Vijay Ramani, PhD
Assistant Professor
Biochemistry and Biophysics
School of Medicine

Websites

Show all (2) Hide

• UCSF Website (kamakshi.ucsf.edu)
• Gladstone Website (gladstone.org)

Publications (23)

Top publication keywords:
Single-Cell AnalysisMolecular ConformationChromosome MappingDNASingle Molecule ImagingSequence Analysis, DNAChromatinDeoxyribonucleasesGene LibraryMicrococcal NucleaseHigh-Throughput Nucleotide SequencingNucleic Acid HybridizationNucleosomesGenome, HumanX Chromosome Inactivation

• The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.
  bioRxiv : the preprint server for biology 2024 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 2023 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 2023 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 2022 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 2021 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

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• Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.
  Genome biology 2021 Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM
• At least two to tango: Choreographing chromatin through cooperative footprints.
  Molecular cell 2021 Abdulhay NJ, Ramani V
• Massively multiplex single-molecule oligonucleosome footprinting.
  eLife 2020 Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V
• Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
  PLoS computational biology 2020 Kim HJ, Yardimci GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS
• Massively multiplex chemical transcriptomics at single-cell resolution.
  Science (New York, N.Y.) 2019 Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C
• Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.
  Methods (San Diego, Calif.) 2019 Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z
• Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.
  Nature communications 2019 Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE
• High Sensitivity Profiling of Chromatin Structure by MNase-SSP.
  Cell reports 2019 Ramani V, Qiu R, Shendure J
• Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
  Science (New York, N.Y.) 2018 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
• Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.
  Nature communications 2018 Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM
• Comprehensive single-cell transcriptional profiling of a multicellular organism.
  Science (New York, N.Y.) 2017 Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J
• Massively multiplex single-cell Hi-C.
  Nature methods 2017 Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J
• Mapping 3D genome architecture through in situ DNase Hi-C.
  Nature protocols 2016 Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z
• Smash and DASH with Cas9.
  Genome biology 2016 Ramani V, Shendure J
• Understanding Spatial Genome Organization: Methods and Insights.
  Genomics, proteomics & bioinformatics 2016 Ramani V, Shendure J, Duan Z
• Bipartite structure of the inactive mouse X chromosome.
  Genome biology 2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM
• High-throughput determination of RNA structure by proximity ligation.
  Nature biotechnology 2015 Ramani V, Qiu R, Shendure J
• 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 2010 Sun Myint A, Mukhopadhyay T, Ramani VS, Perkins K, Snee AJ, Jelley F, Wong H, Lee CD