Falk Hildebrand - Publications

Affiliations: 
VIB Department of Molecular and Cellular Vrije Universiteit Brussel, Elsene, Brussels Hoofdstedelijk Gewest, Belgium 

54 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 Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Research. PMID 35323968 DOI: 10.1093/nar/gkac163  0.409
2022 Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA. Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. Cell Reports Methods. 2: None. PMID 35118437 DOI: 10.1016/j.crmeth.2021.100137  0.398
2021 Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, et al. Towards the biogeography of prokaryotic genes. Nature. PMID 34912116 DOI: 10.1038/s41586-021-04233-4  0.381
2021 Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host & Microbe. PMID 34111423 DOI: 10.1016/j.chom.2021.05.008  0.473
2020 Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. Metagenomic assessment of the global distribution of bacteria and fungi. Environmental Microbiology. PMID 33185929 DOI: 10.1111/1462-2920.15314  0.489
2020 Frioux C, Singh D, Korcsmaros T, Hildebrand F. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. Computational and Structural Biotechnology Journal. 18: 1722-1734. PMID 32670511 DOI: 10.1016/J.Csbj.2020.06.028  0.364
2020 Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L. Plant nutrient-acquisition strategies drive topsoil microbiome structure and function. The New Phytologist. PMID 32279325 DOI: 10.1111/Nph.16598  0.462
2020 Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. The Isme Journal. PMID 32047279 DOI: 10.1038/S41396-020-0600-Z  0.502
2019 Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut. PMID 31203204 DOI: 10.1136/Gutjnl-2019-319045  0.471
2019 Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, et al. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Current Biology : Cb. PMID 31080084 DOI: 10.1016/J.Cub.2019.04.020  0.459
2019 Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Heuerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, et al. Antibiotics-induced monodominance of a novel gut bacterial order. Gut. PMID 30658995 DOI: 10.1136/Gutjnl-2018-317715  0.522
2019 Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U. [The gut microbiome in Parkinson's disease]. Der Nervenarzt. 90: 160-166. PMID 30171304 DOI: 10.1007/S00115-018-0601-6  0.447
2018 Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links. Nature Protocols. PMID 30382244 DOI: 10.1038/S41596-018-0064-Z  0.508
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  0.738
2018 Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH. The gut microbiome is associated with behavioural task in honey bees. Insectes Sociaux. 65: 419-429. PMID 30100619 DOI: 10.1007/S00040-018-0624-9  0.499
2018 Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, et al. Structure and function of the global topsoil microbiome. Nature. PMID 30069051 DOI: 10.1038/S41586-018-0386-6  0.511
2018 Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environmental Microbiology Reports. PMID 30058291 DOI: 10.1111/1758-2229.12684  0.513
2018 Pent M, Hiltunen M, Põldmaa K, Furneaux B, Hildebrand F, Johannesson H, Ryberg M, Bahram M. Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environmental Microbiology. PMID 29441658 DOI: 10.1111/1462-2920.14069  0.351
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, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/S41564-018-0114-X  0.607
2018 Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO. Gut microbiota composition is associated with environmental landscape in honey bees. Ecology and Evolution. 8: 441-451. PMID 29321884 DOI: 10.1002/Ece3.3597  0.555
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, 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  0.644
2017 Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Molecular Systems Biology. 13: 960. PMID 29242367 DOI: 10.15252/Msb.20177589  0.586
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, 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  0.718
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. Genome Medicine. 9: 39. PMID 28449715 DOI: 10.1186/S13073-017-0428-Y  0.427
2017 Saary P, Forslund K, Bork P, Hildebrand F. RTK: efficient rarefaction analysis of large datasets. Bioinformatics (Oxford, England). PMID 28398468 DOI: 10.1093/Bioinformatics/Btx206  0.474
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients (vol 9, pg 39, 2017) Genome Medicine. 9: 61. DOI: 10.3929/Ethz-B-000191807  0.437
2017 Kleinteich J, Hildebrand F, Bahram M, Voigt AY, Wood SA, Jungblut AD, Küpper FC, Quesada A, Camacho A, Pearce DA, Convey P, Vincent WF, Zarfl C, Bork P, Dietrich DR. Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change Frontiers in Ecology and Evolution. 5. DOI: 10.3389/Fevo.2017.00137  0.523
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  0.723
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, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. PMID 27409811 DOI: 10.1038/Nature18646  0.708
2016 Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science (New York, N.Y.). 352: 586-9. PMID 27126044 DOI: 10.1126/Science.Aad8852  0.466
2016 Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection. Ebiomedicine. 5: 135-46. PMID 27077120 DOI: 10.1016/J.Ebiom.2016.01.032  0.414
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, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26633628 DOI: 10.1038/Nature15766  0.746
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, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26618873 DOI: 10.1038/nature15766  0.704
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, ... ... Hildebrand F, 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  0.656
2015 Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi Mycokeys. 10: 1-43. DOI: 10.3897/mycokeys.10.4852  0.391
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  0.568
2015 Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection Ebiomedicine. DOI: 10.1016/j.ebiom.2016.01.032  0.332
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  0.631
2014 Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P. Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. Plos One. 9: e110038. PMID 25369289 DOI: 10.1371/Journal.Pone.0110038  0.307
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, ... ... Hildebrand F, 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  0.636
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  0.523
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  0.505
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  0.562
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: An efficient and user-friendly OTU processing pipeline Microbiome. 2.  0.515
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  0.516
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, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541-6. PMID 23985870 DOI: 10.1038/Nature12506  0.726
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  0.497
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  0.564
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  0.596
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  0.592
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  0.479
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  0.537
2010 Hildebrand F, Meyer A, Eyre-Walker A. Evidence of selection upon genomic GC-content in bacteria. Plos Genetics. 6: e1001107. PMID 20838593 DOI: 10.1371/Journal.Pgen.1001107  0.324
2008 Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, van Soolingen D, Rüsch-Gerdes S, Locht C, Brisse S, Meyer A, Supply P, Niemann S. Origin, spread and demography of the Mycobacterium tuberculosis complex. Plos Pathogens. 4: e1000160. PMID 18802459 DOI: 10.1371/Journal.Ppat.1000160  0.346
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