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Publications |
Selected Recent Publications:
· ANAT: A tool
for constructing and analyzing functional protein networks (with N. Yosef,
E. Zalckvar, A.D. Rubinstein, M. Homilius,
N. Atias, L. Vardi, I.
Berman, H. Zur, A. Kimchi
and E. Ruppin)
Journal:
Science Signaling, 4, pl1, 2011: pdf
· PREDICT: A
method for inferring novel drug indications with application to personalized
medicine (with A.
Gottlieb, G.Y. Stein and E. Ruppin)
Journal:
Molecular Systems Biology, 7, #496, 2011: pdf
· Toward
accurate reconstruction of functional protein networks (with N. Yosef,
L. Ungar,
Journal:
Molecular Systems Biology, 5, #248, 2009: pdf
· A
Systems-level Approach to Mapping the Telomere-length Maintenance Gene
Circuitry
(with R. Shachar, L. Ungar, M. Kupiec and
Journal:
Molecular Systems Biology, 4:#172, 2008: pdf
· Transcriptional
regulation of protein complexes within and across species (with K. Tan, T. Shlomi,
H. Feizi and T. Ideker)
Journal:
Proc. Natl. Acad. Sci. USA 104, pp. 1283-1288, 2007: pdf
· Modeling
cellular machinery through biological network comparison (with T. Ideker)
Journal:
Nature Biotechnology 24, pp. 427-433, 2006: pdf
· Conserved
Patterns of Protein Interaction in Multiple Species (with Silpa
Suthram, Ryan Kelley, Tanja
Kuhn, Scott McCuine, Peter Uetz,
Taylor Sittler, Richard Karp and Trey Ideker)
Journal: Proc. Natl. Acad. Sci. USA 102, pp. 1974-1979, 2005: pdf web-site
Full
List:
2012
· Systematic
identification of gene annotation errors in the widely used yeast mutation
collections (with T.
Ben-Shitrit, N. Yosef, K. Shemesh, E. Ruppin and M. Kupiec)
Journal: Nature Methods, doi:10.1038/nmeth.1890,
2012: pdf
· Reconstructing
Boolean models of signaling (with
R.M. Karp)
Proceedings: RECOMB 2012, to appear: pdf
2011
· ANAT: A tool
for constructing and analyzing functional protein networks (with N. Yosef,
E. Zalckvar, A.D. Rubinstein, M. Homilius,
N. Atias, L. Vardi, I.
Berman, H. Zur, A. Kimchi
and E. Ruppin)
Journal:
Science Signaling, 4, pl1, 2011: pdf
· Competitive
and cooperative metabolic interactions in bacterial communities (with S. Freilich,
R. Zarecki, O. Eilam, E. Shiftman-Segal, C.S. Henry, M. Kupiec,
U. Gophna and E. Ruppin)
Journal:
Nature Communications, 2:#589, 2011: pdf
· A Linearized constraint based approach for modeling signaling
networks (with L. Vardi and E. Ruppin)
Journal:
J. Comput. Biol. (special issue of RECOMB Systems
Biology’11), 19:232-240, 2012: pdf
· Large scale
elucidation of drug response pathways in humans (with Y. Silberberg, A. Gottlieb and
E. Ruppin)
Journal:
J. Comput. Biol. (special issue of RECOMB Systems
Biology’11), 19:163-174, 2012: pdf
· PREDICT: A
method for inferring novel drug indications with application to personalized
medicine (with A.
Gottlieb, G.Y. Stein and E. Ruppin)
Journal:
Molecular Systems Biology, 7, #496, 2011: pdf
· On the approximability of reachability
preserving network orientations
(with M. Elberfeld, V. Bafna,
I. Gamzu, A. Medvedovsky, D.
Segev, D. Silverbush and U.
Zwick)
Journal:
Internet Mathematics, 7, pages 209-232, 2011: pdf
· Gene
expression in the rodent brain is associated with its regional connectivity (with L. Wolf, C. Goldberg, M. Manor
and E. Ruppin)
Journal:
PLoS Computational Biology, 7, #e1002040, 2011: pdf
· Approximation
algorithms for orienting mixed graphs
(with M. Elberfeld, D. Segev,
C.R. Davidson and D. Silverbush)
Proceedings:
CPM, pages 416-428, 2011: pdf
· Optimally
orienting physical networks (with
D. Silverbush and M. Elberfeld)
Proceedings:
RECOMB, pages 424-436, 2011: pdf
Journal:
Journal of Computational Biology, 18, pages 1437-1448, 2011: pdf
· Processes of
fungal proteome evolution and gain of function: Gene duplication and domain
rearrangement (with
I. Cohen-Gihon and R. Nussinov)
Journal:
Physical Biology, 8, #035009, 2011: pdf
· Genome-scale
metabolic modeling elucidates the role of proliferative adaptation in causing
the Warburg effect
(with T. Shlomi, T. Benyamini,
E. Gottlieb and E. Ruppin)
Journal:
PLoS Computational Biology, 7, #e1002018, 2011: pdf
· Evolution of
domain promiscuity in eukaryotic genomes – perspective from the inferred
ancestral domain architectures
(with I. Cohen-Gihon, J.H. Fong, R. Nussinov, T.M. Przytycka and A.R.
Panchenko)
Journal:
Molecular Biosystems, 7, pages 784-792,
2011: pdf
2010
· Combining
drug- and gene similarity measures for drug-target elucidation (with L. Perlman, A. Gottlieb, N. Atias and E. Ruppin)
Journal:
J. Computational Biology (Special issue of RECOMB Systems Biology’10),
18, pages 133-145, 2011: pdf
· A novel
HMM-based method for detecting enriched transcription factor binding sites
reveals RUNX3 as a potential target in pancreatic cancer biology (with L. Levkovitz,
N. Yosef, E. Ruppin and Y. Oron)
Journal:
PLoS One, 5, #e14423, 2011: pdf
· Improved
orientations of physical networks (with
I. Gamzu and D. Segev)
Proceedings:
WABI 2010: pdf
· Transcriptional
Regulation by CHIP/LDB Complexes (with
R. Bronstein, L. Levkovitz, N. Yosef,
M. Yanku, E. Ruppin, H. Westphal, B. Oliver and D. Segal)
Journal:
PLoS Genetics, 6:e1001063: pdf
· Expander: from
expression microarrays to networks and functions (with I. Ulitsky,
A. Maron-Katz, S. Shavit,
D. Sagir, C. Linhart, R. Elkon, A. Tanay, Y. Shiloh and R.
Shamir)
Journal:
Nature Protocols, 5, pages 303-322, 2010: pdf
· MAPK signaling
to the early secretory pathway revealed by kinase/phosphatase functional
screening (with H. Farhan, M.W. Wendeler, S. Mitrovic, E. Fava, Y. Silberberg,
M. Zerial and H.-P. Hauri)
Journal:
Journal of Cell Biology, 189:997-1011, 2010: pdf
· The large
scale organization of the bacterial ecological interaction network (with S. Freilich,
A. Kreimer, U. Gophna and
E. Ruppin)
Journal:
Nucleic Acids Research, 38:3857-68, 2010: pdf
· Translation
efficiency in humans: tissue specificity, global considerations and differences
between developmental stages
(with Y. Waldman, T. Tuller, T. Shlomi
and E. Ruppin)
Journal:
Nucleic Acids Research, doi:10.1093/nar/gkq009, 2010:
pdf
· A systems
level strategy for analyzing the cell death network: implication in exploring
the apoptosis/autophagy connection (with E. Zalckvar,
N. Yosef, S. Reef, Y. Ber,
A. D. Rubinstein, E. Ruppin and A. Kimchi)
Journal:
Cell Death and Differentiation, doi:10.1038/cdd.2010.7,
2010: pdf
· Associating
genes and protein complexes with disease (with Oron Vanunu,
Oded Magger, Eytan Ruppin and Tomer Shlomi)
Journal:
PLoS Computational Biology, 6, #e1000641, 2010: pdf
· Network-free
inference of knockout effects in yeast
(with Tal Peleg, Nir Yosef and Eytan Ruppin)
Proceedings:
RECOMB Systems Biology, accepted for oral presentation.
Journal:
PLoS Computational Biology, 6, #e1000635, 2010: pdf
· Decoupling
environment-dependent and independent genetic robustness across bacterial
species (with Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna and Eytan Ruppin)
Journal:
PLoS Computational Biology, 6, #e1000690, 2010: pdf
· Prediction of
phenotype information from genotype data (with
Journal:
Communications in information and systems, 10, pages 99-114, 2010: pdf
· An algorithmic
framework for predicting side-effects of drugs (with Nir Atias)
Proceedings:
RECOMB, pages 1-14, 2010: pdf
Journal:
Journal of Computational Biology, 18, pages 207-218, 2011: pdf
Recipient
of the Best Paper award at RECOMB’10
2009
· A set-cover
based approach for inexact graph matching (with M. Mongiovi, R. Di Natale, R. Giugno, A. Pulvirenti and A. Ferro)
Proceedings:
CSB, pages 81-90, 2009: pdf
Journal:
Journal of Bioinformatics and Computational Biology, 8, pages 199—218,
2010: pdf
Recipient
of the Best Paper Award at CSB’09.
· Metabolic-network
driven strategies of bacterial ecological strategies (with S. Freilich,
A. Kreimer, E. Borenstein,
N. Yosef, U. Gophna and
Journal:
Genome Biology, doi:10.1186/gb-2009-10-6-r61, 2009: pdf
· Increased microRNA activity in human cancers (with A.
Journal:
PLoS One, 6, #e6045, 2009: pdf
· TP53 cancerous
mutations exhibit selection for translation efficiency (with Yedael
Waldman, Tamir Tuller and Eytan Ruppin)
Journal:
Cancer Research, 69, pages 8807-13, 2009: pdf
· Torque:
Topology-free querying of protein interaction networks (with S. Bruckner, F. Hueffner, R. M. Karp and R. Shamir)
Journal:
Nucleic Acids Research, doi:10.1093/nar/gkp474, 2009:
pdf
· A
complex-centric view of protein network evolution (with N. Yosef,
M. Kupiec and
Journal: Nucleic Acids Research, doi:10.1093/nar/gkp414,
2009: pdf
· A genome-wide
screen yeast genes that affect telomere
length maintenance
(with L. Ungar, N. Yosef,
Y. Sela,
Journal:
Nucleic Acids Research, doi:10.1093/nar/gkp259, 2009:
pdf
· Identification
of protein complexes from co-immunoprecipitation data
(with G. Geva)
Journal:
Bioinformatics, 27, pages 111-117, 2011: pdf
· Toward
accurate reconstruction of functional protein networks (with N. Yosef,
L. Ungar,
Journal:
Molecular Systems Biology, 5, #248, 2009: pdf
· Topology-free
querying of protein interaction networks (with S. Bruckner, F. Huffner,
R.M. Karp and R. Shamir)
Proceedings:
RECOMB'09, pages 74-89, 2009: pdf
Journal:
Journal of Computational Biology, 17, pages 237-252, 2010: pdf
2008
· A
network-based method for predicting disease-causing genes (with
Journal:
Journal of Computational Biology (RECOMB Systems Biology special issue), 16,
pp. 181-189, 2009: pdf
· Structural
similarity of genetically interacting proteins (with O. Dror,
D. Schneidman-Duhovny, A. Shulman-Peleg,
R. Nussinov and H. Wolfson)
Journal:
BMC Systems Biology, 2:69, 2008: pdf
· A propagation
based algorithm for inferring gene-disease associations (with O. Vanunu)
Proceedings:
GCB 2008, to appear: pdf
· An algorithm
for orienting graphs based on cause-effect pairs and its application to
orienting protein networks
(with A. Medvedovsky, V. Bafna
and U. Zwick)
Proceedings: WABI 2008, pp. 222-232: pdf
· Improved
network-based identification of protein orthologs (with
Journal:
Bioinformatics (ECCB'08) 24, pp. i200-i206, 2008: pdf
· Protein
networks in disease
(with T. Ideker)
Journal:
Genome Research, 18, pages 644-652, 2008: pdf
· A
Systems-level Approach to Mapping the Telomere-length Maintenance Gene
Circuitry
(with R. Shachar, L. Ungar, M. Kupiec and
Journal:
Molecular Systems Biology, 4:172, 2008: pdf
· NetworkBLAST: comparative analysis of protein
networks (with M. Kalaev, M. Smoot and T. Ideker)
Journal:
Bioinformatics, 24, pages 594-6, 2008: pdf
· Fast and
accurate alignment of multiple protein networks (with M. Kalaev
and V. Bafna)
Proceedings:
RECOMB 2008, pp. 246-256: pdf
Journal:
Journal of Computational Biology, 16, pages 989-999, 2009: pdf
2007
· Haplotyping with missing data via perfect path
phylogenies (with J.
Gramm, T. Nierhoff and T. Tantau)
Journal:
Discrete Applied Mathematics, 155, pages 788-805, 2007: pdf
· Pepitope: epitope
mapping from affinity-selected peptides (with I. Mayrose et al.)
Journal:
Bioinformatics, 23, pages 3244-6, 2007: pdf
· Systematic
condition-dependent annotation of metabolic genes (with T. Shlomi,
M. Herrgard, V. Portnoy, E.
Naim, B.O. Palsson and
Journal: Genome
research, 17, pages 1626-1633, 2007: pdf
· Constraint-based
functional similarity of metabolic genes: going beyong
network topology (with
O. Rokhlenko, T. Shlomi,
Journal:
Bioinformatics, 23, pages 2139-2146, 2007: pdf
· Comprehensive
analysis of co-occurring domain sets in yeast proteins (with I. Cohen-Gihon
and R. Nussinov)
Journal:
BMC Genomics 8:161, 2007: pdf
· SPINE: A framework
for signaling-regularoty pathway inference from
cause-effect experiments
(with O. Ourfali, T. Shlomi,
T. Ideker and
Journal:
Bioinformatics 23 (ISMB'07), pp. I359-I366, 2007: pdf
· Genetic
interactions in yeast: is robustness going bust (with M. Kupiec
and
Journal:
Molecular Systems Biology 3:97, 2007: pdf
· Transcriptional
regulation of protein complexes within and across species (with K. Tan, T. Shlomi,
H. Feizi and T. Ideker)
Journal:
Proc. Natl. Acad. Sci. USA 104, pp. 1283-1288, 2007: pdf
· Medical
sequencing at the extremes of human body mass (with N. Ahituv et al.)
Journal:
American Journal of Human Genetics 80, pp. 779-791, 2007: pdf
· A genome-scale
computational study of the interplay between transcriptional regulation and
metabolism (with T. Shlomi, Y. Eisenberg and
Journal:
Molecular Systems Biology 3:101, 2007: pdf
· Network-based
prediction of protein function
(with I. Ulitsky and R. Shamir)
Journal:
Molecular Systems Biology 3:88, 2007: pdf
· QNet: A tool for querying protein
interaction networks (with
B. Dost, T. Shlomi, N. Gupta,
Proceedings: RECOMB 2007, pp. 1-15: pdf
Journal: Journal of Computational
Biology 15, pp. 913-925, 2008: pdf
2006
· Structural
similarity is a prominent feature of genetic interactions (with O. Dror,
D. Schneidman-Duhovny, A. Shulman-Peleg,
R. Nussinov and H. Wolfson)
Second Annual RECOMB Satellite Workshop on Systems Biology, accepted for oral
presentation.
· Epitope mapping using combinatorial
phage-display libraries: A graph-based algorithm (with I. Mayrose,
T. Shlomi, N.D. Rubinstein, J.M. Gershoni,
Journal: Nucleic Acids Research, doi: 10.1093/nar/gkl975, 2006: pdf
· Gene loss
rate: A probabilistic measure for the conservation of eukaryotic genes (with E. Borenstein,
T. Shlomi and
Journal:
Nucleic Acids Research, doi: 10.1093/nar/gkl792, 2006: pdf
· On the
complexity of SNP block partitioning under the perfect phylogeny model (with J. Gramm, T. Hartman, T. Nierhoff and T. Tantau)
Proceedings:
WABI 2006, pp. 92-102: pdf
Journal:
Discrete Mathematics, in press: pdf
· Flux based vs.
topology based similarity of metabolic genes (with O. Rokhlenko, T. Shlomi,
Proceedings:
WABI 2006, pp. 274-285: pdf
· Identification
of conserved protein complexes based on a model of protein network evolution (with
Journal:
Bioinformatics 23 (ECCB'06), pp. e170-e176, 2007: pdf
· A supervised
approach for identifying discriminating genotype patterns and its application
to breast cancer data
(with
Journal:
Bioinformatics 23 (ECCB'06), pp. e91-e98, 2007: pdf
· A
sequence-based filtering method for ncRNA
identification and its application to searching for riboswitch
elements (with S.
Zhang, I. Borovok, Y. Aharonowitz
and V. Bafna)
Journal: Bioinformatics 22
(ISMB'06), pp. e557-e565: pdf
· Modeling
cellular machinery through biological network comparison (with T. Ideker)
Journal:
Nature Biotechnology 24, pp. 427-433, 2006: pdf
· QPath: a method for querying pathways in a
protein-protein interaction network
(with T. Shlomi, D. Segal and
Journal: BMC Bioinformatics 7:199, 2006: pdf
· Genetic
variation in putative regulatory loci controlling gene expression in breast
cancer (with V. Kristensen, H. Edvardsen, A. Tsalenko, S. Nordgard, T. Sorlie, A. Vailaya, A. Ben-Dor, P.E. Lonning, S. Lien, S. Omholt, A.-C. Syvanen, Z. Yakhini and A.-L. Borresen-Dale)
Journal:
Proc. Natl. Acad. Sci. USA 103, pp. 7735-40, 2006: pdf
· Reconstructing
chain functions in genetic networks (with
I. Gat-Viks, R.M. Karp and R. Shamir)
Journal:
· Systematic
identification of functional orthologs based on
protein network comparison (with
Journal:
Genome Research 16, pp. 428-435, 2006: pdf cover
2005
· Comparison of
protein-protein interaction confidence assignment schemes (with S. Suthram,
T. Shlomi,
Proceedings:
First Annual RECOMB Satellite Workshop on
Systems Biology,
LNBI 2043, pages 39-50, 2007: pdf
Journal:
BMC Bioinformatics 7:360, 2006: pdf
· A Note on
Phasing Long Regions using Local Haplotype
Predictions (with E. Eskin and
Journal:
Journal of Bioinformatics and Computational Biology 4, pp. 639-647,
2006: pdf
· EXPANDER - an
integrative program suite for microarray data analysis (with Ron Shamir, Adi
Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Yosef Shiloh and Ran Elkon)
Journal: BMC Bioinformatics 6,
p. 232, 2005: pdf
· Analysis of
SNP-Expression Association Matrices (with
Anya Tsalenko, Hege Edvardsen, Vessela Kristensen, Anne-Lise Boressen-Dale, Amir Ben-Dor
and Zohar Yakhini)
Proceedings: CSB 2005, pp. 135-143: pdf
Journal: Journal of Bioinformatics
and Computational Biology 4, pp. 259-274, 2006: pdf
· Islands of
Tractability for Parsimony Haplotyping (with Bjarni
Halldorsson and Sorin Istrail)
Proceedings: CSB 2005, pp. 65-72: pdf
Journal: IEEE/ACM Transactions on Computational
Biology and Bioinformatics, in press: pdf
· A Motif-Based
Framework for Recognizing Sequence Families (with Gene Myers)
Journal:
Bioinformatics 21, Suppl. 1 (ISMB’05), pp. i387-i393, 2005: pdf
· Multiplexing
Schemes for Generic SNP Genotyping Assays (with Jens Gramm, Zohar Yakhini and Amir Ben-Dor)
Journal: Journal of Computational
Biology 12, pp. 514-533, 2005: pdf
· Conserved
Patterns of Protein Interaction in Multiple Species (with Silpa
Suthram, Ryan Kelley, Tanja
Kuhn, Scott McCuine, Peter Uetz,
Taylor Sittler, Richard Karp and Trey Ideker)
Journal: Proc. Natl. Acad. Sci. USA 102, pp. 1974-1979, 2005: pdf web-site
· An Initial
Blueprint for Myogenic differentiation (with Alexander Blais,
Mary Tsikitis, Diego Acosta-Alvear,
Yuval Kluger
and Brian Dynlacht)
Journal: Genes and Development 19, pp. 563-569, 2005: pdf
· Effcient Algorithms for Detecting Signaling
Pathways in Protein Interaction Networks (with Jacob Scott, Trey Ideker
and Richard Karp)
Proceedings: RECOMB 2005, pp. 1-13: pdf
Journal: Journal of Computational Biology 13, pp. 133-144, 2006: pdf
2004
· A
1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals
(with Tzvika Hartman).
Proceedings: WABI 2004, pages 50-61: pdf
Journal: Journal of Computer and System Sciences 70, pp. 300-320, 2005: pdf
· CREME: Cis-Regulatory Module Explorer for the human genome (with Asa
Ben-Hur, Gabriela Loots and Ivan Ovcharenko).
Journal: Nucleic Acids Research 32, pp. W253-W256, 2004: pdf
· PathBLAST: A tool for alignment of protein
interaction networks
(with Brian Kelley, Bingbing Yuan, Fran Lewitter, Brent Stockwell and
Trey Ideker).
Journal: Nucleic Acids Research 32, pp. W83-W88, 2004: pdf
· Bayesian Haplotype Inference via the Dirichlet
Process (with Eric
Xing and Michael Jordan).
Proceedings: ICML 2004, pp. 879-886: pdf
Journal: Journal
of Computational Biology,
14, pages 267-284, 2007: pdf
· Revealing
Modularity and Organization in the Yeast Molecular Network by Integrated
Analysis of Highly Heterogeneous Genome-wide Data (with Amos Tanay,
Martin Kupiec and Ron Shamir).
Journal: Proc. Natl. Acad. Sci. USA 101, pp. 2981-2986, 2004: pdf
· Identification
of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein
Interaction Data
(with Trey Ideker, Brian Kelley, Ron Shamir and
Richard Karp).
Proceedings: RECOMB 2004, pp. 282-289: postscript
Journal: Journal of Computational Biology 12, pp. 835-846, 2005: pdf
· A
Discriminative Model for Identifying Spatial Cis-Regulatory
Modules (with Eran Segal).
Proceedings: RECOMB 2004, pp. 141-149: postscript
Journal: Journal of Computational Biology 12, pp. 822-834, 2005: pdf
Recipient of the Best Paper by a Young Scientist Award at RECOMB'04.
· Incomplete
Directed Perfect Phylogeny
(with Itsik Pe'er, Tal Pupko and Ron Shamir).
Journal:
· Optimal Fully
Dynamic Algorithms for Cograph Recognition (with Ron Shamir).
Journal: Discrete Applied Mathematics, 136, pp. 329-340, 2004: postscript
· Reconstructing
Chain Functions in Genetic Networks
(with Irit Gat-Viks, Ron
Shamir and Richard Karp).
Proceedings: PSB 2004, pp. 498-509: postscript
· Multiplexing
Schemes for Generic SNP Genotyping Assays (with Amir Ben-Dor and Zohar Yakhini).
Proceedings: PSB 2004, pp. 140-151: postscript
2003
· Conserved Pathways
within Bacteria and Yeast as revealed by Global Protein Network Alignment (with Brian Kelley, Richard Karp,
Taylor Sittler, David Root, Brent Stockwell
and Trey Ideker).
Journal: Proc. Natl. Acad. Sci. USA 100, pp. 11394-11399, 2003: pdf
· CREME: A
Framework for Identifying Cis-Regulatory Modules in
Human-Mouse Conserved Segments
(with Ivan Ovcharenko, Asa
Ben-Hur and Richard Karp).
Proceedings: ISMB 2003, pp. 283-291: pdf
· Genome-wide
In-silico Determination of Transcriptional Regulation
Modules Controlling Cell Cycle in Human Cells (with Rani Elkon,
Chaim Linhart, Ron Shamir
and Yossi Shiloh).
Journal: Genome Research 13, pp. 773-780, 2003: pdf
· Optimally
Phasing Long Genomic Regions using Local Haplotype
Predictions (with Eleazar Eskin and Eran Halperin).
Proceedings: Second RECOMB Satellite Workshop on Computational Methods for SNPs
and Haplotypes, to appear.
Technical Report: LTR-2003-78,
· On the
Complexity of Haplotyping via Perfect Phylogeny (with Jens Gramm, Till Nierhoff and Till Tantau).
Proceedings: Second RECOMB Satellite Workshop on Computational Methods for SNPs
and Haplotypes, to appear: postscript
· DEFOG: A
Practical Scheme for Deciphering Families of Genes (with Tania Fuchs et al.).
Journal: Genomics 80(3), pp. 295-302, 2002: pdf
· Identifying
Blocks and Sub-Populations in Noisy SNP Data (with Gad Kimmel and Ron Shamir).
Proceedings: WABI 2003, pp. 303-319: postscript
Journal: INFORMS Journal on Computing, Special Issue on Computational
Biology, 16, pp. 360-370, 2004: pdf
· Towards
Optimally Multiplexed Applications of Universal Arrays (with Amir Ben-Dor,
Tzvika Hartman, Richard Karp, Benno
Schwikowski and Zohar Yakhini).
Proceedings: RECOMB 2003, pp. 48-56: postscript
Journal: Journal of Computational Biology, 11(2-3), pp. 476-492, 2004: pdf
· CLICK and
EXPANDER: A System for Clustering and Visualizing Gene Expression Data (with Adi Maron-Katz and Ron Shamir).
Journal: Bioinformatics 19, pp. 1787-1799, 2003: pdf
· Scoring
Clustering Solutions by their Biological Relevance (with Irit
Gat-Viks and Ron Shamir).
Journal: Bioinformatics, 19, pp. 2381-2389, 2003: pdf
2002
and earlier
· Discovering
Statistically Significant Patterns in Gene Expression Data (with Amos Tanay
and Ron Shamir).
Proceedings: ISMB 2002 (Bioinformatics 18, Supplement 1), pp. 136-144: pdf
· On the
Generality of Phylogenies from Incomplete Directed Characters (with Itsik
Pe'er and Ron Shamir).
Proceedings: SWAT 2002: postscript
· Cluster Graph
Modification Problems
(with Dekel Tsur and Ron
Shamir).
Proceedings: WG 2002, pp. 379-390: postscript
Journal: Discrete Applied Mathematics 144, pp. 173-182, 2004: pdf
· A Chemical
Distance Based Test for Positive Darwinian Selection (with T. Pupko,
M. Hasegawa, R. Shamir and D. Graur).
Proceedings: WABI 2001, pp. 142-155: postscript
Journal: Gene 319, pp. 127-135, 2003: pdf
· CLICK: A
Clustering Algorithm with Applications to Gene Expression Analysis (with Ron Shamir).
Proceedings: ISMB 2000, pp. 307-316: postscript pdf
· Incomplete
Directed Perfect Phylogeny
(with Itsik Pe'er and Ron
Shamir).
Proceedings: CPM 2000, pp. 143-153: postscript
· A Fully
Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs (with Pavol
Hell and Ron Shamir).
Proceedings: ESA 1999, pp. 527-539: postscript
Journal: SIAM Journal on Computing, 31(1), pp. 289-305, 2002: postscript
· Complexity
Classification of Some Edge Modification Problems (with Assaf
Natanzon and Ron Shamir).
Proceedings: WG 1999, pp. 65-77: postscript
Journal: Discrete Applied Mathematics 113, pp. 109-128, 2001: pdf
· On the
Complexity of Positional Sequencing by Hybridization (with Amir Ben-Dor,
Itsik Pe'er and Ron
Shamir).
Proceedings: CPM 1999, pp. 88-100: postscript
Journal: Journal of Computational Biology 8(4), pp. 361-371, 2001: pdf
Full version: Electronic Colloquium on Computational Complexity, Technical
report 01-054, 2001: postscript
· A Polynomial
Approximation Algorithm for the Minimum Fill-In Problem (with Assaf
Natanzon and Ron Shamir).
Proceedings: STOC 1998, pp. 41-47: postscript
Journal:
· A New NC
Algorithm for Perfect Matching in Bipartite Cubic Graphs (with Avi Wigderson).
Proceedings: ISTCS 1996, pp. 202-207: postscript
Book
Chapters:
· Cross-species
analysis of protein-protein interaction networks (with Nir Yosef and Eytan Ruppin)
Book: In Protein-protein
interactions and networks: identification, analysis and prediction, to
appear.
· Biclustering Algorithms: A Survey (with Amos Tanay
and Ron Shamir).
Book: In Handbook of Computational
Molecular Biology, Edited by Srinivas Aluru, Chapman &
Hall/CRC,
Computer and Information Science Series, 2005: ps
· Algorithmic
Approaches to Clustering Gene Expression Data (with Ron Shamir).
Book: Current Topics in Computational Biology, T. Jiang, T. Smith, Y. Xu, M.Q. Zhang eds., MIT Press, pp. 269-299, 2002: pdf
· Cluster
Analysis and its Applications to Gene Expression Data (with R. Elkon
and R. Shamir).
Book: Ernst Schering workshop on Bioinformatics and Genome Analysis, Springer Verlag, 2001: pdf
Theses:
· Graph
Modification Problems and their Applications to Genomic Research
Ph.D. Thesis, School of Computer Science, Tel-Aviv University, 2002.
· Perfect
Matching in Parallel Computation
M.Sc. Thesis,