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Jeroen Raes - Publications

Affiliations: 
VIB Department of Molecular and Cellular  Vrije Universiteit Brussel, Elsene, Brussels Hoofdstedelijk Gewest, Belgium 
Website:
http://www.vib.be/Research/EN/Research+Departments/Department+of+Molecular+and+Cellular+Interactions/Jeroen+Raes/

187 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Procházková N, Falony G, Dragsted LO, Licht TR, Raes J, Roager HM. Advancing human gut microbiota research by considering gut transit time. Gut. PMID 36171079 DOI: 10.1136/gutjnl-2022-328166  0.629
2022 Biclot A, Huys GRB, Bacigalupe R, D'hoe K, Vandeputte D, Falony G, Tito RY, Raes J. Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples. Microbiome. 10: 80. PMID 35644616 DOI: 10.1186/s40168-022-01267-2  0.612
2022 Beller L, Deboutte W, Vieira-Silva S, Falony G, Tito RY, Rymenans L, Yinda CK, Vanmechelen B, Van Espen L, Jansen D, Shi C, Zeller M, Maes P, Faust K, Van Ranst M, ... Raes J, et al. The virota and its transkingdom interactions in the healthy infant gut. Proceedings of the National Academy of Sciences of the United States of America. 119: e2114619119. PMID 35320047 DOI: 10.1073/pnas.2114619119  0.696
2022 Ebrahim Z, Proost S, Tito RY, Raes J, Glorieux G, Moosa MR, Blaauw R. The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial. Nutrients. 14. PMID 35215453 DOI: 10.3390/nu14040805  0.669
2022 Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, ... ... Raes J, et al. Microbiome and metabolome features of the cardiometabolic disease spectrum. Nature Medicine. PMID 35177860 DOI: 10.1038/s41591-022-01688-4  0.78
2022 Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifiti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, ... ... Raes J, et al. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism. Gut. PMID 35017197 DOI: 10.1136/gutjnl-2021-325753  0.786
2022 Goosen C, Proost S, Tito RY, Baumgartner J, Barnabas SL, Cotton MF, Zimmermann MB, Raes J, Blaauw R. The effect of oral iron supplementation on the gut microbiota, gut inflammation, and iron status in iron-depleted South African school-age children with virally suppressed HIV and without HIV. European Journal of Nutrition. PMID 34997267 DOI: 10.1007/s00394-021-02793-9  0.629
2021 Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. Variation and transmission of the human gut microbiota across multiple familial generations. Nature Microbiology. PMID 34969979 DOI: 10.1038/s41564-021-01021-8  0.742
2021 Deutschmann IM, Lima-Mendez G, Krabberød AK, Raes J, Vallina SM, Faust K, Logares R. Correction to: Disentangling environmental effects in microbial association networks. Microbiome. 9: 245. PMID 34933691 DOI: 10.1186/s40168-021-01209-4  0.493
2021 Beller L, Deboutte W, Falony G, Vieira-Silva S, Tito RY, Valles-Colomer M, Rymenans L, Jansen D, Van Espen L, Papadaki MI, Shi C, Yinda CK, Zeller M, Faust K, Van Ranst M, ... Raes J, et al. Successional Stages in Infant Gut Microbiota Maturation. Mbio. 12: e0185721. PMID 34903050 DOI: 10.1128/mBio.01857-21  0.705
2021 Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, ... ... Raes J, et al. Combinatorial, additive and dose-dependent drug-microbiome associations. Nature. 600: 500-505. PMID 34880489 DOI: 10.1038/s41586-021-04177-9  0.78
2021 Gryp T, Faust K, Van Biesen W, Huys GRB, Verbeke F, Speeckaert M, Raes J, Vaneechoutte M, Joossens M, Glorieux G. Gut Microbiome Profiling Uncovers a Lower Abundance of in Advanced Stages of Chronic Kidney Disease. Journal of Personalized Medicine. 11. PMID 34834470 DOI: 10.3390/jpm11111118  0.528
2021 Deutschmann IM, Lima-Mendez G, Krabberød AK, Raes J, Vallina SM, Faust K, Logares R. Disentangling environmental effects in microbial association networks. Microbiome. 9: 232. PMID 34823593 DOI: 10.1186/s40168-021-01141-7  0.523
2021 Vandeputte D, De Commer L, Tito RY, Kathagen G, Sabino J, Vermeire S, Faust K, Raes J. Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nature Communications. 12: 6740. PMID 34795283 DOI: 10.1038/s41467-021-27098-7  0.562
2021 Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, ... ... Raes J, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. PMID 34789871 DOI: 10.1038/s41591-021-01552-x  0.748
2021 Steenackers N, Falony G, Augustijns P, Van der Schueren B, Vanuytsel T, Vieira-Silva S, Wauters L, Raes J, Matthys C. Specific contributions of segmental transit times to gut microbiota composition. Gut. PMID 34642242 DOI: 10.1136/gutjnl-2021-325916  0.588
2021 Pero-Gascon R, Hemeryck LY, Poma G, Falony G, Nawrot TS, Raes J, Vanhaecke L, De Boevre M, Covaci A, De Saeger S. FLEXiGUT: Rationale for exposomics associations with chronic low-grade gut inflammation. Environment International. 158: 106906. PMID 34607040 DOI: 10.1016/j.envint.2021.106906  0.612
2021 Suriano F, Vieira-Silva S, Falony G, Roumain M, Paquot A, Pelicaen R, Régnier M, Delzenne NM, Raes J, Muccioli GG, Van Hul M, Cani PD. Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin. Microbiome. 9: 147. PMID 34183063 DOI: 10.1186/s40168-021-01097-8  0.715
2021 Lloréns-Rico V, Vieira-Silva S, Gonçalves PJ, Falony G, Raes J. Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases. Nature Communications. 12: 3562. PMID 34117246 DOI: 10.1038/s41467-021-23821-6  0.751
2021 Le Roy T, Moens de Hase E, Van Hul M, Paquot A, Pelicaen R, Régnier M, Depommier C, Druart C, Everard A, Maiter D, Delzenne NM, Bindels LB, de Barsy M, Loumaye A, Hermans MP, ... ... Raes J, et al. is a newly isolated human commensal bacterium preventing diet-induced obesity and metabolic disorders in mice. Gut. PMID 34108237 DOI: 10.1136/gutjnl-2020-323778  0.607
2021 Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, ... ... Raes J, et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology. 4: 604. PMID 34021239 DOI: 10.1038/s42003-021-02112-2  0.576
2021 Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, ... ... Raes J, et al. Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health. Gut. PMID 33975870 DOI: 10.1136/gutjnl-2020-323314  0.792
2021 Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, ... ... Raes J, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nature Genetics. PMID 33462485 DOI: 10.1038/s41588-020-00763-1  0.653
2021 Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, ... ... Raes J, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nature Genetics. PMID 33462485 DOI: 10.1038/s41588-020-00763-1  0.653
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Raes J, et al. Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 6448. PMID 33349634 DOI: 10.1038/s41467-020-20412-9  0.773
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Raes J, et al. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 5881. PMID 33208748 DOI: 10.1038/s41467-020-19589-w  0.797
2020 Souffriau J, Timmermans S, Vanderhaeghen T, Wallaeys C, Van Looveren K, Aelbrecht L, Dewaele S, Vandewalle J, Goossens E, Verbanck S, Boyen F, Eggermont M, De Commer L, De Rycke R, De Bruyne M, ... ... Raes J, et al. Zinc inhibits lethal inflammatory shock by preventing microbe-induced interferon signature in intestinal epithelium. Embo Molecular Medicine. e11917. PMID 32914580 DOI: 10.15252/Emmm.201911917  0.314
2020 Hughes DA, Bacigalupe R, Wang J, Rühlemann MC, Tito RY, Falony G, Joossens M, Vieira-Silva S, Henckaerts L, Rymenans L, Verspecht C, Ring S, Franke A, Wade KH, Timpson NJ, ... Raes J, et al. Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nature Microbiology. PMID 32572223 DOI: 10.1038/S41564-020-0743-8  0.664
2020 Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, ... ... Raes J, et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature. 581: 310-315. PMID 32433607 DOI: 10.1038/S41586-020-2269-X  0.777
2019 Park R, Dzialo MC, Spaepen S, Nsabimana D, Gielens K, Devriese H, Crauwels S, Tito RY, Raes J, Lievens B, Verstrepen KJ. Microbial communities of the house fly Musca domestica vary with geographical location and habitat. Microbiome. 7: 147. PMID 31699144 DOI: 10.1186/S40168-019-0748-9  0.413
2019 D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes J. Correction: Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. Elife. 8. PMID 31682225 DOI: 10.7554/Elife.53217  0.715
2019 Vrancken G, Gregory AC, Huys GRB, Faust K, Raes J. Synthetic ecology of the human gut microbiota. Nature Reviews. Microbiology. PMID 31578461 DOI: 10.1038/S41579-019-0264-8  0.629
2019 Le Roy CI, Wells PM, Si J, Raes J, Bell JT, Spector TD. Red Wine Consumption Associated With Increased Gut Microbiota α-diversity in 3 Independent Cohorts. Gastroenterology. PMID 31472153 DOI: 10.1053/J.Gastro.2019.08.024  0.302
2019 Vázquez-Castellanos JF, Biclot A, Vrancken G, Huys GR, Raes J. Design of synthetic microbial consortia for gut microbiota modulation. Current Opinion in Pharmacology. 49: 52-59. PMID 31430629 DOI: 10.1016/J.Coph.2019.07.005  0.383
2019 Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, Schulte B, Schulte D, Franke A, Nikolaus S, Schroeder JO, ... ... Raes J, et al. Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients with Inflammatory Bowel Diseases. Gastroenterology. PMID 31326413 DOI: 10.1053/J.Gastro.2019.07.025  0.331
2019 Depommier C, Everard A, Druart C, Plovier H, Van Hul M, Vieira-Silva S, Falony G, Raes J, Maiter D, Delzenne NM, de Barsy M, Loumaye A, Hermans MP, Thissen JP, de Vos WM, et al. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nature Medicine. PMID 31263284 DOI: 10.1038/S41591-019-0495-2  0.633
2019 Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, Cleynen I, van der Merwe S, Vermeire S, Raes J. Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses. Nature Microbiology. PMID 31209308 DOI: 10.1038/S41564-019-0483-9  0.664
2019 Lloréns-Rico V, Raes J. Tracking humans and microbes. Nature. 569: 632-633. PMID 31142867 DOI: 10.1038/D41586-019-01591-Y  0.311
2019 Ejtahed HS, Tabatabaei-Malazy O, Soroush AR, Hasani-Ranjbar S, Siadat SD, Raes J, Larijani B. Worldwide trends in scientific publications on association of gut microbiota with obesity. Iranian Journal of Basic Medical Sciences. 22: 65-71. PMID 30944710 DOI: 10.22038/Ijbms.2018.30203.7281  0.3
2019 Falony G, Vandeputte D, Caenepeel C, Vieira-Silva S, Daryoush T, Vermeire S, Raes J. The human microbiome in health and disease: hype or hope. Acta Clinica Belgica. 1-12. PMID 30810508 DOI: 10.1080/17843286.2019.1583782  0.632
2019 Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J. The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology. PMID 30718848 DOI: 10.1038/S41564-018-0337-X  0.653
2019 De Paepe K, Verspreet J, Rezaei MN, Hidalgo Martinez S, Meysman F, Van de Walle D, Dewettinck K, Raes J, Courtin C, Van de Wiele T. Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota. Peerj. 7: e6293. PMID 30701133 DOI: 10.7717/Peerj.6293  0.371
2019 Valles-Colomer M, Falony G, Vieira-Silva S, Raes J. Practical guidelines for gut microbiome analysis in microbiota-gut-brain axis research Behavioral and Brain Sciences. 42. DOI: 10.1017/S0140525X18002881  0.629
2018 Joossens M, Faust K, Gryp T, Nguyen ATL, Wang J, Eloot S, Schepers E, Dhondt A, Pletinck A, Vieira-Silva S, Falony G, Vaneechoutte M, Vanholder R, Van Biesen W, Huys GRB, ... Raes J, et al. Gut microbiota dynamics and uraemic toxins: one size does not fit all. Gut. PMID 30464044 DOI: 10.1136/Gutjnl-2018-317561  0.75
2018 Hansen LBS, Roager HM, Søndertoft NB, Gøbel RJ, Kristensen M, Vallès-Colomer M, Vieira-Silva S, Ibrügger S, Lind MV, Mærkedahl RB, Bahl MI, Madsen ML, Havelund J, Falony G, Tetens I, ... ... Raes J, et al. A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults. Nature Communications. 9: 4630. PMID 30425247 DOI: 10.1038/S41467-018-07019-X  0.605
2018 Boesmans L, Valles-Colomer M, Wang J, Eeckhaut V, Falony G, Ducatelle R, Van Immerseel F, Raes J, Verbeke K. Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of to Healthy Volunteers. Msystems. 3. PMID 30417112 DOI: 10.1128/mSystems.00094-18  0.606
2018 D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes J. Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. Elife. 7. PMID 30322445 DOI: 10.7554/Elife.37090  0.726
2018 He Y, Wu W, Wu S, Zheng HM, Li P, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, ... ... Raes J, et al. Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. Microbiome. 6: 172. PMID 30249275 DOI: 10.1186/S40168-018-0557-6  0.35
2018 Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J. Population-level analysis of subtype prevalence and variation in the human gut microbiota. Gut. PMID 30171064 DOI: 10.1136/Gutjnl-2018-316106  0.792
2018 He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, ... ... Raes J, et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nature Medicine. PMID 30150716 DOI: 10.1038/S41591-018-0164-X  0.346
2018 De Paepe K, Verspreet J, Verbeke K, Raes J, Courtin CM, Van de Wiele T. Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community. Environmental Microbiology. PMID 30126070 DOI: 10.1111/1462-2920.14381  0.405
2018 Huys GR, Raes J. Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes. Current Opinion in Microbiology. 44: 1-8. PMID 29908491 DOI: 10.1016/J.Mib.2018.05.002  0.345
2018 Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN, Spector TD, ... ... Raes J, et al. Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative. Microbiome. 6: 101. PMID 29880062 DOI: 10.1186/S40168-018-0479-3  0.381
2018 Falony G, Vieira-Silva S, Raes J. Richness and ecosystem development across faecal snapshots of the gut microbiota. Nature Microbiology. 3: 526-528. PMID 29693658 DOI: 10.1038/S41564-018-0143-5  0.67
2018 Schmidt TSB, Raes J, Bork P. The Human Gut Microbiome: From Association to Modulation. Cell. 172: 1198-1215. PMID 29522742 DOI: 10.1016/J.Cell.2018.02.044  0.593
2018 Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, ... ... Raes J, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/S41564-018-0114-X  0.785
2018 D'hoe K, Conterno L, Fava F, Falony G, Vieira-Silva S, Vermeiren J, Tuohy K, Raes J. Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes. Frontiers in Microbiology. 9: 31. PMID 29416529 DOI: 10.3389/Fmicb.2018.00031  0.649
2018 Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, ... ... Raes J, et al. A global ocean atlas of eukaryotic genes. Nature Communications. 9: 373. PMID 29371626 DOI: 10.1038/S41467-017-02342-1  0.616
2018 Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, ... ... Raes J, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 3: 8-16. PMID 29255284 DOI: 10.1038/S41564-017-0072-8  0.768
2018 Caenepeel C, Vieira-Silva S, Sabino J, Machiels K, Falony G, Ferrante M, Van Assche G, Raes J, Vermeire S. P854 Quantitative microbiome profiling changes the described dysbiotic state in inflammatory bowel disease Journal of Crohn's and Colitis. 12: S548-S549. DOI: 10.1093/Ecco-Jcc/Jjx180.981  0.608
2017 Vandeputte D, Kathagen G, D'hoe K, Vieira-Silva S, Valles-Colomer M, Sabino J, Wang J, Tito RY, De Commer L, Darzi Y, Vermeire S, Falony G, Raes J. Quantitative microbiome profiling links gut community variation to microbial load. Nature. PMID 29143816 DOI: 10.1038/Nature24460  0.702
2017 Raes J. Microbiology: Crowdsourcing Earth's microbes. Nature. PMID 29088699 DOI: 10.1038/Nature24756  0.307
2017 Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. Fems Microbiology Reviews. 41: S154-S167. PMID 28830090 DOI: 10.1093/Femsre/Fux027  0.644
2017 Mamantopoulos M, Ronchi F, Van Hauwermeiren F, Vieira-Silva S, Yilmaz B, Martens L, Saeys Y, Drexler SK, Yazdi AS, Raes J, Lamkanfi M, McCoy KD, Wullaert A. Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition. Immunity. PMID 28801232 DOI: 10.1016/J.Immuni.2017.07.011  0.364
2017 Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P. The resilience of the intestinal microbiota influences health and disease. Nature Reviews. Microbiology. PMID 28626231 DOI: 10.1038/Nrmicro.2017.58  0.404
2017 Gonze D, Lahti L, Raes J, Faust K. Multi-stability and the origin of microbial community types. The Isme Journal. PMID 28475180 DOI: 10.1038/Ismej.2017.60  0.576
2017 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, ... ... Raes J, et al. Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 545: 116. PMID 28470190 DOI: 10.1038/Nature22318  0.77
2017 Mysara M, Njima M, Leys N, Raes J, Monsieurs P. From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data. Gigascience. 6: 1-10. PMID 28369460 DOI: 10.1093/Gigascience/Giw017  0.325
2017 Mysara M, Vandamme P, Props R, Kerckhof FM, Leys N, Boon N, Raes J, Monsieurs P. Reconciliation between Operational Taxonomic Units and Species Boundaries. Fems Microbiology Ecology. PMID 28334218 DOI: 10.1093/Femsec/Fix029  0.332
2017 Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J. Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut. PMID 28213610 DOI: 10.1136/Gutjnl-2016-313271  0.665
2017 Vandeputte D, Falony G, D'hoe K, Vieira-Silva S, Raes J. Water activity does not shape the microbiota in the human colon. Gut. PMID 28062523 DOI: 10.1136/Gutjnl-2016-313530  0.652
2017 Vancamelbeke M, Sabino J, Deroover L, Vandermeulen G, Luypaerts A, Ferrante M, Falony G, Vieira-Silva S, Verbeke K, Raes J, Cleynen I, Vermeire S. P774 Metagenomics and metabolomics of patients with inflammatory bowel disease and their unaffected relatives Journal of Crohn's and Colitis. 11: S476-S477. DOI: 10.1093/Ecco-Jcc/Jjx002.895  0.609
2017 Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ferrante M, Van Assche G, Van Der Merwe S, Matthys C, Raes J, Vermeire S. P767 The FIT trial: anti-inflammatory dietary intervention effects on the intestinal microbiota Journal of Crohn's and Colitis. 11: S473-S473. DOI: 10.1093/Ecco-Jcc/Jjx002.888  0.629
2017 Vancamelbeke M, Sabino J, Deroover L, Vandermeulen G, Luypaerts A, Ferrante M, Falony G, Vieira-Silva S, Verbeke K, Raes J, Cleynen I, Vermeire S. Profiling of the Fecal Microbiota and Metabolome in Patients with Inflammatory Bowel Disease and their Unaffected Relatives Gastroenterology. 152: S991. DOI: 10.1016/S0016-5085(17)33359-0  0.63
2017 Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ferrante M, Van Assche GA, Van Der Merwe S, Matthys C, Raes J, Vermeire S. Therapeutic Manipulation of the Gut Microbiota Through Diet to Reduce Intestinal Inflammation: Results from the FIT Trial Gastroenterology. 152: S1. DOI: 10.1016/S0016-5085(17)30385-2  0.633
2017 Wang H, Wei Z, Mei L, Gu J, Yin S, Faust K, Raes J, Deng Y, Wang Y, Shen Q, Yin S. Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil Soil Biology and Biochemistry. 105: 227-235. DOI: 10.1016/J.Soilbio.2016.11.029  0.599
2016 Pérez-Valera E, Goberna M, Faust K, Raes J, García C, Verdú M. Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks. Environmental Microbiology. PMID 27871135 DOI: 10.1111/1462-2920.13609  0.591
2016 Faust K, Raes J. CoNet app: inference of biological association networks using Cytoscape. F1000research. 5: 1519. PMID 27853510 DOI: 10.12688/F1000Research.9050.2  0.589
2016 Eeckhaut V, Wang J, Van Parys A, Haesebrouck F, Joossens M, Falony G, Raes J, Ducatelle R, Van Immerseel F. The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers. Frontiers in Microbiology. 7: 1416. PMID 27708624 DOI: 10.3389/Fmicb.2016.01416  0.619
2016 Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biology. 17: 189. PMID 27666579 DOI: 10.1186/S13059-016-1052-7  0.337
2016 Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S, Raes J. Species-function relationships shape ecological properties of the human gut microbiome. Nature Microbiology. 1: 16088. PMID 27573110 DOI: 10.1038/Nmicrobiol.2016.88  0.76
2016 Holvoet T, Joossens M, Wang J, Boelens J, Verhasselt B, Laukens D, van Vlierberghe H, Hindryckx P, De Vos M, De Looze D, Raes J. Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating. Gut. PMID 27511198 DOI: 10.1136/Gutjnl-2016-312513  0.323
2016 Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, ... ... Raes J, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. PMID 27409811 DOI: 10.1038/Nature18646  0.774
2016 Darzi Y, Jiao Y, Hasegawa M, Moon H, Núñez G, Inohara N, Raes J. The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity. Plos One. 11: e0158866. PMID 27409077 DOI: 10.1371/Journal.Pone.0158866  0.361
2016 Tito RY, Cypers H, Joossens M, Varkas G, Van Praet L, Glorieus E, Van den Bosch F, De Vos M, Raes J, Elewaut D. Dialister as microbial marker of disease activity in spondyloarthritis. Arthritis & Rheumatology (Hoboken, N.J.). PMID 27390077 DOI: 10.1002/Art.39802  0.3
2016 Günther S, Faust K, Schumann J, Harms H, Raes J, Müller S. Species-sorting and mass-transfer paradigms control managed natural metacommunities. Environmental Microbiology. PMID 27338005 DOI: 10.1111/1462-2920.13402  0.59
2016 Faust K, Raes J. Host-microbe interaction: Rules of the game for microbiota. Nature. 534: 182-3. PMID 27279206 DOI: 10.1038/534182A  0.594
2016 Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ballet V, Ferrante M, Van Assche G, Van der Merwe S, Vermeire S, Raes J. Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD. Gut. PMID 27207975 DOI: 10.1136/Gutjnl-2015-311004  0.638
2016 Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O. A web application for sample size and power calculation in case-control microbiome studies. Bioinformatics (Oxford, England). PMID 27153704 DOI: 10.1093/Bioinformatics/Btw099  0.543
2016 Mysara M, Leys N, Raes J, Monsieurs P. IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. Bmc Bioinformatics. 17: 192. PMID 27130479 DOI: 10.1186/S12859-016-1061-2  0.316
2016 Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, ... ... Raes J, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science (New York, N.Y.). 352: 565-9. PMID 27126040 DOI: 10.1126/Science.Aad3369  0.761
2016 Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, ... ... Raes J, et al. Population-level analysis of gut microbiome variation. Science (New York, N.Y.). 352: 560-4. PMID 27126039 DOI: 10.1126/Science.Aad3503  0.748
2016 Kolmeder CA, Salojärvi J, Ritari J, de Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A, de Vos WM. Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults. Plos One. 11: e0153294. PMID 27070903 DOI: 10.1371/Journal.Pone.0153294  0.682
2016 Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, et al. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Communications. 7: 11071. PMID 27002549 DOI: 10.1038/Ncomms11071  0.567
2016 Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The Isme Journal. PMID 26905627 DOI: 10.1038/Ismej.2015.235  0.602
2016 Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, ... ... Raes J, et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature. PMID 26863193 DOI: 10.1038/Nature16942  0.744
2016 Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Joossens M, Raes J. Meta-omics in IBD research: applications, challenges and guidelines. Journal of Crohn's & Colitis. PMID 26802086 DOI: 10.1093/Ecco-Jcc/Jjw024  0.636
2016 Sabino J, Vieira-Silva S, Cleynen I, Machiels K, Joossens M, Falony G, Wang J, Ballet V, Ferrante M, Van Assche G, Van Der Merwe S, Raes J, Vermeire S. Tu1713 Host-Microbiome Interactions in Primary Sclerosing Cholangitis Gastroenterology. 150: S927-S928. DOI: 10.1016/S0016-5085(16)33144-4  0.615
2016 Sabino J, Vieira-Silva S, Cleynen I, Nys K, Machiels K, Joossens M, Falony G, Wang J, Ballet V, Ferrante M, Van Assche G, Van Der Merwe S, Raes J, Vermeire S. Su1909 Genetic Risk for Crohn's Disease has Little Impact on Intestinal Microbiota Composition Gastroenterology. 150: S585-S586. DOI: 10.1016/S0016-5085(16)32008-X  0.628
2015 Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. Fems Microbiology Reviews. PMID 26657537 DOI: 10.1093/Femsre/Fuv048  0.585
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Raes J, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26633628 DOI: 10.1038/Nature15766  0.811
2015 Darzi Y, Falony G, Vieira-Silva S, Raes J. Towards biome-specific analysis of meta-omics data. The Isme Journal. PMID 26623543 DOI: 10.1038/Ismej.2015.188  0.638
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Raes J, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26618873 DOI: 10.1038/nature15766  0.78
2015 Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J. Cross-biome comparison of microbial association networks. Frontiers in Microbiology. 6: 1200. PMID 26579106 DOI: 10.3389/Fmicb.2015.01200  0.593
2015 Laukens D, Brinkman BM, Raes J, De Vos M, Vandenabeele P. Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design. Fems Microbiology Reviews. PMID 26323480 DOI: 10.1093/Femsre/Fuv036  0.375
2015 Falony G, Vieira-Silva S, Raes J. Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine. Annual Review of Microbiology. 69: 305-21. PMID 26274026 DOI: 10.1146/Annurev-Micro-091014-104422  0.679
2015 Verbeke KA, Boobis AR, Chiodini A, Edwards CA, Franck A, Kleerebezem M, Nauta A, Raes J, van Tol EA, Tuohy KM. Towards microbial fermentation metabolites as markers for health benefits of prebiotics. Nutrition Research Reviews. 28: 42-66. PMID 26156216 DOI: 10.1017/S0954422415000037  0.344
2015 Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. PMID 26069274 DOI: 10.1136/Gutjnl-2015-309618  0.669
2015 Faust K, Lahti L, Gonze D, de Vos WM, Raes J. Metagenomics meets time series analysis: unraveling microbial community dynamics. Current Opinion in Microbiology. 25: 56-66. PMID 26005845 DOI: 10.1016/J.Mib.2015.04.004  0.605
2015 Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, ... ... Raes J, et al. Ocean plankton. Determinants of community structure in the global plankton interactome. Science (New York, N.Y.). 348: 1262073. PMID 25999517 DOI: 10.1126/Science.1262073  0.699
2015 de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, ... ... Raes J, et al. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science (New York, N.Y.). 348: 1261605. PMID 25999516 DOI: 10.1126/Science.1261605  0.598
2015 Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, ... ... Raes J, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science (New York, N.Y.). 348: 1261359. PMID 25999513 DOI: 10.1126/Science.1261359  0.81
2015 Geirnaert A, Wang J, Tinck M, Steyaert A, Van den Abbeele P, Eeckhaut V, Vilchez-Vargas R, Falony G, Laukens D, De Vos M, Van Immerseel F, Raes J, Boon N, Van de Wiele T. Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model. Fems Microbiology Ecology. 91. PMID 25999470 DOI: 10.1093/Femsec/Fiv054  0.66
2015 Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE. Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology. 24: 2433-48. PMID 25809788 DOI: 10.1111/Mec.13172  0.552
2015 Rajili?-Stojanovi? M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, de Vos WM, Manichanh C, Golic N, Enck P, Philippou E, Iraqi FA, Clarke G, Spiller RC, Penders J. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? The American Journal of Gastroenterology. 110: 278-87. PMID 25623659 DOI: 10.1038/Ajg.2014.427  0.338
2015 Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Disease Models & Mechanisms. 8: 1-16. PMID 25561744 DOI: 10.1242/Dmm.017400  0.381
2015 Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P. CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies. Applied and Environmental Microbiology. 81: 1573-84. PMID 25527546 DOI: 10.1128/Aem.02896-14  0.324
2015 Vandeputte D, Vanleeuwen R, Falony G, Joossens M, Raes J. Perspectives and pitfalls of microbiome research through home based fecal sampling: the Flemish Gut Flora Project experience Archives of Public Health. 73. DOI: 10.1186/2049-3258-73-S1-P33  0.622
2015 Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ballet V, Ferrante M, Van Assche GA, Van der Merwe S, Raes J, Vermeire S. 262 Intestinal Dysbiosis in Patients With Primary Sclerosing Cholangitis Gastroenterology. 148: S-60. DOI: 10.1016/S0016-5085(15)30207-9  0.599
2015 Marzorati M, Qin B, Hildebrand F, Klosterbuer A, Roughead Z, Roessle C, Rochat F, Raes J, Possemiers S. Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) Journal of Functional Foods. 16: 211-222. DOI: 10.1016/J.Jff.2015.04.039  0.582
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome. 2: 30. PMID 27367037 DOI: 10.1186/2049-2618-2-30  0.702
2014 Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, ... ... Raes J, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology. 32: 822-8. PMID 24997787 DOI: 10.1038/Nbt.2939  0.804
2014 Kubica M, Hildebrand F, Brinkman BM, Goossens D, Del Favero J, Vercammen K, Cornelis P, Schröder JM, Vandenabeele P, Raes J, Declercq W. The skin microbiome of caspase-14-deficient mice shows mild dysbiosis. Experimental Dermatology. 23: 561-7. PMID 24863253 DOI: 10.1111/Exd.12458  0.535
2014 Ye L, Matthijs S, Bodilis J, Hildebrand F, Raes J, Cornelis P. Analysis of the draft genome of Pseudomonas fluorescens ATCC17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines. Biometals : An International Journal On the Role of Metal Ions in Biology, Biochemistry, and Medicine. 27: 633-44. PMID 24756978 DOI: 10.1007/S10534-014-9734-7  0.526
2014 Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology. 16: 2659-71. PMID 24102695 DOI: 10.1111/1462-2920.12250  0.602
2014 Faust K, Raes J. Comparative analysis of biome-specific microbial association networks F1000research. 5. DOI: 10.7490/F1000Research.1094770.1  0.548
2014 Raes J. The gut microbiome - a new target for understanding, diagnosing and treating disease Archives of Public Health. 72. DOI: 10.1186/2049-3258-72-S1-K3  0.432
2014 Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J. Correction to: LotuS: An efficient and user-friendly OTU processing pipeline [Microbiome, 2, (2014), 30] Microbiome. 2. DOI: 10.1186/2049-2618-2-37  0.635
2014 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Addendum: Enterotypes of the human gut microbiome Nature. 506: 516-516. DOI: 10.1038/Nature13075  0.785
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: An efficient and user-friendly OTU processing pipeline Microbiome. 2.  0.598
2013 Brinkman BM, Becker A, Ayiseh RB, Hildebrand F, Raes J, Huys G, Vandenabeele P. Gut microbiota affects sensitivity to acute DSS-induced colitis independently of host genotype. Inflammatory Bowel Diseases. 19: 2560-7. PMID 24105395 DOI: 10.1097/Mib.0B013E3182A8759A  0.53
2013 Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, ... ... Raes J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541-6. PMID 23985870 DOI: 10.1038/Nature12506  0.794
2013 Ye L, Ballet S, Hildebrand F, Laus G, Guillemyn K, Raes J, Matthijs S, Martins J, Cornelis P. A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies. Biometals : An International Journal On the Role of Metal Ions in Biology, Biochemistry, and Medicine. 26: 561-75. PMID 23877277 DOI: 10.1007/S10534-013-9653-Z  0.516
2013 Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, ... ... Raes J, et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. The Isme Journal. 7: 1678-95. PMID 23575371 DOI: 10.1038/Ismej.2013.59  0.723
2013 Hildebrand F, Nguyen TL, Brinkman B, Yunta RG, Cauwe B, Vandenabeele P, Liston A, Raes J. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biology. 14: R4. PMID 23347395 DOI: 10.1186/Gb-2013-14-1-R4  0.578
2013 Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G. The chemical interactome space between the human host and the genetically defined gut metabotypes. The Isme Journal. 7: 730-42. PMID 23178670 DOI: 10.1038/Ismej.2012.141  0.628
2013 Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J. A metagenomic insight into our gut's microbiome. Gut. 62: 146-58. PMID 22525886 DOI: 10.1136/Gutjnl-2011-301805  0.42
2012 Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. Plos One. 7: e49138. PMID 23209564 DOI: 10.1371/Journal.Pone.0049138  0.366
2012 Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, ... ... Raes J, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 490: 55-60. PMID 23023125 DOI: 10.1038/Nature11450  0.661
2012 Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR. A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). Bmc Genomics. 13: 514. PMID 23020652 DOI: 10.1186/1471-2164-13-514  0.607
2012 Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. Plos Computational Biology. 8: e1002606. PMID 22807668 DOI: 10.1371/Journal.Pcbi.1002606  0.75
2012 Faust K, Raes J. Microbial interactions: from networks to models. Nature Reviews. Microbiology. 10: 538-50. PMID 22796884 DOI: 10.1038/Nrmicro2832  0.576
2012 Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Research. 22: 1974-84. PMID 22665442 DOI: 10.1101/Gr.138198.112  0.652
2012 Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Molecular Systems Biology. 8: 581. PMID 22569339 DOI: 10.1038/Msb.2012.13  0.742
2012 Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. Assessment of metagenomic assembly using simulated next generation sequencing data. Plos One. 7: e31386. PMID 22384016 DOI: 10.1371/Journal.Pone.0031386  0.793
2012 Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The Isme Journal. 6: 1415-26. PMID 22258098 DOI: 10.1038/Ismej.2011.212  0.725
2012 Vermeire S, Joossens M, Verbeke K, Hildebrand F, Machiels K, Van den Broeck K, Van Assche G, Rutgeerts PJ, Raes J. Sa1922 Pilot Study on the Safety and Efficacy of Faecal Microbiota Transplantation in Refractory Crohn's Disease Gastroenterology. 142: S-360. DOI: 10.1016/S0016-5085(12)61356-0  0.505
2011 Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, et al. A holistic approach to marine eco-systems biology. Plos Biology. 9: e1001177. PMID 22028628 DOI: 10.1371/Journal.Pbio.1001177  0.559
2011 Brinkman BM, Hildebrand F, Kubica M, Goosens D, Del Favero J, Declercq W, Raes J, Vandenabeele P. Caspase deficiency alters the murine gut microbiome. Cell Death & Disease. 2: e220. PMID 22012254 DOI: 10.1038/Cddis.2011.101  0.549
2011 Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. Plos One. 6: e22099. PMID 21850220 DOI: 10.1371/Journal.Pone.0022099  0.782
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Raes J, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/Nbt.1823  0.761
2011 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/Nature09944  0.809
2011 Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/Msb.2011.6  0.799
2011 Arumugam M, Raes J, Pelletier E, Paslier DL, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Erratum: Enterotypes of the human gut microbiome (Nature (2011) 473 (174-180)) Nature. 474: 666-666. DOI: 10.1038/Nature10187  0.775
2010 Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, ... ... Raes J, et al. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Standards in Genomic Sciences. 3: 243-8. PMID 21304727 DOI: 10.4056/Sigs.1433550  0.324
2010 Harrington ED, Arumugam M, Raes J, Bork P, Relman DA. SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics (Oxford, England). 26: 2979-80. PMID 20966005 DOI: 10.1093/Bioinformatics/Btq564  0.747
2010 Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics (Oxford, England). 26: 2977-8. PMID 20959381 DOI: 10.1093/Bioinformatics/Btq536  0.756
2010 Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/Nature08821  0.813
2010 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Raes J, et al. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.5252.1  0.579
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/Pnas.0808022106  0.796
2009 Singh AH, Doerks T, Letunic I, Raes J, Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. Journal of Bacteriology. 191: 32-41. PMID 18849420 DOI: 10.1128/Jb.01084-08  0.782
2008 Foerstner KU, Doerks T, Muller J, Raes J, Bork P. A nitrile hydratase in the eukaryote Monosiga brevicollis. Plos One. 3: e3976. PMID 19096720 DOI: 10.1371/Journal.Pone.0003976  0.789
2008 Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P. A molecular study of microbe transfer between distant environments. Plos One. 3: e2607. PMID 18612393 DOI: 10.1371/Journal.Pone.0002607  0.794
2008 Raes J, Bork P. Molecular eco-systems biology: towards an understanding of community function. Nature Reviews. Microbiology. 6: 693-9. PMID 18587409 DOI: 10.1038/Nrmicro1935  0.604
2008 Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology. 4: 198. PMID 18523433 DOI: 10.1038/Msb.2008.35  0.703
2007 Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data. Current Opinion in Microbiology. 10: 490-8. PMID 17936679 DOI: 10.1016/J.Mib.2007.09.001  0.616
2007 Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/Pnas.0702636104  0.788
2007 Raes J, Harrington ED, Singh AH, Bork P. Protein function space: viewing the limits or limited by our view? Current Opinion in Structural Biology. 17: 362-9. PMID 17574832 DOI: 10.1016/J.Sbi.2007.05.010  0.732
2007 von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science (New York, N.Y.). 315: 1126-30. PMID 17272687 DOI: 10.1126/Science.1133420  0.803
2007 Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biology. 8: R10. PMID 17224063 DOI: 10.1186/Gb-2007-8-1-R10  0.773
2006 Rehwinkel J, Raes J, Izaurralde E. Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends in Biochemical Sciences. 31: 639-46. PMID 17010613 DOI: 10.1016/J.Tibs.2006.09.005  0.325
2006 Baele G, Raes J, Van de Peer Y, Vansteelandt S. An improved statistical method for detecting heterotachy in nucleotide sequences. Molecular Biology and Evolution. 23: 1397-405. PMID 16672284 DOI: 10.1093/Molbev/Msl006  0.585
2006 Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biology. 7: R13. PMID 16507168 DOI: 10.1186/Gb-2006-7-2-R13  0.611
2005 Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. Rna (New York, N.Y.). 11: 1530-44. PMID 16199763 DOI: 10.1261/Rna.2160905  0.72
2005 Beysen D, Raes J, Leroy BP, Lucassen A, Yates JR, Clayton-Smith J, Ilyina H, Brooks SS, Christin-Maitre S, Fellous M, Fryns JP, Kim JR, Lapunzina P, Lemyre E, Meire F, et al. Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. American Journal of Human Genetics. 77: 205-18. PMID 15962237 DOI: 10.1086/432083  0.618
2005 Raes J, Van de Peer Y. Functional divergence of proteins through frameshift mutations. Trends in Genetics : Tig. 21: 428-31. PMID 15951050 DOI: 10.1016/J.Tig.2005.05.013  0.588
2005 Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America. 102: 5454-9. PMID 15800040 DOI: 10.1073/Pnas.0501102102  0.627
2005 Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, Couloux A, Déhais P, Deléage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, ... ... Raes J, et al. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Research. 33: D641-6. PMID 15608279 DOI: 10.1093/Nar/Gki115  0.313
2004 Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annual Review of Genetics. 38: 615-43. PMID 15568988 DOI: 10.1146/Annurev.Genet.38.072902.092831  0.323
2003 Raes J, Van de Peer Y. Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. Applied Bioinformatics. 2: 91-101. PMID 15130825  0.576
2003 Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W. Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiology. 133: 1051-71. PMID 14612585 DOI: 10.1104/Pp.103.026484  0.632
2003 De Bodt S, Raes J, Van de Peer Y, Theissen G. And then there were many: MADS goes genomic. Trends in Plant Science. 8: 475-83. PMID 14557044 DOI: 10.1016/J.Tplants.2003.09.006  0.621
2003 Raes J, Vandepoele K, Simillion C, Saeys Y, Van de Peer Y. Investigating ancient duplication events in the Arabidopsis genome. Journal of Structural and Functional Genomics. 3: 117-29. PMID 12836691 DOI: 10.1007/978-94-010-0263-9_12  0.718
2003 De Bodt S, Raes J, Florquin K, Rombauts S, Rouzé P, Theissen G, Van de Peer Y. Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. Journal of Molecular Evolution. 56: 573-86. PMID 12698294 DOI: 10.1007/S00239-002-2426-X  0.602
2002 Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Research. 12: 1792-801. PMID 12421767 DOI: 10.1101/Gr.400202  0.723
2002 Breyne P, Dreesen R, Vandepoele K, De Veylder L, Van Breusegem F, Callewaert L, Rombauts S, Raes J, Cannoot B, Engler G, Inzé D, Zabeau M. Transcriptome analysis during cell division in plants. Proceedings of the National Academy of Sciences of the United States of America. 99: 14825-30. PMID 12393816 DOI: 10.1073/Pnas.222561199  0.561
2002 Vandepoele K, Raes J, De Veylder L, Rouzé P, Rombauts S, Inzé D. Genome-wide analysis of core cell cycle genes in Arabidopsis. The Plant Cell. 14: 903-16. PMID 11971144 DOI: 10.1105/Tpc.010445  0.587
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