Selected Publications

  • Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Kaszei AFA, Shao S, Amitai G, Kranzusch PJ, Sorek R.
    Cyclic CMP and cyclic UMP mediate bacterial immunity against phages
    Cell, 184(23):5728-5739 (2021).

  • Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.
    Prokaryotic viperins produce diverse antiviral molecules
    Nature, 589(7840):120-124 (2021).

  • Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R.
    Bacterial retrons function in anti-phage defense
    Cell, 183(6):1551-1561 (2020).

  • Morehouse B, Govande AA, Millman A, Keszei A, Lowey B, Ofir G, Shao S, Sorek R, Kranzusch PJ
    STING cyclic dinucleotide sensing originated in bacteria
    Nature, 586(7829):429-433 (2020).

  • Bernheim A, Sorek R.
    The pan-immune system of bacteria: antiviral defence as a community resource
    Nature Reviews Microbiology, 18(2):113-119 (2020).

  • Cohen D, Melamed S, Millman A, Shulman G, Oppenheimer-Shaanan Y, Kacen A, Doron S, Amitai G, Sorek R.
    Cyclic GMP-AMP signaling protects bacteria against viral infection
    Nature, 574(7780):691-695 (2019).

  • Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R.
    Systematic discovery of antiphage defense systems in the microbial pangenome
    Science, 359(6379), pii: eaar4120 (2018).

  • Ofir G, Sorek R.
    Contemporary Phage Biology: From Classic Models to New Insights
    Cell, 172:1260-1270 (2018).

  • Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R.
    Communication between viruses guides lysis-lysogeny decisions
    Nature, 541(7638):488-493 (2017).

  • Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P., Sorek R.
    Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
    Science, 352(6282):187 (2016).

  • Amitai G., Sorek R.
    CRISPR-Cas adaptation: insights into the mechanism of action
    Nature Reviews Microbiology, 14(2):67-76 (2016).

  • Levy A., Goren M.G., Yosef I., Auster O., Manor M., Amitai G., Edgar R., Qimron U., Sorek R.
    CRISPR adaptation biases explain preference for acquisition of foreign DNA
    Nature 520(7548):505-10 (2015).

  • Mick E., Sorek R.
    High resolution metagenomics
    Nature Biotechnology, 32(8):750-751 (2014).

  • Mellin J.R., Koutero M., Dar D., Nahori M.A., Sorek R., Cossart P.
    Sequestration of a two-component response regulator by a riboswitch-regulated non-coding RNA
    Science, 345(6199):940-3 (2014).

  • Sorek R, Lawrence CM, Wiedenheft B.
    CRISPR-mediated Adaptive Immune Systems in Bacteria and Archaea.
    Annual Reviews in Biochemistry , 82:237-266 (2013).

  • 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).

  • 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).



  • All Publications

  • Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Kaszei AFA, Shao S, Amitai G, Kranzusch PJ, Sorek R.
    Cyclic CMP and cyclic UMP mediate bacterial immunity against phages
    Cell, 184(23):5728-5739 (2021).

  • Rousset F, Sorek R.
    A treasure trove of molecular scissors
    Science, 374(6563):37-38 (2021).

  • Duncan-Lowey B, McNamara-Bordewick NK, Tal N, Sorek R, Kranzusch PJ.
    Effector-mediated membrane disruption controls cell death in CBASS antiphage defense
    Molecular Cell, in press (2021).

  • Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.
    Prokaryotic viperins produce diverse antiviral molecules
    Nature, 589(7840):120-124 (2021).

  • Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R.
    Bacterial retrons function in anti-phage defense
    Cell, 183(6):1551-1561 (2020).

  • Millman A, Melamed S, Amitai G, Sorek R.
    Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems
    Nature Microbiology, 5(12):1608-1615 (2020).

  • Morehouse B, Govande AA, Millman A, Keszei A, Lowey B, Ofir G, Shao S, Sorek R, Kranzusch PJ
    STING cyclic dinucleotide sensing originated in bacteria
    Nature, 586(7829):429-433 (2020).

  • Lopatina A, Tal N, Sorek R.
    Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy
    Annual Review of Virology, 7:371-384 (2020).

  • Bernheim A, Sorek R.
    The pan-immune system of bacteria: antiviral defence as a community resource
    Nature Reviews Microbiology, 18(2):113-119 (2020).

  • Voichek M, Maass S, Kroniger T, Becher D, Sorek R.
    Peptide-based quorum sensing systems in Paenibacillus polymyxa
    Life Science Alliance, 3(10):e202000847 (2020).

  • Cohen D, Melamed S, Millman A, Shulman G, Oppenheimer-Shaanan Y, Kacen A, Doron S, Amitai G, Sorek R.
    Cyclic GMP-AMP signaling protects bacteria against viral infection
    Nature,574(7780):691-695 (2019).

  • Stokar-Avihail A, Tal N, Erez Z, Lopatina A, Sorek R.
    Widespread utilization of peptide communication in phages infecting soil and pathogenic bacteria
    Cell Host & Microbe, 25:746-755 (2019).

  • Duval M, Dar D, Carvalho P, Rocha EPC, Sorek R, Cossart P.
    HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance
    PNAS, 115(52):13359-13364 (2018).

  • Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R.
    Systematic discovery of antiphage defense systems in the microbial pangenome
    Science, 359(6379), pii: eaar4120 (2018).

  • Bernheim A, Sorek R.
    Viruses cooperate to defeat bacteria
    Nature, 559:482-484 (2018).

  • Dar D, Sorek R.
    Extensive reshaping of bacterial operons by programmed mRNA decay
    PLoS Genetics, 14(4):e1007354 (2018).

  • Dar D, Sorek R.
    High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts
    Nucleic Acids Research, doi: 10.1093/nar/gky274 (2018).

  • Ofir G, Sorek R.
    Contemporary Phage Biology: From Classic Models to New Insights
    Cell, 172:1260-1270 (2018).

  • Dar D, Sorek R.
    Bacterial Noncoding RNAs excised from within protein-coding transcripts
    mBio,9:e01730-18 (2018).

  • Ofir G, Melamed S, Sberro H, Mukamel Z, Silverman S, Yaakov G, Doron S, Sorek R.
    DISARM is a widespread bacterial defence system with broad anti-phage activities
    Nature Microbiology, 3:90-98 (2018).

  • Kimmerling N, Zuqert O, Amitai G, Gurevich T, Armoza-Zvuloni R, Kolesnikov I, Berenshtein I, Melamed S, Gilad S, Benjamin S, Rivlin A, Ohavia M, Paris CB, Holzman R, Kiflawi M, Sorek R.
    Quantitative species-level ecology of reef fish larvae via metabarcoding
    Nature Ecology and Evolution, 2(2):306-316 (2018).

  • Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R.
    Communication between viruses guides lysis-lysogeny decisions
    Nature, 541(7638):488-493 (2017).

  • Amitai G, Sorek R.
    Intracellular signaling in CRISPR-Cas defense
    Science, 357:550-551 (2017).

  • Dar D, Sorek R.
    Regulation of antibiotic-resistance by non-coding RNAs in bacteria
    Current Opinion in Microbiology, 36:111-117 (2017).

  • Ofir G, Sorek R.
    Vesicles spread susceptibility to phages
    Cell, 168:13-15 (2017).

  • Towbin BD, Korem Y, Bren A, Doron S, Sorek R, Alon U.
    Optimality and sub-optimality in a bacterial growth law
    Nature Communications, 8:14123 (2017).

  • Millman A, Dar D, Shamir M, Sorek R.
    Computational prediction of regulatory, premature transcription termination in bacteria
    Nucleic Acids Research, 45(2):886-893 (2017).

  • Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P., Sorek R.
    Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
    Science, 352(6282):187 (2016).

  • Lopatina A, Sorek R.
    CRISPR-Cas: Spacer diversity determines the efficiency of defense
    Current Biology, 26(14):R683-5 (2016).

  • Dar D, Prasse D, Schmitz RA, Sorek R.
    Widespread formation of alternative 3' UTR isoforms via transcription termination in archaea
    Nature Microbiology, 1(10):16143 (2016).

  • Amitai G., Sorek R.
    CRISPR-Cas adaptation: insights into the mechanism of action
    Nature Reviews Microbiology, 14(2):67-76 (2016).

  • Yosef I, Edgar R, Levy A, Amitai G, Sorek R, Munitz A, Qimron U.
    Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model
    Nature Microbiology, 1(6):16047 (2016).

  • Doron S., Fedida A., Hernandez-Prieto M.A., Sabehi G., Karunker I., Stazic D., Feingersch R., Steglich C., Futschik M., Lindell D., Sorek R.
    Transcriptome dynamics of a broad host-range cyanophage and its hosts.
    ISME Journal, 10(6):1437-55 (2016).

  • Cohen O., Doron S., Wurtzel O., Dar D., Edelheit S., Karunker I., Mick E., Sorek R.
    Comparative transcriptomics across the prokaryotic tree of life
    Nucleic Acids Research, 44(W1):W46-W53 (2016).

  • Goren MG, Doron S, Globus R, Amitai G, Sorek R, Qimron U.
    Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array
    Cell Reports, 16(11):2811-8 (2016).

  • Levy A., Goren M.G., Yosef I., Auster O., Manor M., Amitai G., Edgar R., Qimron U., Sorek R.
    CRISPR adaptation biases explain preference for acquisition of foreign DNA
    Nature 520(7548):505-10 (2015).

  • Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Xavier R, Elinav E, Segal E.
    Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
    Science, 349(6252):1101-6 (2015).

  • Goldfarb T., Sberro H., Weinstock E., Cohen O., Doron S., Charpak-Amikam Y., Afik S., Ofir G., Sorek R.
    BREX is a novel phage resistance system widespread in microbial genomes
    EMBO Journal, 34:169-183 (2015).

  • Mick E., Sorek R.
    High resolution metagenomics
    Nature Biotechnology, 32(8):750-751 (2014).

  • Mellin J.R., Koutero M., Dar D., Nahori M.A., Sorek R., Cossart P.
    Sequestration of a two-component response regulator by a riboswitch-regulated non-coding RNA
    Science, 345(6199):940-3 (2014).

  • Huja S., Oren Y., Biran D., Meyer S., Dobrindt U., Bernhard J., Becher D., Hecker M., Sorek R., Ron E.Z.
    Fur Is the Master Regulator of the Extraintestinal Pathogenic Escherichia coli Response to Serum.
    Mbio, 5(4). pii: e01460-14 (2014).

  • 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, 50(1):136-48 (2013).

  • Edelheit S., Schwartz S., Mumbach R., Wurtzl O., Sorek R.
    Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea and yeast reveals m5C within archaeal mRNAs
    PLoS Genetics, 9(6):e1003602 (2013).

  • Sorek R, Lawrence CM, Wiedenheft B.
    CRISPR-mediated Adaptive Immune Systems in Bacteria and Archaea.
    Annual Reviews in Biochemistry , 82:237-266 (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).