Biomedical Informatics
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

Li, G; Bhattacharjee, A; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug target discovery and prioritization. 2023.

Menéndez-Gutiérrez, MP; Porcuna, J; Nayak, R; Paredes, A; Niu, H; Núñez, V; Paranjpe, A; Gómez, MJ; Bhattacharjee, A; Schnell, DJ; et al. Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141:592-608.

Romano, L; Seu, KG; Papoin, J; Muench, DE; Konstantinidis, D; Olsson, A; Schlum, K; Chetal, K; Chasis, JA; Mohandas, N; et al. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140:1621-1634.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VB S; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23.

Dar, AA; Bezrookove, V; Nosrati, M; Ice, R; Patino, JM; Vaquero, EM; Parrett, B; Leong, SP; Kim, KB; Debs, RJ; et al. Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma. Proceedings of the National Academy of Sciences of the United States of America. 2022; 119.

Sun, X; Perl, AK; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; et al. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57:112-145.e2.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; et al. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. 2021.

Fenix, AM; Miyaoka, Y; Bertero, A; Blue, SM; Spindler, MJ; Tan, KK B; Perez-Bermejo, JA; Chan, AH; Mayerl, SJ; Nguyen, TD; et al. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12.

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. Briefings in Bioinformatics. 2021; 22.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; et al. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.

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.

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

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.

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. Computer Applications in the Biosciences. 2020; 36:3773-3780.

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.

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.

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

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.

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.

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.

Salomonis, N. Investigating Cell Fate Decisions with ICGS Analysis of Single Cells. Methods in Molecular Biology. 2019; 1975:251-275.

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.

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.

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.

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-β 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.

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.

Adelman, E; Olsson, A; Qin, T; Lindsley, RC; Bejar, R; Salomonis, N; Grimes, L; Figueroa, ME. Integrative Epigenetic and Single-Cell RNA-Seq Profiling of Human Hematopoietic Stem Cells Reveals Epigenetic Reprogramming of Enhancer and Regulatory Elements during Normal Aging. Blood. 2017; 130:770-770.

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.

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.

Meyer, SE; Qin, T; Muench, DE; Masuda, K; Venkatasubramanian, M; Orr, E; Suarez, L; Gore, SD; Delwel, R; Paietta, E; et al. DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. Cancer Discovery. 2016; 6:501-515.

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.

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

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. Computer Applications in the Biosciences. 2012; 28:2209-2210.

Emig, D; Salomonis, N; Baumbach, J; Lengauer, T; Conklin, BR; Albrecht, M. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research. 2010; 38:W755-W762.

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 the United States of America. 2010; 107:10514-10519.

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; 4.

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 Computational Biology. 2009; 5.

Krishnan, K; Salomonis, N; Guo, S. Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. PLoS ONE. 2008; 3.

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; 8.

Zambon, AC; McDearmon, EL; Salomonis, N; Vranizan, KM; Johansen, KL; Adey, D; Takahashi, JS; Schambelan, M; Conklin, BR. Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biology. 2003; 4.

Doniger, SW; Salomonis, N; Dahlquist, KD; Vranizan, K; Lawlor, SC; Conklin, BR. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biology. 2003; 4.

Dahlquist, KD; Salomonis, N; Vranizan, K; Lawlor, SC; Conklin, BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics. 2002; 31:19-20.

Redfern, CH; Degtyarev, MY; Kwa, AT; Salomonis, N; Cotte, N; Nanevicz, T; Fidelman, N; Desai, K; Vranizan, K; Lee, EK; et al. Conditional expression of a Gi-coupled receptor causes ventricular conduction delay and a lethal cardiomyopathy. Proceedings of the National Academy of Sciences of the United States of America. 2000; 97:4826-4831.

Li, G; Bhattacharjee, A; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug target discovery and prioritization. 2023.

Menéndez-Gutiérrez, MP; Porcuna, J; Nayak, R; Paredes, A; Niu, H; Núñez, V; Paranjpe, A; Gómez, MJ; Bhattacharjee, A; Schnell, DJ; et al. Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141:592-608.

Rosselot, AE; Park, M; Kim, M; Matsu-Ura, T; Wu, G; Flores, DE; Subramanian, KR; Lee, S; Sundaram, N; Broda, TR; et al. Ontogeny and function of the circadian clock in intestinal organoids. EMBO Journal. 2022; 41.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; et al. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2022.

Voulgaridou, A; Elgammal, Y; Husami, A; Emberesh, S; Seu, K; Ramamoorthy, M; Trump, L; Barasa, N; Nelson, AS; Lorsbach, RB; et al. De Novo Germline DHX38 Variant Associated with Alternative Splicing of Multiple Transcripts in Iron-Related Pathways in a Patient with Atypical Congenital Dyserythropoietic Anemia with Ring Sideroblasts. Blood. 2022; 140:1234-1235.

Solomon, M; Song, BA; Govindarajah, V; Good, S; Bartram, J; Cancelas, J; Filippi, M; Salomonis, N; Grimes, HL; Reynaud, D. Hematopoietic Flt3+ Multipotent Progenitors Are Organized in Discrete Functionally and Hierarchically Distinct Populations. Blood. 2022; 140:1981-1982.

Romano, L; Seu, KG; Papoin, J; Muench, DE; Konstantinidis, D; Olsson, A; Schlum, K; Chetal, K; Chasis, JA; Mohandas, N; et al. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140:1621-1634.

Schmidt, AF; Schnell, DJ; Eaton, KP; Chetal, K; Kannan, PS; Miller, LA; Chougnet, CA; Swarr, DT; Jobe, AH; Salomonis, N; et al. Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques. JCI insight. 2022; 7.

Kershner, LJ; Choi, K; Wu, J; Zhang, X; Perrino, M; Salomonis, N; Shern, JF; Ratner, N. Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment. JCI insight. 2022; 7.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VB S; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23.

Dar, AA; Bezrookove, V; Nosrati, M; Ice, R; Patino, JM; Vaquero, EM; Parrett, B; Leong, SP; Kim, KB; Debs, RJ; et al. Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma. Proceedings of the National Academy of Sciences of the United States of America. 2022; 119.

Stevens, J; Steinmeyer, S; Bonfield, M; Peterson, L; Wang, T; Gray, J; Lewkowich, I; Xu, Y; Du, Y; Guo, M; et al. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science Translational Medicine. 2022; 14.

Jin, K; Schnell, D; Li, G; Salomonis, N; Surya Prasath, VB; Szczesniak, R; Aronow, B. CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data. 2022.

Gracia-Maldonado, G; Clark, J; Burwinkel, M; Greenslade, B; Wunderlich, M; Salomonis, N; Leone, D; Gatti, E; Pierre, P; Kumar, AR; et al. LAMP-5 is an essential inflammatory-signaling regulator and novel immunotherapy target for mixed lineage leukemia-rearranged acute leukemia. Haematologica. 2022; 107:803-815.

Jackson, CM; Demmert, M; Mukherjee, S; Isaacs, T; Thompson, R; Chastain, C; Gray, J; Senthamaraikannan, P; Presicce, P; Chetal, K; et al. A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. Mucosal Immunology. 2022; 15:730-744.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; et al. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14.

Avellino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, E; Bindels, E; Grimes, L; et al. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2022; 6:1406-1419.

Sun, X; Perl, AK; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; et al. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57:112-145.e2.

Díaz, PC; Chou, C; Mistry, J; Khan, MD; Salomonis, N; Grimes, HL; Trowbridge, J. 3055 – METALLOTHIONEIN 1 (MT1) AS A TARGETABLE DEPENDENCY IN ACUTE MYELOID LEUKEMIA. Experimental Hematology. 2022; 111.

Leighton Grimes, H; Ferchen, K; Salomonis, N; Song, B; Zhang, X. 2007 – IDENTIFICATION AND ISOLATION OF HEMATOPOIETIC STEM CELLS AND PROGENITORS WITH DISCRETE DEVELOPMENTAL GENE EXPRESSION PROGRAMS. Experimental Hematology. 2022; 111.

Song, B; Ferchen, K; Chou, C; Zhang, X; Steele, H; Herro, R; Salomonis, N; Grimes, HL. 3194 – LIVE BACTERIAL LIGANDS PROGRAM CORE HEMATOPOIETIC GENE EXPRESSION. Experimental Hematology. 2022; 111.

Surumbayeva, A; Kotliar, M; Gabitova-Cornell, L; Kartashov, A; Peri, S; Salomonis, N; Barski, A; Astsaturov, I. Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. STAR Protocols. 2021; 2.

Bono, C; Guerrero, P; Jordán-Pla, A; Erades, A; Salomonis, N; Grimes, HL; Gil, ML; Yáñez, A. GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Frontiers in Immunology. 2021; 12.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; et al. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. 2021.

Jarmas, AE; Brunskill, EW; Chaturvedi, P; Salomonis, N; Kopan, R. Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. Nature Communications. 2021; 12.

Fenix, AM; Miyaoka, Y; Bertero, A; Blue, SM; Spindler, MJ; Tan, KK B; Perez-Bermejo, JA; Chan, AH; Mayerl, SJ; Nguyen, TD; et al. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12.

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. Briefings in Bioinformatics. 2021; 22.

Li, G; Song, B; Singh, H; Prasath, S; Grimes, L; Salomonis, N. scTriangulate, a game-theory based framework for optimal solutions of uni- and multimodal single-cell data. 2021.

Gao, DK; Salomonis, N; Henderlight, M; Woods, C; Thakkar, K; Grom, AA; Thornton, S; Jordan, MB; Wikenheiser-Brokamp, KA; Schulert, GS. IFN-γ is essential for alveolar macrophage-driven pulmonary inflammation in macrophage activation syndrome. JCI insight. 2021; 6.

Kim, KB; Soroceanu, L; de Semir, D; Millis, SZ; Ross, J; Vosoughi, E; Dar, AA; Nosrati, M; Desprez, PY; Ice, R; et al. Prevalence of Homologous Recombination Pathway Gene Mutations in Melanoma: Rationale for a New Targeted Therapeutic Approach. Journal of Investigative Dermatology. 2021; 141:2028-2036.e2.

Chen, D; Wang, Y; Manakkat Vijay, GK; Fu, S; Nash, CW; Xu, D; He, D; Salomonis, N; Singh, H; Xu, H. Coupled analysis of transcriptome and BCR mutations reveals role of OXPHOS in affinity maturation. Nature Immunology. 2021; 22:904-913.

Moreno-Fernandez, ME; Giles, DA; Oates, JR; Chan, CC; Damen, MS M A; Doll, JR; Stankiewicz, TE; Chen, X; Chetal, K; Karns, R; et al. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.

Jackson, C; Demmert, M; Mukherjee, S; Isaacs, T; Gray, J; Senthamaraikannan, P; Presicce, P; Chetal, K; Salomonis, N; Miller, L; et al. A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. 2021.

Schuh, MP; Alkhudairy, L; Potter, A; Potter, SS; Chetal, K; Thakkar, K; Salomonis, N; Kopan, R. The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis. Journal of the American Society of Nephrology : JASN. 2021; 32:1097-1112.

Reiman, D; Vijay, GK M; Xu, H; Sonin, A; Chen, D; Salomonis, N; Singh, H; Khan, AA. Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. PLoS Computational Biology. 2021; 17.

Schmidt, A; Schnell, D; Eaton, K; Chetal, K; Kannan, P; Miller, L; Chougnet, C; Swarr, D; Jobe, A; Salomonis, N; et al. Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques. 2021.

Desprez, PY; Murase, R; Limbad, C; Woo, RW L; Adrados, I; Weitenthaler, K; Soroceanu, L; Salomonis, N; McAllister, SD. Cannabidiol Treatment Results in a Common Gene Expression Response Across Aggressive Cancer Cells from Various Origins. Cannabis and Cannabinoid Research. 2021; 6:148-155.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; et al. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.

Wu, G; Lee, YY; Gulla, EM; Potter, A; Kitzmiller, J; Ruben, MD; Salomonis, N; Whitsett, JA; Francey, LJ; Hogenesch, JB; et al. Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease. eLife. 2021; 10.

Sertorio, M; Nowrouzi, A; Akbarpour, M; Chetal, K; Salomonis, N; Brons, S; Mascia, A; Ionascu, D; McCauley, S; Kupneski, T; et al. Differential transcriptome response to proton versus X-ray radiation reveals novel candidate targets for combinatorial PT therapy in lymphoma. Radiotherapy and Oncology. 2021; 155:293-303.

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. STAR Protocols. 2020; 1.

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. Immunity. 2020; 53:303-318.e5.

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.

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. Computer Applications in the Biosciences. 2020; 36:3773-3780.

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 the United States of America. 2020; 117:9064-9073.

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.

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

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

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.

Tu, Z; Wang, C; Zhao, C; Huang, L; Salomonis, N; Lu, RQ; Zheng, Y. Autism-Associated Chromatin Remodeler CHD8 Governs the Survival and Differentiation of Hematopoietic Stem/Progenitor Cells. Blood. 2019; 134:1191-1191.

Ferraro, F; Miller, CA; Abdalla, A; Helton, N; Salomonis, N; Fulton, RS; Fronick, C; Heath, SE; Westervelt, P; Ley, TJ. The Molecular Basis of Long First Remissions in Normal Karyotype AML Patients. Blood. 2019; 134:3827-3827.

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.

Ice, RJ; Chen, M; McAllister, S; Salomonis, N; Desprez, P; Sidorov, M; Ho, TL; Chan, JK; Soroceanu, L. Dinaciclib persistently inhibits patient-derived high-grade ovarian carcinoma growth. Gynecologic Oncology. 2019; 154.

Salomonis, N. Investigating Cell Fate Decisions with ICGS Analysis of Single Cells. Methods in Molecular Biology. 2019; 1975:251-275.

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.