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

Dr. Salomonis and his group are on the cutting edge of developing new software and algorithms to identify complex functional relationships from whole transcriptome data. They have developed several open source analysis tools including AltAnalyze, LineageProfiler, GO-Elite, and NetPerspective. The advent of single-cell genomic profiles has created many new opportunities for understanding stochastic decisions mediating stem cell differentiation to distinct cell fates and the regulation of distinct gene expression and splicing programs. They are capitalizing on this new technology to explore these decision-making processes at a resolution never previously possible.

Last year, they worked collaboratively with a dozen investigative research teams within Cincinnati Children's to develop new methods for evaluating whole genome transcriptome datasets. These methods include: 1) the detection of distinct gene and splicing populations from bulk and single cell genome profiles, 2) predicting implicated cell types present in complex fetal maternal biological samples and 3) identifying new disease regulatory networks related to pediatric and adult cancers, cardiovascular disease and spinal cord injury.

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

Roedder S, Salomonis N. Loaded, locked, drawn: kSORT validated for patient samples. Nat Rev Nephrol. 2016 Nov 14.  

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.

Sigdel TK, Bestard O, Salomonis N, Hsieh SC, Torras J, Naesens M, Tran TQ, Roedder S, Sarwal MM. Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy. Transplantation. 2016 Oct;100(10):2062-70.

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.

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.