David A. Knowles

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Zoubin GhahramaniProfessor, University of Cambridge, and Distinguished Researcher, GoogleVerified email at eng.cam.ac.uk
Jonathan K PritchardStanford UniversityVerified email at stanford.edu
David GolanStatistics PhD student, Tel Aviv University.Verified email at post.tau.ac.il
Hae Kyung ImAssociate Professor, The University of ChicagoVerified email at uchicago.edu
Yang I LiUniversity of ChicagoVerified email at uchicago.edu
Stephen B MontgomeryProfessor, Pathology, Genetics and Biomedical Data Science, Stanford UniversityVerified email at stanford.edu
Alvaro BarbeiraThe University of ChicagoVerified email at uchicago.edu
Anshul KundajeAssociate Professor, Dept. of Genetics, Dept. of Computer Science, Stanford UniversityVerified email at stanford.edu
Thomas QuertermousProfessor of Medicine, Stanford UniversityVerified email at stanford.edu
Arno RuusaleppTartu University HospitalVerified email at kliinikum.ee
Ke HaoIcahn School of Medicine at Mount SinaiVerified email at mssm.edu
Jack HumphreyInstructor, Mount Sinai School of MedicineVerified email at mssm.edu
Yoav GiladUniversity of ChicagoVerified email at uchicago.edu
Konstantina PallaSpotifyVerified email at spotify.com
Michael WainbergProsserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, TorontoVerified email at stanford.edu
Alexis BattleProfessor, Biomedical Engineering, CS, Genetic Medicine at JHUVerified email at jhu.edu
Tom MinkaSenior Principal Researcher, Microsoft Research, Cambridge UKVerified email at microsoft.com
Tim D SpectorGuys and St Thomas Hospital NHS Trust, Kings College LondonVerified email at kcl.ac.uk
Anil RajPrincipal Data Scientist, Calico LabsVerified email at calicolabs.com
Nasa Sinnott-ArmstrongFred Hutchinson Cancer CenterVerified email at fredhutch.org

David A. Knowles

Columbia University & New York Genome Center

Verified email at columbia.edu - Homepage

Machine learning Computational genomics RNA splicing


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Predicting splicing from primary sequence with deep learning K Jaganathan, SK Panagiotopoulou, JF McRae, SF Darbandi, D Knowles, ... Cell 176 (3), 535-548. e24, 2019	2076	2019
Mapping cis- and trans-regulatory effects across multiple tissues in twins E Grundberg, KS Small, ÅK Hedman, AC Nica, A Buil, S Keildson, JT Bell, ... Nature genetics 44 (10), 1084-1089, 2012	893	2012
Opportunities and challenges for transcriptome-wide association studies M Wainberg, N Sinnott-Armstrong, N Mancuso, AN Barbeira, DA Knowles, ... Nature genetics 51 (4), 592-599, 2019	822	2019
Annotation-free quantification of RNA splicing using LeafCutter YI Li, DA Knowles, J Humphrey, AN Barbeira, SP Dickinson, HK Im, ... Nature genetics 50 (1), 151-158, 2018	707	2018
RNA splicing is a primary link between genetic variation and disease YI Li, B Van De Geijn, A Raj, DA Knowles, AA Petti, D Golan, Y Gilad, ... Science 352 (6285), 600-604, 2016	693	2016
Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice LA Becker, B Huang, G Bieri, R Ma, DA Knowles, P Jafar-Nejad, ... Nature 544 (7650), 367-371, 2017	583	2017
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements E Grundberg, E Meduri, JK Sandling, ÅK Hedman, S Keildson, A Buil, ... The American Journal of Human Genetics 93 (5), 876-890, 2013	399	2013
Batch effects and the effective design of single-cell gene expression studies PY Tung, JD Blischak, CJ Hsiao, DA Knowles, JE Burnett, JK Pritchard, ... Scientific reports 7 (1), 39921, 2017	382	2017
Molecular choreography of acute exercise K Contrepois, S Wu, KJ Moneghetti, D Hornburg, S Ahadi, MS Tsai, ... Cell 181 (5), 1112-1130. e16, 2020	375	2020
Distinct epigenomic features in end-stage failing human hearts M Movassagh, MK Choy, DA Knowles, L Cordeddu, S Haider, T Down, ... Circulation 124 (22), 2411-2422, 2011	320	2011
Gene expression changes with age in skin, adipose tissue, blood and brain D Glass, A Viñuela, MN Davies, A Ramasamy, L Parts, D Knowles, ... Genome biology 14, 1-12, 2013	319	2013
Fixed-form variational posterior approximation through stochastic linear regression T Salimans, DA Knowles Bayesian Analysis 8 (4), 837-882, 2013	274	2013
Landscape of stimulation-responsive chromatin across diverse human immune cells D Calderon, MLT Nguyen, A Mezger, A Kathiria, F Müller, V Nguyen, ... Nature genetics 51 (10), 1494-1505, 2019	260	2019
Gaussian Process Regression Networks AG Wilson, DA Knowles, Z Ghahramani Proceedings of the 29th International Conference on Machine Learning (ICML 2011), 2011	255	2011
Infer.NET 2.4 T Minka, J Winn, J Guiver, D Knowles Microsoft Research Cambridge http://research.microsoft.com/infernet, 2010	234*	2010
Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs K Hadi, X Yao, JM Behr, A Deshpande, C Xanthopoulakis, H Tian, ... Cell 183 (1), 197-210. e32, 2020	213	2020
Infer.NET 2.5 T Minka, J Winn, J Guiver, D Knowles Microsoft Research Cambridge http://research.microsoft.com/infernet, 2012	205*	2012
Nonparametric Bayesian sparse factor models with application to gene expression modeling D Knowles, Z Ghahramani	185	2011
Infinite sparse factor analysis and infinite independent components analysis D Knowles, Z Ghahramani International conference on independent component analysis and signal …, 2007	177	2007
Differential methylation of the TRPA1 promoter in pain sensitivity JT Bell, AK Loomis, LM Butcher, F Gao, B Zhang, CL Hyde, J Sun, H Wu, ... Nature communications 5 (1), 2978, 2014	170	2014

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