Aaron Colak, PhD

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Philip M. KimProfessor, University of TorontoVerified email at kimlab.org
TaeHyung Simon KimUniversity of TorontoVerified email at mail.utoronto.ca
Benjamin J. BlencoweProfessor, University of TorontoVerified email at utoronto.ca
Manuel IrimiaCentre for Genomic RegulationVerified email at crg.eu
Martin EsterDistinguished Professor of Computer Science, Simon Fraser UniversityVerified email at cs.sfu.ca
Brendan FreyFounder & CEO, Deep Genomics; Co-Founder, Vector Institute; Professor, University of TorontoVerified email at psi.toronto.edu
Duncan T OdomUniversity of Heidelberg & German Cancer Research Center/DKFZVerified email at dkfz-heidelberg.de
Hui Yuan XiongRenaissance TechnologiesVerified email at psi.toronto.edu
Stephen WattSanger InstituteVerified email at sanger.ac.uk
Nuno Barbosa-MoraisResearch Group Leader, Instituto de Medicina Molecular - LisbonVerified email at medicina.ulisboa.pt
Claudia KutterPrincipal Investigator, Karolinska Institute and SciLifeLab fellow, Science for Life LaboratoryVerified email at ki.se
Michael D. WilsonUniversity of Toronto and SickKids Research InstituteVerified email at sickkids.ca
Serge GueroussovPostdoctoral associate, Broad InstituteVerified email at broadinstitute.org
Leo J. LeeSenior Research Scientist, University of TorontoVerified email at psi.toronto.edu
Joan TeyraRA at Sidhu lab, University of TorontoVerified email at utoronto.ca
Ugur DogrusozProfessor of Computer Engineering, Bilkent University, Ankara, TurkeyVerified email at cs.bilkent.edu.tr
Emek DemirOHSUVerified email at ohsu.edu
Özgün BaburAssistant Professor at University of Massachusetts BostonVerified email at umb.edu
Alexander SchönhuthProfessor, Faculty for Technology, Bielefeld UniversityVerified email at cebitec.uni-bielefeld.de
Jeff WranaSenior Investigator, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto; Professor, Dept. of Mol. Gen., U. ofVerified email at lunenfeld.ca

Aaron Colak, PhD

Head of AI, Qualtrics

Verified email at qualtrics.com - Homepage

Machine learning data mining NLP genomics


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The evolutionary landscape of alternative splicing in vertebrate species NL Barbosa-Morais, M Irimia, Q Pan, HY Xiong, S Gueroussov, LJ Lee, ... Science 338 (6114), 1587-1593, 2012	1174	2012
Tissue-specific alternative splicing remodels protein-protein interaction networks JD Ellis, M Barrios-Rodiles, R Çolak*, M Irimia, TH Kim, JA Calarco, ... Molecular Cell 46 (6), 884-892, 2012	476	2012
Mining Cohesive Patterns from Graphs with Feature Vectors. F Moser, R Colak, A Rafiey, M Ester SIAM Conference on Data Mining 9, 593-604, 2009	208	2009
Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation N Berliner, J Teyra, R Çolak*, SG Lopez, PM Kim PloS one 9 (9), e107353, 2014	90	2014
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing R Colak, TH Kim, M Michaut, M Sun, M Irimia, J Bellay, CL Myers, ... PLoS Comput Biol, 2013	86	2013
ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity DK Witvliet, A Strokach, AF Giraldo-Forero, J Teyra, R Colak, PM Kim Bioinformatics 32 (10), 1589-1591, 2016	85	2016
Improving Hospital Mortality Prediction with Medical Named Entities and Multimodal Learning M Jin, MT Bahadori, A Colak, P Bhatia, B Celikkaya, R Bhakta, ... Machine Learning for Health (ML4H) Workshop at NeurIPS 2018, 2018	81	2018
Inferring cancer subnetwork markers using density-constrained biclustering P Dao, R Colak, R Salari, F Moser, E Davicioni, A Schönhuth, M Ester Bioinformatics 26 (18), i625-i631, 2010	75	2010
Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization U Dogrusoz, EZ Erson, E Giral, E Demir, O Babur, A Cetintas, R Colak Bioinformatics 22 (3), 374-375, 2006	75	2006
Dense graphlet statistics of protein interaction and random networks R Colak, F Hormozdiari, F Moser, A Schonhuth, J Holman, M Ester, ... Pacific Symposium on Biocomputing 14, 178-189, 2009	41	2009
Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins Y Hao, R Colak, J Teyra*, C Corbi-Verge, A Ignatchenko, H Hahne, ... Cell Reports, 2015	37	2015
Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks R Colak*, F Moser, JSC Chu, A Schönhuth, N Chen, M Ester PloS one 5 (10), e13348, 2010	32	2010
End-to-end Joint Entity Extraction and Negation Detection for Clinical Text P Bhatia, B Celikkaya, M Khalilia, A Colak (AAAI) 2019 Workshop on Health Intelligence, 2019	20	2019
JBASE: joint Bayesian analysis of subphenotypes and epistasis R Colak, TH Kim, H Kazan, Y Oh, M Cruz, A Valladares-Salgado, ... Bioinformatics 32 (2), 203-210, 2016	14	2016
An omics perspective of protein disorder J Bellay, M Michaut, TH Kim, S Han, R Colak, CL Myers, PM Kim Molecular BioSystems 8 (1), 185-193, 2012	13	2012
PATIKAmad: Putting microarray data into pathway context O Babur, R Colak, E Demir, U Dogrusoz Proteomics 8 (11), 2196-2198, 2008	9	2008
Uzaktan Eğitimde Yeni Bir Yaklaşım: e-stüdyo T Yiğit, O Bingöl, H Armağan, E Aruğaslan, R Çolak, G Yakut, H Çivril Muğla Üniversitesi, Akademik Bilişim 1, 97-105, 2010	5	2010
Exploratory analysis of co-change graphs for code refactoring H Khosravi, R Colak Advances in Artificial Intelligence: 22nd Canadian Conference on Artificial …, 2009	5	2009
Towards finding the complete modulome: density constrained biclustering R Colak Simon Fraser University, 2008	5	2008
Implementing recommendation algorithms in a large-scale biomedical science knowledge base J Perrie, Y Hao, Z Hayat, R Colak, K Lyons, S Vembu, S Molyneux arXiv preprint arXiv:1710.08579, 2017	2	2017

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