Michal Ziv-Ukelson

Summary

Publications

  1. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
  2. pmc Gene bi-targeting by viral and human miRNAs
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    BMC Bioinformatics 11:249. 2010
  3. pmc Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    BMC Bioinformatics 13:322. 2012
  4. doi request reprint A faster algorithm for simultaneous alignment and folding of RNA
    Michal Ziv-Ukelson
    Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    J Comput Biol 17:1051-65. 2010
  5. ncbi request reprint A study of accessible motifs and RNA folding complexity
    Ydo Wexler
    Department of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
    J Comput Biol 14:856-72. 2007
  6. doi request reprint Rich parameterization improves RNA structure prediction
    Shay Zakov
    Department of Computer Science, Ben Gurion University of the Negev, Be er Sheva, Israel
    J Comput Biol 18:1525-42. 2011
  7. pmc A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
    Alexander Lan
    Department of Computer Science, National Center for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
    Bioinformatics 29:i210-6. 2013
  8. ncbi request reprint A structure-based flexible search method for motifs in RNA
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    J Comput Biol 14:908-26. 2007
  9. pmc The microRNA Transcriptome of Human Cytomegalovirus (HCMV)
    Mesfin K Meshesha
    Department of Virology and Molecular Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
    Open Virol J 6:38-48. 2012
  10. ncbi request reprint On the repeat-annotated phylogenetic tree reconstruction problem
    Firas Swidan
    Department of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
    J Comput Biol 13:1397-418. 2006

Collaborators

Detail Information

Publications11

  1. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
    ....
  2. pmc Gene bi-targeting by viral and human miRNAs
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    BMC Bioinformatics 11:249. 2010
    ..Our approach to meet this challenge is to identify modules where viral and host miRNAs cooperatively regulate host gene expression...
  3. pmc Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    BMC Bioinformatics 13:322. 2012
    ..In particular, viral and host miRNAs may also have mutual target genes. Based on published evidence linking viral and host miRNAs there are three modes of mutual regulation: competing, cooperating, and compensating modes...
  4. doi request reprint A faster algorithm for simultaneous alignment and folding of RNA
    Michal Ziv-Ukelson
    Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    J Comput Biol 17:1051-65. 2010
    ..Hence, our algorithm speeds up Sankoff's algorithm by a linear factor on average. In simulations, our algorithm speeds up computation by a factor of 3-12 for sequences of length 25-250. Code and data sets are available, upon request...
  5. ncbi request reprint A study of accessible motifs and RNA folding complexity
    Ydo Wexler
    Department of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
    J Comput Biol 14:856-72. 2007
    ..cerevisiae genes and to the mining of exposed binding sites of tissue-specific microRNAs in A. thaliana...
  6. doi request reprint Rich parameterization improves RNA structure prediction
    Shay Zakov
    Department of Computer Science, Ben Gurion University of the Negev, Be er Sheva, Israel
    J Comput Biol 18:1525-42. 2011
    ..e., 30% error rate). That is, the new model yields an error reduction of about 50%. Trained models and source code are available at www.cs.bgu.ac.il/?negevcb/contextfold...
  7. pmc A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
    Alexander Lan
    Department of Computer Science, National Center for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
    Bioinformatics 29:i210-6. 2013
    ..However, the use of single interaction scores fails to capture the tendency of proteins to favour different partners under distinct cellular conditions...
  8. ncbi request reprint A structure-based flexible search method for motifs in RNA
    Isana Veksler-Lublinsky
    Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    J Comput Biol 14:908-26. 2007
    ..Code and data are available at www.cs.bgu.ac.il/vaksler/STRMS...
  9. pmc The microRNA Transcriptome of Human Cytomegalovirus (HCMV)
    Mesfin K Meshesha
    Department of Virology and Molecular Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
    Open Virol J 6:38-48. 2012
    ....
  10. ncbi request reprint On the repeat-annotated phylogenetic tree reconstruction problem
    Firas Swidan
    Department of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
    J Comput Biol 13:1397-418. 2006
    ..Furthermore, the repeats are employed to provide linear-time algorithms for reconstructing both the genomic orders and the phylogeny, which are NP-hard problems under the classical model of sorting by reversals (SBR)...
  11. ncbi request reprint Alignment of metabolic pathways
    Ron Y Pinter
    Department of Computer Science, Technion Israel Institute of Technology, Haifa 32000, Israel
    Bioinformatics 21:3401-8. 2005
    ..g. the enzymes they denote), and allow flexibility by matching similar--rather than identical--pathways...