Author

J. Goecks

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 6 Scientific Communication & Education· 2

Signature Assays, Organisms & Methods

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Organism:human· 6 Approach:experimental assay· 5 Assay:bulk RNA-seq· 4 Research Focus:cell type annotation· 4 Research Focus:differential expression· 4 Assay:spatial transcriptomics· 4 Research Focus:cell-cell communication· 3 Assay:proteomics· 3

Frequent Co-Authors

A. L. Creason· 4 shared L. M. Coussens· 4 shared S. Sivagnanam· 4 shared E. Demir· 3 shared G. B. Mills· 3 shared B. E. Johnson· 2 shared C. B. Betts· 2 shared C. Watson· 2 shared

Activity by Year

2018-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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4 shared papersCancer Biology

A. L. Creason

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging

R. Kirchgaessner, C. Watson, A. L. Creason, K. Keutler, J. Goecks

This paper imputes single-cell protein abundance in multiplex tissue imaging data from a breast cancer cohort using machine learning, showing improved accuracy and biological relevance.

bioRxiv · Dec 5, 2023Cancer Biology

Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer

K. E. Blise, S. Sivagnanam, C. B. Betts, K. Betre, N. Kirchberger, B. Tate, E. E. Furth, A. Dias Costa, J. A. Nowak, B. M. Wolpin, R. H. Vonderheide, J. Goecks, L. M. Coussens, K. Byrne

This study uses machine learning to analyze spatial proteomic data from pancreatic cancer patients, linking T cell function and localization to neoadjuvant CD40 therapy and clinical outcomes.

bioRxiv · Oct 20, 2023Cancer Biology

Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers

A. L. Creason, J. Egger, C. Watson, S. Sivagnanam, K. Chin, K. MacPherson, J.-R. Lin, Y.-A. Chen, B. E. Johnson, H. S. Feiler, D. Galipeau, N. E. Navin, E. Demir, Y. H. Chang, C. L. Corless, , J. Goecks

This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.

bioRxiv · Sep 27, 2023 · PreprintCancer Biology

Ongoing Replication Stress Response and New Clonal T Cell Development Discriminate Between Liver and Lung Recurrence Sites and Patient Outcomes in Pancreatic Ductal Adenocarcinoma

J. M. Link, C. Pelz, P. J. Worth, S. Owen, D. Keith, E. M. Langer, A. Grossblatt-Wait, A. L. Creason, J. Egger, H. Holly, I. English, K. MacPherson, M. Tsuda, J. Goecks, E. Demir, , R. C. Sears

This study identifies transcriptomic and immune features distinguishing liver and lung metastatic sites in PDAC, linking replication stress response and T cell clonal development to patient outcomes.

bioRxiv · May 4, 2022 · PreprintCancer Biology

Single-Cell Spatial Proteomics Analyses of Head and Neck Squamous Cell Carcinoma Reveal Tumor Heterogeneity and Immune Architectures Associated with Clinical Outcome

K. E. Blise, S. Sivagnanam, G. L. Banik, L. M. Coussens, J. Goecks

The paper uses single-cell spatial proteomics to analyze HNSCC tumors, showing that tumor-immune compartmentalization is linked to better clinical outcomes.

bioRxiv · Mar 10, 2021Cancer Biology

An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer

B. E. Johnson, A. L. Creason, J. M. Stommel, J. M. Keck, S. Parmar, C. B. Betts, A. Blucher, C. Boniface, E. Bucher, E. A. Burlingame, T. Camp, K. Chin, J. Eng, J. Estabrook, H. S. Feiler, , J. W. Gray

This paper presents an OMS Atlas from serial biopsies of a metastatic breast cancer patient, linking clinical data to multi-omic and spatial profiles to study therapy-associated heterogeneity and resistance mechanisms.

bioRxiv · Dec 3, 2020Cancer Biology

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

L. Sargent, Y. Liu, W. Leung, N. T. Mortimer, D. Lopatto, J. Goecks, S. C. R. Elgin

Galaxy-based platform builds UCSC Assembly Hubs, JBrowse and Apollo annotation browsers without bioinformatics expertise; parasitoid wasp browsers supported undergraduate research courses producing 192 gene models.

bioRxiv · Oct 2, 2019Scientific Communication & Education✦ In-depth digest

Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results

G. Alterovitz, D. A. Dean, C. Goble, M. R. Crusoe, S. Soiland-Reyes, A. Bell, A. Hayes, A. Suresh, A. Purkayastha, C. H. H. King, D. Taylor, E. Johanson, E. E. Thompson, E. Donaldson, H. Morizono, , R. Mazumder

The paper introduces the BioCompute framework to standardize genomic data reporting, enabling reproducibility and interoperability in precision medicine.

bioRxiv · Nov 5, 2018Scientific Communication & Education