Rotem Sorek

Summary

Affiliation: Compugen Ltd
Country: Israel

Publications

  1. pmc AluGene: a database of Alu elements incorporated within protein-coding genes
    Tal Dagan
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 32:D489-92. 2004
  2. pmc Alu-containing exons are alternatively spliced
    Rotem Sorek
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 12:1060-7. 2002
  3. pmc A novel algorithm for computational identification of contaminated EST libraries
    Rotem Sorek
    Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
    Nucleic Acids Res 31:1067-74. 2003
  4. pmc A non-EST-based method for exon-skipping prediction
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 14:1617-23. 2004
  5. pmc Genomic fossils as a snapshot of the human transcriptome
    Ronen Shemesh
    Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
    Proc Natl Acad Sci U S A 103:1364-9. 2006
  6. ncbi request reprint Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons
    Rotem Sorek
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell 14:221-31. 2004
  7. pmc RNA-editing-mediated exon evolution
    Galit Lev-Maor
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 8:R29. 2007
  8. ncbi request reprint How prevalent is functional alternative splicing in the human genome?
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Trends Genet 20:68-71. 2004
  9. ncbi request reprint The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons
    Galit Lev-Maor
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Science 300:1288-91. 2003
  10. ncbi request reprint Is there any sense in antisense editing?
    Yossef Neeman
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Trends Genet 21:544-7. 2005

Collaborators

Detail Information

Publications25

  1. pmc AluGene: a database of Alu elements incorporated within protein-coding genes
    Tal Dagan
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 32:D489-92. 2004
    ..The Alu elements are annotated with respect to coding region and exon/intron location. This design facilitates queries on Alu sequences, locations, as well as motifs and compositional properties via a one-stop search page...
  2. pmc Alu-containing exons are alternatively spliced
    Rotem Sorek
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 12:1060-7. 2002
    ..Presumably, evolutionary events that cause a constitutive insertion of an Alu sequence into an mRNA are deleterious and selected against...
  3. pmc A novel algorithm for computational identification of contaminated EST libraries
    Rotem Sorek
    Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
    Nucleic Acids Res 31:1067-74. 2003
    ..Our method, along with the identified set of contaminated sequences, will be essential for applications that depend on large EST datasets...
  4. pmc A non-EST-based method for exon-skipping prediction
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 14:1617-23. 2004
    ..We show that a substantial fraction of the splice variants in the human genome could not be identified through current human EST or cDNA data...
  5. pmc Genomic fossils as a snapshot of the human transcriptome
    Ronen Shemesh
    Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
    Proc Natl Acad Sci U S A 103:1364-9. 2006
    ..Our approach can be applied to sequenced metazoan genomes to computationally annotate splicing variation even when expressed sequences are unavailable...
  6. ncbi request reprint Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons
    Rotem Sorek
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell 14:221-31. 2004
    ..Based on these findings, we identified 7810 Alus within the human genome that are prone to exonization. Mutations in these Alus may cause genetic disorders or contribute to human-specific protein diversity...
  7. pmc RNA-editing-mediated exon evolution
    Galit Lev-Maor
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 8:R29. 2007
    ..It was recently shown that Alu elements are also heavily changed by RNA editing in the human genome...
  8. ncbi request reprint How prevalent is functional alternative splicing in the human genome?
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Trends Genet 20:68-71. 2004
    ..We conclude that a significant portion of cassette exons evident in EST databases is not functional, and might result from aberrant rather than regulated splicing...
  9. ncbi request reprint The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons
    Galit Lev-Maor
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Science 300:1288-91. 2003
    ..We revealed a mechanism that governs 3' splice-site selection in these exons during alternative splicing. On the basis of these findings, we identified mutations that activated the exonization of a silent intronic Alu...
  10. ncbi request reprint Is there any sense in antisense editing?
    Yossef Neeman
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Trends Genet 21:544-7. 2005
    ..This observation questions the scope of sense-antisense duplexes formation in-vivo, which is the basis for several proposed regulatory mechanisms...
  11. pmc Assessing the number of ancestral alternatively spliced exons in the human genome
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Genomics 7:273. 2006
    ....
  12. pmc Transcription-mediated gene fusion in the human genome
    Pinchas Akiva
    Compugen Ltd, Tel Aviv 69512, Israel
    Genome Res 16:30-6. 2006
    ..Finally, we provide evidence that transcription-induced chimerism can be a mechanism contributing to the evolution of protein complexes...
  13. pmc Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 13:1631-7. 2003
    ..Our results suggest that the function of many of the intronic sequence blocks that are conserved between human and mouse is the regulation of alternative splicing...
  14. ncbi request reprint Is abundant A-to-I RNA editing primate-specific?
    Eli Eisenberg
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Trends Genet 21:77-81. 2005
    ..The extraordinary frequency of RNA editing in human is explained by the dominance of the primate-specific Alu element in the human transcriptome, which increases the number of double-stranded RNA substrates...
  15. ncbi request reprint Widespread occurrence of antisense transcription in the human genome
    Rodrigo Yelin
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Nat Biotechnol 21:379-86. 2003
    ..Therefore, antisense modulation of gene expression in human cells may be a common regulatory mechanism...
  16. pmc Naturally occurring antisense: transcriptional leakage or real overlap?
    Dvir Dahary
    Compugen Ltd, Tel Aviv 69512 Israel
    Genome Res 15:364-8. 2005
    ..Moreover, our results imply that natural antisense transcription has considerably affected vertebrate genome evolution...
  17. pmc Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious
    Allon Wagner
    The Blavatnik School of Computer Science, Sackler School of Medicine, and Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 110:19166-71. 2013
    ..We expect EDGE to advance our understanding of human pathologies associated with up-regulation of particular transcripts and to facilitate the utilization of gene overexpression in metabolic engineering. ..
  18. ncbi request reprint Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications
    Einat Hazkani-Covo
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, 69978, Ramat Aviv, Israel
    J Mol Evol 56:169-74. 2003
    ..As expected under the assumption that genomic duplications occur at rates that are uninfluenced by content, older numts were found to be duplicated more times than recently inserted ones...
  19. ncbi request reprint In search of antisense
    Giovanni Lavorgna
    Human Molecular Genetics Unit, DIBIT San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
    Trends Biochem Sci 29:88-94. 2004
    ..A range of bioinformatic resources could be used to assist future antisense research...
  20. ncbi request reprint Expressed sequence tags: clean before using. Correspondence re: Z. Wang et al., computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res., 63: 655-657, 2003
    Rotem Sorek
    Cancer Res 63:6996; author reply 6996-7. 2003
  21. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  22. pmc The birth of new exons: mechanisms and evolutionary consequences
    Rotem Sorek
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    RNA 13:1603-8. 2007
    ..This review discusses the molecular mechanisms leading to exonization, its extent in vertebrate genomes, and its evolutionary implications...
  23. ncbi request reprint Accurate identification of alternatively spliced exons using support vector machine
    Gideon Dror
    The Academic College of Tel Aviv Yaffo, Tel Aviv 4044, Israel
    Bioinformatics 21:897-901. 2005
    ..Recently, we have demonstrated that such features can be used to distinguish alternative from constitutive exons. In the current study, we used advanced machine learning methods to generate robust classifier of alternative exons...
  24. ncbi request reprint Genome-wide experimental determination of barriers to horizontal gene transfer
    Rotem Sorek
    Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 318:1449-52. 2007
    ..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...
  25. ncbi request reprint CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea
    Rotem Sorek
    Rotem Sorek, Victor Kunin and Philip Hugenholtz are at the Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Rev Microbiol 6:181-6. 2008
    ..CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism...