Jeremy Goecks

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 24

Top Topics

Machine Learning

Squamous Cell Carcinoma

Top Venues

Cancer immunology research

bioRxiv : the preprint server for biology

PLoS computational biology

NPJ precision oncology

This page only lists publications with an associated author ORCID identifier.

Publications

Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer immunology research 12 (5) (2024)
Raphael Kirchgaessner, Cameron Watson, Allison L Creason, Kaya Keutler, Jeremy Goecks
Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. bioRxiv : the preprint server for biology (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer immunology research 12 (5) (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer immunology research 12 (5) (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer immunology research 12 (5) (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer immunology research 12 (5) (2024)
Katie E Blise, Shamilene Sivagnanam, Courtney B Betts, Konjit Betre, Nell C Kirchberger, Benjamin J Tate, Emma E Furth, Andressa Dias Costa, Jonathan Andrew Nowak, Brian M Wolpin, Robert A Anders, Jeremy Goecks, Lisa M Coussens, Katelyn T Byrne
Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer immunology research (2024)
Raphael Kirchgaessner, Cameron Watson, Allison L Creason, Kaya Keutler, Jeremy Goecks
Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. bioRxiv : the preprint server for biology (2023)
Raphael Kirchgaessner, Cameron Watson, Allison L Creason, Kaya Keutler, Jeremy Goecks
Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. bioRxiv : the preprint server for biology (2023)
Raphael Kirchgaessner, Cameron Watson, Allison L Creason, Kaya Keutler, Jeremy Goecks
Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. bioRxiv : the preprint server for biology (2023)
Katie E Blise, Shamilene Sivagnanam, Grace L Banik, Lisa M Coussens, Jeremy Goecks
Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. NPJ precision oncology 6 (1) (2022)
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L Muhlich, Joshua Hess, Allison L Creason, Ajit J Nirmal, Gregory J Baker, Maulik K Nariya, Jia-Ren Lin, Zoltan Maliga, Connor A Jacobson, Matthew W Hodgman, Juha Ruokonen, Samouil L Farhi, Domenic Abbondanza, Eliot T McKinley, Daniel Persson, Courtney Betts, Shamilene Sivagnanam, Aviv Regev, Jeremy Goecks, D Borden Lacy, Lisa M Coussens, Sandro Santagata, Peter Karl Sorger
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nature methods (2021)
Qiang Gu, Anup Kumar, Simon A Bray, Allison L Creason, Ali Reza Khanteymoori, Vahid Jalili, Bjoern Andreas Gruening, Jeremy Goecks
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLoS computational biology 17 (6) (2021)
Marilyne Labrie, Allen Li, Allison L Creason, Courtney Betts, Jamie Keck, Brett E Johnson, Shamilene Sivagnanam, Christopher Boniface, Hongli Ma, Aurora Blucher, Young Hwan Chang, Koei Chin, Jacqueline Vuky, Alexander R Guimaraes, Molly Downey, Jeong Youn Lim, Lina Gao, Kiara Siex, Swapnil Parmar, Annette Kolodzie, Paul T Spellman, Jeremy Goecks, Lisa M Coussens, Christopher L Corless, Raymond C Bergan, Joe W Gray, Gordon B Mills, Zahi I Mitri
Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ precision oncology 5 (1) (2021)
Luke Sargent, Yating Liu, Wilson Leung, Nathan T Mortimer, David Lopatto, Jeremy Goecks, Sarah C R Elgin
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation. PLoS computational biology 16 (6) (2020)
Prech Uapinyoying, Jeremy Goecks, Susan M Knoblach, Karuna Panchapakesan, Carsten G Bonnemann, Terence A Partridge, Jyoti K Jaiswal, Eric P Hoffman
A long-read RNA-seq approach to identify novel transcripts of very large genes. Genome research 30 (6) (2020)
Gil Alterovitz, Dennis Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H King, Dan Taylor, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimerà, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS biology 16 (12) (2018)