Assaf Gottlieb - Home Page

Assaf Gottlieb

Postdoctoral Fellow, The Blavatnik School of Computer Sciences
Tel Aviv University

Klausner Street, Ramat Aviv, Tel Aviv 69978, Israel.

Tel: +972-(0)3-6407864

I'm the older one,
in case you were wondering...

Academic

I'm a Postdoctoral Fellow under the supervision of Prof. Roded Sharan, Prof. Eytan Ruppin and Prof. Martin Kupiec

My current research interest is in systems medicine, combining multiple drug, target and disease properties to infer various drug traits, e.g. drug targets, drug indications and side effects.
Another research direction is integration of gene expression and protein-protein interaction networks in the context of drugs and diseases

Former research topics include:

Data analysis algorithms.
These include the novel quantum clustering algorithm and novel unsupervised feature filtering algorithm, most suitable in selecting genes from gene-expression microarrays.
I'm also applying and implementing standard machine learning algorithms, such as the Bipartite Spectral CoClustering algorithm
Motif analysis of protein families.
I've used MEX for studying various protein families including enzymes and olfactory receptors.

Publications

Large scale elucidation of drug response pathways in humans
Yael Silberberg , Assaf Gottlieb, Eytan Ruppin and Roded Sharan
Journal: J. Computational Biology (special issue of RECOMB Systems Biology'11), 2012, 19(2): 163-174
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
Common peptides study of aminoacyl-tRNA synthetases
Assaf Gottlieb, Milana Frenkel-Morgenstern, Mark Safro and David Horn
PLoS One 2011, 6(5): e20361
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
*Equal contribution
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 supplementary files
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; Michal Linial
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm528
Novel Unsupervised Feature Filtering of Biological Data
Roy Varshavsky, Assaf Gottlieb, Michal Linial and David Horn
accepted for oral presentation at ISMB 2006. Supplementary Material
Algorithm for data clustering in pattern recognition problems based on quantum mechanics
David Horn and Assaf Gottlieb
Phys. Rev. Lett. 88 (2002) 18702
The Method of Quantum Clustering.
David Horn and Assaf Gottlieb
in proceedings of NIPS*01

M.Sc Thesis - Quantum Clustering

Resources & presentations

Introduction to clustering
COMPACT - Comparative Package for Clustering Assessment can be found here
If you prefer code instead of the COMPACT GUI, you can get Quantum Clustering Matlab files from the following link
Implementation of extended Bipartite Spectral CoClustering algorithm can be found here
Search tool for Olfactory Receptors Common Peptides