Nathan Salomonis, PhD

Academic Affiliations

Assistant Professor, UC Department of Pediatrics

Phone 650-576-1646


Bioinformatics; genomics; alternative splicing; microRNA biology; 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 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.

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

View Pub Med Publications

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

Soreq L, Salomonis N, Bronstein M, Greenberg DS, Israel Z, Bergman H, Soreq H. Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. Front Mol Neurosci. 2013 May 13;6:10.

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, Conklin BR. Stem cell pluripotency: alternative modes of transcription regulation. Cell Cycle. 2010 Aug 15;9(16):3133-4.

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.

Nakamura K, Salomonis N, Tomoda K, Yamanaka S, Conklin BR. G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. PLoS One. 2009 Nov 10;4(11):e7780.

Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol. 2009 Nov;5(11):e1000553.

Stein T, Salomonis N, Nuyten DS, van de Vijver MJ, Gusterson BA. Stein T, Salomonis N, Nuyten DS, van de Vijver MJ, Gusterson BA. A mouse mammary gland involution mRNA signature identifies biological pathways potentially associated with breast cancer metastasis. J Mammary Gland Biol Neoplasia. 2009 Jun;14(2):99-116.

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.