Author

Aliza B. Rubenstein

Icahn School of Medicine at Mount Sinai

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· 1 Biophysics· 1 Genomics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Approach:statistical model· 3 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:ATAC-seq· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Elena ZaslavskyiD· 3 shared Stuart C. SealfoniD· 3 shared Christopher W. WoodsiD· 2 shared Frederique Murielle Ruf-ZamojskiiD· 2 shared Manoj HariharaniD· 2 shared Olga G. TroyanskayaiD· 2 shared Venugopalan D. NairiD· 2 shared Adam M. MichaleasiD· 1 shared

Activity by Year

2017-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersImmunology

Elena ZaslavskyORCID

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Author profile →

4 papers

Recent·Most cited

Innate immune epigenomic landscape following controlled human influenza virus infection

William Thistlethwaite, Sindhu Vangeti, Wan-Sze Cheng, Pankaj Agarwal, Antonio Cappuccio, Wenliang Wang, Bei Wei, Rachel A. Myers, Aliza B. Rubenstein, Daniel G. Chawla, Manoj Hariharan, Micah T. McClain, Thomas W. Burke, Steven H. Kleinstein, Joseph R. Ecker, , Stuart C. Sealfon

The paper analyzes the epigenomic changes in innate immune cells after influenza virus infection and finds coordinated rewiring of the epigenetic landscape.

Cell Reports · Sep 17, 2025Peer-reviewedImmunology

Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Aliza B. Rubenstein, Gregory R. Smith, Zidong Zhang, Xi Chen, Toby L. Chambers, Frederique Murielle Ruf-Zamojski, Natalia Mendelev, Wan Sze Cheng, Michel Zamojski, Mary Anne S. Amper, Venugopalan D. Nair, Andrew R. Marderstein, Stephen B. Montgomery, Olga G. Troyanskaya, Elena Zaslavsky, , Stuart C. Sealfon

The paper uses single-nucleus multiome sequencing to analyze gene regulatory changes in human skeletal muscle after endurance exercise, identifying fiber-type specific regulatory programs and transcription factor networks.

Genome Research · Jul 1, 2025Peer-reviewedGenomics

Comprehensive Guide of Epigenetics and Transcriptomics Data Quality Control

Arianna Comendul, Frederique Murielle Ruf-Zamojski, Colby T. Ford, Pankaj Agarwal, Elena Zaslavsky, German Nudelman, Manoj Hariharan, Aliza B. Rubenstein, Hanna Pinças, Venugopalan D. Nair, Adam M. Michaleas, Philip Fremont‐Smith, Darrell O. Ricke, Stuart C. Sealfon, Christopher W. Woods, , Rafael Jaimes

This paper provides a comprehensive guide for quality control metrics and mitigation strategies for 11 epigenetics and transcriptomics assays to improve exposure signature discovery.

STAR Protocols · Jan 26, 2025Peer-reviewedBioinformatics

Biophysical determinants of mutational robustness in a viral molecular fitness landscape

Manasi A. Pethe, Aliza B. Rubenstein, Dmitri Zorine, Sagar D. Khare

The paper maps the sequence-energetics-function relationship of the HCV NS3/4A protease, revealing mutational robustness and clustering of cleavable/uncleavable motifs.

bioRxiv · Aug 3, 2017 · PreprintBiophysics