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Michael Ku Yu
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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
3802018
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
2772017
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
2412018
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
1922020
Visible machine learning for biomedicine
KY Michael, J Ma, J Fisher, JF Kreisberg, BJ Raphael, T Ideker
Cell 173 (7), 1562-1565, 2018
1522018
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
1482018
Inferring gene ontologies from pairwise similarity data
M Kramer, J Dutkowski, M Yu, V Bafna, T Ideker
Bioinformatics 30 (12), i34-i42, 2014
982014
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
942019
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
832015
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
802016
Structure-based whole-genome realignment reveals many novel noncoding RNAs
S Will, M Yu, B Berger
Genome research 23 (6), 1018-1027, 2013
502013
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
402021
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
362017
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
312023
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
222019
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
212014
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
182021
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
182018
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
122023
The genetic and ecological landscape of plasmids in the human gut
MK Yu, EC Fogarty, AM Eren
https://www.biorxiv.org/content/10.1101/2020.11.01.361691, 2022
122022
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Articles 1–20