de Oliveira IMF, Fredriksen S, Gutiérrez MF, Harmsen HJM, Boekhorst J, van Baarlen P, Wells JM. (2025). Culturomics of the pig tonsil microbiome identifies new species and an untapped source of novel antimicrobials. Microbiome PMID40158143

Chalabi S, Loonen L, Boekhorst J, Li H, Fang L, Harrison PW, Lakhal W, Lluch J, Sokolov A, Djebali S, Rau A, Giuffra E, Wells J. (2025). Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets. Genomics PMID39814241

Zhao T, Pellegrini L, van der Hee B, Boekhorst J, Fernandes A, Brugman S, van Baarlen P, Wells JM. (2025). Choroid plexus organoids reveal mechanisms of Streptococcus suis translocation at the blood-cerebrospinal fluid barrier. Fluids Barriers CNS PMID39930492

Fredriksen S, Neila-Ibáñez C, Hennig-Pauka I, Guan X, Dunkelberger J, de Oliveira IF, Ferrando ML, Correa-Fiz F, Aragon V, Boekhorst J, van Baarlen P, Wells JM. (2024). Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome. Microb Genom PMID39699589

van der Els S, Boekhorst J, Bron PA, Kleerebezem M. (2024). The lactococcal ICE-ome encodes a repertoire of exchangeable traits with potential industrial relevance. BMC Genomics PMID39080539

van der Els S, Sheombarsing R, van Kempen T, Wels M, Boekhorst J, Bron PA, Kleerebezem M. (2024). Detection and classification of the integrative conjugative elements of Lactococcus lactis. BMC Genomics PMID38561675

Fuhren J, Schwalbe M, Boekhorst J, Rösch C, Schols HA, Kleerebezem M. (2024). Prebiotic utilisation provides Lactiplantibacillus plantarum a competitive advantage in vitro, but is not reflected by an increased intestinal fitness. Gut Microbes PMID38656273

Kortman GAM, Timmerman HM, Schaafsma A, Stoutjesdijk E, Muskiet FAJ, Nhien NV, van Hoffen E, Boekhorst J, Nauta A. (2023). Mothers' Breast Milk Composition and Their Respective Infant's Gut Microbiota Differ between Five Distinct Rural and Urban Regions in Vietnam. Nutrients PMID38004196

Tedjo DI, Wilbrink JA, Boekhorst J, Timmerman HM, Nienhuijs SW, Stronkhorst A, Savelkoul PHM, Masclee AAM, Penders J, Jonkers DMAE. (2023). Impact of Sleeve Gastrectomy on Fecal Microbiota in Individuals with Morbid Obesity. Microorganisms PMID37764197

Fredriksen S, de Warle S, van Baarlen P, Boekhorst J, Wells JM. (2023). Resistome expansion in disease-associated human gut microbiomes. Microbiome PMID37507809

Huang Z, Boekhorst J, Fogliano V, Capuano E, Wells JM. (2023). Impact of High-Fiber or High-Protein Diet on the Capacity of Human Gut Microbiota To Produce Tryptophan Catabolites. J Agric Food Chem PMID37126824

Fredriksen S, Ruijten SDE, Murray GGR, Juanpere-Borràs M, van Baarlen P, Boekhorst J, Wells JM. (2023). Transcriptomics in serum and culture medium reveal shared and differential gene regulation in pathogenic and commensal Streptococcus suis. Microb Genom PMID37103997

Zaccaria E, Klaassen T, Alleleyn AME, Boekhorst J, Smokvina T, Kleerebezem M, Troost FJ. (2023). Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial. Microbiome PMID36879297

López Nadal A, Boekhorst J, Lute C, van den Berg F, Schorn MA, Bergen Eriksen T, Peggs D, McGurk C, Sipkema D, Kleerebezem M, Wiegertjes GF, Brugman S. (2023). Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut. Anim Microbiome PMID36869372

Yeak KYC, Boekhorst J, Wels M, Abee T, Wells-Bennik MHJ. (2023). Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members. BMC Microbiol PMID36653740

Zaccaria E, Klaassen T, Alleleyn AME, Boekhorst J, Chervaux C, Smokvina T, Troost FJ, Kleerebezem M. (2023). L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human. Gut Microbes PMID37589280

Huang Z, Boekhorst J, Fogliano V, Capuano E, Wells JM. (2023). Distinct effects of fiber and colon segment on microbiota-derived indoles and short-chain fatty acids. Food Chem PMID35961168

Boekhorst J, Venlet N, Procházková N, Hansen ML, Lieberoth CB, Bahl MI, Lauritzen L, Pedersen O, Licht TR, Kleerebezem M, Roager HM. (2022). Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes. Microbiome PMID36510309

Fredriksen S, Guan X, Boekhorst J, Molist F, van Baarlen P, Wells JM. (2022). Environmental and maternal factors shaping tonsillar microbiota development in piglets. BMC Microbiol PMID36163011

Schoemaker MH, Hageman JHJ, Ten Haaf D, Hartog A, Scholtens PAMJ, Boekhorst J, Nauta A, Bos R. (2022). Prebiotic Galacto-Oligosaccharides Impact Stool Frequency and Fecal Microbiota in Self-Reported Constipated Adults: A Randomized Clinical Trial. Nutrients PMID35057489

Estorninos E, Lawenko RB, Palestroque E, Sprenger N, Benyacoub J, Kortman GAM, Boekhorst J, Bettler J, Cercamondi CI, Berger B. (2022). Term infant formula supplemented with milk-derived oligosaccharides shifts the gut microbiota closer to that of human milk-fed infants and improves intestinal immune defense: a randomized controlled trial. Am J Clin Nutr PMID34617558

Silva V, Alaoui A, Schlünssen V, Vested A, Graumans M, van Dael M, Trevisan M, Suciu N, Mol H, Beekmann K, Figueiredo D, Harkes P, Hofman J, Kandeler E, Abrantes N, Campos I, Martínez MÁ, Pereira JL, Goossens D, Gandrass J, Debler F, Lwanga EH, Jonker M, van Langevelde F, Sorensen MT, Wells JM, Boekhorst J, Huss A, Mandrioli D, Sgargi D, Nathanail P, Nathanail J, Tamm L, Fantke P, Mark J, Grovermann C, Frelih-Larsen A, Herb I, Chivers CA, Mills J, Alcon F, Contreras J, Baldi I, Pasković I, Matjaz G, Norgaard T, Aparicio V, Ritsema CJ, Geissen V, Scheepers PTJ. (2021). Collection of human and environmental data on pesticide use in Europe and Argentina: Field study protocol for the SPRINT project. PLoS One PMID34780516

Alkema W, Boekhorst J, Eijlander RT, Schnittger S, De Gruyter F, Lukovac S, Schilling K, Kortman GAM. (2021). Charting host-microbe co-metabolism in skin aging and application to metagenomics data. PLoS One PMID34758050

Fuhren J, Schwalbe M, Boekhorst J, Rösch C, Schols HA, Kleerebezem M. (2021). Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption. Microbiome PMID34732247

Choudhury R, Middelkoop A, Boekhorst J, Gerrits WJJ, Kemp B, Bolhuis JE, Kleerebezem M. (2021). Early life feeding accelerates gut microbiome maturation and suppresses acute post-weaning stress in piglets. Environ Microbiol PMID34655283

Rahman S, Kortman GAM, Boekhorst J, Lee P, Khan MR, Ahmed F. (2021). Effect of low-iron micronutrient powder (MNP) on the composition of gut microbiota of Bangladeshi children in a high-iron groundwater setting: a randomized controlled trial. Eur J Nutr PMID33634319

Olga L, Petry CJ, van Diepen JA, Prentice PM, Hughes IA, Vervoort J, Boekhorst J, Chichlowski M, Gross G, Dunger DB, Ong KK. (2021). Extensive Study of Breast Milk and Infant Growth: Protocol of the Cambridge Baby Growth and Breastfeeding Study (CBGS-BF). Nutrients PMID34445039

Owolabi AJ, Senbanjo IO, Oshikoya KA, Boekhorst J, Eijlander RT, Kortman GAM, Hageman JHJ, Samuel F, Melse-Boonstra A, Schaafsma A. (2021). Multi-Nutrient Fortified Dairy-Based Drink Reduces Anaemia without Observed Adverse Effects on Gut Microbiota in Anaemic Malnourished Nigerian Toddlers: A Randomised Dose-Response Study. Nutrients PMID34066577

Fuhren J, Nijland R, Wels M, Boekhorst J, Kleerebezem M. (2021). Complete Closed Genome Sequence of the Inulin-Utilizing Lactiplantibacillus plantarum Strain Lp900, Obtained Using a Hybrid Nanopore and Illumina Assembly. Microbiol Resour Announc PMID33927035

Ederveen THA, Smits JPH, Boekhorst J, Schalkwijk J, van den Bogaard EH, Zeeuwen PLJM. (2020). Skin microbiota in health and disease: From sequencing to biology. J Dermatol PMID32804417

Smits JPH, Ederveen THA, Rikken G, van den Brink NJM, van Vlijmen-Willems IMJJ, Boekhorst J, Kamsteeg M, Schalkwijk J, van Hijum SAFT, Zeeuwen PLJM, van den Bogaard EH. (2020). Targeting the Cutaneous Microbiota in Atopic Dermatitis by Coal Tar via AHR-Dependent Induction of Antimicrobial Peptides. J Invest Dermatol PMID31344386

Ederveen THA, Smits JPH, Hajo K, van Schalkwijk S, Kouwenhoven TA, Lukovac S, Wels M, van den Bogaard EH, Schalkwijk J, Boekhorst J, Zeeuwen PLJM, van Hijum SAFT. (2019). A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota. Sci Rep PMID31882601

Paganini D, Uyoga MA, Kortman GAM, Boekhorst J, Schneeberger S, Karanja S, Hennet T, Zimmermann MB. (2019). Maternal Human Milk Oligosaccharide Profile Modulates the Impact of an Intervention with Iron and Galacto-Oligosaccharides in Kenyan Infants. Nutrients PMID31671757

Gommers LMM, Ederveen THA, van der Wijst J, Overmars-Bos C, Kortman GAM, Boekhorst J, Bindels RJM, de Baaij JHF, Hoenderop JGJ. (2019). Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia. FASEB J PMID31299175

van den Bogert B, Boekhorst J, Pirovano W, May A. (2019). On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications. Front Genet PMID31447883

Rogier R, Ederveen THA, Wopereis H, Hartog A, Boekhorst J, van Hijum SAFT, Knol J, Garssen J, Walgreen B, Helsen MM, van der Kraan PM, van Lent PLEM, van de Loo FAJ, Abdollahi-Roodsaz S, Koenders MI. (2019). Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice. PLoS One PMID31283798

Paganini D, Uyoga MA, Kortman GAM, Cercamondi CI, Winkler HC, Boekhorst J, Moretti D, Lacroix C, Karanja S, Zimmermann MB. (2019). Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya. Gut PMID30448776

Chermprapai S, Ederveen THA, Broere F, Broens EM, Schlotter YM, van Schalkwijk S, Boekhorst J, van Hijum SAFT, Rutten VPMG. (2019). The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study. Vet Microbiol PMID30642603

Szopinska JW, Gresse R, van der Marel S, Boekhorst J, Lukovac S, van Swam I, Franke B, Timmerman H, Belzer C, Arias Vasquez A. (2018). Reliability of a participant-friendly fecal collection method for microbiome analyses: a step towards large sample size investigation. BMC Microbiol PMID30189859

Vaidya JD, van den Bogert B, Edwards JE, Boekhorst J, van Gastelen S, Saccenti E, Plugge CM, Smidt H. (2018). The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows. Front Microbiol PMID29445366

Ederveen THA, Ferwerda G, Ahout IM, Vissers M, de Groot R, Boekhorst J, Timmerman HM, Huynen MA, van Hijum SAFT, de Jonge MI. (2018). Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. Microbiome PMID29325581

Paganini D, Uyoga MA, Kortman GAM, Cercamondi CI, Moretti D, Barth-Jaeggi T, Schwab C, Boekhorst J, Timmerman HM, Lacroix C, Karanja S, Zimmermann MB. (2017). Prebiotic galacto-oligosaccharides mitigate the adverse effects of iron fortification on the gut microbiome: a randomised controlled study in Kenyan infants. Gut PMID28774885

Janssen AWF, Dijk W, Boekhorst J, Kuipers F, Groen AK, Lukovac S, Hooiveld GJEJ, Kersten S. (2017). ANGPTL4 promotes bile acid absorption during taurocholic acid supplementation via a mechanism dependent on the gut microbiota. Biochim Biophys Acta Mol Cell Biol Lipids PMID28733267

Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT, Arias Vasquez A. (2017). Gut microbiome in ADHD and its relation to neural reward anticipation. PLoS One PMID28863139

Timmerman HM, Rutten NBMM, Boekhorst J, Saulnier DM, Kortman GAM, Contractor N, Kullen M, Floris E, Harmsen HJM, Vlieger AM, Kleerebezem M, Rijkers GT. (2017). Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures. Sci Rep PMID28827640

Rogier R, Ederveen THA, Boekhorst J, Wopereis H, Scher JU, Manasson J, Frambach SJCM, Knol J, Garssen J, van der Kraan PM, Koenders MI, van den Berg WB, van Hijum SAFT, Abdollahi-Roodsaz S. (2017). Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. Microbiome PMID28645307

Zeeuwen PLJM, Boekhorst J, Ederveen THA, Kleerebezem M, Schalkwijk J, van Hijum SAFT, Timmerman HM. (2017). Reply to Meisel et al. J Invest Dermatol PMID27887953

Zeeuwen PL, Ederveen TH, van der Krieken DA, Niehues H, Boekhorst J, Kezic S, Hanssen DA, Otero ME, van Vlijmen-Willems IM, Rodijk-Olthuis D, Falcone D, van den Bogaard EH, Kamsteeg M, de Koning HD, Zeeuwen-Franssen ME, van Steensel MA, Kleerebezem M, Timmerman HM, van Hijum SA, Schalkwijk J. (2017). Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin. J Allergy Clin Immunol PMID27725187

Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SA, Bachmann H. (2017). Draft Genome Sequences of 24 Lactococcus lactis Strains. Genome Announc PMID28360177

Wels M, Backus L, Boekhorst J, Dijkstra A, Beerthuyzen M, Siezen RJ, Bachmann H, van Hijum SA. (2017). Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains. Genome Announc PMID28302789

Warda AK, Xiao Y, Boekhorst J, Wells-Bennik MHJ, Nierop Groot MN, Abee T. (2017). Analysis of Germination Capacity and Germinant Receptor (Sub)clusters of Genome-Sequenced Bacillus cereus Environmental Isolates and Model Strains. Appl Environ Microbiol PMID27881417

Steegenga WT, Mischke M, Lute C, Boekschoten MV, Lendvai A, Pruis MG, Verkade HJ, van de Heijning BJ, Boekhorst J, Timmerman HM, Plösch T, Müller M, Hooiveld GJ. (2017). Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups. Mol Nutr Food Res PMID27129739

Berendsen EM, Koning RA, Boekhorst J, de Jong A, Kuipers OP, Wells-Bennik MH. (2016). High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn1546 Transposon. Front Microbiol PMID27994575

Krawczyk AO, Berendsen EM, de Jong A, Boekhorst J, Wells-Bennik MH, Kuipers OP, Eijlander RT. (2016). A transposon present in specific strains of Bacillus subtilis negatively affects nutrient- and dodecylamine-induced spore germination. Environ Microbiol PMID27234229

Berendsen EM, Boekhorst J, Kuipers OP, Wells-Bennik MH. (2016). A mobile genetic element profoundly increases heat resistance of bacterial spores. ISME J PMID27105070

Caspers MP, Boekhorst J, de Jong A, Kort R, Nierop Groot M, Abee T. (2016). Draft Genome Sequences of Four Thermophilic Spore Formers Isolated from a Dairy-Processing Environment. Genome Announc PMID27516503

Fernández Ramírez MD, Boekhorst J, de Jong A, Kuipers OP, Abee T, Nierop Groot MN. (2016). Draft Whole-Genome Sequences of Three Lactobacillus plantarum Food Isolates. Genome Announc PMID27313301

Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MH, de Jong A, Kuipers OP, Nierop Groot MN, Abee T. (2016). Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PLoS One PMID27272929

Hayrapetyan H, Boekhorst J, de Jong A, Kuipers OP, Nierop Groot MN, Abee T. (2016). Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates. Genome Announc PMID27257202

Alkema W, Boekhorst J, Wels M, van Hijum SA. (2016). Microbial bioinformatics for food safety and production. Brief Bioinform PMID26082168

Warda AK, Tempelaars MH, Boekhorst J, Abee T, Nierop Groot MN. (2016). Identification of CdnL, a Putative Transcriptional Regulator Involved in Repair and Outgrowth of Heat-Damaged Bacillus cereus Spores. PLoS One PMID26849219

Kortman GA, Dutilh BE, Maathuis AJ, Engelke UF, Boekhorst J, Keegan KP, Nielsen FG, Betley J, Weir JC, Kingsbury Z, Kluijtmans LA, Swinkels DW, Venema K, Tjalsma H. (2015). Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon. Front Microbiol PMID26779139

Berendsen EM, Krawczyk AO, Klaus V, de Jong A, Boekhorst J, Eijlander RT, Kuipers OP, Wells-Bennik MH. (2015). Bacillus thermoamylovorans Spores with Very-High-Level Heat Resistance Germinate Poorly in Rich Medium despite the Presence of ger Clusters but Efficiently upon Exposure to Calcium-Dipicolinic Acid. Appl Environ Microbiol PMID26341201

Kortman GA, Mulder ML, Richters TJ, Shanmugam NK, Trebicka E, Boekhorst J, Timmerman HM, Roelofs R, Wiegerinck ET, Laarakkers CM, Swinkels DW, Bolhuis A, Cherayil BJ, Tjalsma H. (2015). Low dietary iron intake restrains the intestinal inflammatory response and pathology of enteric infection by food-borne bacterial pathogens. Eur J Immunol PMID26046550

Metselaar KI, den Besten HM, Boekhorst J, van Hijum SA, Zwietering MH, Abee T. (2015). Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU. Front Microbiol PMID26005439

Jaeggi T, Kortman GA, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, Njenga J, Mwangi A, Kvalsvig J, Lacroix C, Zimmermann MB. (2015). Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut PMID25143342

Cremers AJ, Zomer AL, Gritzfeld JF, Ferwerda G, van Hijum SA, Ferreira DM, Shak JR, Klugman KP, Boekhorst J, Timmerman HM, de Jonge MI, Gordon SB, Hermans PW. (2014). The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. Microbiome PMID25671106

Steegenga WT, Mischke M, Lute C, Boekschoten MV, Pruis MG, Lendvai A, Verkade HJ, Boekhorst J, Timmerman HM, Plösch T, Müller M. (2014). Sexually dimorphic characteristics of the small intestine and colon of prepubescent C57BL/6 mice. Biol Sex Differ PMID25243059

Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ. (2014). Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A PMID24711427

Brugman S, Schneeberger K, Witte M, Klein MR, van den Bogert B, Boekhorst J, Timmerman HM, Boes ML, Kleerebezem M, Nieuwenhuis EE. (2014). T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut. Gut Microbes PMID25536157

Van den Bogert B, Boekhorst J, Herrmann R, Smid EJ, Zoetendal EG, Kleerebezem M. (2013). Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem. PLoS One PMID24386196

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M. (2013). Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine. Genome Announc PMID24336366

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M. (2013). Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine. Genome Announc PMID24309734

Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid EJ, Boekhorst J, Zoetendal EG, Schaap PJ, Kleerebezem M. (2013). A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics PMID23915218

van den Bogert B, Erkus O, Boekhorst J, de Goffau M, Smid EJ, Zoetendal EG, Kleerebezem M. (2013). Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol PMID23614882

Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JE, Siezen RJ. (2013). Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One PMID23894338

Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, Wels M, van Hijum SA. (2013). Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform PMID22786785

Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ. (2013). Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. PLoS One PMID23527145

Caspers MP, Boekhorst J, Abee T, Siezen RJ, Kort R. (2013). Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment. Genome Announc PMID23469333

Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J, Timmerman HM. (2012). Microbiome dynamics of human epidermis following skin barrier disruption. Genome Biol PMID23153041

Axelsson L, Rud I, Naterstad K, Blom H, Renckens B, Boekhorst J, Kleerebezem M, van Hijum S, Siezen RJ. (2012). Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730). J Bacteriol PMID22493200

Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ. (2012). Database independent proteomics analysis of the ostrich and human proteome. Proc Natl Acad Sci U S A PMID22198768

Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA. (2012). Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol PMID22156394

Boekhorst J, Wilson G, Siezen RJ. (2011). Searching in microbial genomes for encoded small proteins. Microb Biotechnol PMID21518296

Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A. (2011). Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One PMID21437283

Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ, Snel B. (2011). Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One PMID21853102

Bart MJ, van Gent M, van der Heide HG, Boekhorst J, Hermans P, Parkhill J, Mooi FR. (2010). Comparative genomics of prevaccination and modern Bordetella pertussis strains. BMC Genomics PMID21070624

Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, de Vos WM. (2010). Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol PMID20562280

van Schaik W, Top J, Riley DR, Boekhorst J, Vrijenhoek JE, Schapendonk CM, Hendrickx AP, Nijman IJ, Bonten MJ, Tettelin H, Willems RJ. (2010). Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics PMID20398277

Gross G, Snel J, Boekhorst J, Smits MA, Kleerebezem M. (2010). Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin. Benef Microbes PMID21840797

Fokkens L, Botelho SM, Boekhorst J, Snel B. (2010). Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics PMID20152020

Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ. (2010). In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics PMID19770167

Wels M, Bongers RS, Boekhorst J, Molenaar D, Sturme M, de Vos WM, Siezen RJ, Kleerebezem M. (2009). Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome. J Bacteriol PMID19286810

Boekhorst J, van Breukelen B, Heck A, Snel B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol PMID18828897

Zhou M, Boekhorst J, Francke C, Siezen RJ. (2008). LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics PMID18371216

Siezen RJ, Starrenburg MJ, Boekhorst J, Renckens B, Molenaar D, van Hylckama Vlieg JE. (2008). Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Appl Environ Microbiol PMID18039825

Boekhorst J, Snel B. (2007). Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics PMID17888146

Siezen RJ, Renckens B, Boekhorst J. (2007). Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins PMID17348030

Boekhorst J, Wels M, Kleerebezem M, Siezen RJ. (2006). The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology (Reading) PMID17074889

Siezen R, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M. (2006). Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics PMID16723015

Boekhorst J, Helmer Q, Kleerebezem M, Siezen RJ. (2006). Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology (Reading) PMID16385136

Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ. (2005). Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. J Bacteriol PMID15995208

Smid EJ, van Enckevort FJ, Wegkamp A, Boekhorst J, Molenaar D, Hugenholtz J, Siezen RJ, Teusink B. (2005). Metabolic models for rational improvement of lactic acid bacteria as cell factories. J Appl Microbiol PMID15916646

Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, Mercenier A, Kleerebezem M, de Vos WM, Brüssow H, Desiere F. (2004). The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology (Reading) PMID15528649

Kerkhoven R, van Enckevort FH, Boekhorst J, Molenaar D, Siezen RJ. (2004). Visualization for genomics: the Microbial Genome Viewer. Bioinformatics PMID14988111

Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ. (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A PMID12566566

Kim YH, Kapfer DM, Boekhorst J, Lubsen NH, Bächinger HP, Shearer TR, David LL, Feix JB, Lampi KJ. (2002). Deamidation, but not truncation, decreases the urea stability of a lens structural protein, betaB1-crystallin. Biochemistry PMID12437365

total number of publications: 107
Google Scholar: Jos Boekhorst
last updated on Sat May 3 08:05:04 2025