Roded Sharan

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. pmc A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology
    Liron Levkovitz
    Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 5:e14423. 2010
  2. pmc PREDICT: a method for inferring novel drug indications with application to personalized medicine
    Assaf Gottlieb
    The Blavatnik School of Computer Science, Tel Aviv University, Israel
    Mol Syst Biol 7:496. 2011
  3. pmc Identification of protein complexes from co-immunoprecipitation data
    Guy Geva
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 27:111-7. 2011
  4. pmc A method for predicting protein-protein interaction types
    Yael Silberberg
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 9:e90904. 2014
  5. pmc Reconstructing Boolean models of signaling
    Roded Sharan
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 20:249-57. 2013
  6. pmc A direct comparison of protein interaction confidence assignment schemes
    Silpa Suthram
    Department of Bioengineering, University of California, San Diego, CA 92093, USA
    BMC Bioinformatics 7:360. 2006
  7. ncbi request reprint Modeling cellular machinery through biological network comparison
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nat Biotechnol 24:427-33. 2006
  8. ncbi request reprint Multiplexing schemes for generic SNP genotyping assays
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    J Comput Biol 12:514-33. 2005
  9. doi request reprint Expander: from expression microarrays to networks and functions
    Igor Ulitsky
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Nat Protoc 5:303-22. 2010
  10. pmc A genome-wide screen for essential yeast genes that affect telomere length maintenance
    Lior Ungar
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 37:3840-9. 2009

Detail Information

Publications87

  1. pmc A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology
    Liron Levkovitz
    Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 5:e14423. 2010
    ..Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection...
  2. pmc PREDICT: a method for inferring novel drug indications with application to personalized medicine
    Assaf Gottlieb
    The Blavatnik School of Computer Science, Tel Aviv University, Israel
    Mol Syst Biol 7:496. 2011
    ..92). This lays the computational foundation for future personalized drug treatments, where gene expression signatures from individual patients would replace the disease-specific signatures...
  3. pmc Identification of protein complexes from co-immunoprecipitation data
    Guy Geva
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 27:111-7. 2011
    ..Previous methods for detecting protein complexes have been mainly based on analyzing binary protein-protein interaction data, ignoring the more involved co-complex relations obtained from co-immunoprecipitation experiments...
  4. pmc A method for predicting protein-protein interaction types
    Yael Silberberg
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 9:e90904. 2014
    ..We expect the resulting annotated network to facilitate the reconstruction of process-specific subnetworks and assist in predicting protein function or interaction...
  5. pmc Reconstructing Boolean models of signaling
    Roded Sharan
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 20:249-57. 2013
    ....
  6. pmc A direct comparison of protein interaction confidence assignment schemes
    Silpa Suthram
    Department of Bioengineering, University of California, San Diego, CA 92093, USA
    BMC Bioinformatics 7:360. 2006
    ..Here, we perform a rigorous comparative analysis and performance assessment among these different methods...
  7. ncbi request reprint Modeling cellular machinery through biological network comparison
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nat Biotechnol 24:427-33. 2006
    ....
  8. ncbi request reprint Multiplexing schemes for generic SNP genotyping assays
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    J Comput Biol 12:514-33. 2005
    ..Our results show that the algorithms achieve near-optimal designs in many cases and demonstrate the applicability of generic assays to SNP genotyping...
  9. doi request reprint Expander: from expression microarrays to networks and functions
    Igor Ulitsky
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Nat Protoc 5:303-22. 2010
    ..The results of each analysis step can be visualized in a number of ways. The complete protocol can be executed in approximately 1 h...
  10. pmc A genome-wide screen for essential yeast genes that affect telomere length maintenance
    Lior Ungar
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 37:3840-9. 2009
    ..The newly identified genes span a variety of cellular processes, including protein degradation, pre-mRNA splicing and DNA replication...
  11. ncbi request reprint Pepitope: epitope mapping from affinity-selected peptides
    Itay Mayrose
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 23:3244-6. 2007
    ..Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/..
  12. pmc Transcriptional regulation by CHIP/LDB complexes
    Revital Bronstein
    Department of Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 6:e1001063. 2010
    ..Understanding the combinatorial nature of transcription complexes as presented here is crucial to the study of transcription regulation of gene batteries required for development...
  13. pmc Toward accurate reconstruction of functional protein networks
    Nir Yosef
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 5:248. 2009
    ..Surprisingly, we find that the proteasome plays an important role in telomere length regulation through its associations with transcription and DNA repair circuits...
  14. ncbi request reprint Topology-free querying of protein interaction networks
    Sharon Bruckner
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 17:237-52. 2010
    ..Torque detects many more matches than QNet, while giving results that are highly functionally coherent...
  15. pmc Comprehensive analysis of co-occurring domain sets in yeast proteins
    Inbar Cohen-Gihon
    Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    BMC Genomics 8:161. 2007
    ..Indeed, while the number of potential co-occurring domain sets (CDSs) is very large, only a few of these occur in nature. Here we study the principles governing domain content of proteins, using yeast as a model species...
  16. pmc Large-scale elucidation of drug response pathways in humans
    Yael Silberberg
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 19:163-74. 2012
    ..Supplementary Material for this article is available at www.liebertonline.com/cmb...
  17. pmc EXPANDER--an integrative program suite for microarray data analysis
    Ron Shamir
    School of Computer Science, Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 6:232. 2005
    ..Of special need are integrative packages that provide biologist users with advanced but yet easy to use, set of algorithms, together covering the whole range of steps in microarray data analysis...
  18. pmc A systems-level approach to mapping the telomere length maintenance gene circuitry
    Rafi Shachar
    School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    Mol Syst Biol 4:172. 2008
    ..We experimentally validate some of these predictions, demonstrating that our method is remarkably accurate. Our results both uncover the complex cellular network underlying TLM and validate a new method for inferring such networks...
  19. pmc A complex-centric view of protein network evolution
    Nir Yosef
    The Blavatnik School of Computer Science, Department of Molecular Microbiology and Biotechnology and School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 37:e88. 2009
    ....
  20. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010
    ..PRINCE's predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation...
  21. ncbi request reprint Identification of conserved protein complexes based on a model of protein network evolution
    Eitan Hirsh
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 23:e170-6. 2007
    ..The arising challenge is to organize these networks into models of cellular machinery. As in other biological domains, a comparative approach provides a powerful basis for addressing this challenge...
  22. ncbi request reprint A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data
    Nir Yosef
    School of Computer Science, Tel Aviv University Tel Aviv 69978, Israel
    Bioinformatics 23:e91-8. 2007
    ..The discrimination problem becomes even more involved when additional high-throughput data, such as gene expression data, are available for the same cohort...
  23. pmc Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival
    Gideon Y Stein
    Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 7:e45969. 2012
    ..This signature may facilitate personalized therapy by identifying patients who will respond to anti-Met therapy. Moreover, this novel approach may be applied for other tyrosine kinases and other malignancies...
  24. pmc Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks
    Oded Magger
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 8:e1002690. 2012
    ..Furthermore, they allow predicting novel disease-tissue associations, pointing to sub-clinical tissue effects that may escape early detection...
  25. doi request reprint Systematic identification of gene annotation errors in the widely used yeast mutation collections
    Taly Ben-Shitrit
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
    Nat Methods 9:373-8. 2012
    ..These results have important consequences for systems biology, as the mutation collections are extensively used in almost every aspect of the field, from genetic network analysis to functional gene annotation...
  26. pmc Systematic condition-dependent annotation of metabolic genes
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Res 17:1626-33. 2007
    ..The CDA presented is likely to serve as a new reference source for metabolic gene annotation...
  27. ncbi request reprint SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    Oved Ourfali
    School of Computer Science, School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 23:i359-66. 2007
    ....
  28. pmc Genetic interactions in yeast: is robustness going bust?
    Martin Kupiec
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:97. 2007
  29. pmc Network-free inference of knockout effects in yeast
    Tal Peleg
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000635. 2010
    ..In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network...
  30. ncbi request reprint A motif-based framework for recognizing sequence families
    Roded Sharan
    School of Computer Science, Tel Aviv University Tel Aviv 69978, Israel
    Bioinformatics 21:i387-93. 2005
    ..Our goal is a fully automatic pattern recognition system for a family of sequences, which simultaneously discovers the base signals, their spatial relationships and a classifier based upon them...
  31. pmc Environmental stresses disrupt telomere length homeostasis
    Gal Hagit Romano
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel Department of Biological Sciences, Columbia University, New York, New York, United States of America
    PLoS Genet 9:e1003721. 2013
    ..These results demonstrate that telomere length can be manipulated, and that a carefully regulated homeostasis may become markedly deregulated in opposing directions in response to different environmental cues. ..
  32. ncbi request reprint Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    J Comput Biol 12:835-46. 2005
    ..We also compare our results to two alternative methods for detecting complexes and demonstrate that our methodology obtains a much higher specificity...
  33. pmc INDI: a computational framework for inferring drug interactions and their associated recommendations
    Assaf Gottlieb
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 8:592. 2012
    ..cs.tau.ac.il/~bnet/software/INDI, facilitating the inference and exploration of drug interactions and providing important leads for physicians and pharmaceutical companies alike...
  34. doi request reprint Competitive and cooperative metabolic interactions in bacterial communities
    Shiri Freilich
    Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    Nat Commun 2:589. 2011
    ..These findings are important for the future design of consortia optimized towards bioremediation and bio-production applications...
  35. doi request reprint PRINCIPLE: a tool for associating genes with diseases via network propagation
    Assaf Gottlieb
    The Balavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 27:3325-6. 2011
    ..Given a query disease, it prioritizes disease-related genes based on their closeness in a protein-protein interaction network to genes causing phenotypically similar disorders to the query disease...
  36. doi request reprint Optimally orienting physical networks
    Dana Silverbush
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 18:1437-48. 2011
    ..The obtained orientations can lead to a better understanding of the structure and function of the network...
  37. pmc Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes
    Elhanan Borenstein
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 35:e7. 2007
    ....
  38. doi request reprint Fast and accurate alignment of multiple protein networks
    Maxim Kalaev
    1 School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 16:989-99. 2009
    ..We show that our algorithm outperforms previous approaches for the problem, and produces results that are more in line with current biological knowledge...
  39. pmc QPath: a method for querying pathways in a protein-protein interaction network
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 7:199. 2006
    ..The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks...
  40. pmc Structural similarity of genetically interacting proteins
    Oranit Dror
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv, 69978, Israel
    BMC Syst Biol 2:69. 2008
    ..To date, less than 2% of the known genetic interactions in yeast or worm can be accounted for by sequence similarity...
  41. pmc TORQUE: topology-free querying of protein interaction networks
    Sharon Bruckner
    The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel
    Nucleic Acids Res 37:W106-8. 2009
    ..It can handle large queries of up to 25 proteins. The Torque web server is freely available for use at http://www.cs.tau.ac.il/~bnet/torque.html...
  42. pmc The large-scale organization of the bacterial network of ecological co-occurrence interactions
    Shiri Freilich
    Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Nucleic Acids Res 38:3857-68. 2010
    ..Here, we demonstrate its utility for predicting cooperation and inhibition within communities...
  43. doi request reprint TP53 cancerous mutations exhibit selection for translation efficiency
    Yedael Y Waldman
    Department of Molecular Microbiology and Biotechnology, Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    Cancer Res 69:8807-13. 2009
    ..Taken together, these results show that TE plays an important role in the selection of TP53 cancerous mutations...
  44. doi request reprint NetworkBLAST: comparative analysis of protein networks
    Maxim Kalaev
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 24:594-6. 2008
    ..It can analyze a single network or two networks from different species. In the latter case, NetworkBLAST outputs a set of putative complexes that are evolutionarily conserved across the two networks...
  45. pmc Gene expression in the rodent brain is associated with its regional connectivity
    Lior Wolf
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 7:e1002040. 2011
    ..27, p<1e-5 for the incoming). Overall, the association between connectivity and gene expression in a specific extant rodent species' brain is likely to be even stronger than found here, given the limitations of current data...
  46. pmc Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
    Ran Elkon
    The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, and School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Res 13:773-80. 2003
    ..The methods presented here are general and can be applied to the analysis of transcriptional networks controlling any biological process...
  47. pmc Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
    Amos Tanay
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 101:2981-6. 2004
    ....
  48. pmc The approximability of shortest path-based graph orientations of protein-protein interaction networks
    Dima Blokh
    1 Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 20:945-57. 2013
    ..Here we study this variant, provide strong inapproximability results for it, and propose approximation algorithms for the problem, as well as for relaxations where the connecting paths need only be approximately shortest. ..
  49. doi request reprint Combining drug and gene similarity measures for drug-target elucidation
    Liat Perlman
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 18:133-45. 2011
    ..Our framework provides an extensible platform for incorporating additional emerging similarity measures among drugs and genes. Supplementary Material is available at www.liebertonline.com/cmb...
  50. pmc A genetic screen for high copy number suppressors of the synthetic lethality between elg1Δ and srs2Δ in yeast
    Inbal Gazy
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
    G3 (Bethesda) 3:917-26. 2013
    ..We report the identification of 36 such genes, which are enriched for functions related to DNA- and chromatin-binding, chromatin packaging and modification, and mRNA export from the nucleus...
  51. doi request reprint iPoint: an integer programming based algorithm for inferring protein subnetworks
    Nir Atias
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Biosyst 9:1662-9. 2013
    ....
  52. ncbi request reprint Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions
    Ze ev Melamed
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Cell 50:869-81. 2013
    ..Our data present a biological role of alternative splicing in regulation of miRNA biogenesis. ..
  53. pmc Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement
    Inbar Cohen-Gihon
    Department of Human Genetics, Sackler Faculty of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel
    Phys Biol 8:035009. 2011
    ..We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently...
  54. ncbi request reprint Improved network-based identification of protein orthologs
    Nir Yosef
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 24:i200-6. 2008
    ....
  55. pmc Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures
    Inbar Cohen-Gihon
    Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Biosyst 7:784-92. 2011
    ..In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution...
  56. pmc Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm
    Itay Mayrose
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv 69978, Israel
    Nucleic Acids Res 35:69-78. 2007
    ..We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs...
  57. doi request reprint A network-based method for predicting disease-causing genes
    Shaul Karni
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 16:181-9. 2009
    ..In addition, we validate our method on real gene expression data and on gene specific knockouts. Finally, we apply it to suggest possible genes that are involved in myasthenia gravis...
  58. ncbi request reprint Discovering statistically significant biclusters in gene expression data
    Amos Tanay
    School of Computer Science, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
    Bioinformatics 18:S136-44. 2002
    ..In cancer data we are able to detect and relate finer tissue types than was previously possible. We also show that the method outperforms the biclustering algorithm of Cheng and Church (2000)...
  59. doi request reprint A linearized constraint-based approach for modeling signaling networks
    Liram Vardi
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 19:232-40. 2012
    ..Considering the marked computational advantages in terms of scalability and sampling utilization obtained by having a linear mode, these results demonstrate the potential promise of this framework for the study of cellular signaling...
  60. pmc Metabolic-network-driven analysis of bacterial ecological strategies
    Shiri Freilich
    The Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Genome Biol 10:R61. 2009
    ....
  61. pmc Network-based prediction of protein function
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:88. 2007
    ..Although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community...
  62. pmc A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:101. 2007
    ..Overall, SR-FBA enables one to address a host of new questions concerning the interplay between regulation and metabolism...
  63. ncbi request reprint Detecting excess radical replacements in phylogenetic trees
    Tal Pupko
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel
    Gene 319:127-35. 2003
    ..We validate this approach by applying it to two well-studied datasets: the MHC class I glycoproteins serving as a positive control, and the house-keeping gene carbonic anhydrase I serving as a negative control...
  64. ncbi request reprint Islands of tractability for parsimony haplotyping
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    IEEE/ACM Trans Comput Biol Bioinform 3:303-11. 2006
    ..We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable...
  65. doi request reprint An algorithmic framework for predicting side effects of drugs
    Nir Atias
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 18:207-18. 2011
    ..Our method thus represents a promising step toward shortcutting the process and reducing the cost of side effect elucidation...
  66. pmc Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages
    Yedael Y Waldman
    Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:2964-74. 2010
    ..Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms...
  67. ncbi request reprint CLICK and EXPANDER: a system for clustering and visualizing gene expression data
    Roded Sharan
    International Computer Science Institute, 1947 Center St, Suite 600, Berkeley, CA 94704 1198, USA
    Bioinformatics 19:1787-99. 2003
    ..A key step in the analysis of gene expression data is the identification of groups of genes that manifest similar expression patterns. This translates to the algorithmic problem of clustering genes based on their expression patterns...
  68. ncbi request reprint A discriminative model for identifying spatial cis-regulatory modules
    Eran Segal
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021
    J Comput Biol 12:822-34. 2005
    ..Thus, our results provide one of the first comprehensive compendiums of putative cis-regulatory modules in human...
  69. pmc An initial blueprint for myogenic differentiation
    Alexandre Blais
    Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
    Genes Dev 19:553-69. 2005
    ..Our studies suggest unanticipated biological insights into muscle development and highlight new directions for further studies of genes involved in muscle repair and responses to stress and damage...
  70. pmc Conserved patterns of protein interaction in multiple species
    Roded Sharan
    Computer Science Division, University of California, Berkeley, CA 94704, USA
    Proc Natl Acad Sci U S A 102:1974-9. 2005
    ....
  71. pmc CREME: Cis-Regulatory Module Explorer for the human genome
    Roded Sharan
    International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA
    Nucleic Acids Res 32:W253-6. 2004
    ..The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web server is available at http://creme.dcode.org...
  72. ncbi request reprint CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments
    Roded Sharan
    International Computer Science Institute, 1947 Center St, Suite 600, Berkeley CA 94704, USA
    Bioinformatics 19:i283-91. 2003
    ..In this work we establish a framework for finding recurrent cis-regulatory modules in the promoters of a selected set of genes and scoring their statistical significance...
  73. pmc Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    Brian P Kelley
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 100:11394-9. 2003
    ..Analysis of these findings reveals many well characterized interaction pathways as well as many unanticipated pathways, the significance of which is reinforced by their presence in the networks of both species...
  74. pmc PathBLAST: a tool for alignment of protein interaction networks
    Brian P Kelley
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Nucleic Acids Res 32:W83-8. 2004
    ..Just as BLAST enables rapid comparison of protein sequences between genomes, tools such as PathBLAST are enabling comparative genomics at the network level...
  75. pmc Systematic identification of functional orthologs based on protein network comparison
    Sourav Bandyopadhyay
    Program in Bioinformatics, University of California at San Diego, La Jolla, California 92093, USA
    Genome Res 16:428-35. 2006
    ..These results suggest that network analysis can be used to provide a key source of information for refining sequence-based homology searches...
  76. ncbi request reprint Efficient algorithms for detecting signaling pathways in protein interaction networks
    Jacob Scott
    Computer Science Division, University of California, Berkeley, 94720, USA
    J Comput Biol 13:133-44. 2006
    ..The algorithm is very efficient, computing optimal paths of length 8 within minutes and paths of length 10 in about three hours...
  77. pmc Protein networks in disease
    Trey Ideker
    Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, USA
    Genome Res 18:644-52. 2008
    ..Applications in infectious disease, personalized medicine, and pharmacology are also forthcoming as the available protein network information improves in quality and coverage...
  78. ncbi request reprint Constraint-based functional similarity of metabolic genes: going beyond network topology
    Oleg Rokhlenko
    Department of Computer Science, Technion, Haifa 32000, Israel
    Bioinformatics 23:2139-46. 2007
    ..However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data...
  79. ncbi request reprint Bayesian haplotype inference via the Dirichlet process
    Eric P Xing
    School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
    J Comput Biol 14:267-84. 2007
    ..We further generalize the model to treat pedigree relationships (e.g., trios) between the population's genotypes. We apply DP-Haplotyper to the analysis of both simulated and real genotype data, and compare to extant methods...
  80. pmc Transcriptional regulation of protein complexes within and across species
    Kai Tan
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:1283-8. 2007
    ..Our results demonstrate how multiple molecular interaction types can be integrated toward a global wiring diagram of the cell, and they provide insights into the evolutionary dynamics of protein complex regulation...
  81. ncbi request reprint A note on phasing long genomic regions using local haplotype predictions
    Eleazar Eskin
    Computer Science and Engineering, University of California, San Diego, USA
    J Bioinform Comput Biol 4:639-47. 2006
    ..in press; Marchini et al., in preparation). Our method is publicly available via a webserver at http://research.calit2.net/hap/...
  82. ncbi request reprint Analysis of SNP-expression association matrices
    Anya Tsalenko
    Agilent Technologies, 5301 Stevens Creek Blvd, MS23, Santa Clara, CA 95051, USA
    J Bioinform Comput Biol 4:259-74. 2006
    ..We also identify several statistically significant transcript-subsets with common putative regulators that fall into well-defined functional categories...
  83. pmc Genetic variation in putative regulatory loci controlling gene expression in breast cancer
    Vessela N Kristensen
    Department of Genetics, Institute of Cancer Research, Rikshospitalet Radiumhospitalet Medical Center, Montebello, 0310 Oslo, Norway
    Proc Natl Acad Sci U S A 103:7735-40. 2006
    ..It provides the statistical framework for further genotype expression correlation studies in cancer data sets...
  84. ncbi request reprint Towards optimally multiplexed applications of universal arrays
    Amir Ben-Dor
    Agilent Laboratories, 395 Page Mill Road, Palo Alto, CA 94303, USA
    J Comput Biol 11:476-92. 2004
    ..We complement our theoretical analysis by implementing two heuristic approaches and testing their performance on synthetic data as well as on simulated SNP data...
  85. ncbi request reprint A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements
    Shaojie Zhang
    Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Bioinformatics 22:e557-65. 2006
    ....
  86. pmc Medical sequencing at the extremes of human body mass
    Nadav Ahituv
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Am J Hum Genet 80:779-91. 2007
    ..Together, these data suggest that multiple rare alleles contribute to obesity in the population and provide a medical sequencing-based approach to detect them...
  87. ncbi request reprint DEFOG: a practical scheme for deciphering families of genes
    Tania Fuchs
    Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel
    Genomics 80:295-302. 2002
    ..Extremely high degeneracies, reaching over a billion combinations of distinct PCR primer pairs, proved to be very effective and yielded only 0.4% nonspecific products...