Salomonis Lab

Salomonis Research Lab

Genomic Analysis and Tool Development

The Salomonis lab is working to understand the role of alternative splicing in human development and disease and integrate these results with epigenetic, gene expression, proteomic and single-cell sequencing data. They also develop new computational methods for analyzing data generated by emerging sequencing technologies.

The lab’s primary goal is to uncover the origins of human disease through the integration of genetic, molecular and cellular data. To achieve this goal, they build “unsupervised” techniques to extract hidden sources of molecular variation from patient and single-cell genomics datasets as well as accurately quantify the underlying measurements.

The Salomonis team also develops easy-to-use software environments that are accessible to non-computational scientists including new software and algorithms to identify complex functional relationships from whole transcriptome data. Open source computational tools they have developed to understand the impact of gene expression changes on biological pathways include GenMAPP, GO-Elite, and AltAnalyze, an easy-to-use application for the end-to-end analysis of single-cell and bulk RNA-Seq data. These applications have been used in hundreds of studies in laboratories throughout the world.

Join the Lab

The Salomonis lab is recruiting lab members for postdoctoral, graduate and undergraduate positions. Learn more about joining our team.

Publications

Selected Publications

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

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

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

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

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; 537:698-702.

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

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 Medical Genomics. 2015; 8.

Roedder, S; Sigdel, T; Salomonis, N; Hsieh, S; Dai, H; Bestard, O; Metes, D; Zeevi, A; Gritsch, A; Cheeseman, J; et al. The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study. PLoS Medicine. 2014; 11:e1001759-e1001759.

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

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

2020

Li, G; Iyer, B; Prasath, VB S; Ni, Y; Salomonis, N. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. 2020.

Petrany, MJ; Swoboda, CO; Sun, C; Chetal, K; Chen, X; Weirauch, MT; Salomonis, N; Millay, DP. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 2020; 11.

Govindarajah, V; Lee, JM; Solomon, M; Goddard, B; Nayak, R; Nattamai, K; Geiger, H; Salomonis, N; Cancelas, JA; Reynaud, D. FOXO activity adaptation safeguards the hematopoietic stem cell compartment in hyperglycemia. Blood Advances. 2020; 4:5512-5526.

DePasquale, EA K; Schnell, D; Chetal, K; Salomonis, N. Protocol for Identification and Removal of Doublets with DoubletDecon. 2020; 1:100085-100085.

Kwok, I; Becht, E; Xia, Y; Ng, M; Teh, YC; Tan, L; Evrard, M; Li, JL Y; Tran, HT N; Tan, Y; et al. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Journal of Cleaner Production. 2020; 53:303-318.e5.

Venkatasubramanian, M; Chetal, K; Schnell, DJ; Atluri, G; Salomonis, N. Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Bioinformatics. 2020; 36:3773-3780.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; et al. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.

Itskovich, SS; Gurunathan, A; Clark, J; Burwinkel, M; Wunderlich, M; Berger, MR; Kulkarni, A; Chetal, K; Venkatasubramanian, M; Salomonis, N; et al. MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nature Communications. 2020; 11.

DePasquale, E; Schnell, D; Chetal, K; Salomonisi, N. Identification and Removal of Doublets with DoubletDecon. 2020.

de Semir, D; Bezrookove, V; Nosrati, M; Scanlon, KR; Singer, E; Judkins, J; Rieken, C; Wu, C; Shen, J; Schmudermayer, C; et al. PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex. Proceedings of the National Academy of Sciences of USA. 2020; 117:9064-9073.

Petrany, M; Swoboda, C; Sun, C; Chetal, K; Chen, X; Weirauch, M; Salomonis, N; Millay, D. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. 2020.

Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; et al. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.

Holowiecki, A; Linstrum, K; Ravisankar, P; Chetal, K; Salomonis, N; Waxman, JS. Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development (Cambridge). 2020; 147:dev185652-dev185652.

Lucas, D; Salomonis, N; Grimes, HL. Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22:5-6.

2019

DePasquale, EA K; Schnell, D; Dexheimer, P; Ferchen, K; Hay, S; Chetal, K; Valiente-Alandi, I; Blaxall, BC; Grimes, HL; Salomonis, N. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Research. 2019; 47:e138-e138.

DePasquale, EA K; Schnell, DJ; Van Camp, P; Valiente-Alandi, I; Blaxall, BC; Grimes, HL; Singh, H; Salomonis, N. DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell Reports. 2019; 29:1718-1727.e8.

Zusman, E; Sidorov, M; Ayala, A; Chang, J; Singer, E; Chen, M; Desprez, P; McAllister, D; Salomonis, N; Chetal, K; et al. Tissues harvested using an automated surgical approach confirm molecular heterogeneity of glioblastoma and enhance specimen’s translational research value. Frontiers in Oncology. 2019; 9.

Adelman, ER; Huang, HT; Roisman, A; Olsson, A; Colaprico, A; Qin, T; Lindsley, RC; Bejar, R; Salomonis, N; Grimes, HL; et al. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discovery. 2019; 9:1080-1101.

Hulin, A; Hortells, L; Gomez-Stallons, MV; O'Donnell, A; Chetal, K; Adam, M; Lancellotti, P; Oury, C; Potter, SS; Salomonis, N; et al. Maturation of heart valve cell populations during postnatal remodeling. Development (Cambridge). 2019; 146:dev173047-dev173047.

Smith, MA; Choudhary, GS; Pellagatti, A; Choi, K; Bolanos, LC; Bhagat, TD; Gordon-Mitchell, S; Von Ahrens, D; Pradhan, K; Steeples, V; et al. U2AF1 mutations induce oncogenic IRAK4 isoforms and activate innate immune pathways in myeloid malignancies. Nature Cell Biology. 2019; 21:640-650.

Venkatasubramanian, M; Chetal, K; Atluri, G; Salomonis, N. Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. 2019.

Taylor, DM; Aronow, BJ; Tan, K; Bernt, K; Salomonis, N; Greene, CS; Frolova, A; Henrickson, SE; Wells, A; Pei, L; et al. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. 2019; 49:10-29.

Fletcher, JS; Wu, J; Jessen, WJ; Pundavela, J; Miller, JA; Dombi, E; Kim, M; Rizvi, TA; Chetal, K; Salomonis, N; et al. Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice. JCI insight. 2019; 4.

Yang, J; Kalim, KW; Li, Y; Duan, X; Nguyen, P; Hershey, GK K; Kroner, J; Ruff, B; Zhang, L; Salomonis, N; et al. Rational targeting Cdc42 restrains Th2 cell differentiation and prevents allergic airway inflammation. Clinical and Experimental Allergy. 2019; 49:92-107.

Salomonis, N. Investigating cell fate decisions with ICGS analysis of single cells. Methods in molecular biology (Clifton, N.J.). 2019; 1975:251-275.

2018

Hay, SB; Ferchen, K; Chetal, K; Grimes, HL; Salomonis, N. The Human Cell Atlas bone marrow single-cell interactive web portal. Experimental Hematology. 2018; 68:51-61.

Modur, V; Singh, N; Mohanty, V; Chung, E; Muhammad, B; Choi, K; Chen, X; Chetal, K; Ratner, N; Salomonis, N; et al. Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nature Communications. 2018; 9.

Churko, JM; Garg, P; Treutlein, B; Venkatasubramanian, M; Wu, H; Lee, J; Wessells, QN; Chen, S; Chen, W; Chetal, K; et al. Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. Nature Communications. 2018; 9.

Muench, DE; Ferchen, K; Velu, CS; Pradhan, K; Chetal, K; Chen, X; Weirauch, MT; Colmenares, C; Verma, A; Salomonis, N; et al. SKI controls MDS-associated chronic TGF-beta signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132:e24-e34.

Lu, Y; Xavier-Ferrucio, J; Wang, L; Zhang, P; Grimes, HL; Venkatasubramanian, M; Chetal, K; Aronow, B; Salomonis, N; Krause, DS. The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Reports. 2018; 25:2083-2093.e4.

Hayashi, Y; Zhang, Y; Yokota, A; Yan, X; Liu, J; Choi, K; Li, B; Sashida, G; Peng, Y; Xu, Z; et al. Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. Cancer Discovery. 2018; 8:1438-1457.

DePasquale, EA K; Dexheimer, P; Schnell, D; Ferchen, K; Hay, S; Valiente-Alandí, Í; Blaxall, B; Grimes, L; Salomonis, N. cellHarmony: Cell-level matching and holistic comparison of single-cell transcriptomes. 2018.

Meyer, SE; Muench, DE; Rogers, AM; Newkold, TJ; Orr, E; O'Brien, E; Perentesis, JP; Doench, JG; Lal, A; Morris, PJ; et al. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. The Journal of Experimental Medicine. 2018; 215:2115-2136.

DePasquale, EA K; Schnell, D; Valiente-Alandí, Í; Blaxall, B; Grimes, L; Singh, H; Salomonis, N. DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets. 2018.

de Semir, D; Bezrookove, V; Nosrati, M; Dar, AA; Wu, C; Shen, J; Rieken, C; Venkatasubramanian, M; III, MJ R; Desprez, P; et al. PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer. Proceedings of the National Academy of Sciences of USA. 2018; 115:E5766-E5775.

Matsu-ura, T; Dovzhenok, AA; Coradetti, ST; Subramanian, KR; Meyer, DR; Kwon, JJ; Kim, C; Salomonis, N; Glass, NL; Lim, S; et al. Synthetic Gene Network with Positive Feedback Loop Amplifies Cellulase Gene Expression in Neurospora crassa. ACS Synthetic Biology. 2018; 7:1395-1405.

Presicce, P; Park, C; Senthamaraikannan, P; Bhattacharyya, S; Jackson, C; Kong, F; Rueda, CM; DeFranco, E; Miller, LA; Hildeman, DA; et al. mu-1 signaling mediates intrauterine inflammation and chorio-decidua neutrophil recruitment and activation. JCI insight. 2018; 3.

Lee, J; Govindarajah, V; Goddard, B; Hinge, A; Muench, DE; Filippi, M; Aronow, B; Cancelas, JA; Salomonis, N; Grimes, HL; et al. Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression. The Journal of Experimental Medicine. 2018; 215:627-644.

Fang, J; Muto, T; Kleppe, M; Bolanos, LC; Hueneman, KM; Walker, CS; Sampson, L; Wellendorf, AM; Chetal, K; Choi, K; et al. TRAF6 Mediates Basal Activation of NF-kappa B Necessary for Hematopoietic Stem Cell Homeostasis. Cell Reports. 2018; 22:1250-1262.

Salomonis, N. Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers. Methods in molecular biology (Clifton, N.J.). 2018; 1788:89-111.

2017

Daily, K; Sui, SJ H; Schriml, LM; Dexheimer, PJ; Salomonis, N; Schroll, R; Bush, S; Keddache, M; Mayhew, C; Lotia, S; et al. Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. Scientific Data. 2017; 4.

Yanez, A; Coetzee, SG; Olsson, A; Muench, DE; Berman, BP; Hazelett, DJ; Salomonis, N; Grimes, HL; Goodridge, HS. Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Immunity. 2017; 47:890-902.e4.

McLendon, PM; Davis, G; Gulick, J; Singh, SR; Xu, N; Salomonis, N; Molkentin, JD; Robbins, J. An Unbiased High-Throughput Screen to Identify Novel Effectors That Impact on Cardiomyocyte Aggregate Levels. Circulation Research. 2017; 121:604-616.

Johansson, E; Myers, JM B; Martin, LJ; He, H; Pilipenko, V; Mersha, T; Weirauch, M; Salomonis, N; Ryan, P; LeMasters, GK; et al. KIF3A genetic variation is associated with pediatric asthma in the presence of eczema independent of allergic rhinitis. Journal of Allergy and Clinical Immunology. 2017; 140:595-598.e5.

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

Fang, J; Bolanos, LC; Choi, K; Liu, X; Christie, S; Akunuru, S; Kumar, R; Wang, D; Chen, X; Greis, KD; et al. Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nature Immunology. 2017; 18:236-245.

2016

Sigdel, TK; Bestard, O; Salomonis, N; Hsieh, S; 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; 100:2062-2070.