publications

Here is a sampling of some of the papers that guide our lab’s research. You can also find many of these on google scholar and pubmed. #: senior author; *: equal contribution. In cases where a first author is from the lab, all first authors are highlighted in bold.

  1. 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#. "The single-molecule accessibility landscape of newly replicated mammalian chromatin." Cell; 2025 January 9; PMID: 39549698; [pdf]

  2. Nanda AS, Wu K, Irkliyenko I, Woo B, Ostrowski MS, Clugston AS, Sayles LC, Xu L, Satpathy AT, Nguyen HG, Sweet-Cordero EA, Goodarzi H, Kasinathan S#, Ramani V#. "Direct transposition of native DNA for sensitive multimodal single-molecule sequencing." Nature Genetics; 2024 May 9; PMID: 38724748; [pdf]

  3. 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#. "Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler." Nature Structural & Molecular Biology; 2023 Sep 11; PMID: 37696956; [pdf]

  4. 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]

  5. 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]

  6. Ramani V#, Qiu R, Shendure J#. "High-resolution analysis of chromatin structure by MNase-SSP." Cell Reports; 2019 Feb 26; PMID: 30811994; [pdf]

  7. 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]

  8. 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]

  9. 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]

  10. 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]

  11. Ramani V, Qiu R, Shendure J. "High-throughput determination of RNA structure by proximity ligation." Nature Biotechnology; 2015 Aug 3; PMID: 26237516; [pdf]