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

2018Show

Churko JM, Garg P, Treutlein B, Venkatasubramanian M, Wu H, Lee J, Wessells QN, Chen SY, Chen WY, Chetal K, Mantalas G, Neff N, Jabart E, Sharma A, Nolan GP, Salomonis N, Wu JC. Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. Nat Commun. 2018 Nov 21;9(1):4906.

Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, 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 Rep. 2018 Dec 11;25(11):3229.

Modur V, Singh N, Mohanty V, Chung E, Muhammad B, Choi K, Chen X, Chetal K, Ratner N, Salomonis N, Weirauch MT, Waltz S, Huang G, Privette-Vinnedge L, Park JS, Janssen EM, Komurov K. Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nat Commun. 2018 Oct 23;9(1):4410.

Yang JQ, Kalim KW, Li Y, Duan X, Nguyen P, Khurana Hershey GK, Kroner J, Ruff B, Zhang L, Salomonis N, Rochman M, Wen T, Zheng Y, Guo F. Rational targeting Cdc42 restrains Th2 cell differentiation and prevents allergic airway inflammation. Clin Exp Allergy. 2018 Oct 11.

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 Nov 22;132(21):e24-e34.

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

Hayashi Y, Zhang Y, Yokota A, Yan X, Liu J, Choi K, Li B, Sashida G, Peng Y, Xu Z, Huang R, Zhang L, Freudiger GM, Wang J, Dong Y, Zhou Y, Wang J, Wu L, Bu J, Chen A, Zhao X, Sun X, Chetal K, Olsson A, Watanabe M, Romick-Rosendale LE, Harada H, Shih LY, Tse W, Bridges JP, Caligiuri MA, Huang T, Zheng Y, Witte DP, Wang QF, Qu CK, Salomonis N, Grimes HL, Nimer SD, Xiao Z, Huang G. Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. Cancer Discov. 2018 Nov;8(11):1438-1457.

Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. J Exp Med. 2018 Aug 6;215(8):2115-2136.

de Semir D, Bezrookove V, Nosrati M, Dar AA, Wu C, Shen J, Rieken C, Venkatasubramanian M, Miller JR 3rd, Desprez PY, McAllister S, Soroceanu L, Debs RJ, Salomonis N, Schadendorf D, Cleaver JE, Kashani-Sabet M. PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):E5766-E5775.

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. Nat Genet. 2018 May;50(5):699-707.

Matsu-Ura T, Dovzhenok AA, Coradetti ST, Subramanian KR, Meyer DR, Kwon JJ, Kim C, Salomonis N, Glass NL, Lim S, Hong CI. Synthetic Gene Network with Positive Feedback Loop Amplifies Cellulase Gene Expression in Neurospora crassa. ACS Synth Biol. 2018 May 18;7(5):1395-1405.

Presicce P, Park CW, Senthamaraikannan P, Bhattacharyya S, Jackson C, Kong F, Rueda CM, DeFranco E, Miller LA, Hildeman DA, Salomonis N, Chougnet CA, Jobe AH, Kallapur SG. IL-1 signaling mediates intrauterine inflammation and chorio-decidua neutrophil recruitment and activation. JCI Insight. 2018 Mar 22;3(6).

Fang J, Muto T, Kleppe M, Bolanos LC, Hueneman KM, Walker CS, Sampson L, Wellendorf AM, Chetal K, Choi K, Salomonis N, Choi Y, Zheng Y, Cancelas JA, Levine RL, Starczynowski DT. TRAF6 Mediates Basal Activation of NF-κB Necessary for Hematopoietic Stem Cell Homeostasis. Cell Rep. 2018 Jan 30;22(5):1250-1262.

Lee JM, Govindarajah V, Goddard B, Hinge A, Muench DE, Filippi MD, Aronow B, Cancelas JA, Salomonis N, Grimes HL, Reynaud D. Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression. J Exp Med. 2018 Feb 5;215(2):627-644.

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. Dev Biol. 2018 Feb 1;434(1):36-47.

Salomonis N. Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers. Methods Mol Biol. 2018;1788:89-111.

2017Show

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. Nat Biomed Eng. 2017 Oct;1(10):826-837.

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 Nov 21;47(5):890-902.e4.

McLendon PM, Davis G, Gulick J, Singh SR, Xu N, Salomonis N, Molkentin JD, Robbins J. An Unbiased High-Throughput Screen to Identify Novel Effectors That Impact on Cardiomyocyte Aggregate Levels. Circ Res. 2017 Sep 1;121(6):604-616.

Daily K, Ho Sui SJ, Schriml LM, Dexheimer PJ, Salomonis N, Schroll R, Bush S, Keddache M, Mayhew C, Lotia S, Perumal TM, Dang K, Pantano L, Pico AR, Grassman E, Nordling D, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Lutzko C, Aronow BJ, Omberg L. Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. Sci Data. 2017 Mar 28;4:170030.

Johansson E, Biagini Myers JM, Martin LJ, He H, Pilipenko V, Mersha T, Weirauch M, Salomonis N, Ryan P, LeMasters GK, Bernstein DI, Lockey J, Khurana Hershey GK. KIF3A genetic variation is associated with pediatric asthma in the presence of eczema independent of allergic rhinitis. J Allergy Clin Immunol. 2017 Aug;140(2):595-598.e5.

Rindler TN, Hinton RB, Salomonis N, Ware SM. Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics. Sci Rep. 2017 Jan 18;7:39276.

Fang J, Bolanos LC, Choi K, Liu X, Christie S, Akunuru S, Kumar R, Wang D, Chen X, Greis KD, Stoilov P, Filippi MD, Maciejewski JP, Garcia-Manero G, Weirauch MT, Salomonis N, Geiger H, Zheng Y, Starczynowski DT. Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nat Immunol. 2017 Feb;18(2):236-245.

2016Show

Roedder S, Salomonis N. Loaded, locked, drawn: kSORT validated for patient samples. Nat Rev Nephrol. 2016 Nov 14.

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 Sep 29;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, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, Zambidis E, Margolin A, Hide W, Hatzopoulos AK, 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 Jul12;7(1):110-25.

Sigdel TK, Bestard O, Salomonis N, Hsieh SC, Torras J, Naesens M, Tran TQ, Roedder S, Sarwal MM. Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy. Transplantation. 2016 Oct;100(10):2062-70.

Meyer SE, Qin T, Muench DE, Masuda K, Venkatasubramanian M, Orr E, Suarez L, Gore SD, Delwel R, Paietta E, Tallman MS, Fernandez H, Melnick A, Le Beau MM, 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 Discov. 2016 May;6(5):501-15.

Other Significant PublicationsShow

Davis J, Salomonis N, Ghearing N, Lin SC, Kwong JQ, Mohan A, Swanson MS, Molkentin JD. MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response. Nat Commun. 2015 Dec 16;6:10084.

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 Med Genomics. 2015 Oct 22;8:67.

Soreq L, Salomonis N, Israel Z, Bergman H, Soreq H. Analyzing alternative splicing data of splice junction arrays from Parkinson patients' leukocytes before and after deep brain stimulation as compared with control donors. Genom Data. 2015 Jul 16;5:340-3.

Soreq L, Salomonis N, Guffanti A, Bergman H, Israel Z, Soreq H. Whole transcriptome RNA sequencing data from blood leukocytes derived from Parkinson's disease patients prior to and following deep brain stimulation treatment. Genom Data. 2014 Nov 22;3:57-60.

Chen S, Brunskill EW, Potter SS, Dexheimer PJ, Salomonis N, Aronow BJ, Hong CI, Zhang T, Kopan R. Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan. Dev Cell. 2015 Oct 12;35(1):49-62.

Vitalone MJ, Sigdel TK, Salomonis N, Sarwal RD, Hsieh SC, Sarwal MM. Transcriptional Perturbations in Graft Rejection. Transplantation. 2015 Sep;99(9):1882-93.

Roedder S, Sigdel T, Salomonis N, Hsieh S, Dai H, Bestard O, Metes D, Zeevi A, Gritsch A, Cheeseman J, Macedo C, Peddy R, Medeiros M, Vincenti F, Asher N, Salvatierra O, 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 Med. 2014 Nov 11;11(11):e1001759.

Salomonis N. Systems-level perspective of sudden infant death syndrome. Pediatr Res. 2014 Sep;76(3):220-9.

Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell. 2014 Jul 3;15(1):92-101.

Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, Soreq H. Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PLoS Comput Biol. 2014 Mar 20;10(3):e1003517.

Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC. MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. BMC Bioinformatics. 2014 Mar 12;15:69.

Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton DJ, Moore RJ, Hsieh SC, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian WJ, Camp DG 2nd, Sarwal MM. The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics. Mol Cell Proteomics. 2014 Feb;13(2):621-31.

Kreitzer FR, Salomonis N, Sheehan A, Huang M, Park JS, Spindler MJ, Lizarraga P, Weiss WA, So PL, Conklin BR. A robust method to derive functional neural crest cells from human pluripotent stem cells. Am J Stem Cells. 2013 Jun 30;2(2):119-31.

Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, Zambon AC. Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics. 2013 Aug 15;29(16):2059-61.

Soreq L, Salomonis N, Bronstein M, Greenberg DS, Israel Z, Bergman H, Soreq H. Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. Front Mol Neurosci. 2013 May 13;6:10.

Spindler MJ, Burmeister BT, Huang Y, Hsiao EC, Salomonis N, Scott MJ, Srivastava D, Carnegie GK, Conklin BR. AKAP13 Rho-GEF and PKD-binding domain deficient mice develop normally but have an abnormal response to β-adrenergic-induced cardiac hypertrophy. PLoS One. 2013 Apr 26;8(4):e62705.

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 Aug 15;28(16):2209-10.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. Mosaic: making biological sense of complex networks. Bioinformatics. 2012 Jul 15;28(14):1943-4.

Streeper RS, Grueter CA, Salomonis N, Cases S, Levin MC, Koliwad SK, Zhou P, Hirschey MD, Verdin E, Farese RV Jr. Deficiency of the lipid synthesis enzyme, DGAT1, extends longevity in mice. Aging (Albany NY). 2012 Jan;4(1):13-27.

Salomonis N, Conklin BR. Stem cell pluripotency: alternative modes of transcription regulation. Cell Cycle. 2010 Aug 15;9(16):3133-4.

Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62.

Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9.

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 Nov 10;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 Comput Biol. 2009 Nov;5(11):e1000553.

Stein T, Salomonis N, Nuyten DS, van de Vijver MJ, Gusterson BA. A mouse mammary gland involution mRNA signature identifies biological pathways potentially associated with breast cancer metastasis. J Mammary Gland Biol Neoplasia. 2009 Jun;14(2):99-116.

Kita-Matsuo H, Barcova M, Prigozhina N, Salomonis N, Wei K, Jacot JG, Nelson B, Spiering S, Haverslag R, Kim C, Talantova M, Bajpai R, Calzolari D, Terskikh A, McCulloch AD, Price JH, Conklin BR, Chen HS, Mercola M. Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. PLoS One. 2009;4(4):e5046.

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 Jun 24;8:217.

Stein T, Salomonis N, Gusterson BA. Mammary gland involution as a multi-step process. J Mammary Gland Biol Neoplasia. 2007 Mar;12(1):25-35.

Cline MS, Blume J, Cawley S, Clark TA, Hu JS, Lu G, Salomonis N, Wang H, Williams A. ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics. 2005 Jun;21 Suppl 1:i107-15.

Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA. Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8561-6.

Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12.

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 Biol. 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 Biol. 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. Nat Genet. 2002 May;31(1):19-20.