Jeremy Goecks
Overview
Explore the profile of Jeremy Goecks including associated specialties, affiliations and a list of published articles.
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39
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5807
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Recent Articles
1.
Link J, Eng J, Pelz C, MacPherson-Hawthorne K, Worth P, Sivagnanam S, et al.
Nat Cancer
. 2025 Jan;
6(1):123-144.
PMID: 39789181
Patients with metastatic pancreatic ductal adenocarcinoma survive longer if disease spreads to the lung but not the liver. Here we generated overlapping, multi-omic datasets to identify molecular and cellular features...
2.
Karlberg B, Kirchgaessner R, Lee J, Peterkort M, Beckman L, Goecks J, et al.
Genome Biol
. 2024 Dec;
25(1):309.
PMID: 39696541
The accuracy of machine learning methods is often limited by the amount of training data that is available. We proposed to improve machine learning training regimes by augmenting datasets with...
3.
Blise K, Sivagnanam S, Betts C, Betre K, Kirchberger N, Tate B, et al.
Cancer Immunol Res
. 2024 Feb;
12(5):544-558.
PMID: 38381401
Tumor molecular data sets are becoming increasingly complex, making it nearly impossible for humans alone to effectively analyze them. Here, we demonstrate the power of using machine learning (ML) to...
4.
Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J
bioRxiv
. 2023 Dec;
PMID: 38106203
Multiplex tissue imaging are a collection of increasingly popular single-cell spatial proteomics and transcriptomics assays for characterizing biological tissues both compositionally and spatially. However, several technical issues limit the utility...
5.
Blise K, Sivagnanam S, Betts C, Betre K, Kirchberger N, Tate B, et al.
bioRxiv
. 2023 Nov;
PMID: 37961410
Tumor molecular datasets are becoming increasingly complex, making it nearly impossible for humans alone to effectively analyze them. Here, we demonstrate the power of using machine learning to analyze a...
6.
Johnson B, Creason A, Stommel J, Keck J, Parmar S, Betts C, et al.
Cell Rep Med
. 2022 Mar;
3(2):100525.
PMID: 35243422
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms...
7.
Blise K, Sivagnanam S, Banik G, Coussens L, Goecks J
NPJ Precis Oncol
. 2022 Feb;
6(1):10.
PMID: 35217711
There is increasing evidence that the spatial organization of cells within the tumor-immune microenvironment (TiME) of solid tumors influences survival and response to therapy in numerous cancer types. Here, we...
8.
Schatz M, Philippakis A, Afgan E, Banks E, Carey V, Carroll R, et al.
Cell Genom
. 2022 Feb;
2(1).
PMID: 35199087
The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management,...
9.
Schapiro D, Sokolov A, Yapp C, Chen Y, Muhlich J, Hess J, et al.
Nat Methods
. 2021 Nov;
19(3):311-315.
PMID: 34824477
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here,...
10.
Labrie M, Li A, Creason A, Betts C, Keck J, Johnson B, et al.
NPJ Precis Oncol
. 2021 Oct;
5(1):92.
PMID: 34667258
In a pilot study, we evaluated the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities...