Unsupervised Transfer Learning for Rare Disease Transcriptomics

Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, and Greene CS. MultiPLIER: a transfer learning framework reveals systemic features of rare autoimmune diseasebioRxiv. DOI: 10.1101/395947

 

Normalization of Gene Expression Data for Machine Learning Applications

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

 

Analysis of Drug Trials with Molecular Data

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

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 SkinJournal of Investigative Dermatology. 2018. DOI: 10.1016/j.jid.2018.01.006

 

Integrative Functional Genomic Analyses of Systemic Sclerosis

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 sclerosisGenome Medicine 2017 Mar 23;9(1):27. DOI: 10.1186/s13073-017-0417-1

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

 

Molecular Characterization of Systemic Sclerosis Esophageal Disease

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 

 

Reviews and Book Chapters

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

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

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

 

Other Peer-Reviewed Publications

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.

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.

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 SclerosisArthritis Res Ther. 2016 Jan 22;18(1):27. doi: 10.1186/s13075-016-0914-4. 

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

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 SclerodermaArthritis Rheumatol. 2016 Mar 4. doi: 10.1002/art.39658.

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. 80(4):273-85.