| Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms JM Mahoney, J Taroni, V Martyanov, TA Wood, CS Greene, PA Pioli, ... PLoS computational biology 11 (1), e1004005, 2015 | 146 | 2015 |
| Metabolic pathways and immunometabolism in rare kidney diseases PC Grayson, S Eddy, JN Taroni, YL Lightfoot, L Mariani, H Parikh, ... Annals of the rheumatic diseases 77 (8), 1226-1233, 2018 | 131 | 2018 |
| MultiPLIER: a transfer learning framework for transcriptomics reveals systemic features of rare disease JN Taroni, PC Grayson, Q Hu, S Eddy, M Kretzler, PA Merkel, CS Greene Cell systems 8 (5), 380-394. e4, 2019 | 117 | 2019 |
| A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis JN Taroni, CS Greene, V Martyanov, TA Wood, RB Christmann, ... Genome medicine 9, 1-24, 2017 | 114 | 2017 |
| Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts ME Johnson, JM Mahoney, J Taroni, JL Sargent, E Marmarelis, MR Wu, ... PloS one 10 (1), e0114017, 2015 | 87 | 2015 |
| Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures JN Taroni, V Martyanov, CC Huang, JM Mahoney, I Hirano, B Shetuni, ... Arthritis Research & Therapy 17, 1-14, 2015 | 71 | 2015 |
| Mycophenolate mofetil treatment of systemic sclerosis reduces myeloid cell numbers and attenuates the inflammatory gene signature in skin M Hinchcliff, DM Toledo, JN Taroni, TA Wood, JM Franks, MS Ball, ... Journal of Investigative Dermatology 138 (6), 1301-1310, 2018 | 60 | 2018 |
| A multimodal strategy used by a large c-di-GMP network KM Dahlstrom, AJ Collins, G Doing, JN Taroni, TJ Gauvin, CS Greene, ... Journal of bacteriology 200 (8), 10.1128/jb. 00703-17, 2018 | 58 | 2018 |
| Identification of optimal mouse models of systemic sclerosis by interspecies comparative genomics JL Sargent, Z Li, AO Aliprantis, M Greenblatt, R Lemaire, M Wu, J Wei, ... Arthritis & Rheumatology 68 (8), 2003-2015, 2016 | 37 | 2016 |
| Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality MT Dang, MV Gonzalez, KS Gaonkar, KS Rathi, P Young, S Arif, L Zhai, ... Cell reports 34 (13), 2021 | 35 | 2021 |
| Machine learning in rare disease J Banerjee, JN Taroni, RJ Allaway, DV Prasad, J Guinney, C Greene Nature Methods 20 (6), 803-814, 2023 | 34 | 2023 |
| A functional genomic meta-analysis of clinical trials in systemic sclerosis: toward precision medicine and combination therapy JN Taroni, V Martyanov, JM Mahoney, ML Whitfield Journal of Investigative Dermatology 137 (5), 1033-1041, 2017 | 31 | 2017 |
| Roles of mouse sperm‐associated alpha‐L‐fucosidases in fertilization K Phopin, W Nimlamool, LJ Lowe‐Krentz, EW Douglass, JN Taroni, ... Molecular reproduction and development 80 (4), 273-285, 2013 | 30 | 2013 |
| Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously SM Foltz, CS Greene, JN Taroni Communications Biology 6 (1), 222, 2023 | 24* | 2023 |
| OpenPBTA: The Open Pediatric Brain Tumor Atlas JA Shapiro, KS Gaonkar, SJ Spielman, CL Savonen, CJ Bethell, R Jin, ... Cell genomics 3 (7), 2023 | 23 | 2023 |
| Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis ME Johnson, AV Grassetti, JN Taroni, SM Lyons, D Schweppe, JK Gordon, ... Arthritis Research & Therapy 18, 1-13, 2016 | 17 | 2016 |
| Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1 J Banerjee, RJ Allaway, JN Taroni, A Baker, X Zhang, CI Moon, ... Genes 11 (2), 226, 2020 | 16 | 2020 |
| Integrated machine learning pipeline for aberrant biomarker enrichment (i-mAB): characterizing clusters of differentiation within a compendium of systemic lupus erythematosus … TT Le, NO Blackwood, JN Taroni, W Fu, MK Breitenstein AMIA Annual Symposium Proceedings 2018, 1358, 2018 | 12 | 2018 |
| Interspecies comparative genomics identifies optimal mouse models of systemic sclerosis JL Sargent, Z Li, AO Aliprantis, M Greenblatt, R Lemaire, M Wu, J Wei, ... Arthritis & rheumatology (Hoboken, NJ) 68 (8), 2003, 2016 | 10 | 2016 |
| annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions KS Gaonkar, F Marini, KS Rathi, P Jain, Y Zhu, NA Chimicles, MA Brown, ... BMC bioinformatics 21, 1-21, 2020 | 9 | 2020 |
