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Contents

Head of the BioInfo3D Group

Prof. Haim J. Wolfson, School of Computer Science, TAU.

Research Staff

Dr. Naama Hurwitz, School of Computer Science, TAU

Current Graduate Students

Doctoral Students

Name Dept/University Start Year Co-supervisor
Mark Rozanov TAU 2016

Masters Students

Name Dept/University Start Year
Elad Donsky CS,TAU 2007
Aviyah Peri CS,TAU 2008
Dan Cohen CS,TAU 2011
Daniel Zaidman CS,TAU 2011

Former Graduate Students

Doctoral Students

Name Dept/University Thesis Title Period Co-supervisor
Efrat Mashiach CS,TAU Flexible Molecular Docking 2008-2013
Keren Lasker TAU Structure Determination of Macromolecular Assemblies by Data Integration 2008-2012
Yehezkel Lamdan CS,NYU Geometric Hashing 1987-1989 J.T. Schwartz
Daniel Fischer CS,TAU Structural Matching Algorithms in Molecular Biology 1991-1994 R. Nussinov
Raquel Norel CS,TAU Algorithms for Protein Docking 1992-1997 R. Nussinov
Bilha (Billie) Sandak CS,TAU A Method for Biomolecular Structural Recognition allowing Conformational Flexibility 1992-1997 R. Nussinov
Konstantin Kupeev CS,TAU A Structural Method for Shape Recognition 1993-1997 V. Brailovsky
Hadar Benyamini HumGen, MedFac,TAU Applying Novel Geometric Algorithms in the Search for Amyloidogenic Mechanisms 1999-2004 R. Nussinov, MedFac
Inbal Halperin - Landsberg HumGen, MedFac,TAU Improved Docking Schemes Utilizing Biological Information 2001-2005 R. Nussinov, MedFac
Maxim Shatsky CS,TAU The Common Point Set Problem with Applications to Protein Structure Analysis 2001-2006
Nurit Haspel CS,TAU Computational modeling and prediction of self assembling beta-sheet rich protein structures 2001-2006 R. Nussinov
Yuval Inbar CS,TAU Structure Prediction of Multimolecular Protein Complexes 2003-2007
Dina Schneidman-Duhovny CS,TAU Algorithms for Prediction of Molecular Interactions 2003-2008
Oranit Dror CS,TAU Algorithms for Molecular Structure Analysis 2004-2009
Alexandra Shulman-Peleg CS,TAU Algorithms for the Detection and Prediction of 3D Protein Binding Patterns and Interactions 2004-2009
Dan Fishelovitch Human Genetics, MedFac, TAU In Silico prediction of the recognition between small molecules (ligands) and proteins for improved docking and drug design 2004-2009 Ruth Nussinov,MedFac, TAU
Idit Buch Human Genetics, MedFac, TAU In Silico Design, Construction & Validation of Protein Nanostructures 2006-2011 Ruth Nussinov, MedFac, TAU
Ilona Kifer CS,TAU Hierarchical-based Algorithms for Protein Structure Prediction 2005-2011

Masters Students

Name Dept/University Thesis Title Period Co-supervisor
Ephraim (Efi) Cohen CS,BGU Partial Matching of 3-D Objects in CAD/CAM Systems 1993-1995 D. Cohen, CS, BGU
Vladimir Alesker CS,TAU Rapid Macromolecule Comparison by Geometric Secondary Structure Matching 1993-1995
Dan Shappir CS,TAU Mapping of NMR interproton distance onto crystallographically determined protein structures by Computer Vision techniques 1992-1996
Michael Kolko CS,TAU Recognition of Articulated 3D Objects from 2D Images 1993-1996
Georgy Verbitsky CS,TAU Structural Comparison of Flexible Protein Domains 1994-1996
Einat Azarya-Sprinzak HumGen, MedFac,TAU Mutations of Spatially Neighboring Residues in Structurally Conserved Environments 1994-1996 R. Nussinov,
Maria Roiterstein-Rosen CS,TAU Protein Molecule Surface Comparison by Computer Vision Techniques 1994-1997
Nathaniel Leibovitz CS,NYU Multiple Structural Alignment of Protein Ensembles 1997-1999
Maxim Shatsky CS,TAU Flexible Alignment of Protein Molecules 1999-2001
Tal Elkayam HumGen, MedFac,TAU Computational Studies of Protein Binding Sites 1998-2001 R. Nussinov
Nurit Haspel HumGen, MedFac,TAU A Computational Study of Protein Folding Pathways 1999-2002 R. Nussinov
Mark Sadov CS,TAU Flexible Matching of Drug Molecules 1996-2002
Dina Schneidman-Duhovny CS,TAU PatchDock: A Method for Binding Site Detection and Unbound Docking of Rigid Molecules 2000-2003
Adi Barzilay HumGen, MedFac,TAU Detection and Analysis of Folding-Function Inter-relationship in Proteins 2000-2003 R. Nussinov, MedFac
Vladimir Polyak CS,TAU BUDDA: Backbone Unbound Docking Application 2000-2003
Oranit Shem-Tov (Dror) CS,TAU MASS: A Method for Multiple Structural Alignment by Secondary Structures 2000-2003
Yuval Inbar CS,TAU Prediction of Protein Structure by Combinatorial Docking 2001-2003
Alexandra Shulman-Peleg CS,TAU Site-Engine: Functional Sites Structural Search Engine 2002-2004
Assaf Oron HumGen, MedFac,TAU Predicting Electrostatic Steering and Encounter Complexes in Protein-Protein Association Processes 2002-2004 Nussinov, MedFac; N. Ben Tal, Life Sc.
Shira Mintz HumGen, MedFac,TAU Computational Studies of Protein Binding Sites 2003-2005 R. Nussinov
Gilad Weinreb HumGen, MedFac,TAU Templating the Building Blocks and a Secondary-Structure Guided superimposition tool 2003-2005 R. Nussinov
Zipora Fligelman (Shaqed) CS,TAU FLEX MOL: A sequence Order Independent Algorithm for Matching Flexible Molecules by Geometric Hashing 1999-2005
Keren Lasker CS,TAU EMatch: A Method for the Discovery of Protein Substructures in EM Maps 2003-2005
Nelly Bluvshtein-Andrusier CS,TAU FireDock: Fast Interaction REfinement in Molecular Docking 2003-2006 R. Nussinov
Ido Shapira CS,TAU SiteLight 2: An improved method for protein binding site prediction using phage display libraries 2003-2006
Aviad Tsherniak CS,TAU ComaLoop: A Method for Protein Loop Modeling Using Contact Maps Similarity 2004-2006
Efrat Mashiach CS,TAU (transferred to direct Ph.D. track) 2006-2008
Mira Abraham-Cohen CS,TAU DARTS: DAtabase of RNA Tertiary Structure and HARP: geodesic Hashing Alignment of RNA secondary structures including Pseudoknots 2006-2010
Itamar Banitt CS,TAU ParaDock – a flexible DNA rigid protein geometric complementarity based docking algorithm 2009-2010
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