Assaf Gottlieb, PhD
Assaf Gottlieb, Ph.D., joined the UTHealth School of Biomedical Informatics (SBMI) in January 2017 as an assistant professor and one of the core faculty members of the Center for Precision Health.
Gottlieb arrived to SBMI from IBM Research where he served as a research associate at the Machine Learning for Healthcare and Life Science group in Haifa labs. Prior to his position with IBM, Gottlieb was a postdoctoral fellow at both Stanford University and Tel-Aviv University. He has degrees in Physics and Computer Science and has also worked in software and algorithmic development.
Gottlieb is interested in understanding and modeling drugs mode of action and their relation to drug efficacy, adverse reaction and pharmacogenomics, focusing of chronic conditions. His lab employs an integrative computational approach, combining multiple types of data and applying methodologies from systems medicine, machine learning and causal inference domains to identify population and patient-level factors associated with drug efficacy and adverse reactions and to suggest candidates for drug repurposing. Additionally, his research leverages electronic health records for hypothesis generation and validation of therapeutic outcomes.
- PhD, Computational Biology, 2010, Tel Aviv University
- MSc, Physics, 2001, Tel Aviv University
- BSc, Physics and Computer Science, 1998, Tel Aviv University
Areas of Expertise
- Machine Learning
- Systems Medicine
- Causal inference from observational data
- Fast and Efficient Feature Engineering for Multi-Cohort Analysis of EHR Data
Michal Ozery-Flato, Chen Yanover, Assaf Gottlieb, Omer Weissbrod, Naama Parush-Shear-Yashuv, Yaara Goldschmidt
NIPS 2016 Workshop on Machine Learning for Health
- Ranking adverse drug reactions with crowdsourcing
Assaf Gottlieb, Robert Hoehndorf, Michel Dumontier and Russ B. Altman
J Med Internet Res 2015;17(3):e80.
- Three Dimensional Computational Reconstruction of Tissues using Single Cell Gene Expression Data
Robert Durruthy-Durruthy*, Assaf Gottlieb* and Stefan Heller
Nature Protocols, 2015, 10 459–474.
* equal contribution
- Integrating systems biology sources illuminates drug action
Assaf Gottlieb and Russ B. Altman
Clinical Pharmacology and Therapeutics, 2014, (advance online)
- Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single Cell Resolution
Robert Durruthy-Durruthy, Assaf Gottlieb, Byron H. Hartman, Jörg Waldhaus, Roman Laske, Russ Altman and Stefan Heller
Cell, 2014, 157.4: 964-978.
- A community computational challenge to predict the activity of pairs of compounds
Mukesh Bansal, Jichen Yang, Charles Karan, Michael Patrick Menden, James C. Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura Heiser, Ronald Realubit, Michela Mattioli, Mariano Alvarez, Yao Shen, NCI-DREAM consortium* , Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Andrea Califano, Gustavo Stolovitzky
* As part of the NCI-DREAM consortium
Nature Biotechnology, 2014, 32, 1213–1222.
- A community effort to assess and improve drug sensitivity prediction algorithms
James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A. Khan, John-Patrick Mpindi, NCI DREAM Community*, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, Gustavo Stolovitzky
* As part of the NCI-DREAM Community
Nature Biotechnology, 2014, 32, 1202–1212.
- A method for inferring medical diagnoses from patients similarities
Assaf Gottlieb, Gideon Y. Stein, Eytan Ruppin, Russ B. Altman and Roded Sharan
BMC Medicine, 2013 11:194
- Environmental stresses disrupt telomere length homeostasis
Gal Romano, Yaniv Harari, Tal Yehuda, Ariel Podhorzer, Linda Rubinstein, Ron Shamir, Assaf Gottlieb, Yael Silberberg, Dana Pe'er, Eytan Ruppin, Roded Sharan, Martin Kupiec
PLoS Genetics, 2013 9(9): e1003721.
- INDI: A computational framework for inferring drug interactions and their associated recommendations
Assaf Gottlieb, Gideon Y. Stein, Yoram Oron, Eytan Ruppin and Roded Sharan
Molecular Systems Biology, 2012 8:592
- PREDICT: A method for inferring novel drug indications with application to personalized medicine
Assaf Gottlieb, Gideon Y. Stein, Eytan Ruppin and Roded Sharan
Molecular Systems Biology, 2011 7:496
- PRINCIPLE: A tool for associating genes with diseases via network propagation
Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin and Roded Sharan
Bioinformatics, 2011 27 (23): 3325-3326
- Large scale elucidation of drug response pathways in humans,
Yael Silberberg, Assaf Gottlieb, Eytan Ruppin and Roded Sharan
Journal of Computational Biology (special issue of RECOMB Systems Biology’11), 2012, 19(2): 163-174.
- Combining drug and gene similarity measures for drug-target elucidation
Liat Perlman*, Assaf Gottlieb*, Nir Atias, Eytan Ruppin and Roded Sharan
Journal of Computational Biology, 2011, 18(2): 133-145 (Accepted for RECOMB Satellite Meeting on Systems Biology, 2010)
* equal contribution
- Common peptides study of aminoacyl-tRNA synthetases
Assaf Gottlieb, Milana Frenkel-Morgenstern, Mark Safro and David Horn
PLoS One 2011, 6(5): e20361
- UFFizi: A Generic Platform for Ranking Informative Features
Assaf Gottlieb, Roy Varshavsky, Michal Linial and David Horn
BMC Bioinformatics 2010, 11:300
- Stratification of co-evolving genomic groups using ranked phylogenetic profiles
Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka and Christos A Ouzounis
BMC Bioinformatics 2009, 10:355
- Common peptides shed light on evolution of Olfactory Receptors
Assaf Gottlieb, Tsviya Olender, Doron Lancet and David Horn
BMC Evolutionary Biology 2009, 9:91
- Data mining of protein families using common peptides
Assaf Gottlieb, Uri Weingart and David Horn
Accepted talk at AFP / Biosapiens 2008, an ISMB 2008 Special Interest Group meeting
Available at Nature Precedings
- Unsupervised Feature Selection under Perturbations: Meeting the Challenges of Biological Data
Roy Varshavsky, Assaf Gottlieb, David Horn and Michal Linial
Bioinformatics 2007; 23 (24): 3343-3349.
- Novel Unsupervised Feature Filtering of Biological Data
Roy Varshavsky, Assaf Gottlieb, Michal Linial and David Horn
Bioinformatics (2006) 22 (14): e507-e513 (accepted for oral presentation at ISMB 2006).
- Algorithm for data clustering in pattern recognition problems based on quantum mechanics
David Horn and Assaf Gottlieb
Physical Review Letters. 88 (2002) 18702
- The Method of Quantum Clustering.
David Horn and Assaf Gottlieb, in proceedings of NIPS*01