Anna Goldenberg

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Benjamin Haibe-KainsScientist (Principal Investigator), Princess Margaret Cancer Centre, University Health NetworkVerified email at uhnresearch.ca
Petr SmirnovPhD Candidate, Medical Biophysics, University of TorontoVerified email at utoronto.ca
Bo WangLead AI Scientist, PMCC UHN; CIFAR AI Chair, Vector Institute; Assistant Professor, U of TorontoVerified email at vectorinstitute.ai
Michael BrudnoProfessor of Computer Science, University of Toronto; Chief Data Scientist, UHNVerified email at cs.toronto.edu
Stephen E Fienberg 1942-2016Maurice Falk University Professor of Statistics and Social ScienceVerified email at cs.cmu.edu
John QuackenbushHarvard T.H. Chan School of Public Health, Channing Division of Network Medicine, and Dana-FarberVerified email at hsph.harvard.edu
Marc FiumeUniversity of TorontoVerified email at cs.toronto.edu
Edoardo M AiroldiProfessor of Statistics & Data Science Temple University & PI, Harvard UniversityVerified email at fas.harvard.edu
Andrew MooreDean, School of Computer Science, Carnegie MellonVerified email at cs.cmu.edu
Sara MostafaviUniversity of WashingtonVerified email at cs.washington.edu
Quaid MorrisComputational and Systems Biology Program, Memorial Sloan Kettering Cancer CenterVerified email at mskcc.org
Zhuowen TuProfessor, Cognitive Science, Computer Science&Engineering, UC San DiegoVerified email at ucsd.edu
Sohrab ShahMemorial Sloan Kettering Cancer CenterVerified email at mskcc.org
Gary BaderProfessor of Molecular Genetics and Computer Science, The Donnelly Centre, University of TorontoVerified email at utoronto.ca
Galit ShmueliDistinguished Professor, National Tsing Hua UniversityVerified email at iss.nthu.edu.tw
Zhaolei Zhang, ProfessorUniversity of Toronto, Donnelly Centre, Dept of Molecular Genetics, Dept of Computer ScienceVerified email at utoronto.ca
Yue LiMcGill UniversityVerified email at cs.mcgill.ca
Mohammed AlshalalfaBioinformatician and Genomic AnalystVerified email at ucalgary.ca
David BleiProfessor of Statistics and Computer Science, Columbia UniversityVerified email at columbia.edu
Gerald QuonAssistant Professor, University of California, DavisVerified email at ucdavis.edu

Anna Goldenberg

Scientist, SickKids Research Institute; Assistant Professor Department of Computer Science, University of Toronto

Verified email at utoronto.ca - Homepage

machine learning computational biology network modeling disease heterogeneity data integration


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Similarity network fusion for aggregating data types on a genomic scale B Wang, AM Mezlini, F Demir, M Fiume, Z Tu, M Brudno, B Haibe-Kains, ... Nature methods 11 (3), 333-337, 2014	1227	2014
Integrated genomic characterization of pancreatic ductal adenocarcinoma BJ Raphael, RH Hruban, AJ Aguirre, RA Moffitt, JJ Yeh, C Stewart, ... Cancer cell 32 (2), 185-203. e13, 2017	1053	2017
A survey of statistical network models A Goldenberg, AX Zheng, SE Fienberg, EM Airoldi Foundations and Trends® in Machine Learning 2 (2), 129-233, 2010	1015	2010
Intertumoral heterogeneity within medulloblastoma subgroups FMG Cavalli, M Remke, L Rampasek, J Peacock, DJH Shih, B Luu, ... Cancer cell 31 (6), 737-754. e6, 2017	744	2017
Sensitive tumour detection and classification using plasma cell-free DNA methylomes SY Shen, R Singhania, G Fehringer, A Chakravarthy, MHA Roehrl, ... Nature 563 (7732), 579-583, 2018	474	2018
Do no harm: a roadmap for responsible machine learning for health care J Wiens, S Saria, M Sendak, M Ghassemi, VX Liu, F Doshi-Velez, K Jung, ... Nature medicine 25 (9), 1337-1340, 2019	335	2019
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman Information Fusion 50, 71-91, 2019	278	2019
Early statistical detection of anthrax outbreaks by tracking over-the-counter medication sales A Goldenberg, G Shmueli, RA Caruana, SE Fienberg Proceedings of the National Academy of Sciences 99 (8), 5237-5240, 2002	254	2002
TensorFlow: biology’s gateway to deep learning? L Rampasek, A Goldenberg Cell systems 2 (1), 12-14, 2016	232	2016
PharmacoGx: an R package for analysis of large pharmacogenomic datasets P Smirnov, Z Safikhani, N El-Hachem, D Wang, A She, C Olsen, ... Bioinformatics 32 (8), 1244-1246, 2016	188	2016
What clinicians want: contextualizing explainable machine learning for clinical end use S Tonekaboni, S Joshi, MD McCradden, A Goldenberg Machine learning for healthcare conference, 359-380, 2019	183	2019
Explaining image classifiers by counterfactual generation CH Chang, E Creager, A Goldenberg, D Duvenaud arXiv preprint arXiv:1807.08024, 2018	156	2018
Transparency and reproducibility in artificial intelligence B Haibe-Kains, GA Adam, A Hosny, F Khodakarami, L Waldron, B Wang, ... Nature 586 (7829), E14-E16, 2020	149	2020
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data AM Mezlini, EJM Smith, M Fiume, O Buske, GL Savich, S Shah, S Aparicio, ... Genome research 23 (3), 519-529, 2013	141	2013
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma H Suzuki, SA Kumar, S Shuai, A Diaz-Navarro, A Gutierrez-Fernandez, ... Nature 574 (7780), 707-711, 2019	103	2019
Biological embedding of experience: A primer on epigenetics MJ Aristizabal, I Anreiter, T Halldorsdottir, CL Odgers, TW McDade, ... Proceedings of the National Academy of Sciences 117 (38), 23261-23269, 2020	101	2020
Machine learning approaches to drug response prediction: challenges and recent progress G Adam, L Rampášek, Z Safikhani, P Smirnov, B Haibe-Kains, ... NPJ precision oncology 4 (1), 1-10, 2020	97	2020
Subtyping: What it is and its role in precision medicine S Saria, A Goldenberg IEEE Intelligent Systems 30 (4), 70-75, 2015	95	2015
To embed or not: network embedding as a paradigm in computational biology W Nelson, M Zitnik, B Wang, J Leskovec, A Goldenberg, R Sharan Frontiers in genetics 10, 381, 2019	92	2019
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis SK Sieberts, F Zhu, J García-García, E Stahl, A Pratap, G Pandey, ... Nature communications 7 (1), 1-10, 2016	88	2016

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