Vasilis Ntranos, PhD

Title(s)Assistant Professor, Diabetes Center
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSW, #1109
San Francisco CA 94143
ORCID ORCID Icon0000-0002-2477-0670 Additional info
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    Collapse Biography 
    Collapse education and training
    Caltech, Pasadena, CAPostdoc2019Biology & Biological Engineering
    University of California, Berkeley, CAPostdoc2018EECS
    Stanford University, Palo Alto, CAPostdoc2018Electrical Engineering
    University of Southern California, Los Angeles, CAPh.D2015Electrical Engineering
    Technical University of Crete, GreeceDiploma2009ECE

    Collapse Overview 
    Collapse overview
    Vasilis Ntranos obtained his PhD in Electrical Engineering from USC in 2015, working on network information theory problems and their applications in data storage and wireless communications. After his graduate studies, Vasilis moved his focus to computational biology and machine learning, completing his postdoctoral training in EECS and Biological Engineering, working with Lior Pachter and David Tse at UC Berkeley, Stanford, and Caltech.

    Vasilis joined UCSF in November 2019, where he is currently an Assistant Professor in the Department of Epidemiology & Biostatistics and the Diabetes Center. He is a member of the BMS, and BMI Graduate Programs and his lab is affiliated with the Dept. of Bioengineering & Therapeutic Sciences, the Bakar Computational Health Sciences Institute, and HIVE (Health Innovation via Engineering). Vasilis’ main research interests are in computational methods development at the intersection of information theory, genomics, and machine learning, with a primary focus on single cell biology and alternative splicing.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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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. RORγt eTACs mediate oral tolerance and Treg induction. J Exp Med. 2025 Aug 04; 222(8). Sun IH, Qualls AE, Yin HS, Wang J, Arvedson MP, Germino J, Horner NK, Zhong S, Du J, Valdearcos M, Ntranos V, Locksley RM, Ricardo-Gonzalez RR, Gardner JM. PMID: 40298935; PMCID: PMC12039581.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. Phenotypic pleiotropy of missense variants in human B cell-confinement receptor P2RY8. bioRxiv. 2025 Mar 06. LaFlam TN, Billesbølle CB, Dinh T, Wolfreys FD, Lu E, Matteson T, An J, Xu Y, Singhal A, Brandes N, Ntranos V, Manglik A, Cyster JG, Ye CJ. PMID: 40093123; PMCID: PMC11908195.
      View in: PubMed   Mentions:
    3. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell. 2024 Oct 31; 187(22):6393-6410.e16. Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. PMID: 39454576; PMCID: PMC11556465.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    4. nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer. bioRxiv. 2024 Sep 25. Hendley AM, Ashe S, Urano A, Ng M, Phu TA, Peng XL, Luan C, Finger AM, Jang GH, Kerper NR, Berrios DI, Jin D, Lee J, Riahi IR, Gbenedio OM, Chung C, Roose JP, Yeh JJ, Gallinger S, Biankin AV, O'Kane GM, Ntranos V, Chang DK, Dawson DW, Kim GE, Weaver VM, Raffai RL, Hebrok M. PMID: 39399775; PMCID: PMC11468832.
      View in: PubMed   Mentions:
    5. Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions. medRxiv. 2024 May 01. Wei A, Border R, Fu B, Cullina S, Brandes N, Jang SK, Sankararaman S, Kenny E, Udler MS, Ntranos V, Zaitlen N, Arboleda V. PMID: 37745486; PMCID: PMC10516069.
      View in: PubMed   Mentions:
    6. Sox9 regulates alternative splicing and pancreatic beta cell function. Nat Commun. 2024 Jan 18; 15(1):588. Puri S, Maachi H, Nair G, Russ HA, Chen R, Pulimeno P, Cutts Z, Ntranos V, Hebrok M. PMID: 38238288; PMCID: PMC10796970.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    7. Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol. 2023 10 27; 8(88):eabq3109. Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. PMID: 37889983; PMCID: PMC11433069.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    8. Genome-wide prediction of disease variant effects with a deep protein language model. Nat Genet. 2023 09; 55(9):1512-1522. Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V. PMID: 37563329; PMCID: PMC10484790.
      View in: PubMed   Mentions: 101     Fields:    Translation:Humans
    9. Alpha cell dysfunction in type 1 diabetes is independent of a senescence program. Front Endocrinol (Lausanne). 2022; 13:932516. Brawerman G, Ntranos V, Thompson PJ. PMID: 36277717; PMCID: PMC9586489.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    10. Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Sci Immunol. 2021 Nov 12; 6(65):eabl5053. Wang J, Lareau CA, Bautista JL, Gupta AR, Sandor K, Germino J, Yin Y, Arvedson MP, Reeder GC, Cramer NT, Xie F, Ntranos V, Satpathy AT, Anderson MS, Gardner JM. PMID: 34767455; PMCID: PMC8855935.
      View in: PubMed   Mentions: 30     Fields:    Translation:Animals
    11. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 2021 10; 598(7879):103-110. Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. PMID: 34616066; PMCID: PMC8494649.
      View in: PubMed   Mentions: 139     Fields:    Translation:AnimalsCells
    12. Extrathymic Aire-expressing cells support maternal-fetal tolerance. Sci Immunol. 2021 07 16; 6(61). Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC. PMID: 34272228; PMCID: PMC9363019.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    13. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nat Commun. 2021 02 17; 12(1):1096. Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. PMID: 33597545; PMCID: PMC7889611.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansAnimalsCells
    14. Determining sequencing depth in a single-cell RNA-seq experiment. Nat Commun. 2020 02 07; 11(1):774. Zhang MJ, Ntranos V, Tse D. PMID: 32034137; PMCID: PMC7005864.
      View in: PubMed   Mentions: 53     Fields:    
    15. The barcode, UMI, set format and BUStools. Bioinformatics. 2019 11 01; 35(21):4472-4473. Melsted P, Ntranos V, Pachter L. PMID: 31073610.
      View in: PubMed   Mentions: 63     Fields:    
    16. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 2019 03 01; 142(3):647-661. Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, Zhu Y, Brandstadter R, Watson CT, Sharp AJ, Katz Sand I, Casaccia P. PMID: 30698680; PMCID: PMC6821213.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    17. Targeted Elimination of Senescent Beta Cells Prevents Type 1 Diabetes. Cell Metab. 2019 05 07; 29(5):1045-1060.e10. Thompson PJ, Shah A, Ntranos V, Van Gool F, Atkinson M, Bhushan A. PMID: 30799288.
      View in: PubMed   Mentions: 151     Fields:    Translation:HumansAnimalsCells
    18. Deterministic column subset selection for single-cell RNA-Seq. PLoS One. 2019; 14(1):e0210571. McCurdy SR, Ntranos V, Pachter L. PMID: 30682053; PMCID: PMC6347249.
      View in: PubMed   Mentions: 1     Fields:    
    19. A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nat Methods. 2019 02; 16(2):163-166. Ntranos V, Yi L, Melsted P, Pachter L. PMID: 30664774.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansCells
    20. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biol. 2016 05 26; 17(1):112. Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN. PMID: 27230763; PMCID: PMC4881296.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansAnimalsCells
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