Publications

Year:

Computational Discovery and Experimental Validation of Novel Drug Targets in Immuno-oncology

Arthur Machlenkin, Ofer Levy, Galit Rotman, Amir Toporik, Gady Cojocaru, Yair Benita, Liat Dassa, Tal Fridman, Ilan Vaknin, Shirley Sameah-Greenwald, Inbal Barbiro, Spencer Lang, John Hunter, Eyal Neria, Zurit Levine

Nov 03, 2015
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Establishment of a New Target ADC Portfolio Derived from Predictive Discovery

Kyle Hansen, Gady Cojocaru, Andrew Pow, Andrew Drake, Liat Dassa, Itay Spector, Mark White and Mary Haak-Frendscho

Oct 19, 2015
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Computational identification of natural peptides based on analysis of molecular evolution.

Toporik A, Borukhov I, Apatoff A, Gerber D, Kliger Y.

May 08, 2014
Bioinformatics

The Novel Mas agonist, CGEN-856S, Attenuates Isoproterenol-Induced Cardiac Remodeling and Myocardial Infarction Injury in Rats

Sílvia Q. Savergnini, Danielle Ianzer,Mariana B. L. Carvalho,Anderson J. Ferreira, Gerluza A. B. Silva, Fúlvia D. Marques, Antônio Augusto B. Peluso, Merav Beiman, Gady Cojocaru, Yossi Cohen, Alvair P. Almeida, Galit Rotman, Robson A. S. Santos

Mar 01, 2013
PLOS/one, March 2013

Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures

Ifat Shub, Ehud Schreiber, Yossef Kliger

Feb 01, 2013
ISRN Computational Biology, vol. 2013.

CD6 and Syntaxin Binding Protein 6 Variants and Response to Tumor Necrosis Factor Alpha Inhibitors in Danish Patients with Rheumatoid Arthritis.

Sophine B. Krintel, Laurent Essioux, Assaf Wool, Julia S. Johansen , Ehud Schreiber, Tomer Zekharya, Pinchas Akiva, Mikkel Østergaard, Merete L. Hetland

Jun 07, 2012
PLoS ONE 7(6): e38539

A novel angiopoietin-derived peptide displays anti-angiogenic activity and inhibits tumour-induced and retinal neovascularization.

Palmer G, Tiran Z, Zhou Z, Capozzi M, Park W, Coletta C, Pyriochou A, Kliger Y, Levy O, Borukhov I, Dewhirst M, Rotman G, Penn J, Papapetropoulos A.

Mar 07, 2012
Br J Pharmacol. 2012 Mar;165(6):1891-903

Improving classical substructure-based virtual screening to handle extrapolation challenges.

Biniashvili T, Schreiber E, Kliger Y.

Mar 07, 2012
J Chem Inf Model.

Identification of Widespread Ultra-Edited Human RNAs

Carmi S, Borukhov I, Levanon EY

Oct 25, 2011
PLoS Genet 7(10): e1002317

Hidden conformations in protein structures

Haim Ashkenazy, Ron Unger , Yossef Kliger

May 17, 2011
Bioinformatics 2011,10.1093/bioinformatics/btr292

Follow the leader: preference for specific amino acids directly following the initial methionine in proteins of different organisms.

Shemesh R, Novik A, Cohen Y.

Oct 31, 2010
Genomics Proteomics Bioinformatics. 2010 Sep;8(3):180-9.

Computational approaches to therapeutic peptide discovery

Yossef Kliger

Sep 26, 2010
Biopolymers. 2010;94(6):701-10

Prevention of bleomycin induced pulmonary fibrosis by a novel anti-fibrotic peptide with relaxin like activity

Pini A, Shemesh R, Samuel CS, Bathgate RA, Zauberman A, Hermesh C, Wool A, Bani D, Rotman G.

Sep 08, 2010
J Pharmacol Exp Ther. 2010 Sep 8

Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates.

Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, Rechavi G.

Jul 01, 2010
Proc Natl Acad Sci U S A. 2010 Jun 21

Vascular Relaxation, Antihypertensive Effect, and Cardioprotection of a Novel Peptide Agonist of the Mas Receptor

Silvia Quinta˜o Savergnini, Merav Beiman, Roberto Queiroga Lautner, Vanice de Paula-Carvalho,Kyan Allahdadi, Dalton Caires Pessoa, Fabiana Pereira Costa-Fraga, Rodrigo Arau´jo Fraga-Silva,Gady Cojocaru, Yossi Cohen, Michael Bader, Alvair Pinto de Alm

May 30, 2010
Hypertension, May 17th 2010

Cover illustration of “Reducing phylogenetic bias in correlated mutation analysis”.

Haim Ashkenazy,Yossef Kliger

May 12, 2010
Cover illustration of PEDS Volume 23, Number 5, May 2010.

A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing

Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM

May 01, 2010
PLoS Genet. 2010 May 20

Reducing phylogenetic bias in correlated mutation analysis

Haim Ashkenazy, Yossef Kliger

Jan 12, 2010
Protein Engineering Design and Selection, doi:10.1093/protein/gzp078

A novel human heparanase splice variant, T5, endowed with protumorigenic characteristics.

Barash U, Cohen-Kaplan V, Arvatz G, Gingis-Velitski S, Levy-Adam F, Nativ O, Shemesh R, Ayalon-Sofer M, Ilan N, Vlodavsky I.

Jan 05, 2010
FASEB J. 2009 Dec 9

The interaction of TIGIT with PVR and PVRL2 inhibits human NK cell cytotoxicity.

Stanietsky N, Simic H, Arapovic J, Toporik A, Levy O, Novik A, Levine Z, Beiman M, Dassa L, Achdout H, Stern-Ginossar N, Tsukerman P, Jonjic S, Mandelboim O

Oct 05, 2009
Proc Natl Acad Sci U S A. 2009 Oct 20

Peptides modulating conformational changes in secreted chaperones: From in silico design to preclinical proof of concept.

Kliger Y, Levy O, Oren A, Ashkenazy H, Tiran Z, Novik A, Rosenberg A, Amir A, Wool A, Toporik A, Schreiber E, Eshel D, Levine Z, Cohen Y, Nold-Petry C, Dinarello CA, Borukhov I.

Aug 19, 2009
Proc Natl Acad Sci U S A. 2009 Aug 5.

Systematic antigenic profiling of hematopoietic antigens on ovarian carcinoma cells identifies membrane proteins for targeted therapy development

Limor Helpman,MD;Ben-Zion Katz,PhD;Tamar Safra,MD;Letizia Schreiber,MD;Zurit Levin,PhD;Sergey Nemzer,PhD;Yaron Kinar,PhD;Dan Grisaro,MD

Aug 10, 2009
AJOG j, Volume 201, Issue 2, Pages 196.e1-196.e7 (August 2009)

Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins.

Dan A, Ofran Y, Kliger Y.

Jul 17, 2009
Proteins. 2009 Jul 7.

Characterization of natural human antagonistic soluble CD40 isoforms produced through alternative splicing

Dani Eshel, Amir Toporik, Tali Efrati, Sigal Nakav, Aviva Chen, Amos Douvdevani

Dec 01, 2008
Molecular Immunology, Volume 46, Issue 2, December 2008, Pages 250-257

A novel peptide agonist of FPRL1 (ALX) displays anti-inflammatory and cardioprotective effects

Iris Hecht, Rong Jiang, Andre LF Sampaio, Chen Hermesh, Caleb Rutledge, Ronen Shemesh, Amir Toporik, Merav Beiman, Liat Dassa, Hagit Niv, Gady Cojocaru, Arie Zauberman, Galit Rotman, Mauro Perretti, Jakob Vinten-Johansen, Yossi Cohen

Nov 19, 2008
November 20, 2008; DOI: 10.1124/jpet.108.145821

Discovery and validation of novel peptide agonists for G-protein coupled receptors

Ronen Shemesh, Amir Toporik, Zurit Levine, Iris Hecht, Galit Rotman, Assaf Wool, Dvir Dahary, Eyal Gofer, Yossef Kliger, Michal Ayalon Soffer, Avi Rosenberg, Dani Eshel, and Yossi Cohen

Oct 09, 2008
J Biol Chem. 2008 Oct 9.

Optimal data collection for correlated mutation analysis.

Ashkenazy H, Unger R, Kliger Y.

Jul 24, 2008
Proteins. 2008 Jul 24.

A Novel Recombinant Soluble Splice Variant of Met Is a Potent Antagonist of the Hepatocyte Growth Factor/Scatter Factor-Met Pathway

Zohar Tiran, Anat Oren, Chen Hermesh, Galit Rotman, Zurit Levine, Hagit Amitai, Tal Handelsman, Merav Beiman, Aviva Chen, Dalit Landesman-Milo, Liat Dassa, Yair Peres, Cynthia Koifman, Sarit Glezer, Rinat Vidal-Finkelstein et al.

Jul 15, 2008
Clinical Cancer Research 14, 4612-4621, July 15, 2008

Predicting Proteolytic Sites in Extracellular Proteins: Only Halfway There

Yossef Kliger; Eyal Gofer; Assaf Wool; Amir Toporik; Avihay Apatoff; Moshe Olshansky

Mar 04, 2008
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn084

Altered adenosine-to-inosine RNA editing in human cancer

Paz, N., Levanon, EY., Amariglio, N., Heimberger, AB., Ram, Z., Constantini, S., Barbash, ZS., Adamsky, K., Safran, M., Hirschberg, A., Krupsky, M., Ben-Dov, I., Cazacu, S., Mikkelsen, T., Brodie, C., Eisenberg, E., and Rechavi, G.

Nov 01, 2007
Genome Research 17, 1586-95

RNA-Editing-Mediated Exon Evolution

Lev-Maor, G., Sorek, R., Levanon, EY., Paz, N., Eizenberg, E., and Ast, G.

Feb 27, 2007
Genome Biology 8

Large-Scale Unrestricted Identification of Post-Translation Modifications Using Tandem Mass Spectrometry

Havilio, M., and Wool, A.

Jan 17, 2007
Analytical Chemistry 79, 1362-1368

Towards Alignment Independent Quantitative Assessment of Homology Detection

Apatoff, A., Kim, E., and Kliger, Y.

Dec 27, 2006
PLoS ONE 1

Genomic Fossils as a Snapshot of the Human Transcriptome

Shemesh, R., Novik, A., Edelheit, S., and Sorek, R.

Jan 23, 2006
Proceedings of the National Academy of Sciences of the United States of America 10, 1073

Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data

Havilio, M.

Jan 01, 2006
Journal of Computational Biology 13, 63-80

Transcription-Mediated Gene Fusion in the Human Genome

Akiva, P., Toporik, A., Edelheit, S., Peretz, Y., Diber, A., Shemesh, R., Novik, A., and Sorek, R.

Dec 12, 2005
Genome Research 16, 30-36

Discovering Hidden Viral Piracy

Kim, E. and Kliger, Y.

Oct 06, 2005
Bioinformatics 21, 4216-4222

Letter from the Editor: A-to-I RNA Editing in Alu Repeats in the Human Genome

Levanon, K., Eisenberg, E., Rechavi, G., and Levanon, E.Y.

Sep 01, 2005
EMBO Reports 6, 831-835

Is There Any Sense in Antisense Editing?

Neeman, Y., Dahary, D., Levanon, E.Y., Sorek, R., and Eisenberg, E.

Aug 15, 2005
Trends in Genetics 21, 544-547

Identification of RNA Editing Sites in the SNP Database

Eisenberg, E., Adamsky, K., Cohen, L., Amariglio, N., Hirshberg, A., Rechavi, G., and Levanon, E.Y.

Aug 12, 2005
Nucleic Acid Research 33, 4612-4617

Design of a Genome-Wide siRNA Library Using an Artificial Neural Network

Huesken, D., Lange, J., Mickanin, C., Weiler, J., Asselbergs, F., Warner, J., Meloon, B., Engel, S., Rosenberg, A., Cohen, D., Labow, M., Reinhardt, M., Natt, F., and Hall, J.

Jul 17, 2005
Nature Biotechnology 23, 995-1001

Evidence for Abundant Transcription of Non-Coding Regions in the Saccharomyces Cerevisiae Genome

Havilio, M., Levanon, E.Y., Lerman, G., Kupiec, M., and Eisenberg E.

Jun 16, 2005
BMC Genomics 6, 93

From Genome to Antivirals: SARS as a Test Tube

Kliger, Y., Levanon, E.Y., and Gerber, D.

Mar 01, 2005
Drug Discovery Today 10, 345-352

Evolutionarily Conserved Human Targets of Adenosine to Inosine RNA Editing

Levanon, E.Y., Hallegger, M., Kinar, Y., Shemesh, R., Djinovic-Carugo, K., Rechavi, G., Jantsch, M.F., and Eisenberg, E.

Feb 24, 2005
Nucleic Acids Research 33, 1162-1168

Naturally Occurring Antisense: Transcriptional Leakage or Real Overlap?

Dahary, D., Elroy-Stein, O., and Sorek, R.

Feb 14, 2005
Genome Research 15, 364-368

Is Abundant A-to-I RNA Editing Primate-Specific?

Eisenberg, E., Nemzer, S., Kinar, Y., Sorek, R., Rechavi, G., and Levanon, E.Y.

Feb 01, 2005
Trends in Genetics 21, 77-81

Accurate Identification of Alternatively Spliced Exons Using Support Vector Machine

Dror, G., Sorek, R., and Shamir, R.

Nov 05, 2004
Bioinformatics 21, 897-901

A Non-EST-Based Method for Exon-Skipping Prediction

Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G., and Shamir, R.

Aug 01, 2004
Genome Research 14, 1617-1623

Is the G72/G30 Locus Associated with Schizophrenia? Single Nucleotide Polymorphisms, Haplotypes, and Gene Expression Analysis

Korostishevsky, M., Kaganovich, M., Cholostoy, A., Ashkenazi, M., Ratner, Y., Dahary, D., Bernstein, J., Bening-Abu-Shach, U., Ben-Asher, E., Lancet, D., Ritsner, M., and Navon, R.

Aug 01, 2004
Biological Psychiatry 56, 169-176

Systematic Identification of Abundant A-to-I Editing Sites in the Human Transcriptome

Levanon, E.Y., Eisenberg, E., Yelin, R., Nemzer, S., Hallegger, M., Shemesh, R., Fligelman, Z.Y., Shoshan, A., Pollock, S.R., Sztybel, D., Olshansky, M., Rechavi, G., and Jantsch, M.F.

Jul 18, 2004
Nature Biotechnology 22, 1001-1005

An Oligonucleotide Microchip for Genome-Wide MicroRNA Profiling in Human and Mouse Tissues

Liu, C.G., Calin, G.A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C.D., Shimizu, M., Zupo, S., Dono, M., Alder, H., Bullrich, F., Negrini, M., and Croce, C.M.

Jun 21, 2004
Proceedings of the National Academy of Sciences of the United States of America 101, 9740-9744

hCHL2, a Novel Chordin-Related Gene, Displays Differential Expression and Complex Alternative Splicing in Human Tissues and during Myoblast and Osteoblast Maturation

Oren, A., Toporik, A., Biton, S., Almogy, N., Eshel, D., Bernstein, J., Savitsky, K., and Rotman, G.

Apr 28, 2004
Gene 331, 17-31

Sil overexpression in lung cancer characterizes tumors with increased mitotic activity

Ayelet Erez, Marina Perelman, Stephen M Hewitt, Gadi Cojacaru, Iris Goldberg, Iris Shahar, Pnina Yaron, Inna Muler, Stefano Campaner, Ninette Amariglio, Gideon Rechavi, Ilan R Kirsch, Meir Krupsky, Naftali Kaminski and Shai Izraeli

Apr 26, 2004
Oncogene (2004) 23, 5371–5377

Minimal Conditions for Exonization of Intronic Sequences; 5' Splice Site Formation in Alu Exons

Sorek, R., Lev-Maor, G., Reznik, M., Dagan, T., Belinky, F., Graur, D., and Ast, G.

Apr 23, 2004
Molecular Cell 14, 221-231

Evolution of Multicellularity in Metazoa: Comparative Analysis of the Subcellular Localization of Proteins in Saccharomyces, Drosophila and Caenorhabditis

Hazkani-Covo, E., Levanon, E.Y., Rotman, G., Graur, D., and Novik, A.

Feb 20, 2004
Cell Biology International 28, 171-178

Bridging Expressed Sequence Alignments Through Targeted cDNA Sequencing

Xie, H., Diber, A., Pollock, S., Nemzer, S., Safer, H., Meloon, B., Olson, A., Hwang, J.J., Endress, G.A., Savitsky, K., and Gill-More, R.

Jan 27, 2004
Genomics 83, 572-576

In Search of Antisense

Lavorgna, G., Dahary, D., Lehner, B., Sorek, R., Sanderson, C.M., and Casari, G.

Jan 05, 2004
Trends in Biochemical Sciences 29, 88-94

AluGene: a Database of Alu Elements Incorporated within Protein-Coding Genes

Dagan, T., Sorek, R., Sharon, E., Ast, G., and Graur, D.

Jan 01, 2004
Nucleic Acids Research 32, D489-D492

How Prevalent is Functional Alternative Splicing in the Human Genome?

Sorek, R., Shamir, R., and Ast, G.

Dec 23, 2003
Trends in Genetics 20, 68-71

Preferential Attachment in the Protein Network Evolution

Eisenberg, E. and Levanon, E.Y.

Sep 26, 2003
Physical Review Letters 91, 138701

Cloaked Similarity Between HIV-1 and SARS-CoV Suggests an Anti-SARS Strategy

Kliger, Y. and Levanon, E.Y.

Sep 21, 2003
BMC Microbiology 3, 20

Hierarchical Analysis of Large-Scale Two-Dimensional Gel Electrophoresis Experiments

Rubinfeld, A., Keren-Lehrer, T., Hadas, G., and Smilansky, Z.

Jul 23, 2003
Proteomics 3, 1930-1935

Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse

Sorek, R. and Ast, G.

Jul 01, 2003
Genome Research 13, 1631-1637

Human Housekeeping Genes are Compact

Eisenberg, E. and Levanon, E.Y.

Jul 01, 2003
Trends in Genetics 19, 362-365

The Importance of Alternative Splicing in the Drug Discovery Process

Levanon, E.Y. and Sorek, R.

Jun 01, 2003
TARGETS 2, 109-114

The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons

Lev-Maor, G., Sorek, R., Shomron, N., and Ast, G.

May 23, 2003
Science 300, 1288-1291

A Facile Two-Step Synthesis of Novel Ring-A Double Substituted Tryptophan Building Blocks for Combinatorial Chemistry

Gorohovsky, S., Meir, S., Shkoulev, V., Byk, G., and Gellerman, G.

May 08, 2003
SYNLETT 10, 1411-1414

Widespread Occurrence of Antisense Transcription in the Human Genome

Yelin, R., Dahary, D., Sorek, R., Levanon, E.Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., Nemzer, S., Pinner, E., Walach, S., Bernstein, J., Savitsky, K., and Rotman, G.

Mar 17, 2003
Nature Biotechnology 21, 379-386

Intensity-Based Statistical Scorer for Tandem Mass Spectrometry

Havilio, M., Haddad, Y., and Smilansky, Z.

Feb 01, 2003
Analytical Chemistry 75, 435-444

A Novel Algorithm for Computational Identification of Contaminated EST Libraries

Sorek, R. and Safer, H.M.

Feb 01, 2003
Nucleic Acids Research 31, 1067-1074

Evolutionary Dynamics of Large Numts in the Human Genome: Rarity of Independent Insertions and Abundance of Post-Insertion Duplications

Hazkani-Covo, E., Sorek, R., and Graur, D.

Jan 01, 2003
Journal of Molecular Evolution 56, 169-174

Analysing Gene Expression. A Handbook of Methods: Possibilities and Pitfalls. Sections 4.2.1.3 and 7.8.10

Amit, A. (2002), ed. Lorkowski, S. and Cullen, P. Weinheim

Dec 01, 2002
Wiley-VCH

Computational Analysis of Alternative Splicing Using EST Tissue Information

Xie, H., Zhu, W.Y., Wasserman, A., Grebinskiy, V., Olson, A., and Mintz, L.

Sep 01, 2002
Genomics 80, 326-330

Cloning and Characterization of a Novel Human Gene RNF38 Encoding a Conserved Putative Protein with a RING Finger Domain

Eisenberg, I., Hochner, H., Levi, T., Yelin, R., Kahan, T., and Mitrani-Rosenbaum, S.

May 20, 2002
Biochemical and Biophysical Research Communications 294, 1169-1176

Alu-Containing Exons are Alternatively Spliced

Sorek, R., Ast, G., and Graur, D.

May 08, 2002
Genome Research 12, 1060-1067

Large-Scale Protein Annotation through Gene Ontology

Xie, H., Wasserman, A., Levine, Z., Novik, A., Grebinskiy, V., Shoshan, A., and Mintz, L.

Mar 15, 2002
Genome Research 12, 785-794

Precalibration of Matrix-Assisted Laser Desorption/Ionization-Time of Flight Spectra for Peptide Mass Fingerprinting

Wool, A. and Smilansky, Z.

Feb 01, 2002
Proteomics 2, 1365–1373

Identification of Genes Downstream of Pax6 in the Mouse Lens Using cDNA Microarrays

Chauhan, B.K., Reed, N.A., Zhang, W., Duncan, M.K., Kilimann, M., and Cvekl, A.

Jan 14, 2002
Journal of Biological Chemistry 277, 11539-11548

Unusual Alternative Splicing within the Human Kallikrein Genes KLK2 and KLK3 Gives Rise to Novel Prostate-Specific Proteins

David, A., Mabjeesh, N., Azar, I., Biton, S., Engel, S., Bernstein, J., Romano, J., Avidor, Y., Waks, T., Eshhar, Z., Langer, S.Z., Lifschitz-Mercer, B., Matzkin, H., Rotman, G., Toporik, A., Savitsky, K., and Mintz, L.

Jan 01, 2002
Journal of Biological Chemistry 277, 18084-18090

Predicting Splice Variant from DNA Chip Expression Data

Hu, G.K., Madore, S.J., Moldover, B., Jatkoe, T., Balaban, D., Thomas, J., and Wang, Y.

Jul 01, 2001
Genome Research 11, 1237-1245

Designing Oligo Libraries Taking Alternative Splicing into Account

Shoshan, A., Grebinskiy, V., Magen, A., Scolnicov, A., Fink, E., Lehavi, D., and Wasserman, A.

Jun 01, 2001
Proceedings of The International Society for Optical Engineering 4266, 86-95