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Vasilis Ntranos, PhD

Asst Professor In Residence
Diabetes Center
[email protected]

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.

Publications: 

Method of moments framework for differential expression analysis of single-cell RNA sequencing data.

Cell

Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ

nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer.

bioRxiv : the preprint server for biology

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

The genetic underpinnings of variable penetrance and expressivity of pathogenic mutations in cardiometabolic traits.

medRxiv : the preprint server for health sciences

Wei A, Border R, Fu B, Cullina S, Brandes N, Sankararaman S, Kenny EE, Udler MS, Ntranos V, Zaitlen N, Arboleda VA

Sox9 regulates alternative splicing and pancreatic beta cell function.

Nature communications

Puri S, Maachi H, Nair G, Russ HA, Chen R, Pulimeno P, Cutts Z, Ntranos V, Hebrok M

Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance.

Science immunology

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

Genome-wide prediction of disease variant effects with a deep protein language model.

Nature genetics

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

Brawerman G, Ntranos V, Thompson PJ

Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium.

Science immunology

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

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

Extrathymic Aire-expressing cells support maternal-fetal tolerance.

Science immunology

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

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

Zhang MJ, Ntranos V, Tse D

The barcode, UMI, set format and BUStools.

Bioinformatics (Oxford, England)

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

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

Thompson PJ, Shah A, Ntranos V, Van Gool F, Atkinson M, Bhushan A

Deterministic column subset selection for single-cell RNA-Seq.

PloS one

McCurdy SR, Ntranos V, Pachter L

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts.

Genome biology

Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN

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