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.
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.
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.
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.