Selected Publications

  • Sberro H., Leavitt A., Kiro R., Koh E., Peleg Y., Qimron U., Sorek R.
    Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning
    Molecular Cell, in press (2013).

  • Stern A., Mick E., Tirosh I., Sagy O., Sorek R.
    CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
    Genome Research, 22(10):1985-94 (2012).

  • Dominissini D., Moshitch-Moshkovitz S., Schwartz S., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jakob-Hirsch J., Amariglio N., Kupiec M., Sorek R., Rechavi G.
    Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
    Nature, 485(7397):201-6 (2012).

  • Wurtzel O., Sesto N., Mellin J.R., Karunker I., Edelheit S., Becavin C., Archambaud C., Cossart P., Sorek R.
    Comparative transcriptomics of pathogenic and non-pathogenic Listeria species
    Molecular Systems Biology, 8:583 (2012).

  • Kimelman A., Levy A., Sberro H., Kidron S., Leavitt A., Amitai G., Yoder-Himes D., Wurtzel O., Zhu Y., Rubin E.M., Sorek R.
    A vast collection of microbial genes that are toxic to bacteria
    Genome Research, 22(4):802-9 (2012).

  • Avrani S., Wurtzel O., Sharon I., Sorek R., Lindell D
    Genomic island variability facilitates Prochlorococcus-virus coexistence
    Nature, 474(7353):604-608 (2011).

  • Sorek R., Cossart P.
    Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity.
    Nature Reviews Genetics, 11(1):9-16 (2010).

  • Moran N.A., McLaughlin H.J., Sorek R.
    The dynamics and timescale of ongoing genomic erosion in symbiotic bacteria.
    Science, 323(5912):379-382 (2009).

  • Yoder-Himes D.R., Chain P.S.G., Zhu Y., Wurtzel O., Rubin E.M., Tiedje J.M., Sorek R.
    Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.
    PNAS, 106(10):3976-3981 (2009).

  • Sorek R., Kunin V., Hugenholtz P.
    CRISPR - a widespread anti-viral system that provides acquired resistance against viruses in prokaryotes.
    Nature Reviews Microbiology, 6(3):181-6 (2008).

  • Sorek R., Zhu Y., Creevey C., Francino M.P., Bork P., Rubin E.M.
    Genome-wide experimental determination of barriers to horizontal gene transfer.
    Science, 318(5855):1449-1452 (2007).

  • Warnecke F., Luginbuhl P., Ivanova N., Ghassemian M., Richardson T.H., Stege J.T., Cayouette M., Djordjevic G., Aboushadi N., Sorek, R. et al.
    Metagenomic and functional analysis of hindgut microbiota of a wood feeding higher termite.
    Nature, 450(7169):560-565 (2007).

  • Shemesh R., Novik A., Edelheit S., Sorek R.
    Genomic fossils as a snapshot of alternative splicing in the human transcriptome.
    PNAS, 103(5):1364-1369 (2006).

  • Sorek R., Lev-Maor G., Reznik M.*, Dagan T., Belinky F., Graur D., Ast G.
    Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
    Molecular Cell, 14(2): 221-231 (2004).

  • Yelin R.*, Dahary D.*, Sorek R.*, Levanon E.Y., Goldstein O., Shoshan A., Diber A., Biton S., Tamir Y., Khosravi R., Nemzer S., Pinner E., Walach S., Bernstein J., Savitsky K., Rotman G.
    Widespread occurrence of antisense transcription in the human genome.
    Nature Biotechnology, 21(4): 379-386 (2003).

  • Lev-Maor G.*, Sorek R.*, Shomron N., Ast G.
    The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.
    Science, 300(5623): 1288-1291 (2003).

  • Sorek R., Amitai M.
    Piecing together the significance of splicing.
    Nature Biotechnology, 19(3): 196 (2001).


    • All Publications

  • Sberro H., Leavitt A., Kiro R., Koh E., Peleg Y., Qimron U., Sorek R.
    Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning
    Molecular Cell, in press (2013).

  • Mick E., Stern A., Sorek R.
    Holding a grudge: Persisting anti-phage CRISPR immunity in multiple human gut microbiomes
    RNA Biology, 10(5):1-7 (2013).

  • Sesto N., Wurtzel O., Archambaud C., Sorek R., Cossart P.
    The excludon: a new concept in bacterial antisense RNA-mediated gene regulation.
    Nature Reviews Microbiology, 11(2):75-82 (2013).

  • Wurtzel O., Yoder-Himes D., Han K., Dandekar U.., Edelheit S., Greenberg E.P., Sorek R. Lory S.
    The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature
    PLoS Pathogens, 8(9):e1002945 (2012).

  • Stern A., Mick E., Tirosh I., Sagy O., Sorek R.
    CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
    Genome Research, 22(10):1985-94 (2012).

  • Dominissini D., Moshitch-Moshkovitz S., Schwartz S., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jakob-Hirsch J., Amariglio N., Kupiec M., Sorek R., Rechavi G.
    Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
    Nature, 485(7397):201-6 (2012).

  • Wurtzel O., Sesto N., Mellin J.R., Karunker I., Edelheit S., Becavin C., Archambaud C., Cossart P., Sorek R.
    Comparative transcriptomics of pathogenic and non-pathogenic Listeria species
    Molecular Systems Biology, 8:583 (2012).

  • Amitai G., Sorek R.
    PanDaTox: a tool for accelerated metabolic engineering
    Bioengineered Bugs, 3(4):218-2 (2012).

  • Kimelman A., Levy A., Sberro H., Kidron S., Leavitt A., Amitai G., Yoder-Himes D., Wurtzel O., Zhu Y., Rubin E.M., Sorek R.
    A vast collection of microbial genes that are toxic to bacteria
    Genome Research, 22(4):802-9 (2012).

  • Danan M., Schwartz S., Edelheit S., Sorek R.
    Transcriptome-wide discovery of circular RNAs in archaea
    Nucleic Acids Research, 40(7):3131-42 (2012).

  • Michaeli S., Doniger T., Gupta S.K., Wurtzel O., Romano M., Visnovezky D., Sorek R., Unger R., Ullu E
    RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs
    Nucleic Acids Research, 40(3):1282-98 (2012).

  • Sorek R., Serrano L
    Bacterial genomes: from regulatory complexity to engineering
    Current Opinion in Microbiology, 14:1-2 (2011).

  • Avrani S., Wurtzel O., Sharon I., Sorek R., Lindell D
    Genomic island variability facilitates Prochlorococcus-virus coexistence
    Nature, 474(7353):604-608 (2011).

  • Stern A., Sorek R.
    The phage-host arms-race: Shaping the evolution of microbes.
    BioEssays, 33(1):43-51 (2011).

  • He S.*, Wurtzel O.*, Singh K., Froula J., Yilmaz S., Wang Z., Chen F., Lindquist E.A., Sorek R., Hugenholtz P.
    Validation of two commercial ribosomal RNA removal methods for microbial metatranscriptomics.
    Nature Methods, 7:807-812 (2010).

  • Wurtzel O., Dori-Bachash M., Pietrokovski S., Jurkevitch E., Sorek R.
    Mutation detection with next-generation resequencing through a mediator genome.
    PLoS One, 5(12):e15628 (2010).

  • Stern A., Keren L., Wurtzel O., Amitai G., Sorek R.
    Self-targeting by CRISPR: gene regulation or autoimmunity?
    Trends in Genetics, 26(8):335-340 (2010).

  • Sorek R., Cossart P.
    Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity.
    Nature Reviews Genetics, 11(1):9-16 (2010).

  • Wurtzel O., Sapra R., Chen F., Zhu Y., Simmons B., Sorek R.
    A single-base resolution map of an archaeal transcriptome.
    Genome Research, 20(1):133-41 (2010).

  • Sorek R.
    When new exons are born
    Heredity, 103:279–280 (2009).

  • Yoder-Himes D.R., Chain P.S.G., Zhu Y., Wurtzel O., Rubin E.M., Tiedje J.M., Sorek R.
    Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.
    PNAS, 106(10):3976-3981 (2009).

  • Moran N.A., McLaughlin H.J., Sorek R.
    The dynamics and timescale of ongoing genomic erosion in symbiotic bacteria.
    Science, 323(5912):379-382 (2009).

  • Sorek R., Kunin V., Hugenholtz P.
    CRISPR - a widespread anti-viral system that provides acquired resistance against viruses in prokaryotes
    Nature Reviews Microbiology, 6(3):181-6 (2008).

  • Sorek R., Zhu Y., Creevey C., Francino M.P., Bork P., Rubin E.M.
    Genome-wide experimental determination of barriers to horizontal gene transfer.
    Science, 318(5855):1449-1452 (2007).

  • Warnecke F., Luginbuhl P., Ivanova N., Ghassemian M., Richardson T.H., Stege J.T., Cayouette M., Djordjevic G., Aboushadi N., Sorek, R. et al.
    Metagenomic and functional analysis of hindgut microbiota of a wood feeding higher termite.
    Nature, 450(7169):560-565 (2007).

  • Sorek R.
    The birth of new exons: mechanisms and evolutionary consequences.
    RNA, 13(10):1603-1608 (2007).

  • Kunin V.*, Sorek R.*, Hugenholtz P.
    Evolutionary conservation of sequence and secondary structures in CRISPR repeats.
    Genome Biology, 8(4):R61 (2007).

  • Lev-Maor G.*, Sorek R.*, Levanon E.Y., Paz N., Eisenberg E., Ast G.
    RNA-editing mediated exon evolution.
    Genome Biology, 8(2):R29 (2007).

  • Sorek R., Dror G., Shamir R.
    Assessing the fraction of ancestral alternatively spliced exons in the human genome.
    BMC Genomics, 7:273(2006).

  • Shemesh R., Novik A., Edelheit S., Sorek R.
    Genomic fossils as a snapshot of alternative splicing in the human transcriptome.
    PNAS, 103(5):1364-1369 (2006).

  • Akiva P., Toporik A., Edelheit S., Peretz Y., Diber A., Shemesh R., Novik A., Sorek R.
    Transcription-mediated gene fusion in the human genome.
    Genome Research, 16(1):30-36 (2006).

  • Dror G., Sorek R., Shamir R.
    Accurate identification of alternatively spliced exons using support vector machine.
    Bioinformatics, 21(7): 897-901 (2005).

  • Eisenberg E., Nemzer S., Kinar Y., Sorek R., Rechavi G., Levanon E.Y.
    Is abundant A-to-I RNA editing primate-specific?
    Trends in Genetics, 21(2):77-81 (2005).

  • Neeman Y., Dahary D., Levanon E.Y., Sorek R., Eisenberg E.
    Is there any sense in antisense editing?
    Trends in Genetics, 21(10):544-547 (2005).

  • Dahary D., Elroy-Stein O., Sorek R.
    Naturally occurring antisense: Transcriptional leakage or real overlap?
    Genome Research, 15(3): 364-368 (2005).

  • Lavorgna G., Dahary D., Lehner B., Sorek R., Sanderson C.M., Casari G.
    In search of antisense.
    Trends in Biochemical Sciences, 29(2): 88-94 (2004).

  • Dagan T.*, Sorek R.*, Sharon E.*, Ast G., Graur D.
    AluGene: a database of Alu elements incorporated within protein-coding genes.
    Nucleic Acids Research, 32: D489-D492 (2004).

  • Sorek R., Shamir R., Ast G.
    How prevalent is functional alternative splicing in the human genome?
    Trends in Genetics, 20(2): 68-71 (2004).

  • Sorek R.*, Lev-Maor G.*, Reznik M.*, Dagan T., Belinky F., Graur D., Ast G.
    Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
    Molecular Cell, 14(2): 221-231 (2004).

  • Sorek R., Shemesh R., Cohen Y., Basechess O., Ast G., Shamir R.
    A non-EST based method for exon-skipping prediction.
    Genome Research, 14(8): 1617-1623 (2004).

  • Levanon E., Sorek R.
    The importance of alternative splicing in the drug discovery process.
    Targets, 2(3): 109-114 (2003).

  • Hazkani-Covo E., Sorek R., Graur D.
    Evolutionary dynamics of large Numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications.
    Journal of Molecular Evolution, 56(2): 169-174 (2003).

  • Sorek R., Safer H.M.
    A Novel method for computational identification of contaminated EST libraries.
    Nucleic Acids Research, 31(3): 1067-1074 (2003).

  • Yelin R., Dahary D., Sorek R., Levanon E.Y., Goldstein O., Shoshan A., Diber A., Biton S., Tamir Y., Khosravi R., Nemzer S., Pinner E., Walach S., Bernstein J., Savitsky K., Rotman G.
    Widespread occurrence of antisense transcription in the human genome.
    Nature Biotechnology, 21(4): 379-386 (2003).

  • Lev-Maor G.*, Sorek R.*, Shomron N., Ast G.
    The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.
    Science, 300(5623): 1288-1291 (2003).

  • Sorek R., Ast G.
    Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.
    Genome Research, 13(7): 1631-1637 (2003).

  • Sorek R., Basechess O., Safer H.M.
    Expressed sequence tags: clean before using.
    Cancer Research, 63(20):6996 (2003).

  • Sorek R., Ast G., Graur D.
    Alu containing exons are alternatively spliced.
    Genome Research, 12(7): 1060-1067 (2002).

  • Sorek R., Amitai M.
    Piecing together the significance of splicing.
    Nature Biotechnology, 19(3): 196 (2001).