Author

Vidya Subramanian

Broad Institute

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 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:scRNA-seq· 2 Research Focus:cell type annotation· 1 Assay:CRISPR screen· 1 Approach:optimal transport· 1 Research Focus:perturbation response prediction· 1

Frequent Co-Authors

Eric S. LanderiD· 3 shared Benjamin R. DoughtyiD· 2 shared Charles P. FulcoiD· 2 shared Drew T. BergmaniD· 2 shared J EngreitziD· 2 shared Joseph NasseriD· 2 shared Anna GrekaiD· 1 shared Aryeh SolomoniD· 1 shared

Activity by Year

2017-2020 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersGenomics

Eric S. LanderORCID

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3 papers

Recent·Most cited

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

Jamie L. Marshall, Benjamin R. Doughty, Vidya Subramanian, Philine Guckelberger, Qingbo S. Wang, Linlin M. Chen, Samuel G. Rodriques, Kaite Zhang, Charles P. Fulco, Joseph Nasser, Elizabeth J. Grinkevich, Teia Noel, Sarah M. Mangiameli, Drew T. Bergman, Anna Greka, , J Engreitz

HyPR-seq sensitively quantifies up to 100 chosen genes in single cells, achieving high sensitivity for individual transcripts and reducing costs compared to whole-transcriptome scRNA-seq.

Proceedings of the National Academy of Sciences · Dec 21, 2020Peer-reviewedGenomics

Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations

Charles P. Fulco, Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, Rockwell Anyoha, Tejal A. Patwardhan, Tung H. Nguyen, Michael Kane, Benjamin R. Doughty, Elizabeth M. Perez, Neva C. Durand, Elena K. Stamenova, , J Engreitz

The paper introduces CRISPRi-FlowFISH to perturb enhancers and an Activity-by-Contact model to predict enhancer-gene regulatory connections.

bioRxiv · Jan 26, 2019 · PreprintGenetics

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.

Geoffrey R. Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Siyan Liu, Stacie L. Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, , Eric S. Lander

Optimal transport converts a 65,781-cell reprogramming time course into probabilistic fates and trajectories, exposing alternative cell fates and a gene, Obox6, that improves reprogramming efficiency.

bioRxiv · Sep 27, 2017 · PreprintBioinformatics