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Publications:
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From Leiden to Tel-Aviv University (TAU): exploring clustering solutions via a genetic algorithm (with G. Gilad)
PNAS Nexus, 2:1-7, 2023: link
BERTwalk for integrating gene networks to predict gene- and pathway-level properties (with R. Nasser)
Bioinformatics Advances, 2023: link
A mixture model for signature discovery from sparse mutation data
(with I. Sason, Y. Chen and M. Leiserson)
Genome Medicine, 13:#173, 2021: link
Interactome Mapping Provides a Network of
Neurodegenerative Disease Proteins and Uncovers
Widespread Protein Aggregation in Affected Brains (with C. Haenig, E. Wanker et al.)
Cell Reports 32:#108050, 2020: pdf
A systematic approach to orient the human protein-protein interaction network (with D. Silverbush)
Nature Communications 10:#3015, 2019: pdf
Network propagation: a universal amplifier of genetic associations
(with L. Cowen, T. Ideker and B. Raphael)
Nature Reviews Genetics, 18:551-562, 2017: pdf
SPIDER: Constructing cell-type-specific protein-protein interaction networks (with Y. Kupershmidt and S. Kasif)
Bioinformatics Advances, 4:#vbae130, 2024: pdf
Current and future directions in network biology (with M. Zitnik et al.)
Bioinformatics Advances, 4:#vbae099, 2024: pdf
Chronic Lymphocytic Leukemia (CLL)-Derived Extracellular Vesicles Educate Endothelial Cells to Become IL-6-Producing, CLL-Supportive Cells (with O. Uziel et al.)
Biomedicines, 12:#1381, 2024: pdf
Multi-modal contrastive learning of subcellular organization using DICE (with R. Nasser, L. Schaffer and T. Ideker)
Bioinformatics (special issue of ECCB'24), 40, pp. II105-II110, 2024:
pdf
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors ((with R. Sheinin et al.)
npj Systems Biology and Applications, 10:#66, 2024: pdf
D'or: Deep orienter of protein-protein interaction networks (with D. Pirak)
Bioinformatics, 40:#btae355, 2024: pdf
Deep cell-type deconvolution from bulk gene expression data using DECODE (with E. Hermush)
Digital Medicine and Healthcare Technology, 3, pp. 1-11, 2024:
pdf
An integer programming framework for identifying stable components in asynchronous Boolean networks (with S. Jacobson)
Proc. RECOMB'24, pp. 86-98, 2024: pdf
A network-based method for associating genes with autism spectrum disorder (with G. Ast and N. Zadok)
Frontiers in Bioinformatics, 4:#1295600, 2024: pdf
Integer Programming Based Algorithms for Overlapping Correlation Clustering (with B. Mashiach)
From computational logic to computational biology, LNCS 14070, pages 115-127, Springer, 2024: pdf
Batch correction of single cell sequencing data via an autoencoder architecture (with R. Danino and I. Nachman)
Bioinformatics Advances, 2023: link
SARS-CoV-2 variants evolve convergent strategies to remodel the host response (with M. Bouhaddou, N. Krogan et al.)
Cell, 186:4597-4614, 2023: link
BERTwalk for integrating gene networks to predict gene- and pathway-level properties (with R. Nasser)
Bioinformatics Advances, 2023: link
From Leiden to Tel-Aviv University (TAU): exploring clustering solutions via a genetic algorithm (with G. Gilad)
PNAS Nexus, 2:1-7, 2023: link
A mutation-level covariate model for mutational signatures (with I. Kahane and M. Leiserson)
PLoS Computational Biology, 5:#e1011195, 2023: pdf
A biterm topic model for sparse mutation data (with I. Sason, Y. Chen and M. Leiserson)
Cancers, 15:#1601, 2023: pdf
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder
(with A. Gervits)
Journal: Frontiers in Bioinformatics, doi.org/10.3389/fbinf.2022.1025783, 2022: pdf
A comparative analysis of telomere length maintenance circuits in fission and budding yeast
(with I. Peretz and M. Kupiec)
Journal: Frontiers in Genetics, doi:10.3389/fgene.2022.1033113, 2022: pdf
Exosomal telomerase transcripts reprogram the microRNA transcriptome profile of fibroblasts and partially contribute to CAF formation
(with D. Likonen, O. Uziel et al.)
Journal: Scientific Reports, 12, \#16415, 2022: pdf
Multi-task learning for predicting SARS-CoV-2 antibody escape
(with B. Gross)
Journal: Frontiers in Genetics, 13:#886649, 2022: pdf
Gene architecture directs splicing outcome in separate nuclear spatial regions
(with L. Tammer, G. Ast et al.)
Journal: Molecular Cell, 82:1021-1034, 2022: pdf
Deep unfolding for non-negative matrix factorization with application to mutational signature analysis
(with R. Nasser and Y. Eldar)
Journal: J. Computational Biology (RECOMB'21 special issue), 29, pages 45-55, 2022:
pdf
ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures
(with N. Franzese, J. Fan and M. Leiserson)
Journal: J. Computational Biology (RECOMB'21 special issue), 29, pages 56-73, 2022: pdf
A mixture model for signature discovery from sparse mutation data
(with I. Sason, Y. Chen and M. Leiserson)
Proceedings: RECOMB 2020, pp. 271-2.
Journal: Genome Medicine, 13:#173, 2021: link
Effect of SARS-CoV-2 proteins on vascular permeability
(with R. Rauti et al.)
Journal: eLife, 10:e69314, 2021: pdf
A data-driven approach for constructing mutation categories for mutational signature analysis
(with G. Gilad and M. Leiserson)
Journal: PLoS Computational Biology, 17:#e1009542, 2021: pdf
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution
(with S. Margalit, Y. Ebenstein et al.)
Journal: Bioinformatics 37 (ISMB'21 special issue), pages I327-I333, 2021:
pdf
Mutations signatures: from methods to mechanisms
(with Y.-A. Kim, M. Leiserson, P. Moorjani, D. Wojtowicz and T. Przytycka)
Journal: Annual Review of Biomedical Data Science 4:189-206, 2021:
link
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage specific transcriptional plasticity (with O. Shani, N. Erez et al.)
Journal: eLife, 10:e60745, 2021:pdf
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
(with J. Ma, T. Ideker et al.)
Journal: Nature Cancer, 2, pp. 233-244, 2021: pdf
Prediction of cancer dependencies from expression data using deep learning (with N. Itzhacky)
Journal: Molecular Omics, 17, pp. 66-71, 2021: pdf
An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning
(with G. Gilad and I. Sason)
Journal: Machine Learning: Science and Technology, 2021:
pdf
Interactome Mapping Provides a Network of
Neurodegenerative Disease Proteins and Uncovers
Widespread Protein Aggregation in Affected Brains (with C. Haenig, E. Wanker et al.)
Journal: Cell Reports 32:#108050, 2020: pdf
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality (with A. Levitan, A. Gale, E. Dallon, D. Kozan, K. Cunningham and J. Berman)
Journal: Current Genetics, DOI: 10.1007/s00294-020-01096-6, 2020: pdf
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions (with A. Gale, R. Sakhawala, A. Levitan, J. Berman, W. Timp and K. Cunningham)
Journal: G3, 10:3859-3870, 2020: pdf
Network-based Approaches Elucidate Differences Within APOBEC and Clock-Like Signatures in Breast Cancer (with Y.-A. Kim, D. Wojtowicz, R. Sarto Basso, I. Sason, W. Robinson, D. Hochbaum, M. Leiserson, F. Vandin and T. Przytycka)
Journal: Genome Medicine, 12:#52, 2020: pdf
G2G: A web-server for the prediction of human synthetic lethal interactions (with Y. Almozlino, I. Peretz and M. Kupiec)
Journal: Computational and Structural Biotechnology J., 18, pp. 1028-1031, 2020: pdf
DNA repair footprint uncovers contribution of DNA repair mechanisms to mutational signatures (with D. Wojtowicz, M. Leiserson and T. Przytycka)
Proceedings: PSB 25:262-273, 2020: pdf
Genome architecture and stability in the Saccharomyces cerevisiae knockout collection (with F. Puddu et al.)
Journal: Nature, 573:416-420, 2019: pdf
A systematic approach to orient the human protein-protein interaction network (with D. Silverbush)
Journal: Nature Communications 10:#3015, 2019: pdf
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance (with W. Song and I. Ovcharenko)
Genome Biology, 20:197, 2019: pdf
Assessment of network module identification across complex diseases
(with The DREAM Module Identification Challenge Consortium)
Journal: Nature Methods, 16:843-852, 2019:pdf
The EXPANDER Integrated Platform for Transcriptome Analysis
(with T. Hait, A. Maron-Katz, D. Sagir, D. Amar, I. Ulitsky, C. Linhart, A. Tanay, Y. Shiloh, R. Elkon and R. Shamir)
Journal: J. Molecular Biology, 431:2398-2406, 2019: pdf
Hidden Markov Models Lead to Higher Resolution Maps of Mutation Signature Activity in Cancer
(with D. Wojtowicz, I. Sason, X. Huang, Y.-A. Kim, M. Leiserson and T. Przytycka)
Journal: Genome Medicine, 11:#49, 2019: pdf
Modeling Clinical and Molecular Covariates of Mutational Process Activity in Cancer
(with W. Robinson and M. Leiserson)
Journal: Bioinformatics (ISMB'19 special issue), 35, pp. I492-I500, 2019:
pdf
To embed or not: Network embedding as a paradigm in computational biology (with W. Nelson, M. Zitnik, B. Wang, J. Leskovec and A. Goldenberg)
Journal: Frontiers in Genetics, 10:#381, 2019: pdf
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules
(with D. Silverbush, S. Cristea, G. Yanovich, T. Geiger and N. Beerenwinkel)
Proceedings: RECOMB, pp. 283-284, 2018.
Journal: Cell Systems, doi: 10.1016/j.cels.2019.04.005, 2019: pdf
A Robustness Analysis of Dynamic
Boolean Models of Cellular Circuits
(with Ariel Bruner)
Proceedings: ISBRA, pp. 183-195, 2019.
Journal: J. Computational Biology, 27, pp. 133-143, 2020: pdf
A sticky multinomial mixture model of strand-coordinated
mutational processes in cancer
(with I. Sason, D. Wojtowicz, W. Robinson, M. Leiserson and T. Przytycka)
Proceedings: RECOMB, pp. 243-255, 2019.
Journal: iScience, 23:#100900, 2020: pdf
Comparative analysis of normalization methods for network propagation (with H. Biran and M. Kupiec)
Journal: Frontiers in Genetics, 10:#4, 2019: pdf
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans
(with E.S. Segal, V. Gritsenko, A. Levitan, B. Yadav, N. Dror, J.L. Steenwyk, Y. Silberberg, K. Mielich, A. Rokas, N.A.R. Gow, R. Kunze and J. Berman)
Journal: mBio, 9, e02048-18, 2018: pdf
Using deep learning to model the hierarchical structure and function of a cell
(with J. Ma, M. Yu, S. Fong, K. Ono, E. Sage, B. Demchak and T. Ideker)
Journal: Nature Methods, 2018: pdf
A dynamic algorithm for network propagation
(with B. Sternberg)
Proceedings: WABI, pp. 1-13, 2018: pdf
Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas
(with A. Atak, S. Khurana, K. Gollapalli, P.J. Reddy, R. Levy, S. Ben-Salmon,
D. Hollander, M. Donyo, A. Heit, A. Hotz-Wagenblatt, H. Biran, S. Rane,
A. Shelar, G. Ast and S. Srivastava)
Journal: Oncotarget 9:13530-13544, 2018: pdf
An optimization framework for network annotation
(with S. Patkar)
Journal: Bioinformatics 34 (ISMB'18), pp. I502-I508, 2018: pdf
WebPropagate: a web-server for network propagation
(with H. Biran, T. Almozlino and M. Kupiec)
Journal: J. Molecular Biology, 430, pp. 2231-2236, 2018: pdf
Network propagation: a universal amplifier of genetic associations
(with L. Cowen, T. Ideker and B. Raphael)
Journal: Nature Reviews Genetics, 18:551-562, 2017: pdf
ANAT 2.0: reconstructing functional protein subnetworks
(with Y. Almozlino, N. Atias and D. Silverbush)
Journal: BMC Bioinformatics, 18:#495, 2017: pdf
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer
(with S. Patkar, A. Magen and S. Hannenhalli)
Journal: PLoS Computational Biology, in press.
GLADIATOR: a global approach for elucidating disease modules
(with Y. Silberberg and M. Kupiec)
Journal: Genome Medicine, 9:#48, 2017: pdf
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence
and Functional Interactions
(with P. Dao, Y.-A. Kim, D. Wojtowicz, S. Madan and T. Przytycka)
Proceedings: RECOMB 2017, pp. 370-371.
Abstract: Cell Systems, in press.
Journal: PLoS Computational Biology, 13:e1005695, 2017: pdf
Genome Rearrangement with ILP
(with T. Hartmann, N. Wieseke, M. Middendorf and M. Bernt)
Proceedings: APBC 2017.
Journal: IEEE/ACM Trans. Comput. Biol. Bioinform., in press.
Elucidation of Signaling Pathways
from Large-Scale Phosphoproteomic
Data Using Protein Interaction Networks
(with J.D. Rudolph, M. de Graauw, B. van de Water and T. Geiger)
Journal: Cell Systems, 3:585-593, 2016: pdf
Quantifying deleterious effects of regulatory variants
(with S. Li, R.V. Alvarez, D. Landsman and I. Ovcharenko)
Journal: Nucleic Acid Research, doi:10.1093/nar/gkw1263, 2016: pdf
Utilizing yeast
chemogenomic profiles for the prediction of pharmacogenomic associations in
humans
(with Y. Silberberg and M. Kupiec)
Journal: Scientific Reports, 6:#23703, 2016: pdf
Systematic Identification and Correction of Annotation Errors in the Genetic
Interaction Map of Saccharomyces Cerevisiae
(with N. Atias and M. Kupiec)
Journal: Nucleic Acids Rsearch, 44:#e50, 2016: pdf
Copy-Number Evolution Problems: Complexity and Algorithms
(with M. El-Kebir, B. Raphael, R. Shamir, S. Zaccaria, M. Zehavi and R. Zeira)
Proceedings: WABI, pp. 137-149, 2016.
Journal: Algorithms for Molecular Biology 12:#13, 2017: pdf
An integer programming framework for inferring disease complexes from network data
(with A. Mazza, K. Klockmeier and E. Wanker)
Journal: Bioinformatics (ISMB'16), 32:i271-i277, 2016: pdf
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
(with D. Hollander, M. Donyo, N. Atias, K. Mekahel, Z. Melamed, S. Yannai, G. Lev-Maor, A. Shilo, S. Schwartz, I. Barshackand and G. Ast)
Journal: Genome Research, 26, pp. 541-553, 2016: pdf
Metabolic network prediction of drug side effects
(with I. Shaked, M. Oberhardt, N. Atias and E. Ruppin)
Journal: Cell Systems, 2, pp. 209-213, 2016: pdf
Translation of genotype to phenotype by a hierarchy of cell subsystems
(with M. Yu, M. Kramer, J. Dutkowski, R. Srivas, K. Licon, J. Kreisberg, C. Ng, N. Krogan and T. Ideker)
Journal: Cell Systems, 2, pp. 77-88, 2016: pdf
Proteomic analysis of dynein-interacting proteins in Amyotrophic Lateral Sclerosis synaptosomes reveals alterations in the RNA-binding protein Staufen1
(with N. Gershoni-Emek, A. Mazza, M. Chein, T. Gradus-Pery, X. Xiang, K.W. Li and E. Perlson)
Journal: Molecular and Cellular Proteomics, 15, pp. 506-522, 2016: pdf
Inference of personalized drug targets via network propagation
(with O. Shnaps, E. Perry and D. Silverbush)
Proceedings: Pacific Symposium on Biocomputing, pp. 156-167, 2016: pdf
Network-based integration of disparate omic data to identify silent players in cancer
(with M. Ruffalo and M. Koyuturk)
Journal: PLoS Computational Biology, 11:#e1004595, 2015: pdf
Functional
Alignment of Metabolic networks
(with A. Mazza, A. Wagner and E. Ruppin)
Proceedings: RECOMB, pp. 243-255, 2015: pdf
Journal: J. of Computational Biology, 23, pp. 390-399, 2016: pdf
Prediction of human population responses to toxic compounds by a
collaborative competition
(with The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration)
Journal: Nature Biotechnology, 2015: pdf
Human protein interaction networks across tissues and diseases
(with E. Yeger-Lotem)
Journal: Frontiers in Genetics, 6:257, 2015: pdf
Regulation
of Sec16 levels and dynamics links proliferation and secretion
(with
K.D. Tillmann, V. Reiterer, F. Baschieri, J. Hoffmann, V. Millarte,
M.A. Hauser, A. Mazza, N. Atias, D.F. Legler, M. Weiss and H. Farhan)
Journal: J. of Cell Science, 128, pp. 670-682, 2015: pdf
The
effects of telomere shortening on cancer cells: Network model of
proteomic and microRNA analysis (with O. Uziel et al.)
Journal: Genomics, 105, pp. 5-16, 2015: pdf
Experimental
design schemes for learning
Boolean network mdoels (with N. Atias, M. Gershenzon and K.
Labazin)
Journal: Bioinformatics (ECCB'14 special issue), 30, pp. I445-I452,
2014: pdf
Modelling
the yeast interactome (with V. Janjic and N. Przulj)
Journal: Scientific Reports, 4:#4273, 2014: pdf
Network
orientation via shortest paths
(with D. Silverbush)
Journal: Bioinformatics, 30, pp. 1449-55, 2014: pdf
A method
for predicting protein-protein interaction types (with Y.
Silberberg and M. Kupiec)
Journal: PLoS One, 9:#e90904, 2014: pdf
Elucidating
Influenza inhibition pathways
via network reconstruction (with A. Mazza and I. Gat-Viks)
Journal: J. Computational Biology (Special issue of RECOMB Systems
Genomics'13), 21, pp. 394-404, 2014: pdf
Pathways
of Toxicity (t4 workshop report)
(with A. Kleensang et al.)
Journal: ALTEX, 31, pp. 53-61, 2014: pdf
Pathway-based
analysis of genomic variation data (with N. Atias and
S.Istrail)
Journal: Current Opinion in Genetics and Development, 23, pp. 622-626 ,
2013: pdf
Toward a
role model
Journal: EMBO Reports, 14, p. 948, 2013: pdf
A method
for inferring medical diagnoses from patient similarities (with
A. Gottlieb, G. Stein, E. Ruppin and R. Altman)
Journal: BMC Medicine, 11:#194, 2013: pdf.
Network-based
interpretation of genomic variation data (with B.
Halldorsson)
Journal: J. of Molecular Biology, 425, pp. 3964-3969, 2013: pdf.
A
minimum labeling approach for reconstructing protein networks across
multiple conditions (with A. Mazza, I. Gat-Viks and H.
Farhan)
Proceedings: WABI, pp. 33-44, 2013.
Journal: Algorithms in Molecular Biology, 9:#1, 2014: pdf
Environmental
stresses disrupt telomere length homeostasis (with
G. Romano, Y. Harari, T. Yehuda, A. Podhorzer, L. Rubinstein, R.
Shamir, A. Gottlieb, Y. Silberberg, D. Peer, E. Ruppin and M. Kupiec)
Journal: PLoS Genetics, 9:#e1003721, 2013:
pdf.
A genetic screen for high copy number
suppressors of the synthetic lethality between Elg1 and Srs2 in yeast (with
I. Gazy, B. Liefshitz, A. Bronstein, O. Parnas, N. Atias and M. Kupiec)
Journal: G3, 3, pp. 917-926, 2013: pdf.
Alternative splicing regulates biogenesis of
miRNAs located across exon-intron junctions (with Z.
Melamed, A. Levy, R. Ashwal-Fluss, G. Lev-Maor, K. Mekahel, N. Atias,
S. Gilad, C. Levy, S. Kadener and G. Ast)
Journal: Molecular Cell, 50, pp. 869-881, 2013: pdf.
Simultaneous identification of multiple
driver pathways in cancer (with M.
Leiserson, D. Blokh and B. Raphael)
Journal: PLoS Computational Biology, 9:#e1003054, 2013: pdf.
iPoint: an integer programming based
algorithm for inferring protein subnetworks (with N. Atias)
Journal: Molecular Biosystems, DOI: 10.1039/C3MB25432A, 2013: pdf.
Enhancing
the prioritization of disease-causing genes through tissue-specific
protein interaction networks (with O. Magger, Y.Y. Waldman
and E. Ruppin)
Journal: PLoS Computational Biology, 8:#e1002690, 2012.: pdf
Met
kinetic signature derived from the response to HGF/SF in a cellular
model predicts breast cancer patient survival (with G.Y.
Stein, N. Yosef, H. Reichman, J. Horev, A. Laser-Azogui, A. Berens, J.
Resau, E. Ruppin and I. Tsarfaty),
Journal: PLoS One, 7, #e45969, 2012: pdf.
INDI: A
computational framework for inferring drug interactions and their
associated recommendations (with A. Gottlieb, G. Stein, Y.
Oron and E. Ruppin)
Journal: Molecular Systems Biology, 8:#592, 2012: pdf
Estimating
population size via line graph reconstruction (with B.
Halldorsson and D. Blokh),
Proceedings: WABI, Lecture Notes in Computer Science 7534, pp.
69-80, 2012 pdf
Journal: Algorithms for Molecular Biology, 8:#17, 2013: pdf
Sign
assignment problems on protein networks (with S. Houri)
Proceedings: WABI 2012, Lecture Notes in Computer Science 7534, pp
338-345, 2012 pdf
Comparative
analysis of protein networks: Hard problems, practical solutions (with
N. Atias)
Journal: Communications of the ACM, 55, pp. 88-97, 2012 (cover story): pdf
Approximation
algorithms and hardness results for shortest path based graph
orientations (with D. Blokh and D. Segev)
Proceedings: CPM 2012, Lecture Notes in Computer Science 7354, pp
70-82, 2012: pdf
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
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.
Reconstructing
Boolean models of signaling (with R.M. Karp)
Proceedings: RECOMB, pp. 261-271, 2012: pdf.
Journal: J. Comput. Biol., 20, pp. 249-257, 2013: pdf.
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
PRINCIPLE:
A tool for associating genes with diseases via network propagation (with
A. Gottlieb, O. Magger, I. Berman and E. Ruppin)
Journal: Bioinformatics, 27, pages 3325-6, 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
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
Journal: Theoretical Computer Science, 483, pp. 96-103, 2013: preprint; publisher-link
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
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'10, pp. 215-225, 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 via network propagation (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 S. Freilich, A. Kreimer, E.
Boirenstein, U. Gophna and E. Ruppin)
Journal: PLoS Computational Biology,
6, #e1000690, 2010: pdf
Prediction
of phenotype information from genotype data (with N. Yosef,
J. Gramm, Q.-f. Wang, W.S. Noble and R. M. Karp)
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
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 E.
Ruppin)
Journal: Genome Biology, doi:10.1186/gb-2009-10-6-r61, 2009: pdf.
Increased
microRNA activity in human cancers (with A.
Israel, E. Ruppin and E. Galun)
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 E. Ruppin)
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, E. Ruppin and M. Kupiec)
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, E. Zalckvar, A. Kimchi, M. Kupiec and E. Ruppin)
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.
A
network-based method for predicting disease-causing genes (with
S. Karni and H. Soreq)
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 N.
Yosef and W. S. Noble)
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 E.
Ruppin)
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. Bafn)
Proceedings: RECOMB 2008, pp. 246-256: pdf.
Journal: Journal of Computational Biology, 16, pages 989-999, 2009: pdf.
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 E. Ruppin)
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, E. Ruppin and R.Y.
Pinter)
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 E.
Ruppin)
Journal: Bioinformatics 23 (ISMB'07), pp. I359-I366, 2007: pdf.
Genetic
interactions in yeast: is robustness going bust (with M.
Kupiec and E. Ruppin)
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 E. Ruppin)
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, E. Ruppin and V. Bafna)
Proceedings: RECOMB 2007, pp. 1-15: pdf.
Journal: Journal of Computational Biology 15, pp. 913-925, 2008: pdf.
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, E. Ruppin and T. Pupko)
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 E. Ruppin)
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, E. Ruppin and R.Y. Pinter)
Proceedings: WABI 2006, pp. 274-285: pdf.
Identification
of conserved protein complexes based on a model of protein network
evolution (with E. Hirsh)
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 N. Yosef, Z.
Yakhini, A. Tsalenko, V. Kristensen, A.-L. Borresen-Dale and E. Ruppin)
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.
QPath: a
method for querying pathways in a protein-protein interaction network (with
T. Shlomi, D. Segal and E. Ruppin)
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-D)
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: SIAM J. Discrete Mathematics 20, pp. 727-740, 2007: pdf.
Systematic
identification of functional orthologs based on protein network
comparison (with S. Bandyopadhyay and T. Ideker)
Journal: Genome Research 16, pp. 428-435, 2006: pdf, Cover.
Comparison
of protein-protein interaction confidence assignment schemes (with
S. Suthram, T. Shlomi, E. Ruppin and T. Ideker)
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 E. Halperin)
Journal: Journal of Bioinformatics and Computational Biology 4, pp.
639-647, 2006: pdf
Modeling
cellular machinery through biological network comparison
(with T. Ideker)
Journal: Nature Biotechnology 24, pp. 427-433, 2006: 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.
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.
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.
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.
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.
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)
Proceedings: RECOMB 2005, pp. 1-13: pdf.
Journal: Journal of Computational Biology 13, pp. 133-144, 2006: 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: pdf.
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: pdf.
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: SIAM Journal on Computing, 33(3), pp. 590-607, 2004: pdf.
Optimal
Fully Dynamic Algorithms for Cograph Recognition (with Ron
Shamir)
Journal: Discrete Applied Mathematics, 136, pp. 329-340, 2004: pdf.
Reconstructing
Chain Functions in Genetic Networks (with Irit Gat-Viks, Ron
Shamir and Richard Karp)
Proceedings: PSB 2004, pp. 498-509: pdf.
Multiplexing
Schemes for Generic SNP Genotyping Assays (with Amir Ben-Dor
and Zohar Yakhini)
Proceedings: PSB 2004, pp. 140-151: pdf.
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, LNBI, Springer, 2004 pdf.
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, LNBI, Springer, 2004 pdf.
Technical Report: LTR-2003-78, Leibniz Center, Hebrew University, 2003:
pdf.
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, LNBI, Springer, 2004 pdf.
Identifying
Blocks and Sub-Populations in Noisy SNP Data (with Gad
Kimmel and Ron Shamir)
Proceedings: WABI 2003, pp. 303-319: pdf.
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: pdf.
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.
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: ISMB 2003, pp. 283-291: pdf.
Cluster
Graph Modification Problems (with Dekel Tsur and Ron Shamir)
Proceedings: WG 2002, pp. 379-390: pdf.
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: pdf.
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: pdf.
Incomplete
Directed Perfect Phylogeny (with I. Pe'er and R. Shamir)
Proceedings: CPM 2000, pp. 143-153: pdf.
A Fully
Dynamic Algorithm for Recognizing and Representing Proper Interval
Graphs (with P. Hell and R. Shamir)
Proceedings: ESA 1999, pp. 527-539: pdf.
Journal: SIAM Journal on Computing, 31(1), pp. 289-305, 2002: pdf.
Complexity
Classification of Some Edge Modification Problems (with A.
Natanzon and R. Shamir)
Proceedings: WG 1999, pp. 65-77: pdf.
Journal: Discrete Applied Mathematics 113, pp. 109-128, 2001: pdf.
On the
Complexity of Positional Sequencing by Hybridization (with
A. Ben-Dor, I. Pe'er and R. Shamir)
Proceedings: CPM 1999, pp. 88-100: pdf.
Journal: Journal of Computational Biology 8(4), pp. 361-371, 2001: pdf.
Full version: Electronic Colloquium on Computational Complexity,
Technical report 01-054, 2001: pdf.
A
Polynomial Approximation Algorithm for the Minimum Fill-In Problem (with
A. Natanzon and R. Shamir)
Proceedings: STOC 1998, pp. 41-47: pdf.
Journal: Journal of Computational Biology 8(4), pp. 361-371, 2001: pdf.
Journal: SIAM Journal on Computing 30(4), pp. 1067-1079, 2000: pdf.
A
Polynomial Approximation Algorithm for the Minimum Fill-In Problem (with
A. Natanzon and R. Shamir)
Proceedings: STOC 1998, pp. 41-47: pdf.
Journal: SIAM Journal on Computing 30(4), pp. 1067-1079, 2000: pdf.
A New NC
Algorithm for Perfect Matching in Bipartite Cubic Graphs (with
A. Wigderson)
Proceedings: ISTCS 1996, pp. 202-207: pdf.
Global
alignment of protein-protein interaction networks
(with Misael Mongiovi)
Book: Data mining for systems biology: Methods and protocols, Mamitsuka
et al. eds., Springer, 2013: pdf
Cross-species
analysis of protein-protein interaction networks (with N.
Yosef and E. Ruppin)
Book: In Protein-protein interactions and networks: identification,
analysis and prediction, 2008.
Biclustering
Algorithms: A Survey (with A, Tanay and R. Shamir)
Book: In Handbook of Computational Molecular Biology, Edited by
Srinivas Aluru, Chapman & Hall/CRC, Computer and Information
Science Series, 2005: pdf.
Algorithmic
Approaches to Clustering Gene Expression Data (with R.
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.
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, School of Computer Science, Hebrew University, 1995.
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