Bassel F. El‐Rayes, Shishir K. Maithel, H. Jean Khoury, James Taylor, Michael R. Rossi
Cancer Medicine
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04 Jan 2015
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doi:10.1002/cam4.360
2014
The Bioinformatics Open Source Conference (BOSC) 2013
Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp
Bioinformatics
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14 Jul 2014
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doi:10.1093/bioinformatics/btu413
Dietary and Flight Energetic Adaptations in a Salivary Gland Transcriptome of an Insectivorous Bat
Carleton J. Phillips, Caleb D. Phillips, Jeremy Goecks, Enrique P. Lessa, Cibele G. Sotero-Caio, Bernard Tandler, Michael R. Gannon, Robert J. Baker
PLoS ONE
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14 Jan 2014
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doi:10.1371/journal.pone.0083512
2013
Web-based visual analysis for high-throughput genomics
Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor
BMC Genomics
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13 Jun 2013
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doi:10.1186/1471-2164-14-397
Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms
Jeremy Goecks, Nathan T. Mortimer, James A. Mobley, Gregory J. Bowersock, James Taylor, Todd A. Schlenke
PLoS ONE
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23 May 2013
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doi:10.1371/journal.pone.0064125
Parasitoid wasp venom SERCA regulates
Drosophila
calcium levels and inhibits cellular immunity
Nathan T. Mortimer, Jeremy Goecks, Balint Z. Kacsoh, James A. Mobley, Gregory J. Bowersock, James Taylor, Todd A. Schlenke
Proceedings of the National Academy of Sciences
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20 May 2013
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doi:10.1073/pnas.1222351110
2012
NGS analyses by visualization with Trackster
Jeremy Goecks, Nate Coraor, The Galaxy Team, Anton Nekrutenko, James Taylor
Nature Biotechnology
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01 Nov 2012
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doi:10.1038/nbt.2404
Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses
Jeremy Goecks, The Galaxy Team, Anton Nekrutenko, James Taylor
2012 IEEE 8th International Conference on E-Science
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01 Oct 2012
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doi:10.1109/eScience.2012.6404442
Turning pipe dreams into reality
Peter Li, Jeremy Goecks, Tin-Lap Lee
Genome Biology
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01 Jan 2012
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doi:10.1186/gb-2012-13-8-318
2011
The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool
Jeremy Goecks, Kanwei Li, Dave Clements, The Galaxy Team, James Taylor
2011 IEEE Symposium on Biological Data Visualization (BioVis).
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01 Oct 2011
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doi:10.1109/BioVis.2011.6094046
Galaxy: A Gateway to Tools in e-Science
Enis Afgan, Jeremy Goecks, Dannon Baker, Nate Coraor, Anton Nekrutenko, James Taylor
Computer Communications and Networks
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01 Jan 2011
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doi:10.1007/978-0-85729-439-5_6
2010
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team
Genome Biology
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01 Jan 2010
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doi:10.1186/gb-2010-11-8-r86