| A catalogue of small proteins from the global microbiome Y Duan, CD Santos Júnior, TSB Schmidt, A Fullam, BLS de Almeida, ... BioRxiv, 2023.12. 27.573469, 2023 | 2 | 2023 |
| 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 | 8 | 2024 |
| 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 | 148 | 2018 |
| A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut EC Fogarty, MS Schechter, K Lolans, ML Sheahan, I Veseli, R Moore, ... bioRxiv, 2023 | 4 | 2023 |
| 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 | 36 | 2017 |
| 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 | 18 | 2021 |
| Annotating gene sets by mining large literature collections with protein networks S Wang, J Ma, MK Yu, F Zheng, EW Huang, J Han, J Peng, T Ideker Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 23, 602, 2018 | 18 | 2018 |
| Clustering with or without the Approximation F Schalekamp, M Yu, A Van Zuylen Journal of Combinatorial Optimization 25, 393-429, 2013 | 12 | 2013 |
| 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 | 85 | 2015 |
| 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 | 22 | 2019 |
| 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 | 4 | 2024 |
| 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, 1-11, 2017 | 285 | 2017 |
| Hierarchical Models of Biological Systems MK Yu University of California, San Diego, 2017 | | 2017 |
| 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 | 94 | 2019 |
| Inferring gene ontologies from pairwise similarity data M Kramer, J Dutkowski, M Yu, V Bafna, T Ideker Bioinformatics 30 (12), i34-i42, 2014 | 99 | 2014 |
| Inferring the hierarchical structure and function of a cell from millions of biological measurements M Yu, O Summit Ontology Summit, 2017 | 2 | 2017 |
| 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 | 42 | 2021 |
| 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 | 33 | 2023 |
| 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, ... bioRxiv, 2023 | 12 | 2023 |
| Multi-scale mapping of the physical and functional architecture of the cancer cell F Zheng, MK Yu, M Kim, K Ono, M Flagg, JF Kreisberg, N Krogan, T Ideker Cancer Research 78 (13_Supplement), 1317-1317, 2018 | | 2018 |
