Author

Mark J. Berger

Stanford University

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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Genomics· 3 Genetics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:differential expression· 2 Organism:human· 2 Organism:mouse· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Aaron M. NewmaniD· 1 shared Alicia Yiran ZhouiD· 1 shared Amanda Faith SpielmaniD· 1 shared Angera H. KuoiD· 1 shared Anjali D. ZimmeriD· 1 shared Anjan BharadwajiD· 1 shared Anoop ManjunathiD· 1 shared Cynthia L. NebeniD· 1 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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1 shared paperGenomics

Aaron M. NewmanORCID

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Author profile →

4 papers

Recent·Most cited

Allele-specific expression reveals genetic drivers of tissue regeneration in mice

Heather Elizabeth desJardins-Park, Katya L. Mack, M. Griffin, Nicholas J. Guardino, Jennifer B. Laufey Parker, Amanda Faith Spielman, Michael F. Davitt, Shamik Mascharak, Mark J. Berger, Derrick C. Wan, Hunter B. Fraser, Michael Thornton Longaker

The paper identifies cis-regulatory variation in MRL mice associated with ear regeneration using allele-specific expression analysis.

bioRxiv · Sep 23, 2022 · PreprintGenomics

Single-cell transcriptional diversity is a hallmark of developmental potential

Gunsagar Singh Gulati, Shaheen S. Sikandar, Daniel J. Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J. Berger, Francisco Ilagan, Angera H. Kuo, Robert W. Hsieh, Shang Cai, Maider Zabala, Ferenc A. Scheeren, Neethan A. Lobo, Dalong Qian, Feiqiao Brian Yu, , Aaron M. Newman

The paper introduces CytoTRACE, a method using transcriptional diversity to predict differentiation states from scRNA-seq data, outperforming existing methods and identifying stem cells and tumor-related genes.

Science · Jan 23, 2020Peer-reviewedGenomics

Color Data v2: a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets

Mark J. Berger, Hannah Williams, Ryan Barrett, Anjali D. Zimmer, Wendy McKennon, Huy Hong, Jeremy Ginsberg, Alicia Yiran Zhou, Cynthia L. Neben

Color Data v2 provides an updated open-access database with genetic and phenotypic data on hereditary cancer and cardiovascular conditions, including polygenic risk scores and clinical risk models.

Database · Jan 1, 2020Peer-reviewedGenetics

Comment on "A genetic signature of the evolution of loss of flight in the Galapagos cormorant"

Mark J. Berger, Gill Bejerano

The paper identifies 48 limb enhancers with accelerated evolution in Galapagos cormorants, suggesting non-coding regions contribute to flightlessness.

bioRxiv · Sep 8, 2017 · PreprintGenomics