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: 

Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion.

Current opinion in genetics & development

Corin A, Nora EP, Ramani V

Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.

Nature neuroscience

Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.

Nature neuroscience

Bonev B, Gonçalo CB, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Bayraktar O, Habib N, Nowakowski TJ

The single-molecule accessibility landscape of newly replicated mammalian chromatin.

Cell

Ostrowski MS, Yang MG, McNally CP, Abdulhay NJ, Wang S, Renduchintala K, Irkliyenko I, Biran A, Chew BTL, Midha AD, Wong EV, Sandoval J, Jain IH, Groth A, Nora EP, Goodarzi H, Ramani V