Salomonis Research Lab

Selected Publications

Li, G; Song, B; Singh, H; Surya Prasath, VB; Leighton Grimes, H; Salomonis, N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications. 2023; 14:406.

Li, G; Bhattacharjee, A; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug target discovery and prioritization. 2023; 4:2023.03.03.530994.

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:bbac324.

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 USA. 2022; 119:e2206824119.

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; Preprint:2021.12.05.471312.

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; 12:6324.

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:bbab160.

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; 11:6374.

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

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. Editor, Ponty Y. 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; 11:2369.

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: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.

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.

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.

Salomonis, N. Investigating Cell Fate Decisions with ICGS Analysis of Single Cells. Methods in molecular biology (Clifton, N.J.). 2019; 1975:251-275.

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; 9:4906.

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.

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.

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; 7:39276.

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; 8:67.

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. Editor, Remuzzi G. PLoS Medicine. 2014; 11:e1001759.

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. Bioinformatics. 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 USA. 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. Editor, Verfaillie CM. PloS one. 2009; 4: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. Editor, Ares M. PLoS Computational Biology. 2009; 5:e1000553.

Krishnan, K; Salomonis, N; Guo, S. Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. Editor, Tora L. PloS one. 2008; 3:e3621.

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; 8:217.

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: biology for the post-genomic era. 2003; 4:R61.

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: biology for the post-genomic era. 2003; 4:R7.

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 USA. 2000; 97:4826-4831.

2024

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; et al. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16:eade2886.

Ozga, M; Nicolet, D; Mrózek, K; Yilmaz, AS; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; et al. Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG). Leukemia. 2024; 38:45-57.

Solomon, M; Song, B; Govindarajah, V; Good, S; Arasu, A; Hinton, EB; Thakkar, K; Bartram, J; Filippi, MD; Cancelas, JA; et al. Slow cycling and durable Flt3+ progenitors contribute to hematopoiesis under native conditions. The Journal of Experimental Medicine. 2024; 221:e20231035.

2023

Guo, M; Morley, MP; Jiang, C; Wu, Y; Li, G; Du, Y; Zhao, S; Wagner, A; Cakar, AC; Kouril, M; et al. Guided construction of single cell reference for human and mouse lung. Nature Communications. 2023; 14:4566.

Gafranek, JT; D’Aniello, E; Ravisankar, P; Thakkar, K; Vagnozzi, RJ; Lim, HW; Salomonis, N; Waxman, JS. Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart. Nature Communications. 2023; 14:5509.

Li, G; Song, B; Singh, H; Surya Prasath, VB; Leighton Grimes, H; Salomonis, N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications. 2023; 14:406.

Stiff, A; Nicolet, D; Fornerod, M; Kelly, B; Miller, K; Mrózek, K; Boateng, I; Kain, BN; Garfinkle, E; Hu, EY; et al. Genomic Profiles and Associated Survival Prognosticators in Black Patients with Acute Myeloid Leukemia. Blood. 2023; 142:837.

Verweyen, EL; Thakkar, K; Dhakal, S; Baker, E; Chetal, K; Schnell, D; Canna, S; Grom, AA; Salomonis, N; Schulert, GS. Population-level single-cell genomics reveals conserved gene programs in systemic juvenile idiopathic arthritis. The Journal of Clinical Investigation. 2023; 133:e166741.

Pathak, B; Lange, TE; Lampe, K; Hollander, E; Oria, M; Murphy, KP; Salomonis, N; Sertorio, M; Oria, M. Development of a Single-Neurosphere Culture to Assess Radiation Toxicity and Pre-Clinical Cancer Combination Therapy Safety. Cancers. 2023; 15:4916.

Dean, ST; Ishikawa, C; Zhu, X; Walulik, S; Nixon, T; Jordan, JK; Henderson, S; Wyder, M; Salomonis, N; Wunderlich, M; et al. Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development. Blood Advances. 2023; 7:4822-4837.

Basu, J; Olsson, A; Ferchen, K; Titerina, EK; Chetal, K; Nicolas, E; Czyzewicz, P; Levchenko, D; Ge, L; Hua, X; et al. ThPOK is a critical multifaceted regulator of myeloid lineage development. Nature Immunology. 2023; 24:1295-1307.

Ferchen, K; Salomonis, N; Grimes, HL. pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. Editor, Kelso J. Bioinformatics. 2023; 39:btad287.

Song, B; Zhang, X; Bennett, S; Ma, S; Ferchen, K; Salomonis, N; Grimes, HL. High-throughput workflow leveraging spectral flow cytometry and CITE-seq to characterize human bone marrow across race and gender. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:250.13.

Ferchen, K; Song, B; Potter, C; Zhang, X; Chou, C; Khodoun, M; Finkelman, FD; Salomonis, N; Grimes, HL. Th2 immune responses induced by helminth infection reprogram multilineage progenitors to produce successive waves of neutrophils, basophils, and eosinophils. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:65.01.

Song, B; Zhang, X; Steele, H; Chou, C; Ferchen, K; Salomonis, N; Herro, R; Grimes, HL. Live bacterial ligands universally regulate mTOR activity but are not essential for homeostatic innate immunity. Journal of immunology (Baltimore, Md. : 1950). 2023; 210:65.05.

Doll, JR; Moreno-Fernandez, ME; Stankiewicz, TE; Wayland, JL; Wilburn, A; Weinhaus, B; Chougnet, CA; Giordano, D; Cappelletti, M; Presicce, P; et al. BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth. Cell Reports. 2023; 42:112352.

Li, G; Bhattacharjee, A; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug target discovery and prioritization. 2023; 4:2023.03.03.530994.

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.

2022

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. The EMBO Journal. 2022; 41:e106973.

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.

Dean, S; Ishikawa, C; Zhu, X; Nixon, T; Walulik, S; Wyder, M; Jordan, J; Wunderlich, M; Starczynowski, DT; Salomonis, N; et al. TRIM13 Is a Novel Cell Cycle Hub Regulated By CHAF1B to Promote Acute Myeloid Leukemogenesis. Blood. 2022; 140:2978-2979.

Colom Diaz, PA; Chou, C; Mistry, JJ; Salomonis, N; Daud Khan, M; Grimes, HL; Trowbridge, JJ. Metallothionein 1 (MT1) Is Selectively Required for DNMT3A;NPM1-Mutant Acute Myeloid Leukemia Proliferation. Blood. 2022; 140:9103-9104.

Ozga, MP; Nicolet, D; Mrózek, K; Yilmaz, S; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; et al. Sex-Associated Differences in Frequencies and Outcome Prognostication of Recurrent Molecular Features in Adults with Acute Myeloid Leukemia (AML) (AMLCG, CALGB [Alliance]). Blood. 2022; 140:936-939.

Ferchen, K; Song, BA; Chou, C; Zhang, X; Salomonis, N; Grimes, HL. Identification and Isolation of Hematopoietic Stem Cells and Progenitors with Discrete Developmental Gene Expression Programs. Blood. 2022; 140:2856.

Zhang, X; Song, BA; Khan, MD; Ferchen, K; Chou, C; Li, G; DeZern, AE; Ghiaur, G; Halene, S; Salomonis, N; et al. Single-Cell Multiomics Reveal Hypomethylating Agent Partially Restores Hematopoiesis in a LR-MDS Patient at the Cost of Leukemic Transformation. Blood. 2022; 140:9759-9760.

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:e162101.

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:e154513.

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:bbac324.

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 USA. 2022; 119:e2206824119.

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:eabl3981.

Vijay, GK M; Thakkar, K; Chetal, K; Hay, S; Fan, J; Joglekar, AV; Salomonis, N; Singh, H. Developmental dynamics and genomic programming of GC-derived precursors that give rise to long lived plasma cells. Journal of immunology (Baltimore, Md. : 1950). 2022; 208:168.08.

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.

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: the hematology journal. 2022; 107:803-815.

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:eabl8574.

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:s72.

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:s35.

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:s142.

2021

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; 2:100989.

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; 12:790309.

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; Preprint:2021.12.05.471312.

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; 12:6324.

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; 12:6332.

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:bbab160.

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; 2021.10.16.464640.

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:e147593.

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.

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. Editor, Haugh JM. PLoS Computational Biology. 2021; 17:e1008094.

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.

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:e63003.

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.

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; 11:6374.

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; 1:100085.

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. Immunity. 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. Editor, Ponty Y. 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; 11:2369.

DePasquale, E; Schnell, D; Chetal, K; Salomonisi, N. Identification and Removal of Doublets with DoubletDecon. 2020; 2020.04.23.058156.

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.

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.

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

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