| Using deep learning to model the hierarchical structure and function of a cell J Ma, MK Yu, S Fong, K Ono, E Sage, B Demchak, R Sharan, T Ideker Nature methods 15 (4), 290-298, 2018 | 496 | 2018 |
| Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment T Wang, B Tsui, JF Kreisberg, NA Robertson, AM Gross, MK Yu, H Carter, ... Genome biology 18 (1), 57, 2017 | 334 | 2017 |
| Systematic evaluation of molecular networks for discovery of disease genes JK Huang, DE Carlin, MK Yu, W Zhang, JF Kreisberg, P Tamayo, T Ideker Cell systems 6 (4), 484-495. e5, 2018 | 302 | 2018 |
| The cancer microbiome: distinguishing direct and indirect effects requires a systemic view JB Xavier, VB Young, J Skufca, F Ginty, T Testerman, AT Pearson, ... Trends in cancer 6 (3), 192-204, 2020 | 248 | 2020 |
| Visible machine learning for biomedicine KY Michael, J Ma, J Fisher, JF Kreisberg, BJ Raphael, T Ideker Cell 173 (7), 1562-1565, 2018 | 187 | 2018 |
| A global transcriptional network connecting noncoding mutations to changes in tumor gene expression W Zhang, A Bojorquez-Gomez, DO Velez, G Xu, KS Sanchez, JP Shen, ... Nature genetics 50 (4), 613-620, 2018 | 160 | 2018 |
| Inferring gene ontologies from pairwise similarity data M Kramer, J Dutkowski, M Yu, V Bafna, T Ideker Bioinformatics 30 (12), i34-i42, 2014 | 109 | 2014 |
| Identifying epistasis in cancer genomes: a delicate affair J Van De Haar, S Canisius, KY Michael, EE Voest, LFA Wessels, T Ideker Cell 177 (6), 1375-1383, 2019 | 107 | 2019 |
| Conserved piRNA expression from a distinct set of piRNA cluster loci in eutherian mammals G Chirn, R Rahman, YA Sytnikova, JA Matts, M Zeng, D Gerlach, M Yu, ... PLoS genetics 11 (11), e1005652, 2015 | 100 | 2015 |
| Translation of genotype to phenotype by a hierarchy of cell subsystems MK Yu, M Kramer, J Dutkowski, R Srivas, K Licon, JF Kreisberg, CT Ng, ... Cell systems 2 (2), 77-88, 2016 | 91 | 2016 |
| Metabolic independence drives gut microbial colonization and resilience in health and disease AR Watson, J Füssel, I Veseli, JZ DeLongchamp, M Silva, F Trigodet, ... Genome Biology 24 (1), 78, 2023 | 85 | 2023 |
| Interpretation of cancer mutations using a multiscale map of protein systems F Zheng, MR Kelly, DJ Ramms, ML Heintschel, K Tao, B Tutuncuoglu, ... Science 374 (6563), eabf3067, 2021 | 80 | 2021 |
| Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess MK Yu, EC Fogarty, AM Eren Nature Microbiology 9 (3), 830-847, 2024 | 56 | 2024 |
| A cryptic plasmid is among the most numerous genetic elements in the human gut EC Fogarty, MS Schechter, K Lolans, ML Sheahan, I Veseli, RM Moore, ... Cell 187 (5), 1206-1222. e16, 2024 | 53 | 2024 |
| Microbes with higher metabolic independence are enriched in human gut microbiomes under stress I Veseli, YT Chen, MS Schechter, C Vanni, EC Fogarty, AR Watson, ... Elife 12, RP89862, 2025 | 52 | 2025 |
| Structure-based whole-genome realignment reveals many novel noncoding RNAs S Will, M Yu, B Berger Genome research 23 (6), 1018-1027, 2013 | 51 | 2013 |
| Active interaction mapping reveals the hierarchical organization of autophagy MH Kramer, JC Farre, K Mitra, MK Yu, K Ono, B Demchak, K Licon, ... Molecular cell 65 (4), 761-774. e5, 2017 | 37 | 2017 |
| DDOT: a Swiss army knife for investigating data-driven biological ontologies MK Yu, J Ma, K Ono, F Zheng, SH Fong, A Gary, J Chen, B Demchak, ... Cell systems 8 (3), 267-273. e3, 2019 | 28 | 2019 |
| Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut AR Watson, J Füssel, I Veseli, JZ DeLongchamp, M Silva, F Trigodet, ... bioRxiv, 2021.03. 02.433653, 2021 | 21 | 2021 |
| NeXO Web: the NeXO ontology database and visualization platform J Dutkowski, K Ono, M Kramer, M Yu, D Pratt, B Demchak, T Ideker Nucleic acids research 42 (D1), D1269-D1274, 2014 | 21 | 2014 |
