Jeremy Goecks, PhD

Cancer data science, Machine learning for biomedicine, Computational infrastructure for biomedicine, precision medicine, spatial and multimodal tumor biology.

Associations

• Biostatistics and Bioinformatics
• Machine Learning
• Molecular Medicine Program

My research interests lie at the intersection of biomedical data science, high-performance computing, and precision oncology. I have two active areas of research: Software Tools for Biomedicine: I build software tools for cancer and biomedical data science, including individual analysis packages, machine learning applications, interactive visualizations, and software platforms/infrastructure. I am a lead investigator for the Galaxy computational workbench (https://galaxyproject.org/), which is used by thousands of scientists across the world. Precision Cancer Medicine: I apply computational tools and software platforms to identify biomarkers associated with cancer susceptibility, progression, and response to therapy. Recently I have led the creation and analysis of multimodal, spatial, and single-cell molecular tumor atlases to identify tumor adaptations to therapy and potential approaches to mitigate these adaptations.

• Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J. Imputing single-cell protein abundance in multiplex tissue imaging. Nat Commun. 2025 May.16(1):4747. Pubmedid: 40404617. Pmcid: PMC12098973.
• Obermayer A, Davis J, Talada DP, Teng M, Eschrich S, Yin V, Spakowicz D, Dhrubo D, Rounbehler RJ, Churchman ML, Tarhini AA, Wang X, Gupta S, Markowitz J, Goecks J, Li R, Rodriguez-Pessoa R, Manley BJ, Tan AC, Grass GD, Chen DT, Shaw TI. ShinyEvents: harmonizing longitudinal data for real world survival estimation. Res Sq. 2025 Aug. Pubmedid: 40799741. Pmcid: PMC12340904.
• Noller K, Botsis T, Camara PG, Ciotti L, Cooper LA, Goecks J, Griffith M, Haas BJ, Ideker T, Karchin R, Kontos D, Lai J, Marcus D, Meyer CA, Naegle K, Pati S, Peters B, Pratt D, Raphael BJ, Reich M, Savova GK, Wright C, Fertig EJ, Bakas S. Informatics at the Frontier of Cancer Research. Cancer Res. 2025 Aug.85(16):2967-2986. Pubmedid: 40600473. Pmcid: PMC12355178.
• Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate BJ, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer Immunol Res. 2024 May.12(5):544-558. Pubmedid: 38381401. Pmcid: PMC11065586.
• Karlberg B, Kirchgaessner R, Lee J, Peterkort M, Beckman L, Goecks J, Ellrott K. SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions. Genome Biol. 2024 Dec.25(1):309. Pubmedid: 39696541. Pmcid: PMC11658131.
• Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate B, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. bioRxiv. 2023 Oct. Pubmedid: 37961410. Pmcid: PMC10634700.
• Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J. Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. bioRxiv. 2023 Dec. Pubmedid: 38106203. Pmcid: PMC10723289.
• Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods. 2022 Mar.19(3):311-315. Pubmedid: 34824477. Pmcid: PMC8916956.
• Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan.2(1). Pubmedid: 35199087. Pmcid: PMC8863334.
• Blise KE, Sivagnanam S, Banik GL, Coussens LM, Goecks J. Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. NPJ Precis Oncol. 2022 Feb.6(1):10. Pubmedid: 35217711. Pmcid: PMC8881577.
• Banik G, Betts CB, Liudahl SM, Sivagnanam S, Kawashima R, Cotechini T, Larson W, Goecks J, Pai SI, Clayburgh DR, Tsujikawa T, Coussens LM. High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers. Methods Enzymol. 2021 Jun.635:1-20. Pubmedid: 32122539. Pmcid: PMC7390987.
• Gu Q, Kumar A, Bray S, Creason A, Khanteymoori A, Jalili V, Grüning B, Goecks J. Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLoS Comput Biol. 2021 Jun.17(6):e1009014. Pubmedid: 34061826. Pmcid: PMC8213174.
• Liudahl SM, Betts CB, Sivagnanam S, Morales-Oyarvide V, da Silva A, Yuan C, Hwang S, Grossblatt-Wait A, Leis KR, Larson W, Lavoie MB, Robinson P, Dias Costa A, Väyrynen SA, Clancy TE, Rubinson DA, Link J, Keith D, Horton W, Tempero MA, Vonderheide RH, Jaffee EM, Sheppard B, Goecks J, Sears RC, Park BS, Mori M, Nowak JA, Wolpin BM, Coussens LM. Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome. Cancer Discov. 2021 Aug.11(8):2014-2031. Pubmedid: 33727309. Pmcid: PMC8338775.
• Uapinyoying P, Goecks J, Knoblach SM, Panchapakesan K, Bonnemann CG, Partridge TA, Jaiswal JK, Hoffman EP. A long-read RNA-seq approach to identify novel transcripts of very large genes. Genome Res. 2020 Jun.30(6):885-897. Pubmedid: 32660935. Pmcid: PMC7370890.
• Sargent L, Liu Y, Leung W, Mortimer NT, Lopatto D, Goecks J, Elgin SCR. G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation. PLoS Comput Biol. 2020 Jun.16(6):e1007863. Pubmedid: 32497138. Pmcid: PMC7272004.
• Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res. 2020 Jul.48(W1):W395-W402. Pubmedid: 32479607. Pmcid: PMC7319590.
• Jalili V, Afgan E, Taylor J, Goecks J. Cloud bursting galaxy: federated identity and access management. Bioinformatics. 2020 Jan.36(1):1-9. Pubmedid: 31197310. Pmcid: PMC6956780.
• Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. Corrigendum: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res. 2020 Aug.48(14):8205-8207. Pubmedid: 32585001. Pmcid: PMC7641327.
• Goecks J, Jalili V, Heiser LM, Gray JW. How Machine Learning Will Transform Biomedicine. Cell. 2020 Apr.181(1):92-101. Pubmedid: 32243801. Pmcid: PMC7141410.
• Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genetics. 2020 Apr.52(4):448-457. Pubmedid: 32246132. Pmcid: PMC7127986.
• Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr.181(2):236-249. Pubmedid: 32302568. Pmcid: PMC7376497.
• Liu Y, Sargent L, Leung W, Elgin SCR, Goecks J. G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes. Bioinformatics. 2019 Nov.35(21):4422-4423. Pubmedid: 31070714. Pmcid: PMC6821377.
• Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D. Biology Needs Evolutionary Software Tools: Let's Build Them Right. Mol Biol Evol. 2018 Jun.35(6):1372-1375. Pubmedid: 29688462. Pmcid: PMC5967460.
• 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 Syst. 2018 Jun.6(6):631-635. Pubmedid: 29953862. Pmcid: PMC6263957.
• Simonyan V, Goecks J, Mazumder R. Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA J Pharm Sci Technol. 2018 Jun.71(2):136-146. Pubmedid: 27974626. Pmcid: PMC5510742.
• Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-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 Res. 2018 Jul.46(W1):W537-W544. Pubmedid: 29790989. Pmcid: PMC6030816.
• Afgan E, Jalili V, Goonasekera N, Taylor J, Goecks J. Federated Galaxy: Biomedical Computing at the Frontier. IEEE Int Conf Cloud Comput. 2018 Jul.2018. Pubmedid: 34386295. Pmcid: PMC8356149.
• Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biol. 2018 Dec.16(12):e3000099. Pubmedid: 30596645. Pmcid: PMC6338479.
• Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriguez J, Voskanian A, Wan Q, Mazumder R. Impact of germline and somatic missense variations on drug binding sites. Pharmacogenomics J. 2017 Mar.17(2):128-136. Pubmedid: 26810135. Pmcid: PMC5380835.
• Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von 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 Res. 2016 Jul.44(W1):W3-W10. Pubmedid: 27137889. Pmcid: PMC4987906.
• 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 Med. 2015 Mar.4(3):392-403. Pubmedid: 25594743. Pmcid: PMC4380965.
• Harris NL, Cock PJ, Chapman BA, Goecks J, Hotz HR, Lapp H. The Bioinformatics Open Source Conference (BOSC) 2013. Bioinformatics. 2015 Jan.31(2):299-300. Pubmedid: 25024288. Pmcid: PMC4287938.
• Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N. A quick guide for building a successful bioinformatics community. PLoS Comput Biol. 2015 Feb.11(2):e1003972. Pubmedid: 25654371. Pmcid: PMC4318577.
• Phillips CJ, Phillips CD, Goecks J, Lessa EP, Sotero-Caio CG, Tandler B, Gannon MR, Baker RJ. Dietary and flight energetic adaptations in a salivary gland transcriptome of an insectivorous bat. PLoS One. 2014 Jan.9(1):e83512. Pubmedid: 24454705. Pmcid: PMC3891661.
• Goecks J, Mortimer NT, Mobley JA, Bowersock GJ, Taylor J, Schlenke TA. Integrative approach reveals composition of endoparasitoid wasp venoms. PLoS One. 2014 Jan.8(5):e64125. Pubmedid: 23717546. Pmcid: PMC3662768.
• Goecks J, Eberhard C, Too T, Nekrutenko A, Taylor J. Web-based visual analysis for high-throughput genomics. BMC Genomics. 2013 Jun.14:397. Pubmedid: 23758618. Pmcid: PMC3691752.
• 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. Proc Natl Acad Sci U S A. 2013 Jun.110(23):9427-9432. Pubmedid: 23690612. Pmcid: PMC3677475.
• Goecks J, Coraor N, Nekrutenko A, Taylor J. NGS analyses by visualization with Trackster. Nat Biotechnol. 2012 Nov.30(11):1036-1039. Pubmedid: 23138293. Pmcid: PMC3889118.
• Li P, Goecks J, Lee TL. Turning pipe dreams into reality. Genome Biol. 2012 Aug.13(8):318. Pubmedid: 22943297. Pmcid: PMC3491365.
• Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2011 Jan.11(8):R86. Pubmedid: 20738864. Pmcid: PMC2945788.

• Title: Developing a Cancer Galaxy Computational Workbench to Meet Emerging Cancer Data Analysis Needs
  Award Number: 5U24CA284167-02
  Sponsor: National Cancer Institute (NCI)
  Goecks, J. (PD/PI)
• Title: Expanding the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)
  Award Number: 5U24HG010263
  Sponsor: National Cancer Institute (NCI)
  Goecks, J. (PD/PI)
• Title: Democratization of Data Analysis in Life Sciences Through Galaxy
  Award Number: 2U24HG006620
  Sponsor: National Institutes of Health (NIH)
  Goecks, J. (PD/PI)