Assaf Gottlieb, PhD

Assistant Professor

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.

Contact

Assaf.Gottlieb@uth.tmc.edu
Phone: 713.500.3698
Fax: 713.500.3929

Staff Support

Susan Rojas
Phone: 713.500.3654

Education

  • 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

  • Pharmacogenomics
  • Machine Learning
  • Systems Medicine
  • Causal inference from observational data

Publications

  1. 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
  2. Ranking adverse drug reactions with crowdsourcing
    Assaf Gottlieb, Robert Hoehndorf, Michel Dumontier and Russ B. Altman
    J Med Internet Res 2015;17(3):e80.
  3. 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
  4. Integrating systems biology sources illuminates drug action
    Assaf Gottlieb and Russ B. Altman
    Clinical Pharmacology and Therapeutics, 2014, (advance online)
  5. 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.
  6. 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.
  7. 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.
  8. 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
  9. 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.
  10. 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
  11. 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
  12. 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
  13. 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.
  14. 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
  15. Common peptides study of aminoacyl-tRNA synthetases
    Assaf Gottlieb, Milana Frenkel-Morgenstern, Mark Safro and David Horn
    PLoS One 2011, 6(5): e20361
  16. UFFizi: A Generic Platform for Ranking Informative Features
    Assaf Gottlieb, Roy Varshavsky, Michal Linial and David Horn
    BMC Bioinformatics 2010, 11:300
  17. 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
  18. Common peptides shed light on evolution of Olfactory Receptors
    Assaf Gottlieb, Tsviya Olender, Doron Lancet and David Horn
    BMC Evolutionary Biology 2009, 9:91
  19. 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
  20. 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.
  21. 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).
  22. Algorithm for data clustering in pattern recognition problems based on quantum mechanics
    David Horn and Assaf Gottlieb
    Physical Review Letters. 88 (2002) 18702
  23. The Method of Quantum Clustering.
    David Horn and Assaf Gottlieb, in proceedings of NIPS*01