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Vijay Ramani, PhD

Title(s)Assistant Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone. Sci Adv. 2025 Aug 15; 11(33):eads4473. Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ. PMID: 40815652; PMCID: PMC12356256.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. Transcriptional Elongation-Associated RNA Processing Errors in Induced Cellular Growth Arrest. bioRxiv. 2025 Jun 23. Parast S, Wang S, Iwanaszko M, He Y, Olgun DG, Gold SR, Aoi Y, Zeidner JM, Howard BC, Thakur WR, Ramani V, Shilatifard A. PMID: 40599158; PMCID: PMC12212439.
      View in: PubMed   Mentions:
    3. Acquired resistance to immune checkpoint therapy is caused by glycoprotein non-metastatic melanoma protein B signal cascade. Commun Med (Lond). 2025 Mar 20; 5(1):79. Chung JS, Ramani V, Guo L, Popat V, Cruz PD, Xu L, Hammers H, Ariizumi K. PMID: 40114009; PMCID: PMC11926377.
      View in: PubMed   Mentions:
    4. Aging activates escape of the silent X chromosome in the female mouse hippocampus. Sci Adv. 2025 Mar 07; 11(10):eads8169. Gadek M, Shaw CK, Abdulai-Saiku S, Saloner R, Marino F, Wang D, Bonham LW, Yokoyama JS, Panning B, Benayoun BA, Casaletto KB, Ramani V, Dubal DB. PMID: 40043106; PMCID: PMC11881916.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    5. Relating DNA sequence, organization, and function. Science. 2025 Feb 07; 387(6734):580. Fudenberg G, Ramani V. PMID: 39913601.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    6. The PRC2.1 subcomplex opposes G1 progression through regulation of CCND1 and CCND2. Elife. 2025 Feb 04; 13. 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. PMID: 39903505; PMCID: PMC11793871.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    7. Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers. bioRxiv. 2025 Jan 22. Yang MG, Richter HJ, Wang S, McNally CP, Harris N, Dhillon S, Maresca M, de Wit E, Willenbring H, Maher J, Goodarzi H, Ramani V. PMID: 39896524; PMCID: PMC11785029.
      View in: PubMed   Mentions:
    8. Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2025 Jan; 28(1):216. 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. PMID: 39681663; PMCID: PMC12138952.
      View in: PubMed   Mentions:    Fields:    
    9. Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion. Curr Opin Genet Dev. 2025 Feb; 90:102298. Corin A, Nora EP, Ramani V. PMID: 39709822; PMCID: PMC12058310.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    10. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2024 Dec; 27(12):2292-2309. 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. PMID: 39627587; PMCID: PMC11999325.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    11. Cooperative Atomically Dispersed Fe-N4 and Sn-Nx Moieties for Durable and More Active Oxygen Electroreduction in Fuel Cells. J Am Chem Soc. 2024 Dec 11; 146(49):33569-33578. Xia F, Li B, An B, Zachman MJ, Xie X, Liu Y, Xu S, Saha S, Wu Q, Gao S, Abdul Razak IB, Brown DE, Ramani V, Wang R, Marks TJ, Shao Y, Cheng Y. PMID: 39620942.
      View in: PubMed   Mentions:    Fields:    
    12. Split-pool barcoding serves up an epigenomic smorgasbord. Nat Genet. 2024 Dec; 56(12):2596-2597. Ramani V. PMID: 39587359.
      View in: PubMed   Mentions:    Fields:    
    13. The single-molecule accessibility landscape of newly replicated mammalian chromatin. Cell. 2025 Jan 09; 188(1):237-252.e19. 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. PMID: 39549698; PMCID: PMC12176082.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    14. Endogenous neuronal DNA double-strand breaks are not sufficient to drive brain aging and neurodegeneration. bioRxiv. 2024 Oct 23. Cohen S, Cheradame L, Pratt KJB, Collins S, Barillas A, Carlson A, Ramani V, Legube G, Villeda SA, Mullins RD, Schwer B. PMID: 39484383; PMCID: PMC11526996.
      View in: PubMed   Mentions:
    15. The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. bioRxiv. 2024 Oct 16. 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. PMID: 38562687; PMCID: PMC10983909.
      View in: PubMed   Mentions:
    16. ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers. bioRxiv. 2024 Sep 10. Moore C, Wong E, Kaur U, Chio US, Zhou Z, Ostrowski M, Wu K, Irkliyenko I, Wang S, Ramani V, Narlikar GJ. PMID: 39314305; PMCID: PMC11418981.
      View in: PubMed   Mentions:
    17. HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA. bioRxiv. 2024 Aug 24. Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ. PMID: 39229246; PMCID: PMC11370580.
      View in: PubMed   Mentions:
    18. Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. Nat Genet. 2024 Jun; 56(6):1300-1309. Nanda AS, Wu K, Irkliyenko I, Woo B, Ostrowski MS, Clugston AS, Sayles LC, Xu L, Satpathy AT, Nguyen HG, Alejandro Sweet-Cordero E, Goodarzi H, Kasinathan S, Ramani V. PMID: 38724748; PMCID: PMC11176058.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    19. A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies. Genes Dev. 2024 04 17; 38(5-6):253-272. Freie B, Carroll PA, Varnum-Finney BJ, Ramsey EL, Ramani V, Bernstein I, Eisenman RN. PMID: 38565249; PMCID: PMC11065175.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    20. Timing of radiotherapy (RT) after radical prostatectomy (RP): long-term outcomes in the RADICALS-RT trial (NCT00541047). Ann Oncol. 2024 Jul; 35(7):656-666. Parker CC, Petersen PM, Cook AD, Clarke NW, Catton C, Cross WR, Kynaston H, Parulekar WR, Persad RA, Saad F, Bower L, Durkan GC, Logue J, Maniatis C, Noor D, Payne H, Anderson J, Bahl AK, Bashir F, Bottomley DM, Brasso K, Capaldi L, Chung C, Cooke PW, Donohue JF, Eddy B, Heath CM, Henderson A, Henry A, Jaganathan R, Jakobsen H, James ND, Joseph J, Lees K, Lester J, Lindberg H, Makar A, Morris SL, Oommen N, Ostler P, Owen L, Patel P, Pope A, Popert R, Raman R, Ramani V, Røder A, Sayers I, Simms M, Srinivasan V, Sundaram S, Tarver KL, Tran A, Wells P, Wilson J, Zarkar AM, Parmar MKB, Sydes MR, RADICALS investigators. PMID: 38583574; PMCID: PMC7617161.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    21. A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies. bioRxiv. 2023 Oct 25. Freie B, Carroll PA, Varnum-Finney BJ, Ramani V, Bernstein I, Eisenman RN. PMID: 37961183; PMCID: PMC10634767.
      View in: PubMed   Mentions: 1  
    22. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Nat Struct Mol Biol. 2023 10; 30(10):1571-1581. 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. PMID: 37696956; PMCID: PMC10584690.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    23. A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Mol Cell. 2022 06 02; 82(11):2098-2112.e4. Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ. PMID: 35597239; PMCID: PMC9351570.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    24. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. PLoS Biol. 2021 10; 19(10):e3001085. 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. PMID: 34669700; PMCID: PMC8528285.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    25. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biol. 2021 09 27; 22(1):279. 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. PMID: 34579774; PMCID: PMC8474932.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    26. Mechanism of Anti-Inflammatory Activity of TLR4-Interacting SPA4 Peptide. Immunohorizons. 2021 08 24; 5(8):659-674. Awasthi S, Kumar G, Ramani V, Awasthi V, Rodgers KK, Xie J, Beierle J, Kyere-Davies G, Singh B, Rahman N, Chowdhury AA, Chataut N. PMID: 34429343; PMCID: PMC8673433.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    27. At least two to tango: Choreographing chromatin through cooperative footprints. Mol Cell. 2021 04 15; 81(8):1591-1593. Abdulhay NJ, Ramani V. PMID: 33861946.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    28. Massively multiplex single-molecule oligonucleosome footprinting. Elife. 2020 12 02; 9. Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V. PMID: 33263279; PMCID: PMC7735760.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    29. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput Biol. 2020 09; 16(9):e1008173. Kim HJ, Yardimci GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. PMID: 32946435; PMCID: PMC7526900.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    30. Unsupervised manifold alignment for single-cell multi-omics data. ACM BCB. 2020 Sep; 2020:1-10. Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. PMID: 33954299; PMCID: PMC8095090.
      View in: PubMed   Mentions: 24  
    31. The Role of Frozen Section Examination During Inguinal Exploration in Men with Inconclusive Testicular Tumors: A Systematic Review and Meta-analysis. Eur Urol Focus. 2021 11; 7(6):1400-1402. Fankhauser CD, Roth L, Kranzbühler B, Eberli D, Bode P, Moch H, Oliveira P, Ramani V, Beyer J, Hermanns T. PMID: 32684510.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    32. Massively multiplex chemical transcriptomics at single-cell resolution. Science. 2020 01 03; 367(6473):45-51. 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. PMID: 31806696; PMCID: PMC7289078.
      View in: PubMed   Mentions: 168     Fields:    Translation:HumansCells
    33. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods. 2020 01 01; 170:61-68. Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. PMID: 31536770; PMCID: PMC6949367.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    34. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nat Commun. 2019 04 04; 10(1):1538. Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. PMID: 30948719; PMCID: PMC6449405.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansCells
    35. MRE11 as a Predictive Biomarker of Outcome After Radiation Therapy in Bladder Cancer. Int J Radiat Oncol Biol Phys. 2019 07 15; 104(4):809-818. Walker AK, Karaszi K, Valentine H, Strauss VY, Choudhury A, McGill S, Wen K, Brown MD, Ramani V, Bhattarai S, Teo MTW, Yang L, Myers KA, Deshmukh N, Denley H, Browning L, Love SB, Iyer G, Clarke NW, Hall E, Huddart R, James ND, Hoskin PJ, West CML, Kiltie AE. PMID: 30885775; PMCID: PMC6588678.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    36. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep. 2019 02 26; 26(9):2465-2476.e4. Ramani V, Qiu R, Shendure J. PMID: 30811994; PMCID: PMC6582983.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    37. Genomic Evaluation of Multiparametric Magnetic Resonance Imaging-visible and -nonvisible Lesions in Clinically Localised Prostate Cancer. Eur Urol Oncol. 2019 02; 2(1):1-11. Parry MA, Srivastava S, Ali A, Cannistraci A, Antonello J, Barros-Silva JD, Ubertini V, Ramani V, Lau M, Shanks J, Nonaka D, Oliveira P, Hambrock T, Leong HS, Dhomen N, Miller C, Brady G, Dive C, Clarke NW, Marais R, Baena E. PMID: 30929837; PMCID: PMC6472613.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    38. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science. 2018 09 28; 361(6409):1380-1385. 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. PMID: 30166440; PMCID: PMC6571013.
      View in: PubMed   Mentions: 464     Fields:    Translation:HumansAnimalsCells
    39. Primary Mutational Landscape Linked with Pre-Docetaxel Lactate Dehydrogenase Levels Predicts Docetaxel Response in Metastatic Castrate-Resistant Prostate Cancer. Eur Urol Focus. 2019 Sep; 5(5):831-841. Hiew K, Hart CA, Ali A, Elliott T, Ramani V, Sangar V, Lau M, Maddineni S, Brown M, Clarke N. PMID: 29699892.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    40. Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nat Commun. 2018 04 13; 9(1):1445. Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM. PMID: 29654302; PMCID: PMC5899087.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    41. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017 08 18; 357(6352):661-667. 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. PMID: 28818938; PMCID: PMC5894354.
      View in: PubMed   Mentions: 726     Fields:    Translation:HumansAnimalsCells
    42. Massively multiplex single-cell Hi-C. Nat Methods. 2017 03; 14(3):263-266. Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. PMID: 28135255; PMCID: PMC5330809.
      View in: PubMed   Mentions: 308     Fields:    Translation:HumansCells
    43. Mapping 3D genome architecture through in situ DNase Hi-C. Nat Protoc. 2016 11; 11(11):2104-21. Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. PMID: 27685100; PMCID: PMC5547819.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansCells
    44. Smash and DASH with Cas9. Genome Biol. 2016 Mar 05; 17:42. Ramani V, Shendure J. PMID: 26944856; PMCID: PMC4779193.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    45. Understanding Spatial Genome Organization: Methods and Insights. Genomics Proteomics Bioinformatics. 2016 Feb; 14(1):7-20. Ramani V, Shendure J, Duan Z. PMID: 26876719; PMCID: PMC4792841.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    46. Hierarchically Structured Nanomaterials for Electrochemical Energy Conversion. Angew Chem Int Ed Engl. 2016 Jan 04; 55(1):122-48. Trogadas P, Ramani V, Strasser P, Fuller TF, Coppens MO. PMID: 26549054.
      View in: PubMed   Mentions: 11     Fields:    
    47. Bipartite structure of the inactive mouse X chromosome. Genome Biol. 2015 Aug 07; 16:152. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. PMID: 26248554; PMCID: PMC4539712.
      View in: PubMed   Mentions: 149     Fields:    Translation:HumansAnimalsCells
    48. High-throughput determination of RNA structure by proximity ligation. Nat Biotechnol. 2015 Sep; 33(9):980-4. Ramani V, Qiu R, Shendure J. PMID: 26237516; PMCID: PMC4564351.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    49. Can increasing the dose of radiation by HDR brachytherapy boost following pre operative chemoradiotherapy for advanced rectal cancer improve surgical outcomes? Colorectal Dis. 2010 Aug; 12 Suppl 2:30-6. Sun Myint A, Mukhopadhyay T, Ramani VS, Perkins K, Snee AJ, Jelley F, Wong H, Lee CD. PMID: 20618365.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
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