Publications

NCBI Bibliography | ORCiD

2020

Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. bioRxiv. 2020. DOI: 10.1101/839738

Dang MT, Gonzalez M, Gaonkar KS, Rathi KS, Young P, Arif S, Zhai L, Alam MZ, Devalaraja S, To TK, Folkert IW, Raman P, Rokita JL, Martinez D, Taroni JN, Shapiro JA, Greene CS, Savonen C, Hakonarson H, Curran T, Haldar M. Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment. bioRxiv. 2020. DOI: 10.1101/2020.02.12.945642

Banerjee J, Allaway RJ, Taroni JN, Baker A, Zhang X, Moon CI, Pratilas CA, Blakeley JO, Guinney J, Hirbe A, Greene CS, Gosline SJ. Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1. Genes (Basel). 2020 Feb 21;11(2). doi: 10.3390/genes11020226.

2019

Taroni JN. Making Workshops Work: Insights from EDAMAME. mSystems. 2019 Aug 20;4(4). doi: 10.1128/mSystems.00467-19.

Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, Greene CS. MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. Cell Syst. 2019 May 22;8(5):380-394.e4. DOI: 10.1016/j.cels.2019.04.003.

2018

Le TT, Blackwood NO, Taroni JN, Fu W, Breitenstein MK. Integrated machine learning pipeline for aberrant biomarker enrichment (i-mAB): characterizing clusters of differentiation within a compendium of systemic lupus erythematosus patients. AMIA Annu Symp Proc. 2018; 2018: 1358–1367. 

Grayson PC, Eddy S, Taroni JN, Lightfoot YL, Mariani L, Parikh H, Lindenmeyer MT, Ju W, Greene CS, Godfrey B, Cohen CD, Krischer J, Kretzler M, Merkel PA; Vasculitis Clinical Research Consortium, the European Renal cDNA Bank cohort, and the Nephrotic Syndrome Study Network. Metabolic pathways and immunometabolism in rare kidney diseases. Ann Rheum Dis. 2018 Aug;77(8):1226-1233. doi: 10.1136/annrheumdis-2017-212935.

Hinchcliff M, Toledo DM, Taroni JN, Wood TA, Franks JM, Ball MS, Hoffmann A, Amin SM, Tan AU, Tom K, Nesbeth Y, Lee J, Ma M, Aren K, Carns MA, Pioli PA, Whitfield ML. Mycophenolate Mofetil Treatment of Systemic Sclerosis Reduces Myeloid Cell Numbers and Attenuates the Inflammatory Gene Signature in Skin. Journal of Investigative Dermatology. 2018. DOI: 10.1016/j.jid.2018.01.006

Dahlstrom KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA. A Multimodal Strategy Used by a Large c-di-GMP Network. J Bacteriol. 2018 Mar 26;200(8). pii: e00703-17. doi: 10.1128/JB.00703-17.

2017

Taroni JN, Mahoney JM, Whitfield ML. The mechanistic implications of gene expression studies in SSc: Insights from Systems Biology. Curr Treatm Opt Rheumatol. 2017 Sep;3(3):181-192. doi: 10.1007/s40674-017-0072-0

Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann R, Farber HW,  Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Medicine 2017 Mar 23;9(1):27. DOI: 10.1186/s13073-017-0417-1

Taroni JN, Greene CS. Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously. bioRxiv. 2017. DOI: 10.1101/118349

2016 and earlier

Taroni JN, Martyanov V, Mahoney JM, Whitfield ML. A functional genomic meta-analysis of clinical trials in systemic sclerosis: towards precision medicine and combination therapy. Journal of Investigative Dermatology. 2016. DOI: 10.1016/j.jid.2016.12.007

Krishnan A, Taroni JN, Greene CS. Integrative networks illuminate biological factors underlying gene-disease associations. Curr Genet Med Rep. 2016. 

Sargent JL, Li Z, Aliprantis AO, Greenblatt M, Lemaire R, Wu M, Wei J, Taroni J, Harris A, Long K, Burgwin C, Artlett CM, Blankenhorn EP, Lafyatis R, Varga J, Clark SH, Whitfield ML. Interspecies Comparative Genomics Identifies Optimal Mouse Models of Scleroderma. Arthritis Rheumatol. 2016 Mar 4. doi: 10.1002/art.39658.

Mahoney JM, Taroni JN, Whitfield ML. Systems Biology Approaches to Understanding the Pathogenesis of Systemic Sclerosis. Scleroderma: From Pathogenesis to Comprehensive Management. 2nd edition.

Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML. Stress Granules and RNA Processing Bodies are Novel Autoantibody Targets in Systemic Sclerosis. Arthritis Res Ther. 2016 Jan 22;18(1):27. doi: 10.1186/s13075-016-0914-4. 

Taroni JN, Martyanov V, Huang CC, Mahoney JM, Hirano I, Shetuni B, Yang G, Brenner D, Jung B, Wood TA, Bhattacharyya S, Almagor O, Lee J, Sirajuddin A, Chang RW, Varga J, Whitfield ML, Hinchcliff M. Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures. Arthritis Res Ther 17, (2015). DOI: 10.1186/s13075-015-0695-1 

Johnson ME, Mahoney JM, Taroni J, Sargent JL, Marmarelis E, Wu MR, Spotts K, Hinchcliff M, Whitfield ML. Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts. PLoS One 2015; 10(1):e0114017

Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff M, Whitfield ML. Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. PLoS Comput Biol 2015 Jan; 11(1):e1004005

Phopin K, Nimlamool W, Lowe-Krentz LJ, Douglass EW, Taroni JN, Bean BS. Roles of mouse sperm-associated alpha-L-fucosidases in fertilization. Mol Reprod Dev. 2013 Apr;80(4):273-85. doi: 10.1002/mrd.22164.