Author

Michael F. Ochs

The College of New Jersey

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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Bioinformatics· 2 Cancer Biology· 1 Genomics· 1 Systems Biology· 1 Zoology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 4 Organism:human· 4 Approach:statistical model· 4 Research Focus:clustering· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Approach:machine learning (classical)· 2 Assay:spatial transcriptomics· 2

Frequent Co-Authors

Elana Judith FertigiD· 5 shared Genevieve Stein-O’BrieniD· 4 shared Alexander V. FavoroviD· 3 shared Daria A. GaykalovaiD· 2 shared Emily L. FlamiD· 2 shared Kathleen NolleriD· 2 shared Luciane Tsukamoto KagoharaiD· 2 shared Michael ConsidineiD· 2 shared

Activity by Year

2017-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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5 shared papersBioinformatics

Elana Judith FertigORCID

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Author profile →

6 papers

Recent·Most cited

Clear cell renal cell carcinoma consensus transcriptomic programs reveal converging trajectories towards aggressive disease

Roy M. Elias, Vivek Nimgaonkar, Bingrui Emily Xie, Yuqi Zhang, Archana Balan, Kathleen Noller, Nirmish Singla, Yasser M. A. Ged, Ezra G. Baraban, Payal Kapur, James Brugarolas, Genevieve Stein-O’Brien, Michael F. Ochs, Elana Judith Fertig, Atul J Deshpande, Srinivasan Yegnasubramanian

The paper identifies 17 consensus transcriptomic programs in ccRCC using NMF and links them to cellular sources and clinical outcomes, revealing converging trajectories toward aggressive disease.

The Oncologist · Sep 1, 2026Peer-reviewedCancer Biology

Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas

Kathleen Noller, Jiaying Lai, Daniel Lesperance, Ricky S. Adkins, Ahmed M. Elhossiny, Paola A. Guerrero, Kimal Rajapakshe, Anirban Maitra, Michelle Gwinn Giglio, Anup Mahurkar, Owen R. White, Marina Pasca di Magliano, Michael F. Ochs, Luciane Tsukamoto Kagohara, Laura DeLong Wood, , Elana Judith Fertig

The paper identifies multi-omic phenotypes in pancreatic precursor lesions to distinguish progressive from indolent precancers using integrative transcriptomic, genomic, and spatial data.

bioRxiv · Nov 3, 2025 · PreprintBioinformatics

Unsupervised learning reveals rapid gait adaption after leg loss and regrowth in spiders

Suzanne Amador Kane, Brooke L. Quinn, Xuanyi Kris Wu, Sarah Y. Xi, Michael F. Ochs, S. Tonia Hsieh

Gait-space clustering shows juvenile tarantulas losing two same-tetrapod legs immediately adopt variable tripod-like gaits, regaining pre-autotomy speed within a day without evidence of learning.

Journal of Experimental Biology · Jun 15, 2025Peer-reviewedZoology✦ In-depth digest

Enter the matrix: factorization uncovers knowledge from omics

Genevieve Stein-O’Brien, Raman Arora, Aedín C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana Judith Fertig

This paper reviews matrix factorization applications for systems-level omics analysis, highlighting their ability to uncover biological knowledge from high-dimensional data.

Trends in Genetics · Aug 21, 2018Peer-reviewedSystems Biology

Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer

Bahman Afsari, Theresa W. Guo, Michael Considine, Liliana Florea, Luciane Tsukamoto Kagohara, Genevieve Stein-O’Brien, Dylan Z. Kelley, Emily L. Flam, Kristina Diana A. Zambo, Patrick K. Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana Judith Fertig

SEVA identifies differential heterogeneity in gene isoform usage between cancer subtypes using RNA-seq data.

Bioinformatics · Jan 11, 2018Peer-reviewedGenomics

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

Genevieve Stein-O’Brien, Jacob Carey, Wai Shing Lee, Michael Considine, Alexander V. Favorov, Emily L. Flam, Theresa W. Guo, Sijia Li, Luigi Marchionni, Thomas D. Sherman, Shawn Sivy, Daria A. Gaykalova, Ronald D.G. McKay, Michael F. Ochs, Carlo Colantuoni, Elana Judith Fertig

The paper introduces PatternMarkers and GWCoGAPS to identify data-driven biomarkers from whole-genome data using NMF, demonstrating their application on GTex data.

Bioinformatics · Jan 30, 2017Peer-reviewedBioinformatics