Vasilis Ntranos, PhD
Assistant Professor
Diabetes Center
School of Medicine

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.

• Genome-wide prediction of disease variant effects with a deep protein language model.
  Nature genetics 2023 Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V
• Alpha cell dysfunction in type 1 diabetes is independent of a senescence program.
  Frontiers in endocrinology 2022 Brawerman G, Ntranos V, Thompson PJ
• Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium.
  Science immunology 2021 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
• A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.
  Nature 2021 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, …
• Extrathymic Aire-expressing cells support maternal-fetal tolerance.
  Science immunology 2021 Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC
• Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.
  Nature communications 2021 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
• Determining sequencing depth in a single-cell RNA-seq experiment.
  Nature communications 2020 Zhang MJ, Ntranos V, Tse D
• The barcode, UMI, set format and BUStools.
  Bioinformatics (Oxford, England) 2019 Melsted P, Ntranos V, Pachter L
• Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis.
  Brain : a journal of neurology 2019 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
• Targeted Elimination of Senescent Beta Cells Prevents Type 1 Diabetes.
  Cell metabolism 2019 Thompson PJ, Shah A, Ntranos V, Van Gool F, Atkinson M, Bhushan A
• Deterministic column subset selection for single-cell RNA-Seq.
  PloS one 2019 McCurdy SR, Ntranos V, Pachter L
• A discriminative learning approach to differential expression analysis for single-cell RNA-seq.
  Nature methods 2019 Ntranos V, Yi L, Melsted P, Pachter L
• Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts.
  Genome biology 2016 Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN