Vijay Ramani, PhD

Assistant Professor
Assistant Investigator
Gladstone Institute for Data Science & Biotechnology
Department of Biochemistry and Biophysics
[email protected]
Research Overview: 

Featured Publications

  1. Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V#. "Massively multiplex single-molecule oligonucleosome footprinting." eLife; 2020 Dec 14; PMID: 33263279; [pdf]
  2. Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers FJ, Shendure J, Trapnell C. "Massively multiplex chemical transcriptomics at single-cell resolution." Science; 2019 Dec 5; PMID: 31806696; [pdf]
  3. Ramani V#, Qiu R, Shendure J#. "High-resolution analysis of chromatin structure by MNase-SSP." Cell Reports; 2019 Feb 26; PMID: 30811994; [pdf]
  4. Cao J, Cusanovich DA*, Ramani V*, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J. "Joint profiling of chromatin accessibility and gene expression in thousands of single cells." Science; 2018 Aug 30; PMID: 30166440; [pdf]
  5. Cao J, Packer J, Ramani V*, Cusanovich DA*, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. "Comprehensive single cell transcriptional profiling of a multicellular organism." Science; 2017 Aug 18; PMID: 28818938; [pdf]
  6. Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. "Massively multiplex single-cell Hi-C." Nature Methods; 2017 Jan 30; PMID: 28135255; [pdf]
  7. Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. "Mapping three-dimensional genome architecture through in situ DNase Hi-C." Nature Protocols; 2016 Sep 29; PMID: 27685100; [pdf]
  8. Ramani V, Qiu R, Shendure J. "High-throughput determination of RNA structure by proximity ligation." Nature Biotechnology; 2015 Aug 3; PMID: 26237516; [pdf]

#: senior author; *: equal contribution. In cases where a first author is from the lab, all first authors are highlighted in bold

Primary Thematic Area: 
Human Genetics
Secondary Thematic Area: 
Cancer Biology & Cell Signaling
Research Summary: 
Our lab develops new genome-scale methods to study mammalian chromatin structure and transcriptional regulation

Websites

Publications: 

The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.

bioRxiv : the preprint server for biology

Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP

A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies.

bioRxiv : the preprint server for biology

Freie B, Carroll PA, Varnum-Finney BJ, Ramani V, Bernstein I, Eisenman RN

Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler.

Nature structural & molecular biology

Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V

A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function.

Molecular cell

Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ

The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis.

PLoS biology

Carroll PA, Freie BW, Cheng PF, Kasinathan S, Gu H, Hedrich T, Dowdle JA, Venkataramani V, Ramani V, Wu X, Raftery D, Shendure J, Ayer DE, Muller CH, Eisenman RN