Nathan Salomonis, PhD

Academic Affiliation

Assistant Professor

UC Department of Biomedical Informatics

Phone 650-576-1646


Bioinformatics; genomics; cancer genomics; single-cell RNA-Seq analysis; alternative splicing; pathway analysis; pathway visualization; pathway curation; SIDS; stem cell biology; cardiac specification; renal graft dysfunction

Our understanding of human health and ability to treat disease is being radically transformed by new technologies to read genomes and transcriptomes at an unprecedented resolution. To capitalize on these technologies it is essential that we develop holistic models of gene biology that will best inform clinicians of disease risk. Dr. Salomonis uses computational approaches to examine the interplay between diverse modes of gene regulation, including transcription, alternative splicing and microRNA regulation that underlie important cellular interaction networks.

By applying such techniques to human disease and cellular dysfunction paradigms, we strive to shed new light on existing problems. To achieve these goals, we develop community available tools, such AltAnalyze, GenMAPP, ICGS, LineageProfiler and GO-Elite, to analyze and interpret genome-level data that is accessible by both untrained and skilled computational biologists alike. To identify global trends from complex data sets, we take advantage of pathway-driven approaches, such as WikiPathways models and aggregate large amounts of publically available data from a broad range of developmental and disease datasets available in the public domain. With these tools in hand, we strive to validate predicted functional effects in the laboratory with a diverse team of collaborative scientists.

BS: University of California, Los Angeles, CA, 1998.

PhD: University of California, San Francisco, CA, 2008.

Postdoctoral Fellow: Gladstone Institutes, San Francisco, CA, 2012.

View Pub Med Publications

Olsson A, Venkatasubramanian M, Chaudhri VK, Aronow BJ, Salomonis N, Singh H, Grimes HL. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016.

Salomonis N, Dexheimer PJ, Omberg L, Schroll R, Bush S, Huo J, Schriml L, Ho Sui S, Keddache M, Mayhew C, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, Zambidis E, Margolin A, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Aronow BJ, Lutzko C. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Stem Cell Reports. 2016 Jul 12;7(1):110-25.

Meyer SE, Qin T, Muench DE, Masuda K, Venkatasubramanian M, Orr E, Suarez L, Gore SD, Delwel R, Paietta E, Tallman MS, Fernandez H, Melnick A, Le Beau MM, Kogan S, Salomonis N, Figueroa ME, Grimes HL. DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. Cancer Discov. 2016 May;6(5):501-15.

Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y. Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. BMC Med Genomics. 2015 Oct 22;8(1):67.

Salomonis N, Roedder S, Sigdel T, Hsieh S, Dai H, Bestard O, Metes D, Zeevi A, Gritsch A, Cheeseman J, Macedo C, Peddy R, Medeiros M, Vincenti F, Asher N, Salvatierra O, Shapiro R, Kirk A, Reed EF, Sarwal MM. The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Med. 2014 Nov 11;11(11):e1001759.

Salomonis N. Systems-level perspective of sudden infant death syndrome. Pediatr Res. 2014 Sep;76(3):220-9.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012 Aug 15;28(16):2209-10.

Salomonis N, Emig D*, Baumbach J, Lengauer T, Conklin BR, Albrecht M. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62.

Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9.

Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:217.

Bioinformatics Core for the Progenitor Cell Biology Consortium. Co-Principle Investigator. National Institutes of Health, Heart, Lung and Blood Institute. May 2013-April 2016. U01HL099997.

Identifying Therapeutic Targets for RNA Splicing-Related Cardiomyopathy. Co-Investigator. National Institutes of Health, Heart, Lung and Blood Institute. Dec 2015-Nov 2019. R01 HL130533-01

Mechanisms of Granulocyte Homeostasis. Co-Investigator. National Institutes of Health, Heart, Lung and Blood Institute. July 2015-June 2020. R01 HL122661

A Rapid Spontaneous Murine Model of CN-AML. Co-Investigator. National Cancer Institute. July 2016-June 2019. R01 CA196658.