Falk Hildebrand - Publications

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

45 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
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.32
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.64
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  0.8
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  0.8
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  0.8
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  0.64
2015 Tedersoo L, Bahram M, Põlme S, Anslan S, Riit T, Kõljalg U, Nilsson RH, Hildebrand F, Abarenkov K. FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi". Science (New York, N.Y.). 349: 936. PMID 26315429 DOI: 10.1126/science.aaa5594  0.32
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  0.64
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  0.64
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  0.64
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  0.8
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  0.8
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  0.64
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  0.64
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  0.64
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  0.64
2014 Dingemans J, Ye L, Hildebrand F, Tontodonati F, Craggs M, Bilocq F, De Vos D, Crabbé A, Van Houdt R, Malfroot A, Cornelis P. The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung. Pathogens and Disease. 71: 26-38. PMID 24659602 DOI: 10.1111/2049-632X.12170  0.64
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  0.64
2014 Kleinteich J, Hildebrand F, Wood SA, CirÌs S, Agha R, Quesada A, Pearce DA, Convey P, Küpper FC, Dietrich DR. Diversity of toxin and non-toxin containing cyanobacterial mats of meltwater ponds on the Antarctic Peninsula: A pyrosequencing approach Antarctic Science. 26: 521-532. DOI: 10.1017/S0954102014000145  0.64
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: An efficient and user-friendly OTU processing pipeline Microbiome. 2.  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
2012 Wei Q, Minh PN, Dötsch A, Hildebrand F, Panmanee W, Elfarash A, Schulz S, Plaisance S, Charlier D, Hassett D, Häussler S, Cornelis P. Global regulation of gene expression by OxyR in an important human opportunistic pathogen. Nucleic Acids Research. 40: 4320-33. PMID 22275523 DOI: 10.1093/nar/gks017  0.64
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  0.64
2011 Qiu H, Hildebrand F, Kuraku S, Meyer A. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. Bmc Genomics. 12: 325. PMID 21699680 DOI: 10.1186/1471-2164-12-325  0.64
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  0.64
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  0.64
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