A photo of Nathan Salomonis.

Associate Professor, UC Department of Pediatrics

650-576-1646

Biography & Affiliation

Biography

I am a trained computational and experimental biologist who develops approaches to examine the interplay between diverse modes of gene regulation, including transcription, alternative splicing, genetics and epigenetics that underlie disease interaction networks.

I have co-authored more than 80 publications related to computational genomics and have more than 20 years’ experience directing the development of highly-used software applications for computational experts and biologists alike. My research group actively applies these and many other computational genomics techniques to diverse biological problems, including understanding the role of alternative splicing and neoantigen creation in cancer while defining lineage fate choices in differentiation and defining novel molecular mechanisms in human cardiovascular diseases.

We continue to develop new approaches for the integrative analysis of diverse molecular omics technologies including those for single-cell transcriptomics/epigenomics/ proteomics. We hope to ultimately apply insights from these computational approaches to develop new therapeutic strategies for difficult to treat pediatric cancers.

I have been fortunate to receive support from various internal awards, including:

  • Cincinnati Children’s Hospital Medical Center Endowed Scholar recognition (2019)
  • Academic and Research Committee (ARC) Award (2018)
  • Trustee Award and Procter Scholar (TAPS) Program Award (2017)

Our work has been published in numerous high impact journals, including Nature, Nature Genetics, Cancer Discovery, Nature Methods, Cell Stem Cell and Nucleic Acids Research.

Research Interests

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

Academic Affiliation

Associate Professor, UC Department of Pediatrics

Research Divisions

Biomedical Informatics, Fibrosis



Education

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

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

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

Publications

Selected Publication

Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; et al. Nature Genetics. 2018; 50:699-707.

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. Magella, B; Adam, M; Potter, AS; Venkatasubramanian, M; Chetal, K; Hay, SB; Salomonis, N; Potter, SS. Developmental Biology. 2018; 434:36-47.

Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. Churko, JM; Lee, J; Ameen, M; Gu, M; Venkatasubramanian, M; Diecke, S; Sallam, K; Im, H; Wang, G; Gold, JD; et al. Nature Biomedical Engineering. 2017; 1:826-837.

Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics. Rindler, TN; Hinton, RB; Salomonis, N; Ware, SM. Scientific Reports. 2017; 7.

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Olsson, A; Venkatasubramanian, M; Chaudhri, VK; Aronow, BJ; Salomonis, N; Singh, H; Grimes, HL. Nature: New biology. 2016; 537:698-702.

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Salomonis, N; Dexheimer, PJ; Omberg, L; Schroll, R; Bush, S; Huo, J; Schriml, L; Sui, SH; Keddache, M; Mayhew, C; et al. Stem Cell Reports. 2016; 7:110-125.

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

The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. Roedder, S; Sigdel, T; Salomonis, N; Hsieh, S; Dai, H; Bestard, O; Metes, D; Zeevi, A; Gritsch, A; Cheeseman, J; et al. PLoS Medicine. 2014; 11.

Systems-level perspective of sudden infant death syndrome. Salomonis, N. Pediatric Research. 2014; 76:220-229.

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Salomonis, N; Schlieve, CR; Pereira, L; Wahlquist, C; Colas, A; Zambon, AC; Vranizan, K; Spindler, MJ; Pico, AR; Cline, MS; et al. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107:10514-10519.