Salomonis Lab

Salomonis Research Lab

Genomic Analysis and Tool Development

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

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

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

Join the Lab

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

Publications

Selected Publications

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

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

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

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

Olsson, A; Venkatasubramanian, M; Chaudhri, VK; Aronow, BJ; Salomonis, N; Singh, H; Grimes, HL. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702.

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

Kamath-Rayne, BD; Du, Y; Hughes, M; Wagner, EA; Muglia, LJ; DeFranco, EA; Whitsett, JA; Salomonis, N; Xu, Y. Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. BMC Medical Genomics. 2015; 8.

Roedder, S; Sigdel, T; Salomonis, N; Hsieh, S; Dai, H; Bestard, O; Metes, D; Zeevi, A; Gritsch, A; Cheeseman, J; et al. The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Medicine. 2014; 11.

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

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

2022

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.

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.

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.

2020

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

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

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

2019

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

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.

2018

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

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

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

Muench, DE; Ferchen, K; Velu, CS; Pradhan, K; Chetal, K; Chen, X; Weirauch, MT; Colmenares, C; Verma, A; Salomonis, N; et al. SKI controls MDS-associated chronic TGF-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.

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

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

Muench, D; Ferchen, K; Pham, G; Hay, S; Zhang, K; Myers, K; Kappes, D; Way, SS; Salomonis, N; Grimes, HL. 3121 Severe Congenital Neutropenia-Associated Mutations Reveal Stage-Specific GFI1-Dependent Checkpoints in Myeloid Development. Experimental Hematology. 2018; 64.

Muench, D; Ferchen, K; Olsson, A; Dwivedi, P; Greis, K; Verma, A; Salomonis, N; Grimes, HL. 3122 Understanding Early Stage Myelodysplastic Syndrome Pathobiology. Experimental Hematology. 2018; 64.

Yáñez, A; Coetzee, S; Olsson, A; Muench, D; Berman, B; Hazelett, D; Salomonis, N; Grimes, HL; Goodridge, H. 3195 Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Experimental Hematology. 2018; 64.

Grimes, H; Venkatasubramanian, M; Chou, C; Olsson, A; Chen, X; Chetal, K; Newkold, T; Kulkarni, A; Meyers, K; Weirauch, M; et al. 3050 Global Unsupervised Splicing Analysis of Leukemia Reveals a Persistent Prognostic Signature That Precurses Oncogenesis. Experimental Hematology. 2018; 64.

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

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

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

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

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

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

Salomonis, N. Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers. Methods in Molecular Biology. 2018; 1788:89-111.