
Assistant Professor
Assistant Investigator
Gladstone Institute for Data Science & Biotechnology
Department of Biochemistry and Biophysics
Primary Thematic Area
Secondary Thematic Area
Research Summary
Our lab develops new genome-scale methods to study mammalian chromatin structure and transcriptional regulation
Featured Publications
- 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]
- 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]
- Ramani V#, Qiu R, Shendure J#. "High-resolution analysis of chromatin structure by MNase-SSP." Cell Reports; 2019 Feb 26; PMID: 30811994; [pdf]
- 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]
- 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]
- 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]
- 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]
- 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
Websites
Publications
Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers.
bioRxiv : the preprint server for biology
Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Nature neuroscience
Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion.
Current opinion in genetics & development
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Nature neuroscience
Split-pool barcoding serves up an epigenomic smorgasbord.
Nature genetics
Endogenous neuronal DNA double-strand breaks are not sufficient to drive brain aging and neurodegeneration.
bioRxiv : the preprint server for biology
The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.
bioRxiv : the preprint server for biology
ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers.
bioRxiv : the preprint server for biology
HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA.
bioRxiv : the preprint server for biology
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing.
Nature genetics
A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies.
bioRxiv : the preprint server for biology
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler.
Nature structural & molecular biology
A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function.
Molecular cell
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.
Genome biology
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
PLoS computational biology
Massively multiplex chemical transcriptomics at single-cell resolution.
Science (New York, N.Y.)
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.
Methods (San Diego, Calif.)
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.
Nature communications
Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Science (New York, N.Y.)
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.
Nature communications
Comprehensive single-cell transcriptional profiling of a multicellular organism.
Science (New York, N.Y.)
Massively multiplex single-cell Hi-C.
Nature methods
Mapping 3D genome architecture through in situ DNase Hi-C.
Nature protocols
Smash and DASH with Cas9.
Genome biology
Understanding Spatial Genome Organization: Methods and Insights.
Genomics, proteomics & bioinformatics
Bipartite structure of the inactive mouse X chromosome.
Genome biology
High-throughput determination of RNA structure by proximity ligation.
Nature biotechnology
Can increasing the dose of radiation by HDR brachytherapy boost following pre operative chemoradiotherapy for advanced rectal cancer improve surgical outcomes?
Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland