Publications

2024

Endocrinology in the multi-omics era

Shilo S. & Segal E. (2024) Nature Reviews Endocrinology. 20, p. 73-74

Competitive fungal commensalism mitigates candidiasis pathology

Sekeresova Kralova J., Donic C., Dassa B., Livyatan I., Jansen P. M., Ben-Dor S., Fidel L., Trzebanski S., Narunsky-Haziza L., Asraf O., Brenner O., Dafni H., Jona G., Boura-Halfon S., Stettner N., Segal E., Brunke S., Pilpel Y., Straussman R., Zeevi D., Bacher P., Hube B., Shlezinger N. & Jung S. (2024) Journal of Experimental Medicine. 221, 5, e20231686.

Melanoma and microbiota: Current understanding and future directions

Routy B., Jackson T., Mählmann L., Baumgartner C. K., Blaser M., Byrd A., Corvaia N., Couts K., Davar D., Derosa L., Hang H. C., Hospers G., Isaksen M., Kroemer G., Malard F., McCoy K. D., Meisel M., Pal S., Ronai Z., Segal E., Sepich-Poore G. D., Shaikh F., Sweis R. F., Trinchieri G., van den Brink M., Weersma R. K., Whiteson K., Zhao L., McQuade J., Zarour H. & Zitvogel L. (2024) Cancer Cell. 42, 1, p. 16-34

Genome-wide association studies and polygenic risk score phenome-wide association studies across complex phenotypes in the human phenotype project

Levine Z., Kalka I., Kolobkov D., Rossman H., Godneva A., Shilo S., Keshet A., Weissglas-Volkov D., Shor T., Diament A., Talmor-Barkan Y., Aviv Y., Sharon T., Weinberger A. & Segal E. (2024) Med. 5, 1, p. 90-101.e4

Quantification of beta cell carrying capacity in prediabetes

Woller A., Tamir Y., Bar A., Mayo A., Rein M., Godneva A., Cohen N. M., Segal E., Toledano Y., Shilo S., Gonze D. & Alon U. (2024) BioRxiv.

Continuous glucose monitoring and intrapersonal variability in fasting glucose

Shilo S., Keshet A., Rossman H., Godneva A., Talmor-Barkan Y., Aviv Y. & Segal E. (2024) Nature Medicine. 30, 5, p. 1424-1431

2023

Head-to-head efficacy and safety of rivaroxaban, apixaban, and dabigatran in an observational nationwide targeted trial

Talmor-Barkan Y., Yacovzada N., Rossman H., Witberg G., Kalka I., Kornowski R. & Segal E. (2023) European heart journal. Cardiovascular pharmacotherapy. 9, 1, p. 26-37

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Kennedy K. M., de Goffau M. C., Perez-Muñoz M. E., Arrieta M., Bäckhed F., Bork P., Braun T., Bushman F. D., Dore J., de Vos W. M., Earl A. M., Eisen J. A., Elovitz M. A., Ganal-Vonarburg S. C., Gänzle M. G., Garrett W. S., Hall L. J., Hornef M. W., Huttenhower C., Konnikova L., Lebeer S., Macpherson A. J., Massey R. C., McHardy A. C., Koren O., Lawley T. D., Ley R. E., O'Mahony L., O'Toole P. W., Pamer E. G., Parkhill J., Raes J., Rattei T., Salonen A., Segal E., Segata N., Shanahan F., Sloboda D. M., Smith G. C. S., Sokol H., Spector T. D., Surette M. G., Tannock G. W., Walker A. W., Yassour M. & Walter J. (2023) Nature. 613, 7945, p. 639-649

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

Bourgonje A. R., Andreu-Sánchez S., Vogl T., Hu S., Vich Vila A., Gacesa R., Leviatan S., Kurilshikov A., Klompus S., Kalka I. N., van Dullemen H. M., Weinberger A., Visschedijk M. C., Festen E. A., Faber K. N., Wijmenga C., Dijkstra G., Segal E., Fu J., Zhernakova A. & Weersma R. K. (2023) Immunity. 56, 6, p. 1393-1409.e6

Wearable and digital devices to monitor and treat metabolic diseases

Keshet A., Reicher L., Bar N. & Segal E. (2023) Nature metabolism. 5, 4, p. 563-571

A randomized clinical trial comparing low-fat with precision nutrition–based diets for weight loss: impact on glycemic variability and HbA1c

Kharmats A. Y., Popp C., Hu L., Berube L., Curran M., Wang C., Pompeii M. L., Li H., Bergman M., St-Jules D. E., Segal E., Schoenthaler A., Williams N., Schmidt A. M., Barua S. & Sevick M. A. (2023) American Journal of Clinical Nutrition. 118, 2, p. 443-451

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

Andreu-Sánchez S., Bourgonje A. R., Vogl T., Kurilshikov A., Leviatan S., Ruiz-Moreno A. J., Hu S., Sinha T., Vich Vila A., Klompus S., Kalka I. N., de Leeuw K., Arends S., Jonkers I., Withoff S., Brouwer E., Weinberger A., Wijmenga C., Segal E. & Weersma R. K. (2023) Immunity. 56, 6, p. 1376-1392

Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes

Ben-Yacov O., Godneva A., Rein M., Shilo S., Lotan-Pompan M., Weinberger A. & Segal E. (2023) Gut. 72, 8, p. 1486-1496

Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines

Shoer S., Shilo S., Godneva A., Ben-Yacov O., Rein M., Wolf B. C., Lotan-Pompan M., Bar N., Weiss E. I., Houri-Haddad Y., Pilpel Y., Weinberger A. & Segal E. (2023) Nature Communications. 14, 5384.

Bacterial SNPs in the human gut microbiome associate with host BMI

Zahavi L., Lavon A., Reicher L., Shoer S., Godneva A., Leviatan S., Rein M., Weissbrod O., Weinberger A. & Segal E. (2023) Nature Medicine. 29, 11, p. 2785-2792

2022

Nowcasting the spread of SARS-CoV-2

Rossman H. & Segal E. (2022) Nature Microbiology. 7, 1, p. 16-17

An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents

Rothschild D., Leviatan S., Hanemann A., Cohen Y., Weissbrod O. & Segal E. (2022) PLoS ONE. 17, 3 March, e0265756.

Recording bacterial responses to changes in the gut environment

Zahavi L. & Segal E. (2022) Science (American Association for the Advancement of Science). 376, 6594, p. 697-698

DOP53 In-depth characterisation of the serum antibody epitope repertoire in Inflammatory Bowel Disease by high-throughput phage-displayed immunoprecipitation sequencing

Bourgonje A. R., Andreu-Sánchez S., Vogl T., Hu S., Vich Vila A., Leviatan S., Kurilshikov A., Klompus S., Kalka I. N., van Dullemen H. M., Weinberger A., Visschedijk M. C., Festen E. A. M., Faber K. N., Wijmenga C., Dijkstra G., Segal E., Fu J., Zhernakova A. & Weersma R. K. (2022) Journal of Crohn's and Colitis. 16, Supplement_1, p. i100-i102

Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3′UTR protect against ALS

Eitan C., Siany A., Barkan E., Olender T., Yanowski E., Marmor-Kollet H., Chapnik E., Ainbinder E., Ben-Dor S., Segal E. & Hornstein E. (2022) Nature Neuroscience. 25, 4, p. 433-445

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species

Leviatan S., Shoer S., Rothschild D., Gorodetski M. & Segal E. (2022) Nature Communications. 13, 3863.

Estimating the effect of cesarean delivery on long-term childhood health across two countries

Keshet A., Rossman H., Shilo S., Barbash-Hazan S., Amit G., Bivas-Benita M., Yanover C., Girshovitz I., Akiva P., Ben-Haroush A., Hadar E., Wiznitzer A. & Segal E. (2022) PLoS ONE. 17, 10, e0268103.

BIPS—A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library

Leviatan S., Kalka I. N., Vogl T., Klompas S., Weinberger A. & Segal E. (2022) PLoS Computational Biology. 18, 11, e1010663.

Genome-Wide Association Analysis of Over 170,000 Individuals from the UK Biobank Identifies Seven Loci Associated with Dietary Approaches to Stop Hypertension (DASH) Diet

Mompeo O., Freidin M. B., Gibson R., Hysi P. G., Christofidou P., Segal E., Valdes A. M., Spector T. D., Menni C. & Mangino M. (2022) Nutrients. 14, 20, 4431.

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients

Vogl T., Kalka I. N., Klompus S., Leviatan S., Weinberger A. & Segal E. (2022) Science advances. 8, 38, eabq2422.

Research gaps and opportunities in precision nutrition: an NIH workshop report

Lee B. Y., Ordovás J. M., Parks E. J., Anderson C. A., Barabási A. L., Clinton S. K., de la Haye K., Duffy V. B., Franks P. W., Ginexi E. M., Hammond K. J., Hanlon E. C., Hittle M., Ho E., Horn A. L., Isaacson R. S., Mabry P. L., Malone S., Martin C. K., Mattei J., Meydani S. N., Nelson L. M., Neuhouser M. L., Parent B., Pronk N. P., Roche H. M., Saria S., Scheer F. A., Segal E., Sevick M. A., Spector T. D., Van Horn L., Varady K. A., Voruganti V. S. & Martinez M. F. (2022) The American journal of clinical nutrition. 116, 6, p. 1877-1900

Soluble Receptor for Advanced Glycation End Products (sRAGE) Isoforms Predict Changes in Resting Energy Expenditure in Adults with Obesity during Weight Loss

Popp C. J., Zhou B., Manigrasso M. B., Li H., Curran M., Hu L., St-Jules D. E., Alemán J. O., Vanegas S. M., Jay M., Bergman M., Segal E., Sevick M. A. & Schmidt A. M. (2022) Current Developments in Nutrition. 6, 5, nzac046.

New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease

Elmaleh D. R., Downey M. A., Kundakovic L., Wilkinson J. E., Neeman Z. & Segal E. (2022) Handbook of Microbiome and Gut-Brain-Axis in Alzheimer's Disease . Pasinetti G. M.(eds.). p. 117-145

Microbiome and metabolome features of the cardiometabolic disease spectrum

Fromentin S., Forslund S. K., Chechi K., Bar N. & Segal E. (2022) Nature Medicine. 28, 2, p. 303-314

Antibody signatures in inflammatory bowel disease: current developments and future applications

Bourgonje A. R., Vogl T., Segal E. & Weersma R. K. (2022) Trends in Molecular Medicine. 28, 8, p. 693-705

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

Suez J., Cohen Y., Valdés-Mas R., Mor U., Dori-Bachash M., Federici S., Zmora N., Leshem A., Heinemann M., Linevsky R., Zur M., Ben-Zeev Brik R., Bukimer A., Eliyahu-Miller S., Metz A., Fischbein R., Sharov O., Malitsky S., Itkin M., Stettner N., Harmelin A., Shapiro H., Stein-Thoeringer C. K., Segal E. & Elinav E. (2022) Cell. 185, 18, p. 3307-3328.e19

Phenotypic correlates of the working dog microbiome

Craddock H. A., Godneva A., Rothschild D., Motro Y., Grinstein D., Lotem-Michaeli Y., Narkiss T., Segal E. & Moran-Gilad J. (2022) npj Biofilms and Microbiomes. 8, 66.

Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis

Mashiah J., Karady T., Fliss-Isakov N., Sprecher E., Slodownik D., Artzi O., Samuelov L., Ellenbogen E., Godneva A., Segal E. & Maharshak N. (2022) Immunity, inflammation and disease. 10, 3, e570.

Effects of personalized diets by prediction of glycemic responses on glycemic control and metabolic health in newly diagnosed T2DM: a randomized dietary intervention pilot trial

Rein M., Ben-Yacov O., Godneva A., Shilo S., Zmora N., Kolobkov D., Cohen-Dolev N., Wolf B., Kosower N., Lotan-Pompan M., Weinberger A., Halpern Z., Zelber-Sagi S., Elinav E. & Segal E. (2022) BMC Medicine. 20, 56.

BREAst Cancer Personalised NuTrition (BREACPNT): dietary intervention in breast cancer survivors treated with endocrine therapy – a protocol for a randomised clinical trial

Rein M. S., Dadiani M., Godneva A., Bakalenik-Gavry M., Morzaev-Sulzbach D., Vachnish Y., Kolobkov D., Lotan-Pompan m., Weinberger A., Segal E. & Gal-Yam E. N. (2022) BMJ Open. 12, 11, e062498.

Prediction of Personal Glycemic Responses to Food for Individuals With Type 1 Diabetes Through Integration of Clinical and Microbial Data

Shilo S., Godneva A., Rachmiel M., Korem T., Kolobkov D., Karady T., Bar N., Wolf B. C., Glantz-Gashai Y., Cohen M., Zuckerman Levin N., Shehadeh N., Gruber N., Levran N., Koren S., Weinberger A., Pinhas-Hamiel O. & Segal E. (2022) Diabetes Care. 45, 3, p. 502-511

The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control

Shilo S., Godneva A., Rachmiel M., Korem T., Bussi Y., Kolobkov D., Karady T., Bar N., Wolf B. C., Glantz-Gashai Y., Cohen M., Levin N. Z., Shehadeh N., Gruber N., Levran N., Koren S., Weinberger A., Pinhas-Hamiel O. & Segal E. (2022) Diabetes Care. 45, 3, p. 555-563

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease

Talmor-Barkan Y., Bar N., Shaul A. A., Shahaf N., Godneva A., Bussi Y., Lotan-Pompan M., Weinberger A., Shechter A., Chezar-Azerrad C., Arow Z., Hammer Y., Chechi K., Forslund S. K., Fromentin S., Dumas M., Ehrlich S. D., Pedersen O., Kornowski R. & Segal E. (2022) Nature Medicine. 28, 2, p. 295-302

Effect of a Personalized Diet to Reduce Postprandial Glycemic Response vs a Low-fat Diet on Weight Loss in Adults with Abnormal Glucose Metabolism and Obesity: A Randomized Clinical Trial

Popp C. J., Hu L., Kharmats A. Y., Curran M., Berube L., Wang C., Pompeii M. L., Illiano P., St-Jules D. E., Mottern M., Li H., Williams N., Schoenthaler A., Segal E., Godneva A., Thomas D., Bergman M., Schmidt A. M. & Sevick M. A. (2022) JAMA network open. 5, 9,

Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals

Leviatan S., Vogl T., Klompus S., Kalka I. N., Weinberger A. & Segal E. (2022) Immunity. 55, 12, p. 2454-2469.e6

2021

New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease

Elmaleh D. R., Downey M. A., Kundakovic L., Wilkinson J. E., Neeman Z. & Segal E. (2021) Journal of Alzheimer's Disease. 82, 4, p. 1373-1401

Stress-related emotional and behavioural impact following the first COVID-19 outbreak peak

Benjamin A., Kuperman Y., Eren N., Rotkopf R., Amitai M., Rossman H., Shilo S., Meir T., Keshet A., Nuttman-Shwartz O., Segal E. & Chen A. (2021) Molecular Psychiatry. 26, 11, p. 6149-6158

Evidence for cutaneous dysbiosis in dystrophic epidermolysis bullosa

Bar J., Sarig O., Lotan-Pompan M., Dassa B., Miodovnik M., Weinberger A., Sprecher E., Segal E. & Samuelov L. (2021) Clinical and Experimental Dermatology. 46, 7, p. 1223-1229

Reporting guidelines for human microbiome research: the STORMS checklist

Elinav E. & Segal E. (2021) Nature Medicine. 27, 11, p. 1885-1892

Structured elements drive extensive circular RNA translation

Chen C. K., Cheng R., Demeter J., Chen J., Weingarten-Gabbay S., Jiang L., Snyder M. P., Weissman J. S., Segal E., Jackson P. K. & Chang H. Y. (2021) Molecular Cell. 81, 20, p. 4300-4318.e13

Large-scale association analyses identify host factors influencing human gut microbiome composition

Kurilshikov A., Medina-Gomez C., Bacigalupe R., Barkan E., Segal E. & Rothschild Bup D. (2021) Nature Genetics. 53, 2, p. 156-165

Challenges of conducting a remote behavioral weight loss study: Lessons learned and a practical guide

Hu L., Illiano P., Pompeii M. L., Popp C. J., Kharmats A. Y., Curran M., Perdomo K., Chen S., Bergman M., Segal E. & Sevick M. A. (2021) Contemporary Clinical Trials. 108, 106522.

Prediction of Childhood Obesity from Nationwide Health Records

Rossman H., Shilo S., Barbash-Hazan S., Artzi N. S., Hadar E., Balicer R. D., Feldman B., Wiznitzer A. & Segal E. (2021) Journal of Pediatrics. 233, p. 132-140.e1

Signals of hope: gauging the impact of a rapid national vaccination campaign

Shilo S., Rossman H. & Segal E. (2021) Nature Reviews Immunology. 21, p. 198-199

Anosmia, ageusia, and other COVID-19-like symptoms in association with a positive SARS-CoV-2 test, across six national digital surveillance platforms: an observational study

Sudre C. H., Keshet A., Graham M. S., Joshi A. D., Shilo S., Rossman H., Murray B., Molten E., Klaser K., Canas L. D., Antonelli M., Nguyen L. H., Drew D. A., Modat M., Pujol J. C., Ganesh S., Wolf J., Meir T., Chan A. T., Steves C. J., Spector T. D., Brownstein J. S., Segal E., Ourselin S. & Astley C. M. (2021) The Lancet. Digital health. 3, 9, p. e577-e586

SARS-CoV-2 antibody testing for estimating COVID-19 prevalence in the population

Vogl T., Leviatan S. & Segal E. (2021) Cell Reports Medicine. 2, 2, 100191.

The gut microbiome: a key player in the complexity of amyotrophic lateral sclerosis (ALS)

Boddy S. L., Giovannelli I., Sassani M., Cooper-Knock J., Snyder M. P., Segal E., Elinav E., Barker L. A., Shaw P. J. & McDermott C. J. (2021) BMC Medicine. 19, 1, 13.

Hospital load and increased COVID-19 related mortality in Israel

Rossman H., Meir T., Somer J., Shilo S., Gutman R., Ben Arie A., Segal E., Shalit U. & Gorfine M. (2021) Nature Communications. 12, 1, 1904.

Estimating heritability of glycaemic response to metformin using nationwide electronic health records and population-sized pedigree

Kalka I. N., Gavrieli A., Shilo S., Rossman H., Artzi N. S., Yacovzada N. & Segal E. (2021) Communications Medicine. 1, 1, 55.

Unified platform for genetic and serological detection of COVID-19 with single-molecule technology

Furth N., Shilo S., Cohen N., Erez N., Fedyuk V., Schrager A. M., Weinberger A., Dror A. A., Zigron A., Shehadeh M., Sela E., Srouji S., Amit S., Levy I., Segal E., Dahan R., Jones D., Douek D. C. & Shema E. (2021) PLoS ONE. 16, 7, e0255096.

COVID-19 dynamics after a national immunization program in Israel

Rossman H., Shilo S., Meir T., Gorfine M., Shalit U. & Segal E. (2021) Nature Medicine. 27, p. 1055-1061

The long-term genetic stability and individual specificity of the human gut microbiome

Chen L., Wang D., Garmaeva S., Kurilshikov A. & Segal E. (2021) Cell. 184, 9, p. 2302-2315.e12

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

Thomas V., Shelley K., Sigal L., N K. I., Adina W., Cisca W., Jingyuan F., Alexandra Z., K W. R. & Segal E. (2021) Nature Medicine. 27, 8, p. 1442-1450

Identification of bacteria-derived HLA-bound peptides in melanoma

Kalaora S., Nagler A., Nejman D., Alon M., Barbolin C., Barnea E., Ketelaars S. L. C., Cheng K., Vervier K., Shental N., Bussi Y., Rotkopf R., Levy R., Benedek G., Trabish S., Dadosh T., Levin-Zaidman S., Geller L. T., Wang K., Greenberg P., Yagel G., Peri A., Fuks G., Bhardwaj N., Reuben A., Hermida L., Johnson S. B., Galloway-Peña J. R., Shropshire W. C., Bernatchez C., Haymaker C., Arora R., Roitman L., Eilam R., Weinberger A., Lotan-Pompan M., Lotem M., Levin Y., Lawley T. D., Adams D. J., Levesque M. P., Besser M. J., Schachter J., Golani O., Segal E., Ruppin E., Kvistborg P., Peterson S. N., Wargo J. A., Straussman R. & Samuels Y. (2021) Nature (London). 592, 7852, p. 138-143

Cross-reactive antibodies against human coronaviruses and the animal coronavirome suggest diagnostics for future zoonotic spillovers

Klompus S., Leviatan S., Vogl T., Mazor R., Kalka I., Stoler-Barak L., Nathan N., Peres A., Moss L., Godneva A., Kagan Ben Tikva S., Shinar E., Dvashi H. C., Gabizon R., London N., Diskin R., Yaari G., Weinberger A., Shulman Z. & Segal E. (2021) Science immunology. 6, 61, eabe9950.

Potential role of indolelactate and butyrate in multiple sclerosis revealed by integrated microbiome-metabolome analysis

Levi I., Gurevich M., Perlman G., Magalashvili D., Menascu S., Bar N., Godneva A., Zahavi L., Chermon D., Kosower N., Wolf B. C., Malka G., Lotan-Pompan M., Weinberger A., Yirmiya E., Rothschild D., Leviatan S., Tsur A., Didkin M., Dreyer S., Eizikovitz H., Titngi Y., Mayost S., Sonis P., Dolev M., Stern Y., Achiron A. & Segal E. (2021) Cell Reports Medicine. 2, 4, 100246.

10 K: a large-scale prospective longitudinal study in Israel

Shilo S., Bar N., Keshet A., Talmor-Barkan Y., Rossman H., Godneva A., Aviv Y., Edlitz Y., Reicher L., Kolobkov D., Wolf B. C., Lotan-Pompan M., Levi K., Cohen O., Saranga H., Weinberger A. & Segal E. (2021) European Journal of Epidemiology. 36, 11, p. 1187-1194

A Prediction Model to Prioritize Individuals for a SARS-CoV-2 Test Built from National Symptom Surveys

Shoer S., Karady T., Keshet A., Shilo S., Rossman H., Gavrieli A., Meir T., Lavon A., Kolobkov D., Kalka I., Godneva A., Cohen O., Kariv A., Hoch O., Zer-Aviv M., Castel N., Sudre C., Zohar A. E., Irony A., Spector T., Geiger B., Hizi D., Shalev V., Balicer R. & Segal E. (2021) Med. 2, 2, p. 196-208.e4

Diversity and functional landscapes in the microbiota of animals in the wild

Levin D., Raab N., Pinto Y., Rothschild D., Zanir G., Godneva A., Mellul N., Futorian D., Gal D., Leviatan S., Zeevi D., Bachelet I. & Segal E. (2021) Science. 372, 6539, eabb5352.

Personalized Postprandial Glucose Response–Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes

Ben-Yacov O., Godneva A., Rein M., Shilo S., Kolobkov D., Koren N., Cohen Dolev N., Travinsky Shmul T., Wolf B. C., Kosower N., Sagiv K., Lotan-Pompan M., Zmora N., Weinberger A., Elinav E. & Segal E. (2021) Diabetes Care. 44, 9, p. 1980-1991

2020

Axes of a revolution: challenges and promises of big data in healthcare

Shilo S., Rossman H. & Segal E. (2020) Nature Medicine. 26, 1, p. 29-38

Prediction of gestational diabetes based on nationwide electronic health records

Artzi N. S., Shilo S., Hadar E., Rossman H., Barbash-Hazan S., Ben-Haroush A., Balicer R. D., Feldman B., Wiznitzer A. & Segal E. (2020) Nature Medicine. 26, 1, p. 71-76

Rich data sets could end costly drug discovery

Segal E. (2020) Nature (London). 577, 7792, p. S19-S19

Clinically Accurate Prediction of Glucose Levels in Patients with Type 1 Diabetes

Amar Y., Shilo S., Oron T., Amar E., Phillip M. & Segal E. (2020) Diabetes Technology and Therapeutics. 22, 8, p. 562-569

Visualizing the structure and motion of the long noncoding RNA HOTAIR

Spokoini-Stern R., Stamov D., Jessel H., Aharoni L., Haschke H., Giron J., Unger R., Segal E., Abu-Horowitz A. & Bachelet I. (2020) RNA. 26, 5, p. 629-636

Building an international consortium for tracking coronavirus health status

Segal E., Zhang F., Lin X., King G., Shalem O., Shilo S., Allen W. E., Alquaddoomi F., Altae-Tran H., Anders S., Balicer R., Bauman T., Bonilla X., Booman G., Chan A. T., Cohen O., Coletti S., Davidson N., Dor Y., Drew D. A., Elemento O., Evans G., Ewels P., Gale J., Gavrieli A., Grad Y. H., Greene C. S., Hajirasouliha I., Jerala R., Kahles A., Kallioniemi O., Keshet A., Kocarev L., Landua G., Meir T., Muller A., Nguyen L. H., Oresic M., Ovchinnikova S., Peterson H., Prodanova J., Rajagopal J., Ratsch G., Rossman H., Rung J., Sboner A., Sigaras A., Spector T., Steinherz R., Stevens I., Vilo J. & Wilmes P. (2020) Nature Medicine. 26, 8, p. 1161-1165

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome (vol 182, pg 1460, 2020): Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome (Cell (2020) 182(6) (1460–1473.e17), (S0092867420309983), (10.1016/j.cell.2020.08.007))

Mars R. A., Yang Y., Ward T., Houtti M., Priya S., Lekatz H. R., Tang X., Sun Z., Kalari K. R., Korem T., Bhattarai Y., Zheng T., Bar N., Frost G., Johnson A. J., van Treuren W., Han S., Ordog T., Grover M., Sonnenburg J., D'Amato M., Camilleri M., Elinav E., Segal E., Blekhman R., Farrugia G., Swann J. R., Knights D. & Kashyap P. C. (2020) Cell. 183, 4, p. 1137-1140

High-throughput interrogation of programmed ribosomal frameshifting in human cells

Mikl M., Pilpel Y. & Segal E. (2020) Nature Communications. 11, 1, 3061.

A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys

Rossman H., Keshet A., Shilo S., Gavrieli A., Bauman T., Cohen O., Shelly E., Balicer R., Geiger B., Dor Y. & Segal E. (2020) Nature Medicine. 26, 5, p. 634-638

The road ahead in genetics and genomics

McGuire A. L., Gabriel S., Tishkoff S. A., Wonkam A., Chakravarti A., Furlong E. E. M., Treutlein B., Meissner A., Chang H. Y., Lopez-Bigas N., Segal E. & Kim J. (2020) Nature Reviews Genetics. 21, 10, p. 581-596

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

Mars R. A. T., Ward T., Houtti M., Priya S., Lekatz H. R., Tang X., Sun Z., Kalari K. R., Bhattarai Y., Zheng T., Bar N., Frost G., Johnson A. J., van Treuren W., Han S., Ordog T., Grover M., Sonnenburg J., D'Amato M., Camilleri M., Elinav E., Segal E., Blekhman R., Farrugia G., Swann J. R., Knights D. & Kashyap P. C. (2020) Cell. 182, 6, p. 1460-1473

Identifying gut microbes that affect human health

Leviatan S. & Segal E. (2020) Nature. 587, 7834, p. 373-374

A reference map of potential determinants for the human serum metabolome

Bar N., Korem T., Weissbrod O., Zeevi D., Rothschild Bup D., Peled-Leviatan S., Kosower N., Lotan-Pompan M., Weinberger A. & Segal E. (2020) Nature. 588, 7836, p. 135-140

The gut microbiome and individual-specific responses to diet

Leshem A., Segal E. & Elinav E. (2020) mSystems. 5, 5, e00665-20.

The human tumor microbiome is composed of tumor type-specific intracellular bacteria

Nejman D., Livyatan I., Fuks G., Gavert N., Zwang Y., Geller L. T., Rotter-Maskowitz A., Weiser R., Mallel G., Gigi E., Meltser A., Douglas G. M., Kamer I., Gopalakrishnan V., Dadosh T., Levin-Zaidman S., Avnet S., Atlan T., Cooper Z. A., Arora R., Cogdill A. P., Khan M. A. W., Ologun G., Bussi Y., Weinberger A., Lotan-Pompan M., Golani O., Perry G., Rokah M., Bahar-Shany K., Rozeman E. A., Blank C. U., Ronai A., Shaoul R., Amit A., Dorfman T., Kremer R., Cohen Z. R., Harnof S., Siegal T., Yehuda-Shnaidman E., Gal-Yam E. N., Shapira H., Baldini N., Langille M. G. I., Ben-Nun A., Kaufman B., Nissan A., Golan T., Dadiani M., Levanon K., Bar J., Yust-Katz S., Barshack I., Peeper D. S., Raz D. J., Segal E., Wargo J. A., Sandbank J., Shental N. & Straussman R. (2020) Science. 368, 6494, p. 973-980

Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex

Zuckerman B., Ron M., Mikl M., Segal E. & Ulitsky I. (2020) Molecular Cell. 79, 2, p. 251-267

Longitudinal symptom dynamics of COVID-19 infection

Mizrahi B., Shilo S., Rossman H., Kalkstein N., Marcus K., Barer Y., Keshet A., Shamir-Stein N., Shalev V., Zohar A. E., Chodick G. & Segal E. (2020) Nature Communications. 11, 1, 6208.

Rationale and design of a randomised controlled trial testing the effect of personalised diet in individuals with pre-diabetes or type 2 diabetes mellitus treated with metformin

Htet T. D., Godneva A., Liu Z., Chalmers E., Kolobkov D., Snaith J. R., Richens R., Toth K., Danta M., Hng T. M., Elinav E., Segal E., Greenfield J. R. & Samocha-Bonet D. (2020) BMJ Open. 10, 10, e037859.

2019

Systematic interrogation of human promoters

Weingarten-Gabbay S., Nir R., Lubliner S., Sharon E., Kalma Y., Weinberger A. & Segal E. (2019) Genome Research. 29, 2, p. 171-183

A Significant Expansion of Our Understanding of the Composition of the Human Microbiome

Leviatan S. & Segal E. (2019) mSystems. 4, 1, e00010-19.

The pros, cons, and many unknowns of probiotics

Suez J., Zmora N., Segal E. & Elinav E. (2019) Nature Medicine. 25, 5, p. 716-729

Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries

Mikl M., Hamburg A., Pilpel Y. & Segal E. (2019) Nature Communications. 10, 4572.

Sequence determinants of polyadenylation-mediated regulation

Slutskin I. V., Weinberger A. & Segal E. (2019) Genome Research. 29, 10, p. 1635-1647

Erratum: Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast (Proceedings of the National Academy of Sciences of the United States of America (2013) 110 (E2792–E2801) DOI: 10.1073/pnas.1222534110)

Dvir S., Velten L., Sharon E., Zeevi D., Carey L. B., Weinberger A. & Segal E. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116, 27, p. 13701

Potential roles of gut microbiome and metabolites in modulating ALS in mice

Blacher E., Bashiardes S., Shapiro H., Rothschild D., Mor U., Dori-Bachash M., Kleimeyer C., Moresi C., Harnik Y., Zur M., Zabari M., Brik R. B., Kviatcovsky D., Zmora N., Cohen Y., Bar N., Levi I., Amar N., Mehlman T., Brandis A., Biton I., Kuperman Y., Tsoory M., Alfahel L., Harmelin A., Schwartz M., Israelson A., Arike L., Johansson M. E. V., Hansson G. C., Gotkine M., Segal E. & Elinav E. (2019) Nature. 572, 7770, p. 474-480

Structural variation in the gut microbiome associates with host health

Zeevi D., Korem T., Godneva A., Bar N., Kurilshikov A., Lotan-Pompan M., Weinberger A., Fu J., Wijmenga C., Zhernakova A. & Segal E. (2019) Nature. 568, 7750, p. 43-48

The rationale and design of the personal diet study, a randomized clinical trial evaluating a personalized approach to weight loss in individuals with pre-diabetes and early-stage type 2 diabetes

Popp C. J., St-Jules D. E., Hu L., Ganguzza L., Illiano P., Curran M., Li H., Schoenthaler A., Bergman M., Schmidt A. M., Segal E., Godneva A. & Sevick M. A. (2019) Contemporary Clinical Trials. 79, p. 80-88

2018

Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

Slutskin I. V., Weingarten-Gabbay S., Nir R., Weinberger A. & Segal E. (2018) Nature Communications. 9, 529.

Probiotics administration following sleeve gastrectomy surgery: a randomized double-blind trial

Sherf-Dagan S., Zelber-Sagi S., Zilberman-Schapira G., Webb M., Buch A., Keidar A., Raziel A., Sakran N., Goitein D., Goldenberg N., Mahdi J. A., Pevsner-Fischer M., Zmora N., Dori-Bachash M., Segal E., Elinav E. & Shibolet O. (2018) International Journal of Obesity. 42, 2, p. 147-155

Role of the gut microbiota in nutrition and health

Valdes A. M., Walter L., Segal E. & Spector T. D. (2018) British Medical Journal. 361, 2179.

Prediction of acute myeloid leukaemia risk in healthy individuals

Abelson S., Collord G., Ng S. W. K., Weissbrod O., Mendelson Cohen N., Niemeyer E., Barda N., Zuzarte P. C., Heisler L., Sundaravadanam Y., Luben R., Hayat S., Wang T. T., Zhao Z., Cirlan I., Pugh T. J., Soave D., Ng K., Latimer C., Hardy C., Raine K., Jones D., Hoult D., Britten A., McPherson J. D., Johansson M., Mbabaali F., Eagles J., Miller J. K., Pasternack D., Timms L., Krzyzanowski P., Awadalla P., Costa R., Segal E., Bratman S. V., Beer P., Behjati S., Martincorena I., Wang J. C. Y., Bowles K. M., Quirós J. R., Karakatsani A., La Vecchia C., Trichopoulou A., Salamanca-Fernández E., Huerta J. M., Barricarte A., Travis R. C., Tumino R., Masala G., Boeing H., Panico S., Kaaks R., Krämer A., Sieri S., Riboli E., Vineis P., Foll M., McKay J., Polidoro S., Sala N., Khaw K., Vermeulen R., Campbell P. J., Papaemmanuil E., Minden M. D., Tanay A., Balicer R. D., Wareham N. J., Gerstung M., Dick J. E., Brennan P., Vassiliou G. S. & Shlush L. I. (2018) Nature. 559, 7714, p. 400-404

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

Kotler E., Shani O., Goldfeld G., Lotan-Pompan M., Tarcic O., Gershoni A., Hopf T. A., Marks D. S., Oren M. & Segal E. (2018) Molecular Cell. 71, 1, p. 178-190.e8

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Suez J., Zmora N., Zilberman-Schapira G., Mor U., Dori-Bachash M., Bashiardes S., Zur M., Regev-Lehavi D., Brik R. B., Federici S., Horn M., Cohen Y., Moor A. E., Zeevi D., Korem T., Kotler E., Harmelin A., Itzkovitz S., Maharshak N., Shibolet O., Pevsner-Fischer M., Shapiro H., Sharon I., Halpern Z., Segal E. & Elinav E. (2018) Cell. 174, 6, p. 1406-1423.e16

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

Zmora N., Zilberman-Schapira G., Suez J., Mor U., Dori-Bachash M., Bashiardes S., Kotler E., Zur M., Regev-Lehavi D., Brik R. B., Federici S., Cohen Y., Linevsky R., Rothschild D., Moor A. E., Ben-Moshe S., Harmelin A., Itzkovitz S., Maharshak N., Shibolet O., Shapiro H., Pevsner-Fischer M., Sharon I., Halpern Z., Segal E. & Elinav E. (2018) Cell. 174, 6, p. 1388-1405.e21

Host genetics and microbiome associations through the lens of genome wide association studies

Weissbrod O., Rothschild D., Barkan E. & Segal E. (2018) Current Opinion in Microbiology. 44, p. 9-19

The Helix Twist: Damage and Repair Follows the DNA Minor Groove

Kotler E. & Segal E. (2018) Cell. 175, 4, p. 902-904

Functional characterization of the p53 "mutome"

Kotler E., Segal E. & Oren M. (2018) Molecular & cellular oncology. 5, 6, 1511207.

What Can Immunologists Learn from Systems Approaches?

Segal E., Vogl T., Klompus S., Peled-Leviatan S. & Weinberger A. (2018) Trends in Immunology. 39, 3, p. 163-166

Towards utilization of the human genome and microbiome for personalized nutrition

Bashiardes S., Godneva A., Elinav E. & Segal E. (2018) Current Opinion in Biotechnology. 51, p. 57-63

Environment dominates over host genetics in shaping human gut microbiota

Rothschild D., Weissbrod O., Barkan E., Kurilshikov A., Korem T., Zeevi D., Costea P. I., Godneva A., Kalka I. N., Bar N., Shilo S., Lador D., Vila A. V., Zmora N., Pevsner-Fischer M., Israeli D., Kosower N., Malka G., Wolf B. C., Avnit-Sagi T., Lotan-Pompan M., Weinberger A., Halpern Z., Carmi S., Fu J., Wijmenga C., Zhernakova A., Elinav E. & Segal E. (2018) Nature. 555, 7695, p. 210-215

2017

Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

Van Dijk D. D., Sharon E., Lotan-Pompan M., Weinberger A., Segal E. & Carey L. (2017) Genome Research. 27, 1, p. 87-94

Involvement of a gut-retina axis in protection against dietary glycemia-induced age-related macular degeneration

Rowan S., Jiang S., Korem T., Szymanski J., Chang M., Szelog J., Cassalman C., Dasuri K., McGuire C., Nagai R., Du X., Brownlee M., Rabbani N., Thornalley P. J., Baleja J. D., Deik A. A., Pierce K. A., Scott J. M., Clish C. B., Smith D. E., Weinberger A., Avnit Sagi T., Lotan-Pompan M., Segal E. & Taylor A. (2017) Proceedings of the National Academy of Sciences of the United States of America. 114, 22, p. E4472-E4481

Microbiome at the Frontier of Personalized Medicine

Kashyap P. C., Chia N., Nelson H., Segal E. & Elinav E. (2017) Mayo Clinic Proceedings. 92, 12, p. 1855-1864

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Gritsenko A. A., Weingarten-Gabbay S., Elias-Kirma S., Nir R., De Ridder R. D. & Segal E. (2017) PLoS Computational Biology. 13, 9, e1005734.

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

Levo M., Avnit-Sagi T., Lotan-Pompan M., Kalma Y., Weinberger A., Yakhini Z. & Segal E. (2017) Molecular Cell. 65, 4, p. 604-+

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses

Korem T., Zeevi D., Zmora N., Weissbrod O., Bar N., Lotan-Pompan M., Avnit Sagi S. T., Kosower N., Malka G., Rein M., Suez J., Goldberg B. Z., Weinberger A., Levy A., Elinav E. & Segal E. (2017) Cell Metabolism. 25, 6, p. 1243-1253

2016

Comparative genetics: Systematic discovery of cap-independent translation sequences in human and viral genomes

Weingarten-Gabbay S., Elias-Kirma S., Nir R., Gritsenko A. A., Stern-Ginossar N., Yakhini Z., Weinberger A. & Segal E. (2016) Science. 351, 6270, aad4939.

Talking about cross-talk: The immune system and the microbiome

Zeevi D., Korem T. & Segal E. (2016) GENOME BIOLOGY. 17, 1, 50.

A minimalistic resource allocation model to explain ubiquitous increase in protein expression with growth rate

Barenholz U., Keren L., Segal E. & Milo R. (2016) PLoS ONE. 11, 4, 0153344.

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

Keren L., Hausser J., Lotan-Pompan M., Vainberg Slutskin I., Alisar H., Kaminski S., Weinberger A., Alon U., Milo R. & Segal E. (2016) Cell. 166, 5, p. 1282-1294.e18

Persistent microbiome alterations modulate the rate of post-dieting weight regain

Thaiss C. A., Itav S., Rothschild D., Meijer M. T., Levy M., Moresi C., Dohnalová L., Braverman S., Rozin S., Malitsky S., Dori-Bachash M., Kuperman Y., Biton I., Gertler A., Harmelin A., Shapiro H., Halpern Z., Aharoni A., Segal E. & Elinav E. (2016) Nature. 540, 7634, p. 544-551

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaiss C., Levy M., Korem T., Dohnalova L., Shapiro H., Jaitin D., David E., Winter D., Gury-BenAri M., Tatirovsky E., Tuganbaev T., Federici S., Zmora N., Zeevi D., Dori-Bachash M., Pevsner-Fischer M., Kartvelishvily E., Brandis A., Harmelin A., Shibolet O., Halpern Z., Honda K., Amit I., Segal E. & Elinav E. (2016) Cell. 167, 6, p. 1495-1510.e12

Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease

Zmora N., Zeevi D., Korem T., Segal E. & Elinav E. (2016) Cell Host & Microbe. 19, 1, p. 12-20

2015

Artificial Sweeteners Induce Glucose Intolerance by Altering the Gut Microbiota: Editorial comment

Suez J., Korem T., Zeevi D., Zilberman-Schapira G., Thaiss C. A., Maza O., Israeli D., Zmora N., Gilad S., Weinberger A., Kuperman Y., Harmelin A., Kolodkin-Gal I., Shapiro H., Halpern Z., Segal E. & Elinav E. (2015) Obstetrical & Gynecological Survey. 70, 1, p. 31-32

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

Shalem O., Sharon E., Lubliner S., Regev I., Lotan-Pompan M., Yakhini Z. & Segal E. (2015) PLoS Genetics. 11, 4, e1005147.

GenoExp: A web tool for predicting gene expression levels from single nucleotide polymorphisms

Manor O. & Segal E. (2015) Bioinformatics. 31, 11, p. 1848-1850

Editorial overview: Genome architecture and expression

Panning B. & Segal E. (2015) Current opinion in genetics & development. 31, p. v-vi

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

Noise in gene expression is coupled to growth rate

Keren L., Van Dijk D. D., Weingarten-Gabbay S., Davidi D., Jona G., Weinberger A., Milo R. & Segal E. (2015) Genome Research. 25, p. 1893-1902

Personalized Nutrition by Prediction of Glycemic Responses

Zeevi D., Korem T., Zmora N., Israeli D., Rothschild D., Weinberger A., Ben-Yacov O., Lador D., Avnit Sagi S. T., Lotan-Pompan M., Suez J., Mahdi J. A., Matot E., Malka G., Kosower N., Rein M., Zilberman-Schapira G., Dohnalova L., Pevsner-Fischer M., Bikovsky R., Halpern Z., Elinav E. & Segal E. (2015) Cell. 163, 5, p. 1079-1094

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling

Levy M., Thaiss C. A., Zeevi D., Dohnalova L., Zilberman-Schapira G., Mahdi J. A., David E., Savidor A., Korem T., Herzig Y., Pevsner-Fischer M., Shapiro H., Christ A., Harmelin A., Halpern Z., Latz E., Flavell R. A., Amit I., Segal E. & Elinav E. (2015) Cell. 163, 6, p. 1428-1443

2014

Landscape and variation of RNA secondary structure across the human transcriptome

Wan Y., Qu K., Zhang Q. C., Flynn R. A., Manor O., Ouyang Z., Zhang J., Spitale R. C., Snyder M. P., Segal E. & Chang H. Y. (2014) Nature. 505, 7485, p. 706-709

The grammar of transcriptional regulation

Weingarten-Gabbay S. & Segal E. (2014) Human Genetics. 133, 6, p. 701-711

In pursuit of design principles of regulatory sequences

Levo M. & Segal E. (2014) Nature Reviews Genetics. 15, 7, p. 453-468

Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters

Zeevi D., Lubliner S., Lotan-Pompan M., Hodis E., Vesterman R., Weinberger A. & Segal E. (2014) Genome Research. 24, 12, p. 1991-1999

A shared architecture for promoters and enhancers

Weingarten-Gabbay S. & Segal E. (2014) Nature Genetics. 46, 12, p. 1253-1254

Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis

Thaiss C. A., Zeevi D., Levy M., Zilberman-Schapira G., Suez J., Tengeler A. C., Abramson L., Katz M. N., Korem T., Zmora N., Kuperman Y., Biton I., Gilad S., Harmelin A., Shapiro H., Halpern Z., Segal E. & Elinav E. (2014) Cell. 159, 3, p. 514-529

Host-parasite network structure is associated with community-level immunogenetic diversity

Pilosof S., Fortuna M. A., Cosson J. F., Galan M., Kittipong C., Ribas A., Segal E., Krasnov B. R., Morand S. & Bascompte J. (2014) Nature Communications. 5, 5172.

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

Sharon E., Van Dijk D. D., Kalma Y., Keren L., Manor O., Yakhini Z. & Segal E. (2014) Genome Research. 24, 10, p. 1698-1706

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Suez J., Korem T., Zeevi D., Zilberman-Schapira G., Thaiss C. A., Maza O., Israeli D., Zmora N., Gilad S., Weinberger A., Kuperman Y., Harmelin A., Kolodkin-Gal I., Shapiro H., Halpern Z., Segal E. & Elinav E. (2014) Nature. 514, 7521, p. 181-186

2013

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

Dvir S., Velten L., Sharon E., Zeevi D., Carey L. B., Weinberger A. & Segal E. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110, 30, p. E2792-E2801

Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein

Zalckvar E., Paulus C., Tillo D., Asbach-Nitzsche A., Lubling Y., Winterling C., Strieder N., Mücke K., Goodrum F., Segal E. & Nevels M. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110, 32, p. 13126-13131

Fixated on fixation: using ChIP to interrogate the dynamics of chromatin interactions

Keren L. & Segal E. (2013) GENOME BIOLOGY. 14, 11,

Promoters maintain their relative activity levels under different growth conditions

Keren L., Zackay O., Lotan-Pompan M., Barenholz U., Dekel E., Sasson V., Aidelberg G., Bren A., Zeevi D., Weinberger A., Alon U., Milo R. & Segal E. (2013) Molecular Systems Biology. 9, 701.

Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

Shalem O., Carey L., Zeevi D., Sharon E., Keren L., Weinberger A., Dahan O., Pilpel Y. & Segal E. (2013) PLoS Computational Biology. 9, 3, e1002934.

Determinants of nucleosome positioning

Struhl K. & Segal E. (2013) Nature Structural & Molecular Biology. 20, 3, p. 267-273

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity

Lubliner S., Keren L. & Segal E. (2013) Nucleic Acids Research. 41, 11, p. 5569-5581

Promoter Sequence Determines the Relationship between Expression Level and Noise

Carey L. B., van Dijk D., Sloot P. M., Kaandorp J. A. & Segal E. (2013) PLoS Biology. 11, 4, e1001528.

Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms

Manor O. & Segal E. (2013) PLoS Computational Biology. 9, 8, e1003200.

Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise

Dadiani M., Van Dijk D. D., Segal B., Field Y., Ben Artzi A. G., Raveh - Sadka -. S. T., Levo M., Kaplow I., Weinberger A. & Segal E. (2013) Genome Research. 23, 6, p. 966-976

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Meyer P., Siwo G., Zeevi D., Sharon E., Norel R., Segal E., Stolovitzky G., Rider A. K., Tan A., Pinapati R. S., Emrich S., Chawla N., Ferdig M. T., Tung Y. A., Chen Y. S., Chen M. J. M., Chen C. Y., Knight J. M., Sahraeian S. M. E. & Esfahani M. S. (2013) Genome Research. 23, 11, p. 1928-1937

2012

Genome-wide Measurement of RNA Folding Energies

Wan Y., Qu K., Ouyang Z., Kertesz M., Li J., Tibshirani R., Makino D. L., Nutter R. C., Segal E. & Chang H. Y. (2012) Molecular Cell. 48, 2, p. 169-181

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

Raveh - Sadka -. S. T., Levo M., Shabi U., Shany B., Keren L., Lotan-Pompan M., Zeevi D., Sharon E., Weinberger A. & Segal E. (2012) Nature Genetics. 44, 7, p. 743-750

Cell lineage analysis of the mammalian female germline

Reizel Y., Itzkovitz S., Adar R., Elbaz J., Jinich A., Chapal Ilani I. N., Maruvka Y. E., Nevo N., Marx Z., Horovitz I., Wasserstrom A., Mayo A., Shur I., Benayahu D., Skorecki K., Segal E., Dekel N. & Shapiro E. (2012) PLoS Genetics. 8, 2, e1002477.

From catalogue to function

Segal E. (2012) Nature. 489, 7414, p. 55-55

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

Sharon E., Kalma Y., Sharp A., Raveh - Sadka -. S. T., Levo M., Zeevi D., Keren L., Yakhini Z., Weinberger A. & Segal E. (2012) Nature Biotechnology. 30, 6, p. 521-+

New insights into replication origin characteristics in metazoans

Cayrou C., Coulombe P., Puy A., Rialle S., Kaplan N., Segal E. & Mechali M. (2012) Cell Cycle. 11, 4, p. 658-667

2011

Understanding the transcriptome through RNA structure

Wan Y., Kertesz M., Spitale R. C., Segal E. & Chang H. Y. (2011) Nature Reviews Genetics. 12, 9, p. 641-655

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

Ercan S., Lubling Y., Segal E. & Lieb J. D. (2011) Genome Research. 21, 2, p. 237-244

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Zeevi D., Sharon E., Lotan-Pompan M., Lubling Y., Shipony Z., Raveh - Sadka -. S. T., Keren L., Levo M., Weinberger A. & Segal E. (2011) Genome Research. 21, 12, p. 2114-2128

How Transcription Factors Identify Regulatory Sites in Genomic Sequence

Field Y., Sharon E. & Segal E. (2011) Handbook Of Transcription Factors . p. 193-204 (trueSubcellular Biochemistry).

Computational Prediction of RNA Structural Motifs Involved in Post-Transcriptional Regulatory Processes

Rabani M., Kertesz M. & Segal E. (2011) Rna Detection And Visualization : Methods And Protocols . p. 467-479

2010

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

Nili E. L., Field Y., Lubling Y., Widom J., Oren M. & Segal E. (2010) Genome Research. 20, 10, p. 1361-1368

Overlapping codes within protein-coding sequences

Itzkovitz S., Hodis E. & Segal E. (2010) Genome Research. 20, 11, p. 1582-1589

Nucleosome sequence preferences influence in vivo nucleosome organization

Kaplan N., Moore I., Fondufe-Mittendorf Y., Gossett A. J., Tillo D., Field Y., Hughes T. R., Lieb J. D., Widom J. & Segal E. (2010) Nature Structural & Molecular Biology. 17, 8, p. 918-920

Contribution of histone sequence preferences to nucleosome organization: Proposed definitions and methodology

Kaplan N., Hughes T. R., Lieb J. D., Widom J. & Segal E. (2010) GENOME BIOLOGY. 11, 11, 140.

Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast

Kenigsberg E., Bar A., Segal E. & Tanay A. (2010) PLoS Computational Biology. 6, 12, e1001039.

Genome-wide measurement of RNA secondary structure in yeast

Kertesz M., Wan Y., Mazor E., Rinn J. L., Nutter R. C., Chang H. Y. & Segal E. (2010) Nature. 467, 7311, p. 103-107

High nucleosome occupancy is encoded at human regulatory sequences

Tillo D., Kaplan N., Moore I. K., Fondufe-Mittendorf Y., Gossett A. J., Field Y., Lieb J. D., Widom J., Segal E. & Hughes T. R. (2010) PLoS ONE. 5, 2, e9129.

Long noncoding RNA as modular scaffold of histone modification complexes

Tsai M., Manor O., Wan Y., Mosammaparast N., Wang J. K., Lan F., Shi Y., Segal E. & Chang H. Y. (2010) Science. 329, 5992, p. 689-693

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Gerstein M. B., Lu Z. J., Van Nostrand E. L., Cheng C., Arshinoff B. I., Liu T., Yip K. Y., Robilotto R., Rechtsteiner A., Ikegami K., Alves P., Chateigner A., Perry M., Morris M., Auerbach R. K., Feng X., Leng J., Vielle A., Niu W., Rhrissorrakrai K., Agarwal A., Alexander R. P., Barber G., Brdlik C. M., Brennan J., Brouillet J. J., Carr A., Cheung M. S., Clawson H., Contrino S., Dannenberg L. O., Dernburg A. F., Desai A., Dick L., Dosé A. C., Du J., Egelhofer T., Ercan S., Euskirchen G., Ewing B., Feingold E. A., Gassmann R., Good P. J., Green P., Gullier F., Gutwein M., Guyer M. S., Habegger L., Han T., Henikoff J. G., Henz S. R., Hinrichs A., Holster H., Hyman T., Iniguez A. L., Janette J., Jensen M., Kato M., Kent W. J., Kephart E., Khivansara V., Khurana E., Kim J. K., Kolasinska-Zwierz P., Lai E. C., Latorre I., Leahey A., Lewis S., Lloyd P., Lochovsky L., Lowdon R. F., Lubling Y., Lyne R., MacCoss M., Mackowiak S. D., Mangone M., McKay S., Mecenas D., Merrihew G., Miller D. M., Muroyama A., Murray J. I., Ooi S. L., Pham H., Phippen T., Preston E. A., Rajewsky N., Rätsch G., Rosenbaum H., Rozowsky J., Rutherford K., Ruzanov P., Sarov M., Sasidharan R., Sboner A., Scheid P., Segal E., Shin H., Shou C., Slack F. J., Slightam C., Smith R., Spencer W. C., Stinson E. O., Taing S., Takasaki T., Vafeados D., Voronina K., Wang G., Washington N. L., Whittle C. M., Wu B., Yan K. K., Zeller G., Zha Z., Zhong M., Zhou X., Ahringer J., Strome S., Gunsalus K. C., Micklem G., Liu X. S., Reinke V., Kim S. K., Hillier L. W., Henikoff S., Piano F., Snyder M., Stein L., Lieb J. D. & Waterston R. H. (2010) Science. 330, 6012, p. 1775-1787

2009

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

Field Y., Fondufe-Mittendorf Y., Moore I. K., Mieczkowski P., Kaplan N., Lubling Y., Lieb J. D., Widom J. & Segal E. (2009) Nature Genetics. 41, 4, p. 438-445

Incorporating nucleosomes into thermodynamic models of transcription regulation

Raveh - Sadka -. S. T., Levo M. & Segal E. (2009) Genome Research. 19, 8, p. 1480-1496

The DNA-encoded nucleosome organization of a eukaryotic genome

Kaplan N., Moore I. K., Fondufe-Mittendorf Y., Gossett A. J., Tillo D., Field Y., LeProust E. M., Hughes T. R., Lieb J. D., Widom J. & Segal E. (2009) Nature. 458, 7236, p. 362-366

From DNA sequence to transcriptional behaviour: A quantitative approach

Segal E. & Widom J. (2009) Nature Reviews Genetics. 10, 7, p. 443-456

Poly(dA:dT) tracts: major determinants of nucleosome organization

Segal E. & Widom J. (2009) Current Opinion in Structural Biology. 19, 1, p. 65-71

What controls nucleosome positions?

Segal E. & Widom J. (2009) Trends in Genetics. 25, 8, p. 335-343

Proteome-wide prediction of acetylation substrates

Basu A., Rose K. L., Zhang J., Beavis R. C., Ueberheide B., Garcia B. A., Chait B., Zhao Y., Hunt D. F., Segal E., Allis C. D. & Hake S. B. (2009) Proceedings of the National Academy of Sciences of the United States of America. 106, 33, p. 13785-13790

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

Lubliner S. & Segal E. (2009) Bioinformatics. 25, 12, p. i348-i355

2008

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

Wang J., Fondufe-Mittendorf Y., Xi L., Tsai G., Segal E. & Widom J. (2008) PLoS Computational Biology. 4, 9,

Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells

Minsky N., Shema E., Field Y., Schuster M., Segal E. & Oren M. (2008) Nature Cell Biology. 10, 4, p. 483-488

Reconstruction of Cell Lineage Trees in Mice

Wasserstrom A., Adar R., Shefer G., Frumkin D., Itzkovitz S., Stern T., Shur I., Zangi L., Kaplan S., Harmelin A., Reisner Y., Benayahu D., Tzahor E., Segal E. & Shapiro E. (2008) PLoS ONE. 3, 4, 1939.

Estimating cell depth from somatic mutations

Wasserstrom A., Frumkin D., Adar R., Itzkovitz S., Stern T., Kaplan S., Shefer G., Shur I., Zangi L., Reizel Y., Harmelin A., Dor Y., Dekel N., Reisner Y., Benayahu D., Tzahor E., Segal E. & Shapiro E. (2008) PLoS Computational Biology. 4, 5, 1000058.

Revealing targeted therapy for human cancer by gene module maps

Wong D. J., Nuyten D. S., Regev A., Lin M., Adler A. S., Segal E., Van De Vijver M. J. & Chang H. Y. (2008) Cancer Research. 68, 2, p. 369-378

Stemness, cancer and cancer stem cells

Wong D. J., Segal E. & Chang H. Y. (2008) Cell Cycle. 7, 23, p. 3622-3624

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

Field Y., Kaplan N., Fondufe-Mittendorf Y., Moore I. K., Sharon E., Lubling Y., Widom J. & Segal E. (2008) PLoS Computational Biology. 4, 11, e1000216.

Reversal of aging by NFκB blockade

Adler A. S., Kawahara T. L., Segal E. & Chang H. Y. (2008) Cell Cycle. 7, 5, p. 556-559

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

Rabani M., Kertesz M. & Segal E. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105, 39, p. 14885-14890

Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code

Itzkovitz S., Baruch L., Shapiro E. & Segal E. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105, 27, p. 9278-9283

Predicting expression patterns from regulatory sequence in Drosophila segmentation

Segal E., Raveh - Sadka -. S. T., Schroeder M., Unnerstall U. & Gaul U. (2008) Nature. 451, 7178, p. 535-540

Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity

Baruch L., Itzkovitz S., Golan Mashiach M. M., Shapiro E. & Segal E. (2008) PLoS Computational Biology. 4, 7, e1000120.

A feature-based approach to modeling protein-DNA interactions

Sharon E., Lubliner S. & Segal E. (2008) PLoS Computational Biology. 4, 8, e1000154.

Systematic functional characterization of cis-regulatory motifs in human core promoters

Sinha S., Adler A. S., Field Y., Chang H. Y. & Segal E. (2008) Genome Research. 18, 3, p. 477-488

Module Map of Stem Cell Genes Guides Creation of Epithelial Cancer Stem Cells

Wong D. J., Liu H., Ridky T. W., Cassarino D., Segal E. & Chang H. Y. (2008) Cell Stem Cell. 2, 4, p. 333-344

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

Shalem O., Dahan O., Levo M., Martinez M. R., Furman I., Segal E. & Pilpel Y. (2008) Molecular Systems Biology. 4, 4.

2007

Motif module map reveals enforcement of aging by continual NF-κB activity

Adler A. S., Sinha S., Kawahara T. L., Zhang J. Y., Segal E. & Chang H. Y. (2007) GENES & DEVELOPMENT. 21, 24, p. 3244-3257

Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

Rinn J. L., Kertesz M., Wang J. K., Squazzo S. L., Xu X., Brugmann S. A., Goodnough L. H., Helms J. A., Farnham P. J., Segal E. & Chang H. Y. (2007) Cell. 129, 7, p. 1311-1323

Decoding global gene expression programs in liver cancer by noninvasive imaging

Segal E., Sirlin C. B., Ooi C., Adler A. S., Gollub J., Chen X., Chan B. K., Matcuk G. R., Barry C. T., Chang H. Y. & Kuo M. D. (2007) Nature biotechnology. 25, 6, p. 675-680

The role of site accessibility in microRNA target recognition

Kertesz M., Iovino N., Unnerstall U., Gaul U. & Segal E. (2007) Nature Genetics. 39, 10, p. 1278-1284

A transcriptional program mediating entry into cellular quiescence

Liu H., Adler A. S., Segal E. & Chang H. Y. (2007) PLoS Genetics. 3, 6, p. 996-1008

A feature-based approach to modeling protein-DNA interactions

Sharon E. & Segal E. (2007) RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, PROCEEDINGS. 4453, p. 77-91

InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

Wang H., Segal E., Ben-Hur A., Li Q. R., Vidal M. & Koller D. (2007) GENOME BIOLOGY. 8, 9, R192.

A module of negative feedback regulators defines growth factor signaling

Amit I., Citri A., Shay T., Lu Y., Katz M., Zhang F., Tarcic G., Siwak D., Lahad J., Jacob-Hirsch J., Amariglio N., Vaisman N., Segal E., Rechavi G., Alon U., Mills G. B., Domany E. & Yarden Y. (2007) Nature Genetics. 39, 4, p. 503-512

Zinc-ion binding and cytokine activity regulation pathways predicts outcome in relapsing-remitting multiple sclerosis

Achiron A., Gurevich M., Snir Y., Segal E. & Mandel M. (2007) Clinical and Experimental Immunology. 149, 2, p. 235-242

2006

A genomic code for nucleosome positioning

Segal E., Fondufe-Mittendorf Y., Chen L., Thastroem A., Field Y., Moore I. K., Wang J. Z. & Widom J. (2006) Nature. 442, 7104, p. 772-778

2005

Separating the contribution of translational and rotational diffusion to protein association

Kuttner Y., Kozer N., Segal E., Schreiber G. & Haran G. (2005) Journal of the American Chemical Society. 127, 43, p. 15138-15144

2003

Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data

Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D. & Friedman N. (2003) Nature Genetics. 34, 2, p. 166-176

2001

Exact Inference in Networks with Discrete Children of Continuous Parents

Lerner U., Segal E. & Koller D. (2001) Conference on Uncertainty in Artificial Intelligence : UAI2001 . p. 319-328