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   ·   01 Jun 2021   ·   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   ·   29 Sep 2023   ·   doi:10.1101/2023.09.27.557464

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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   ·   21 Apr 2022   ·   doi:10.1093/nar/gkac247

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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   ·   25 Feb 2022   ·   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   ·   01 Feb 2022   ·   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   ·   01 Jan 2022   ·   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   ·   25 Nov 2021   ·   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   ·   19 Oct 2021   ·   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   ·   01 Jun 2021   ·   doi:10.1371/journal.pcbi.1009014

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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   ·   16 Mar 2021   ·   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   ·   04 Jun 2020   ·   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   ·   01 Jun 2020   ·   doi:10.1093/nar/gkaa434

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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   ·   01 Jun 2020   ·   doi:10.1101/gr.259903.119

How Machine Learning Will Transform Biomedicine

Jeremy Goecks, Vahid Jalili, Laura M. Heiser, Joe W. Gray

Cell   ·   01 Apr 2020   ·   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   ·   01 Apr 2020   ·   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   ·   01 Apr 2020   ·   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   ·   01 Jan 2020   ·   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   ·   01 Oct 2019   ·   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   ·   01 Sep 2019   ·   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   ·   14 Jun 2019   ·   doi:10.1093/bioinformatics/btz472

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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   ·   09 May 2019   ·   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)   ·   01 Jul 2018   ·   doi:10.1109/cloud.2018.00124

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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   ·   01 Jun 2018   ·   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   ·   22 May 2018   ·   doi:10.1093/nar/gky379

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Biology Needs Evolutionary Software Tools: Let’s Build Them Right

Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg

Molecular Biology and Evolution   ·   23 Apr 2018   ·   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   ·   14 Dec 2016   ·   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   ·   26 Jan 2016   ·   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   ·   05 Feb 2015   ·   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   ·   04 Jan 2015   ·   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   ·   14 Jul 2014   ·   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   ·   14 Jan 2014   ·   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   ·   13 Jun 2013   ·   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   ·   23 May 2013   ·   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   ·   20 May 2013   ·   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   ·   01 Nov 2012   ·   doi:10.1038/nbt.2404

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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   ·   01 Oct 2012   ·   doi:10.1109/eScience.2012.6404442

Turning pipe dreams into reality

Peter Li, Jeremy Goecks, Tin-Lap Lee

Genome Biology   ·   01 Jan 2012   ·   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).   ·   01 Oct 2011   ·   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   ·   01 Jan 2011   ·   doi:10.1007/978-0-85729-439-5_6

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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   ·   01 Jan 2010   ·   doi:10.1186/gb-2010-11-8-r86

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