Publications

2024

Diversification of molecular pattern recognition in bacterial NLR-like proteins

Béchon N., Tal N., Stokar-Avihail A., Savidor A., Kupervaser M., Melamed S., Amitai G. & Sorek R. (2024) Nature Communications. 15, 9860.

Phage genome engineering with retrons

Osterman I. & Sorek R. (2024) Nature biotechnology.

Phages reconstitute NAD+ to counter bacterial immunity

Osterman I., Samra H., Rousset F., Loseva E., Itkin M., Malitsky S., Yirmiya E., Millman A. & Sorek R. Nature, 634(8036):1160-1167 (2024)

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

Hör J., Wolf S. G. & Sorek R. Nature, 631:850-856 (2024)

The SARM1 TIR domain produces glycocyclic ADPR molecules as minor products

Garb J., Amitai G., Lu A., Ofir G., Brandis A., Mehlman T., Kranzusch P. J. & Sorek R. PLoS ONE, 19, 4 , e0302251 (2024).

Activation of Thoeris antiviral system via SIR2 effector filament assembly

Tamulaitiene G., Sabonis D., Sasnauskas G., Ruksenaite A., Silanskas A., Avraham C., Ofir G., Sorek R., Zaremba M. & Siksnys V. Nature, 627:431-436 (2024)

Structural basis of Gabija anti-phage defence and viral immune evasion

Antine S. P., Johnson A. G., Mooney S. E., Leavitt A., Mayer M. L., Yirmiya E., Amitai G., Sorek R. & Kranzusch P. J. Nature, 625:360-365 (2024).

Phages overcome bacterial immunity via diverse anti-defence proteins

Yirmiya E., Leavitt A., Lu A., Ragucci A. E., Avraham C., Osterman I., Garb J., Antine S. P., Mooney S. E., Hobbs S. J., Kranzusch P. J., Amitai G. & Sorek R. Nature, 625:352-359 (2024).

2023

A conserved family of immune effectors cleaves cellular ATP upon viral infection

Rousset F., Yirmiya E., Nesher S., Brandis A., Mehlman T., Itkin M., Malitsky S., Millman A., Melamed S. & Sorek R. Cell, 186:3619-3631.e13 (2023).

The evolutionary success of regulated cell death in bacterial immunity

Rousset F. & Sorek R. Current Opinion in Microbiology. 74, 102312 (2023).

CARD-like domains mediate anti-phage defense in bacterial gasdermin systems

Wein T., Johnson A. G., Millman A., Lange K., Yirmiya E., Hadary R., Garb J., Steinruecke F., Hill A. B., Kranzusch P. J. & Sorek R. (2023) BioRxiv.

The defense island repertoire of the Escherichia coli pan-genome

Hochhauser D., Millman A. & Sorek R. PLoS Genetics, 19:4, e1010694(2023).

Discovery of phage determinants that confer sensitivity to bacterial immune systems

Stokar-Avihail A., Fedorenko T., Hör J., Garb J., Leavitt A., Millman A., Shulman G., Wojtania N., Melamed S., Amitai G. & Sorek R. Cell, 186:1863-1876  (2023).

Cryo-EM structure of the RADAR supramolecular anti-phage defense complex

Duncan-Lowey B., Tal N., Johnson A. G., Rawson S., Mayer M. L., Doron S., Millman A., Melamed S., Fedorenko T., Kacen A., Brandis A., Mehlman T., Amitai G., Sorek R. & Kranzusch P. J. Cell, 186:987-998 (2023).

2022

An expanded arsenal of immune systems that protect bacteria from phages

Millman A., Melamed S., Leavitt A., Doron S., Bernheim A., Hör J., Garb J., Bechon N., Brandis A., Lopatina A., Ofir G., Hochhauser D., Stokar-Avihail A., Tal N., Sharir S., Voichek M., Erez Z., Ferrer J. L. M., Dar D., Kacen A., Amitai G. & Sorek R. (2022) Cell Host and Microbe. 30, 11, p. 1556-1569e5

Viruses inhibit TIR gcADPR signalling to overcome bacterial defence

Leavitt A., Yirmiya E., Amitai G., Lu A., Garb J., Herbst E., Morehouse B. R., Hobbs S. J., Antine S. P., Sun Z. J., Kranzusch P. J. & Sorek R. Nature , 611(7935):326-331 (2022)

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD(+) depletion

Zaremba M., Dakineviciene D., Golovinas E., Zagorskaite E., Stankunas E., Lopatina A., Sorek R., Manakova E., Ruksenaite A., Silanskas A., Asmontas S., Grybauskas A., Tylenyte U., Jurgelaitis E., Grigaitis R., Timinskas K., Venclovas C. & Siksnys V. (2022) Nature Microbiology. 7, 11, p. 1857-1869

Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion

Garb J., Lopatina A., Bernheim A., Zaremba M., Siksnys V., Melamed S., Leavitt A., Millman A., Amitai G. & Sorek R. Nature Microbiology, 7(11):1849-1856 (2022)

Bacterial origins of human cell-autonomous innate immune mechanisms

Wein T. & Sorek R. Nature Reviews in Immunology, 22:629-638 (2022) 

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

Federici S., Kredo-Russo S., Valdes Mas R., Kviatcovsky D., Weinstock E., Matiuhin Y., Silberberg Y., Atarashi K., Furuichi M., Oka A., Liu B., Fibelman M., Weiner I., Khabra E., Cullin N., Ben-Yishai N., Inbar D., Ben David H., Nicenboim J., Kowalsman N., Lieb W., Kario E., Cohen T., Friedman Geffen Y., Zelcbuch L., Cohen A., Rappo U., Gahali-Sass I., Golembo M., Lev Goldman V., Dori-Bachash M., Shapiro H., Moresi C., Cuevas Sierra A., Mohapatra G., Kern L., Zheng D., Nobs S. P., Suez J., Harmelin A., Stettner N., Zak N., Puttagunta S., Bassan M., Honda K., Sokol H., Bang C., Franke A., Schramm C., Maharshak N., Balfour Sartor R., Sorek R. & Elinav E.  Cell, 185(16):2879-2898.e24 (2022)

Bacteria deplete deoxynucleotides to defend against bacteriophage infection

Tal N., Millman A., Stokar Avihail A., Fedorenko T., Leavitt A., Melamed S., Yirmiya E., Avraham C., Brandis A., Mehlman T., Amitai G. & Sorek R. (2022) Nature Microbiology. 7, 8, p. 1200-1209

The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA

LeRoux M., Srikant S., Teodoro G. I., Zhang T., Littlehale M. L., Doron S., Badiee M., Leung A. K., Sorek R. & Laub M. T. (2022) Nature Microbiology. 7, 7, p. 1028-1040

Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity

Hobbs S. J., Wein T., Lu A., Morehouse B. R., Schnabel J., Leavitt A., Yirmiya E., Sorek R. & Kranzusch P. J. (2022) Nature. 605, 7910, p. 522-526

SnapShot: Bacterial immunity

Tal N. & Sorek R. Cell, 185(3):578-578.e1 (2022).

Bacterial gasdermins reveal an ancient mechanism of cell death

Johnson A. G., Wein T., Mayer M. L., Duncan-Lowey B., Yirmiya E., Oppenheimer-Shaanan Y., Amitai G., Sorek R. & Kranzusch P. J. (2022) Science (American Association for the Advancement of Science). 375, 6577, p. 221-225

2021

Antiviral activity of bacterial TIR domains via immune signalling molecules

Ofir G., Herbst E., Baroz M., Cohen D., Millman A., Doron S., Tal N., Malheiro D. B. A., Malitsky S., Amitai G. & Sorek R. Nature, 600(7887):116-120 (2021)

Effector-mediated membrane disruption controls cell death in CBASS antiphage defense

Duncan-Lowey B., McNamara-Bordewick N. K., Tal N., Sorek R. & Kranzusch P. J. Molecular Cell, 81(24):5039 -5051.e5 (2021)

Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

Tal N., Morehouse B. R., Millman A., Stokar-Avihail A., Avraham C., Fedorenko T., Yirmiya E., Herbst E., Brandis A., Mehlman T., Oppenheimer-Shaanan Y., Keszei A. F., Shao S., Amitai G., Kranzusch P. J. & Sorek R. Cell, 184(23):5728-5739 (2021)

Prokaryotic viperins produce diverse antiviral molecules

Bernheim A., Millman Dayan A. J., Ofir G., Meitav G., Avraham C., Shomar H., Rosenberg M. M., Tal N., Melamed S., Amitai G. & Sorek R. Nature, 589(7840):120-124 (2021) 

2020

Bacterial Retrons Function In Anti-Phage Defense

Millman A., Bernheim A., Stokar-Avihail A., Fedorenko T., Voichek M., Leavitt A., Oppenheimer-Shaanan Y. & Sorek R. Cell, 183(6):551-1561 (2020)

Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems

Millman A., Melamed S., Amitai G. & Sorek R. (2020) Nature Microbiology. 5, 12, p. 1608-1615

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Hofmeister B. T., Denkena J., Colomé-Tatché M., Shahryary Y., Hazarika R., Grimwood J., Mamidi S., Jenkins J., Grabowski P. P., Sreedasyam A., Shu S., Barry K., Lail K., Adam C., Lipzen A., Sorek R., Kudrna D., Talag J., Wing R., Hall D. W., Jacobsen D., Tuskan G. A., Schmutz J., Johannes F. & Schmitz R. J. (2020) Genome Biology. 21, 1, p. 259 259.

STING cyclic dinucleotide sensing originated in bacteria

Morehouse B. R., Govande A. A., Millman A., Keszei A. F. A., Lowey B., Ofir G., Shao S., Sorek R. & Kranzusch P. J. (2020) Nature. 586, 7829, p. 429-433

Peptide-based quorum sensing systems in Paenibacillus polymyxa

Voichek M., Maaß S., Kroniger T., Becher D. & Sorek R. (2020) Life Science Alliance. 3, 10, 202000847.

Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy

Lopatina A., Tal N. & Sorek R. (2020) Annual Review of Virology. 7, p. 371-384

The pan-immune system of bacteria: antiviral defence as a community resource

Bernheim A. & Sorek R. (2020) Nature Reviews Microbiology. 18, 2, p. 113-119

2019

Cyclic GMP-AMP signalling protects bacteria against viral infection

Cohen D., Melamed S., Millman A., Shulman G., Oppenheimer-Shaanan Y., Kacen A., Doron S., Amitai G. & Sorek R. Nature, 574(7780):691-695  (2019)

A rhlI 5' UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa

Thomason M. K., Voichek M., Dar D., Addis V., Fitzgerald D., Gottesman S., Sorek R. & Greenberga E. P. (2019) mBio. 10, 5, e02253-19.

Widespread Utilization of Peptide Communication in Phages Infecting Soil and Pathogenic Bacteria

Stokar-Avihail A., Tal N., Erez Z., Lopatina A. & Sorek R. (2019) Cell Host & Microbe. 25, 5, p. 746-755.e5

Consent insufficient for data release−Response

Amann R. I., Baichoo S., Blencowe B. J., Bork P., Borodovsky M., Brooksbank C., Chain P. S., Colwell R. R., Daffonchio D. G., Danchin A., de Lorenzo V., Dorrestein P. C., Finn R. D., Fraser C. M., Gilbert J. A., Hallam S. J., Hugenholtz P., Ioannidis J. P., Jansson J. K., Kim J. F., Klenk H. P., Klotz M. G., Knight R., Konstantinidis K. T., Kyrpides N. C., Mason C. E., McHardy A. C., Meyer F., Ouzounis C. A., Patrinos A. A., Podar M., Pollard K. S., Ravel J., Muñoz A. R., Roberts R. J., Rosselló-Móra R., Sansone S. A., Schloss P. D., Schriml L. M., Setubal J. C., Sorek R., Stevens R. L., Tiedje J. M., Turjanski A., Tyson G. W., Ussery D. W., Weinstock G. M., White O., Whitman W. B. & Xenarios I. (2019) Science. 364, 6439, p. 446

Successful Brincidofovir Treatment of Metagenomics-detected Adenovirus Infection in a Severely Ill Signal Transducer and Activator of Transcription-1-deficient Patient

Averbuch D., Safadi R., Dar D., Wolf D., Cherniak M., Sorek R. & Amit S. (2019) Pediatric Infectious Disease Journal. 38, 3, p. 297-299

Toward unrestricted use of public genomic data: Publication interests should not limit access to public data

Amann R. I., Baichoo S., Blencowe B. J., Bork P., Borodovsky M., Brooksbank C., Chain P. S. G., Colwell R. R., Daffonchio D. G., Danchin A., de Lorenzo V., Dorrestein P. C., Finn R. D., Fraser C. M., Gilbert J. A., Hallam S. J., Hugenholtz P., Ioannidis J. P. A., Jansson J. K., Kim J. F., Klenk H., Klotz M. G., Knight R., Konstantinidis K. T., Kyrpides N. C., Mason C. E., McHardy A. C., Meyer F., Ouzounis C. A., Patrinos A. A. N., Podar M., Pollard K. S., Ravel J., Munoz A. R., Roberts R. J., Rossello-Mora R., Sansone S., Schloss P. D., Schriml L. M., Setubal J. C., Sorek R., Stevens R. L., Tiedje J. M., Turjanski A., Tyson G. W., Ussery D. W., Weinstock G. M., White O., Whitman W. B. & Xenarios I. (2019) Science. 363, 6425, p. 350-352

2018

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance

Duval M., Dar D., Carvalho F., Rocha E. P. C., Sorek R. & Cossart P. (2018) Proceedings of the National Academy of Sciences of the United States of America. 115, 52, p. 13359-13364

High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts

Dar D. & Sorek R. (2018) Nucleic Acids Research. 46, 13, p. 6797-6805

Viruses cooperate to defeat bacteria

Bernheim A. & Sorek R. (2018) Nature. 559, 7715, p. 482-484

Extensive reshaping of bacterial operons by programmed mRNA decay

Dar D. & Sorek R. (2018) PLoS Genetics. 14, 4, e1007354.

Contemporary Phage Biology: From Classic Models to New Insights

Ofir G. & Sorek R. (2018) Cell. 172, 6, p. 1260-1270

Quantitative species-level ecology of reef fish larvae via metabarcoding

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 C. B., Holzman R., Kiflawi M. & Sorek R. (2018) Nature ecology & evolution. 2, 2, p. 306-316

Systematic discovery of antiphage defense systems in the microbial pangenome

Doron S., Melamed S., Ofir G., Leavitt A., Lopatina A., Keren M., Amitai G. & Sorek R. Science, 359(6379):eaar4120 (2018)

DISARM is a widespread bacterial defence system with broad anti-phage activities

Ofir G., Melamed S., Sberro H., Mukamel Z., Silverman S., Yaakov G., Doron S. & Sorek R. (2018) Nature Microbiology. 3, 1, p. 90-98

2017

Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli

Benhalevy D., Biran I., Bochkareva E. S., Sorek R. & Bibi E. (2017) PLoS ONE. 12, 8, e0183862.

Intracellular signaling in CRISPR-Cas defense

Amitai G. & Sorek R. (2017) Science. 357, 6351, p. 550-551

Regulation of antibiotic-resistance by non-coding RNAs in bacteria

Dar D. & Sorek R. (2017) Current Opinion in Microbiology. 36, p. 111-117

Communication between viruses guides lysis-lysogeny decisions

Erez Z., Steinberger-Levy I., Shamir M., Doron S., Stokar Avihail A. A., Peleg Y., Melamed S., Leavitt A., Savidor A., Albeck S., Amitai G. & Sorek R. Nature, 541(7638):488-493 (2017)

Optimality and sub-optimality in a bacterial growth law

Towbin B. D., Korem Y., Bren A., Doron S., Sorek R. & Alon U. (2017) Nature Communications. 8, 14123.

Vesicles Spread Susceptibility to Phages

Ofir G. & Sorek R. (2017) Cell. 168, 1-2, p. 13-15

Computational prediction of regulatory, premature transcription termination in bacteria

Millman A., Dar D., Shamir M. & Sorek R. (2017) Nucleic Acids Research. 45, 2, p. 886-893

2016

Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array

Goren M. G., Doron S., Globus R., Amitai G., Sorek R. & Qimron U. (2016) Cell Reports. 16, 11, p. 2811-2818

Widespread formation of alternative 3' UTR isoforms via transcription termination in archaea

Dar D., Prasse D., Schmitz R. A. & Sorek R. (2016) Nature Microbiology. 1, 10, 16143.

CRISPRCas: Spacer Diversity Determines the Efficiency of Defense

Lopatina A. & Sorek R. (2016) Current Biology. 26, 14, p. R683-R685

Transcriptome dynamics of a broad host-range cyanophage and its hosts

Doron S., Fedida A., Hernndez-Prieto M. A., Sabehi G., Karunker I., Stazic D., Feingersch R., Steglich C., Futschik M., Lindell D. & Sorek R. (2016) ISME Journal. 10, 6, p. 1437-1455

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

Dar D., Shamir M., Mellin J. R., Koutero M., Stern-Ginossar N., Cossart P. & Sorek R. (2016) Science. 352, 6282, aad9822.

Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model

Yosef I., Edgar R., Levy A., Amitai G., Sorek R., Munitz A., Qimron U., Mueller B., Tarkowski P. & Weiss D. (2016) Nature Microbiology. 1, 6, 16047.

CRISPR-Cas adaptation: Insights into the mechanism of action

Amitai G. & Sorek R. (2016) Nature Reviews Microbiology. 14, 2, p. 67-76

Comparative transcriptomics across the prokaryotic tree of life

Cohen O., Doron S., Wurtzel O., Dar D., Edelheit S., Karunker I., Mick E. & Sorek R. (2016) Nucleic Acids Research. 44, W1, p. W46-W53

2015

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

Korem T., Zeevi D., Suez J., Weinberger A., Avnit Sagi S. T., Pompan-Lotan M., Matot E., Jona G., Harmelin A., Cohen N., Sirota-Madi A., Thaiss C. A., Pevsner-Fischer M., Sorek R., Xavier R. J., Elinav E. & Segal E. (2015) Science (New York, N.Y.). 349, 6252, p. 1101-1106

CRISPR adaptation biases explain preference for acquisition of foreign DNA

Levy A., Goren M. G., Yosef I., Auster O., Manor M., Amitai G., Edgar R., Qimron U. & Sorek R. (2015) Nature. 520, 7548, p. 505-510

BREX is a novel phage resistance system widespread in microbial genomes

Goldfarb T., Sberro H., Weinstock E., Cohen O., Doron S., Charpak-Amikam Y., Afik S., Ofir G. & Sorek R. (2015) EMBO Journal. 34, 2, p. 169-183

2014

Pregnancy-associated listeriosis: Clinical characteristics and geospatial analysis of a 10-year period in Israel

Elinav H., Hershko-Klement A., Valinsky L., Jaffe J., Wiseman A., Shimon H., Braun E., Paitan Y., Block C., Sorek R. & Nir-Paz R. (2014) Clinical Infectious Diseases. 59, 7, p. 953-961

Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA

Mellin J. R., Koutero M., Dar D., Nahori M. A., Sorek R. & Cossart P. (2014) Science. 345, 6199, p. 940-943

Fur is the master regulator of the extraintestinal pathogenic Escherichia coli response to serum

Huja S., Oren Y., Biran D., Meyer S., Dobrindt U., Bernhard J., Becher D., Hecker M., Sorek R. & Ron E. Z. (2014) mBio. 5, 4, e01460-14.

High-resolution metagenomics

Mick E. & Sorek R. (2014) Nature biotechnology. 32, 8, p. 750-751

Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia

Singh G., Srinivasan R., Cheng J., Peng Z., Fujimura K., Baek M. S., Panzer A. R., Tringe S. G., Chen F., Sorek R., Weng L., Bristow J., Wiener-Kronish J. P. & Lynch S. V. (2014) Journal of Clinical Microbiology. 52, 7, p. 2430-2438

2013

Computational evaluation of cellular metabolic costssuccessfully predicts genes whose expression is deleterious

Wagner A., Zarecki R., Reshef L., Gochev C., Sorek R., Gophna U. & Ruppin E. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110, 47, p. 19166-19171

Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins

Rockah-Shmuel L., Toth-Petroczy A., Sela A., Wurtzel O., Sorek R. & Tawfik D. (2013) PLoS Genetics. 9, 10, e1003882.

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

Edelheit S., Schwartz S., Mumbach M. R., Wurtzel O. & Sorek R. (2013) PLoS Genetics. 9, 6, e1003602.

Differential translation tunes uneven production of operon-encoded proteins

Quax T. E. F., Wolf Y. I., Koehorst J. J., Wurtzel O., van der Oost d. O. R., Ran W., Blombach F., Makarova K. S., Brouns S. J. J., Forster A. C., Wagner E. G. H., Sorek R., Koonin E. V. & van der Oost d. O. J. (2013) Cell Reports. 4, 5, p. 938-944

Holding a grudge: Persisting anti-phage CRISPR immunity in multiple human gut microbiomes

Mick E., Stern A. & Sorek R. (2013) RNA Biology. 10, 5, p. 900-906

A Global Transcriptional Switch between the Attack and Growth Forms of Bdellovibrio bacteriovorus

Karunker I., Rotem O., Dori-Bachash M., Jurkevitch E. & Sorek R. (2013) PLoS ONE. 8, 4, e61850.

Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

Sberro H., Leavitt A., Kiro R., Koh E., Peleg Y., Qimron U. & Sorek R. (2013) Molecular Cell. 50, 1, p. 136-148

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

Sesto N., Wurtzel O., Archambaud C., Sorek R. & Cossart P. (2013) Nature Reviews Microbiology. 11, 2, p. 75-82

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

Sorek R., Lawrence C. M. & Wiedenheft B. (2013) Annual Review of Biochemistry. 82, p. 237-266

2012

Roles of CRISPR in regulation of physiological processes

Amitai G. & Sorek R. (2012) CRISPR-Cas Systems : RNA-Mediated Adaptive Immunity in Bacteria and Archaea . van der Oost J. & Barrangou R.(eds.). p. 251-266

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

Stern A., Mick E., Tirosh I., Sagy O. & Sorek R. (2012) Genome Research. 22, 10, p. 1985-1994

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

Wurtzel O., Yoder-Himes D. R., Han K., Dandekar A. A., Edelheit S., Greenberg E. P., Sorek R. & Lory S. (2012) PLoS Pathogens. 8, 9, e1002945.

PanDaTox: A tool for accelerated metabolic engineering

Amitai G. & Sorek R. (2012) Bioengineered. 3, 4, p. 218-221

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

Dominissini D., Moshitch-Moshkovitz S., Schwartz S., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jacob-Hirsch J., Amariglio N., Kupiec M., Sorek R. & Rechavi G. (2012) Nature. 485, 7397, p. 201-206

A vast collection of microbial genes that are toxic to bacteria

Kimelman A., Levy A., Sberro H., Kidron S., Leavitt A., Amitai G., Yoder-Himes D. R., Wurtzel O., Zhu Y., Rubin E. M. & Sorek R. (2012) Genome Research. 22, 4, p. 802-809

Transcriptome-wide discovery of circular RNAs in Archaea

Danan M., Schwartz S., Edelheit S. & Sorek R. (2012) Nucleic Acids Research. 40, 7, p. 3131-3142

RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

Michaeli S., Doniger T., Gupta S. K., Wurtzel O., Romano M., Visnovezky D., Sorek R., Unger R. & Ullu E. (2012) Nucleic Acids Research. 40, 3, p. 1282-1298

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

Wurtzel O., Sesto N., Mellin J. R., Karunker I., Edelheit S., Becavin C., Archambaud C., Cossart P. & Sorek R. (2012) Molecular Systems Biology. 8, 1, 583.

2011

Bacterial genomes: From regulatory complexity to engineering

Sorek R. & Serrano L. (2011) Current Opinion in Microbiology. 14, 5, p. 577-578

Genomic island variability facilitates Prochlorococcusvirus coexistence

Avrani S., Wurtzel O., Sharon I., Sorek R. & Lindell D. (2011) Nature. 474, 7353, p. 604-608

The phage-host arms race: Shaping the evolution of microbes

Stern A. & Sorek R. (2011) BioEssays. 33, 1, p. 43-51

2010

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

He S., Wurtzel O., Singh K., Froula J. L., Yilmaz S., Tringe S. G., Wang Z., Chen F., Lindquist E. A., Sorek R. & Hugenholtz P. (2010) Nature Methods. 7, 10, p. 807-812

Self-targeting by CRISPR: Gene regulation or autoimmunity?

Stern A., Keren L., Wurtzel O., Amitai G. & Sorek R. (2010) Trends in Genetics. 26, 8, p. 335-340

A single-base resolution map of an archaeal transcriptome

Wurtzel O., Sapra R., Chen F., Zhu Y., Simmons B. A. & Sorek R. (2010) Genome Research. 20, 1, p. 133-141

Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity

Sorek R. & Cossart P. (2010) Nature Reviews Genetics. 11, 1, p. 9-16

Mutation detection with next-generation resequencing through a mediator genome

Wurtzel O., Dori-Bachash M., Pietrokovski S., Jurkevitch E. & Sorek R. (2010) PLoS ONE. 5, 12, e15628.

2009

When new exons are born

Sorek R. (2009) Heredity. 103, 4, p. 279-280

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

Yoder-Himes D. R., Chain P. S. G., Zhu Y., Wurtzel O., Rubin E. M., Tiedje J. M. & Sorek R. (2009) Proceedings of the National Academy of Sciences of the United States of America. 106, 10, p. 3976-3981

The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria

Moran N. A., McLaughlin H. J. & Sorek R. (2009) Science. 323, 5912, p. 379-382

2008

CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea

Sorek R., Kunin V. & Hugenholtz P. (2008) Nature Reviews Microbiology. 6, 3, p. 181-186

2007

Genome-wide experimental determination of barriers to horizontal gene transfer

Sorek R., Zhu Y., Creevey C. J., Francino M. P., Bork P. & Rubin E. M. (2007) Science. 318, 5855, p. 1449-1452

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

Warnecke F., Luginbühl P., Ivanova N., Ghassemian M., Richardson T. H., Stege J. T., Cayouette M., McHardy A. C., Djordjevic G., Aboushadi N., Sorek R., Tringe S. G., Podar M., Martin H. G., Kunin V., Dalevi D., Madejska J., Kirton E., Platt D., Szeto E., Salamov A., Barry K., Mikhailova N., Kyrpides N. C., Matson E. G., Ottesen E. A., Zhang X., Hernández M., Murillo C., Acosta L. G., Rigoutsos I., Tamayo G., Green B. D., Chang C., Rubin E. M., Mathur E. J., Robertson D. E., Hugenholtz P. & Leadbetter J. R. (2007) Nature. 450, 7169, p. 560-565

The birth of new exons: Mechanisms and evolutionary consequences

Sorek R. (2007) RNA. 13, 10, p. 1603-1608

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Kunin V., Sorek R. & Hugenholtz P. (2007) GENOME BIOLOGY. 8, 4, R61.

RNA-editing-mediated exon evolution

Lev-Maor G., Sorek R., Levanon E. Y., Paz N., Eisenberg E. & Ast G. (2007) GENOME BIOLOGY. 8, 2, R29.

2006

Assessing the number of ancestral alternatively spliced exons in the human genome

Sorek R., Dror G. & Shamir R. (2006) BMC Genomics. 7, 273.

Genomic fossils as a snapshot of the human transcriptome

Shemesh R., Novik A., Edelheit S. & Sorek R. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103, 5, p. 1364-1369

Transcription-mediated gene fusion in the human genome

Akiva P., Toporik A., Edelheit S., Peretz Y., Diber A., Shemesh R., Novik A. & Sorek R. (2006) Genome Research. 16, 1, p. 30-36

2005

Is there any sense in antisense editing?

Neeman Y., Dahary D., Levanon E. Y., Sorek R. & Eisenberg E. (2005) Trends in Genetics. 21, 10, p. 544-547

Accurate identification of alternatively spliced exons using support vector machine

Dror G., Sorek R. & Shamir R. (2005) Bioinformatics. 21, 7, p. 897-901

Naturally occurring antisense: Transcriptional leakage or real overlap?

Dahary D., Elroy-Stein O. & Sorek R. (2005) Genome Research. 15, 3, p. 364-368

Is abundant A-to-I RNA editing primate-specific?

Eisenberg E., Nemzer S., Kinar Y., Sorek R., Rechavi G. & Levanon E. Y. (2005) Trends in Genetics. 21, 2, p. 77-81

2004

A non-EST-based method for exon-skipping prediction

Sorek R., Shemesh R., Cohen Y., Basechess O., Ast G. & Shamir R. (2004) Genome Research. 14, 8, p. 1617-1623

Minimal conditions for exonization of intronic sequences: 5 splice site formation in Alu exons

Sorek R., Lev-Maor G., Reznik M., Dagan T., Belinky F., Graur D. & Ast G. (2004) Molecular Cell. 14, 2, p. 221-231

How prevalent is functional alternative splicing in the human genome?

Sorek R., Shamir R. & Ast G. (2004) Trends in Genetics. 20, 2, p. 68-71

In search of antisense

Lavorgna G., Dahary D., Lehner B., Sorek R., Sanderson C. M. & Casari G. (2004) Trends in Biochemical Sciences. 29, 2, p. 88-94

AluGene: A database of Alu elements incorporated within protein-coding genes

Dagan T., Sorek R., Sharon E., Ast G. & Graur D. (2004) Nucleic Acids Research. 32, Suppl.1, p. D489-D492

2003

Intronic sequences flanking alternatively spliced exons are conserved between human and mouse

Sorek R. & Ast G. (2003) Genome Research. 13, 7, p. 1631-1637

The birth of an alternatively spliced exon: 3 Splice-site selection in Alu exons

Lev-Maor G., Sorek R., Shomron N. & Ast G. (2003) Science. 300, 5623, p. 1288-1291

Widespread occurrence of antisense transcription in the human genome

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. (2003) Nature biotechnology. 21, 4, p. 379-386

A novel algorithm for computational identification of contaminated EST libraries

Sorek R. & Safer H. M. (2003) Nucleic Acids Research. 31, 3, p. 1067-1074

Evolutionary dynamics of large Numts in the human genome: Rarity of independent insertions and abundance of post-insertion duplications

Hazkani-Covo E., Sorek R. & Graur D. (2003) Journal of Molecular Evolution. 56, 2, p. 169-174

The importance of alternative splicing in the drug discovery process

Levanon E. Y. & Sorek R. (2003) Drug Discovery Today: TARGETS. 2, 3, p. 109-114

2002

Alu-containing exons are alternatively spliced

Sorek R., Ast G. & Graur D. (2002) Genome Research. 12, 7, p. 1060-1067

2001

Piecing together the significance of splicing

Sorek R. & Amitai M. (2001) Nature biotechnology. 19, 3, p. 196