Publications

Selected Publications

Venkatasubramanian, M; Schwartz, L; Ramachandra, N; Bennett, J; Subramanian, KR; Chen, X; Gordon-Mitchell, S; Fromowitz, A; Pradhan, K; Shechter, D; Grimes, HL; Starczynowski, DT; Verma, A; Salomonis, N. Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias. Science Translational Medicine. 2025; 17(797):eadr1471.

Lambourne, L; Mattioli, K; Santoso, C; Sheynkman, G; Inukai, S; Kaundal, B; Berenson, A; Spirohn-Fitzgerald, K; Bhattacharjee, A; Rothman, E; Sahni, N; Vidal, M; Bulyk, ML; Fuxman Bass, JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Molecular Cell. 2025; 85(7):1445-1466.e13.

Li, G; Schnell, D; Bhattacharjee, A; Yarmarkovich, M; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery. Cell Reports: Methods. 2024; 4(11):100900.

Stiff, A; Fornerod, M; Kain, BN; Nicolet, D; Kelly, BJ; Miller, KE; Mrózek, K; Boateng, I; Bollas, A; Garfinkle, EAR; Salomonis, N; Grimes, HL; Mardis, ER; Eisfeld, A-K. Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia. Nature Genetics. 2024; 56(11):2434-2446.

Zhang, X; Song, B; Carlino, MJ; Li, G; Ferchen, K; Chen, M; Thompson, EN; Kain, BN; Schnell, D; Thakkar, K; Singh, H; Krause, DS; Salomonis, N; Grimes, HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology. 2024; 25(4):703-715.

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; Sheynkman, GM; Tilburgs, T; Salomonis, N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16(730):eade2886.

Menéndez-Gutiérrez, MP; Porcuna, J; Nayak, R; Paredes, A; Niu, H; Núñez, V; Paranjpe, A; Gómez, MJ; Bhattacharjee, A; Schnell, DJ; Sánchez-Cabo, F; Welch, JS; Salomonis, N; Cancelas, JA; Ricote, M. Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141(6):592-608.

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(1):406.

Romano, L; Seu, KG; Papoin, J; Muench, DE; Konstantinidis, D; Olsson, A; Schlum, K; Chetal, K; Chasis, JA; Mohandas, N; Grimes, HL; Salomonis, N; Blanc, L; Kalfa, TA. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140(14):1621-1634.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VBS; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23(5).

Dar, AA; Bezrookove, V; Nosrati, M; Ice, R; Patino, JM; Vaquero, EM; Parrett, B; Leong, SP; Kim, KB; Debs, RJ; Cleaver, JE; Salomonis, N; Mcallister, S; Kashani-Sabet, M. 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(34):e2206824119.

Sun, X; Perl, A-K; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; Xu, Y; Pryhuber, G; Whitsett, J; Morrisey, EE. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57(1):112-145.e2.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; Tickle, T; Aronow, BJ; Salomonis, N; Consortium, NL. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. bioRxiv. 2021; 2021.12.05.471312.

Li, G; Iyer, B; Prasath, VBS; Ni, Y; Salomonis, N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics. 2021; 22(6).

Fenix, AM; Miyaoka, Y; Bertero, A; Blue, SM; Spindler, MJ; Tan, KKB; Perez-Bermejo, JA; Chan, AH; Mayerl, SJ; Nguyen, TD; Yeo, GW; Murry, CE; Conklin, BR; Salomonis, N. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12(1):6324.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D'alessandro, A; Way, SS; Salomonis, N; Grimes, HL; Lucas, D. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590(7846):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(1):6374.

Depasquale, EAK; Schnell, D; Chetal, K; Salomonis, N. Protocol for Identification and Removal of Doublets with DoubletDecon. STAR Protocols. 2020; 1(2):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. Bioinformatics. 2020; 36(12):3773-3780.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; Kappes, DJ; Way, SS; Salomonis, N; Grimes, HL. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582(7810):109-114.

Itskovich, SS; Gurunathan, A; Clark, J; Burwinkel, M; Wunderlich, M; Berger, MR; Kulkarni, A; Chetal, K; Venkatasubramanian, M; Salomonis, N; Kumar, AR; Lee, LH. MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nature Communications. 2020; 11(1):2369.

Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; Mulloy, J; Kofron, M; Salomonis, N; Grimes, HL; Filippi, M-D. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26(3):420-430.e6.

Lucas, D; Salomonis, N; Grimes, HL. Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22(1):5-6.

Depasquale, EAK; Schnell, D; Dexheimer, P; Ferchen, K; Hay, S; Chetal, K; Valiente-Alandí, Í; Blaxall, BC; Grimes, HL; Salomonis, N. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Research (NAR). 2019; 47(21):e138.

Depasquale, EAK; Schnell, DJ; Van Camp, P-J; Valiente-Alandí, Í; Blaxall, BC; Grimes, HL; Singh, H; Salomonis, N. DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell reports. 2019; 29(6):1718-1727.e8.

Adelman, ER; Huang, H-T; Roisman, A; Olsson, A; Colaprico, A; Qin, T; Lindsley, RC; Bejar, R; Salomonis, N; Grimes, HL; Figueroa, ME. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discovery. 2019; 9(8):1080-1101.

Smith, MA; Choudhary, GS; Pellagatti, A; Choi, K; Bolanos, LC; Bhagat, TD; Gordon-Mitchell, S; Von Ahrens, D; Pradhan, K; Steeples, V; Komurov, K; Boultwood, J; Verma, A; Starczynowski, DT. U2AF1 mutations induce oncogenic IRAK4 isoforms and activate innate immune pathways in myeloid malignancies. Nature Cell Biology. 2019; 21(5):640-650.

Taylor, DM; Aronow, BJ; Tan, K; Bernt, K; Salomonis, N; Greene, CS; Frolova, A; Henrickson, SE; Wells, A; Pei, L; Kong, SW; Bönnemann, CG; Mandl, KD; White, PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. 2019; 49(1):10-29.

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

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; Grimes, HL. SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132(21):e24-e34.

Churko, JM; Garg, P; Treutlein, B; Venkatasubramanian, M; Wu, H; Lee, J; Wessells, QN; Chen, S-Y; Chen, W-Y; Chetal, K; Sharma, A; Nolan, GP; Salomonis, N; Wu, JC. Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. Nature Communications. 2018; 9(1):4906.

Lu, Y-C; Sanada, C; Xavier-Ferrucio, J; Wang, L; Zhang, P-X; 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(8):2083-2093.e4.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; Barski, A; Salomonis, N; Kaufman, KM; Kottyan, LC; Weirauch, MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50(5):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(1):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(Suppl_1):770.

Yáñez, 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(5):890-902.e4.

Churko, JM; Lee, J; Ameen, M; Gu, M; Venkatasubramanian, M; Diecke, S; Sallam, K; Im, H; Wang, G; Gold, JD; Salomonis, N; Snyder, MP; Wu, JC. Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. Nature Biomedical Engineering. 2017; 1(10):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(7622):698-702.

Salomonis, N; Dexheimer, PJ; Omberg, L; Schroll, R; Bush, S; Huo, J; Schriml, L; Ho Sui, S; Keddache, M; Mayhew, C; 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; 7(1):110-125.

Meyer, SE; Qin, T; Muench, DE; Masuda, K; Venkatasubramanian, M; Orr, E; Suarez, L; Gore, SD; Delwel, R; Paietta, E; 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 Discovery. 2016; 6(5):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; Shapiro, R; Kirk, A; Reed, EF; Sarwal, MM. The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Medicine. 2014; 11(11):e1001759.

Salomonis, N. Systems-level perspective of sudden infant death syndrome. Pediatric Research. 2014; 76(3):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(16):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 (NAR). 2010; 38(Web Server issue):W755-W762.

Salomonis, N; Schlieve, CR; Pereira, L; Wahlquist, C; Colas, A; Zambon, AC; Vranizan, K; Spindler, MJ; Pico, AR; Cline, MS; Samal, E; Mercola, M; Merrill, BJ; Conklin, BR. 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(23):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(11):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. PLoS Computational Biology. 2009; 5(11):e1000553.

Stein, T; Salomonis, N; Nuyten, DSA; Van De Vijver, MJ; Gusterson, BA. A Mouse Mammary Gland Involution mRNA Signature Identifies Biological Pathways Potentially Associated with Breast Cancer Metastasis. Journal of Mammary Gland Biology and Neoplasia. 2009; 14(2):117-119.

Krishnan, K; Salomonis, N; Guo, S. Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. PLoS ONE. 2008; 3(11):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. 2003; 4(10):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. 2003; 4(1):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(1):19-20.

Redfern, CH; Degtyarev, MY; Kwa, AT; Salomonis, N; Cotte, N; Nanevicz, T; Fidelman, N; Desai, K; Vranizan, K; Lee, EK; Fishman, GI; Bernstein, D; Baker, AJ; Conklin, BR. 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(9):4826-4831.

2025

Thapa, C; Walling, I; Chaturvedi, P; Baumgartner, S; Fleming, M; Biesiada, J; Salomonis, N; Crone, SA. Diverse Transcriptional Alterations in V2a Propriospinal Neurons Following Spinal Cord Injury. Journal of Neuroscience. 2025; 45(48).

Peters, AL; Depasquale, EAK; Begum, G; Roskin, KM; Kotliar, M; Barski, A; Salomonis, N; Shi, T; Ranganathan, S; Woodle, ES; Hildeman, DA. Single-cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells. American Journal of Transplantation. 2025; 25(11):2345-2360.

Kudira, R; Yang, ZF; Osuji, I; Damen, MSMA; Yang Vom Hofe, A; Singh, M; Karns, R; Bariya, P; Pfuhler, L; Mullen, M; Subramanian, S; Salomonis, N; Miraldi, ER; Miethke, AG. Bile acids engage the SIPR-STAT3 signaling axis to modulate regulatory T cell responses in fibrosing cholangiopathies. Journal of Hepatology. 2025; 83(5):1128-1141.

Ferchen, K; Zhang, X; Thakkar, K; Li, G; Bernardicius, D; Sen, S; Rawat, P; Olsson, A; Bennett, SN; Potter, C; Morris, S; Singh, H; Salomonis, N; Grimes, HL. A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice. Nature Immunology. 2025; 26(11):2086-2099.

Peters, M; Teodorescu, P; Pasca, S; Zhang, X; Wang, R; Yegnasubramanian, S; Grimes, LH; Salomonis, N; Gondek, LP; Ghiaur, G. Comprehensive characterization of human bone marrow microenvironment shows age-related changes. Haematologica. 2025; 110(11):2844-2848.

Khan, I; Rodriguez-Brotons, A; Bhattacharjee, A; Bezrookove, V; Dar, A; De Semir, D; Nosrati, M; Ice, R; Soroceanu, L; Leong, SP; Bosenberg, M; Salomonis, N; Mcallister, S; Kashani-Sabet, M. Combinatorial therapy regimens targeting preclinical models of melanoma resistant to immune checkpoint blockade. Journal of Clinical Investigation. 2025; 135(18).

Johnstone, ME; Leck, AL; Lange, TE; Wilcher, KE; Shephard, MS; Paranjpe, A; Schutte, S; Wells, SI; Kappes, F; Salomonis, N; Privette Vinnedge, LM. DEK promotes mammary hyperplasia and is associated with H3K27me3 epigenetic modifications. Life Science Alliance. 2025; 8(9).

Lape, M; Schnell, D; Parameswaran, S; Ernst, K; O'connor, S; Salomonis, N; Martin, LJ; Harnett, BM; Kottyan, LC; Weirauch, MT. A survey of pathogenic involvement in non-communicable human diseases. Communications Medicine. 2025; 5(1):242.

Venkatasubramanian, M; Schwartz, L; Ramachandra, N; Bennett, J; Subramanian, KR; Chen, X; Gordon-Mitchell, S; Fromowitz, A; Pradhan, K; Shechter, D; Grimes, HL; Starczynowski, DT; Verma, A; Salomonis, N. Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias. Science Translational Medicine. 2025; 17(797):eadr1471.

Lambourne, L; Mattioli, K; Santoso, C; Sheynkman, G; Inukai, S; Kaundal, B; Berenson, A; Spirohn-Fitzgerald, K; Bhattacharjee, A; Rothman, E; Sahni, N; Vidal, M; Bulyk, ML; Fuxman Bass, JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Molecular Cell. 2025; 85(7):1445-1466.e13.

Alarcon, PC; Ulanowicz, CJ; Damen, MSMA; Eom, J; Sawada, K; Chung, H; Alahakoon, T; Oates, JR; Wayland, JL; Stankiewicz, TE; Moreno-Fernandez, ME; Zacharias, WJ; Salomonis, N; Divanovic, S. Obesity Uncovers the Presence of Inflammatory Lung Macrophage Subsets With an Adipose Tissue Transcriptomic Signature in Influenza Virus Infection. Journal of Infectious Diseases. 2025; 231(2):e317-e327.

2024

Li, G; Schnell, D; Bhattacharjee, A; Yarmarkovich, M; Salomonis, N. Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery. Cell Reports: Methods. 2024; 4(11):100900.

Stiff, A; Fornerod, M; Kain, BN; Nicolet, D; Kelly, BJ; Miller, KE; Mrózek, K; Boateng, I; Bollas, A; Garfinkle, EAR; Salomonis, N; Grimes, HL; Mardis, ER; Eisfeld, A-K. Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia. Nature Genetics. 2024; 56(11):2434-2446.

Bezrookove, V; Khan, I; Bhattacharjee, A; Fan, J; Jones, R; Sharma, A; Nosrati, M; Desprez, P-Y; Salomonis, N; Shi, Y; Dar, A; Kashani-Sabet, M. miR-876-3p is a tumor suppressor on 9p21 that is inactivated in melanoma and targets ERK. Journal of Translational Medicine. 2024; 22(1):758.

Li, G; Salomonis, N. RNA Isoforms as Broad Targets for Cancer Immunotherapy. DNA and Cell Biology. 2024; 43(8):363-368.

Manakkat Vijay, GK; Zhou, M; Thakkar, K; Rothrauff, A; Chawla, AS; Chen, D; Lau, LC-W; Gerges, PH; Chetal, K; Chhibbar, P; Borghesi, L; Salomonis, N; Xu, H; Singh, H. Temporal dynamics and genomic programming of plasma cell fates. Nature Immunology. 2024; 25(6):1097-1109.

Zhang, X; Song, B; Carlino, MJ; Li, G; Ferchen, K; Chen, M; Thompson, EN; Kain, BN; Schnell, D; Thakkar, K; Singh, H; Krause, DS; Salomonis, N; Grimes, HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology. 2024; 25(4):703-715.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; Xu, Y; Tickle, T; Aronow, BJ; Salomonis, N. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2024; 70(2):129-139.

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; Sheynkman, GM; Tilburgs, T; Salomonis, N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16(730):eade2886.

Solomon, M; Song, B; Govindarajah, V; Good, S; Arasu, A; Hinton, EB; Thakkar, K; Bartram, J; Filippi, M-D; Cancelas, JA; Salomonis, N; Grimes, HL; Reynaud, D. Slow cycling and durable Flt3+ progenitors contribute to hematopoiesis under native conditions. Journal of Experimental Medicine (JEM). 2024; 221(1).

Ozga, M; Nicolet, D; Mrózek, K; Yilmaz, AS; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; Salomonis, N; Herold, T; Mims, AS; Eisfeld, A-K. Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG). Leukemia. 2024; 38(1):45-57.

2023

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. Journal of Clinical Investigation. 2023; 133(22).

Stiff, A; Nicolet, D; Fornerod, M; Kelly, B; Miller, K; Mrózek, K; Boateng, I; Kain, BN; Garfinkle, E; Hu, EY; Byrd, JC; Grimes, HL; Mardis, ER; Eisfeld, A-K. Genomic Profiles and Associated Survival Prognosticators in Black Patients with Acute Myeloid Leukemia. Blood. 2023; 142(Supplement 1):837.

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(20).

Dean, ST; Ishikawa, C; Zhu, X; Walulik, S; Nixon, T; Jordan, JK; Henderson, S; Wyder, M; Salomonis, N; Wunderlich, M; Greis, KD; Starczynowski, DT; Volk, AG. Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development. Blood advances. 2023; 7(17):4822-4837.

Gafranek, JT; D'aniello, E; Ravisankar, P; Thakkar, K; Vagnozzi, RJ; Lim, H-W; 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(1):5509.

Basu, J; Olsson, A; Ferchen, K; Titerina, EK; Chetal, K; Nicolas, E; Czyzewicz, P; Levchenko, D; Ge, L; Hua, X; Grimes, HL; Salomonis, N; Kappes, DJ. ThPOK is a critical multifaceted regulator of myeloid lineage development. Nature Immunology. 2023; 24(8):1295-1307.

Guo, M; Morley, MP; Jiang, C; Wu, Y; Li, G; Du, Y; Zhao, S; Wagner, A; Cakar, AC; Kouril, M; Sun, X; Morrisey, EE; Whitsett, JA; Xu, Y. Guided construction of single cell reference for human and mouse lung. Nature Communications. 2023; 14(1):4566.

Ferchen, K; Salomonis, N; Grimes, HL. pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. Bioinformatics. 2023; 39(5).

Ferchen, K; Song, B; Potter, C; Zhang, X; Chou, C-H; 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. 2023; 210(Supplement_1):65.01-65.01.

Song, B; Zhang, X; Steele, H; Chou, C-H; 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. 2023; 210(Supplement_1):65.05-65.05.

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. 2023; 210(Supplement_1):250.13-250.13.

Doll, JR; Moreno-Fernandez, ME; Stankiewicz, TE; Wayland, JL; Wilburn, A; Weinhaus, B; Chougnet, CA; Giordano, D; Cappelletti, M; Presicce, P; Kallapur, SG; Salomonis, N; Tilburgs, T; Divanovic, S. BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth. Cell reports. 2023; 42(4):112352.

Menéndez-Gutiérrez, MP; Porcuna, J; Nayak, R; Paredes, A; Niu, H; Núñez, V; Paranjpe, A; Gómez, MJ; Bhattacharjee, A; Schnell, DJ; Sánchez-Cabo, F; Welch, JS; Salomonis, N; Cancelas, JA; Ricote, M. Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141(6):592-608.

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(1):406.

2022

Rosselot, AE; Park, M; Kim, M; Matsu-Ura, T; Wu, G; Flores, DE; Subramanian, KR; Lee, S; Sundaram, N; Broda, TR; Wells, JM; Hogenesch, JB; Moore, SR; Hong, CI. Ontogeny and function of the circadian clock in intestinal organoids. EMBO Journal. 2022; 41(2):e106973.

Solomon, M; Song, B; Govindarajah, V; Good, S; Bartram, J; Cancelas, J; Filippi, M-D; Salomonis, N; Grimes, HL; Reynaud, D. Hematopoietic Flt3+ Multipotent Progenitors Are Organized in Discrete Functionally and Hierarchically Distinct Populations. Blood. 2022; 140(Supplement 1):1981-1982.

Voulgaridou, A; Elgammal, Y; Husami, A; Emberesh, S; Seu, K; Ramamoorthy, M; Trump, L; Barasa, N; Nelson, AS; Lorsbach, RB; Romano, L; Salomonis, NA; Zhang, W; Lutzko, C; Kalfa, TA. 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(Supplement 1):1234-1235.

Ozga, MP; Nicolet, D; Mrózek, K; Yilmaz, S; Kohlschmidt, J; Larkin, KT; Blachly, JS; Oakes, CC; Buss, J; Walker, CJ; Salomonis, N; Herold, T; Mims, AS; Eisfeld, A-K. 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(Supplement 1):936-939.

Zhang, X; Song, B; Khan, MD; Ferchen, K; Chou, C-H; Li, G; Dezern, AE; Ghiaur, G; Halene, S; Salomonis, N; Grimes, HL. Single-Cell Multiomics Reveal Hypomethylating Agent Partially Restores Hematopoiesis in a LR-MDS Patient at the Cost of Leukemic Transformation. Blood. 2022; 140(Supplement 1):9759-9760.

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

Ferchen, K; Song, B; Chou, C-H; Zhang, X; Salomonis, N; Grimes, HL. Identification and Isolation of Hematopoietic Stem Cells and Progenitors with Discrete Developmental Gene Expression Programs. Blood. 2022; 140(Supplement 1):2856.

Romano, L; Seu, KG; Papoin, J; Muench, DE; Konstantinidis, D; Olsson, A; Schlum, K; Chetal, K; Chasis, JA; Mohandas, N; Grimes, HL; Salomonis, N; Blanc, L; Kalfa, TA. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140(14):1621-1634.

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(18).

Schmidt, AF; Schnell, DJ; Eaton, KP; Chetal, K; Kannan, PS; Miller, LA; Chougnet, CA; Swarr, DT; Jobe, AH; Salomonis, N; Kamath-Rayne, BD. Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques. JCI Insight. 2022; 7(18).

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VBS; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23(5).

Dar, AA; Bezrookove, V; Nosrati, M; Ice, R; Patino, JM; Vaquero, EM; Parrett, B; Leong, SP; Kim, KB; Debs, RJ; Cleaver, JE; Salomonis, N; Mcallister, S; Kashani-Sabet, M. 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(34):e2206824119.

Stevens, J; Steinmeyer, S; Bonfield, M; Peterson, L; Wang, T; Gray, J; Lewkowich, I; Xu, Y; Du, Y; Guo, M; Miller, L; Chougnet, C; O'connor, DH; Deshmukh, H. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science Translational Medicine. 2022; 14(649):eabl3981.

Vijay, GKM; 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. 2022; 208(Supplement_1):168.08-168.08.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VBS; Szczesniak, R; Aronow, BJ. CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data. bioRxiv. 2022; 2022.04.13.488194.

Gracia-Maldonado, G; Clark, J; Burwinkel, M; Greenslade, B; Wunderlich, M; Salomonis, N; Leone, D; Gatti, E; Pierre, P; Kumar, AR; Lee, LH. LAMP-5 is an essential inflammatory-signaling regulator and novel immunotherapy target for mixed lineage leukemia-rearranged acute leukemia. Haematologica. 2022; 107(4):803-815.

Jackson, CM; Demmert, M; Mukherjee, S; Isaacs, T; Thompson, R; Chastain, C; Gray, J; Senthamaraikannan, P; Presicce, P; Chetal, K; Zacharias, WJ; Lewkowich, IP; Deshmukh, H; Chougnet, CA. A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. Mucosal Immunology. 2022; 15(4):730-744.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; Chougnet, CA; Jobe, AH; Deshmukh, H; Zacharias, WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14(638):eabl8574.

Avellino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, E; Bindels, E; Grimes, L; Delwel, R. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood advances. 2022; 6(5):1406-1419.

Sun, X; Perl, A-K; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; Xu, Y; Pryhuber, G; Whitsett, J; Morrisey, EE. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57(1):112-145.e2.

Song, B; Ferchen, K; Chou, C-H; Zhang, X; Steele, H; Herro, R; Salomonis, N; Grimes, HL. 3194 – LIVE BACTERIAL LIGANDS PROGRAM CORE HEMATOPOIETIC GENE EXPRESSION. Experimental Hematology. 2022; 111:s142.

Díaz, PC; Chou, C-H; 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.

Grimes, HL; 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.

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