A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
Marnix H. Medema Miaomiao Zhou Sacha A.F.T. van Hijum Jolein Gloerich Hans J.C.T Wessels Roland J. Siezen Marc Strous
Jolein Gloerich
Gloerich Jolein
ORCID: 0000-0001-5976-8426
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Marnix H. Medema
Medema Marnix H.
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Marc Strous
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Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem 10.1038/ismej.2008.75
Assessing species biomass contributions in microbial communities via metaproteomics 10.1038/s41467-017-01544-x
Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria 10.1042/BST0330205
Designer microbiomes for environmental, energy and health biotechnology 10.1016/j.mib.2017.12.007
Cell division ring, a new cell division protein and vertical inheritance of a bacterial organelle in anammox planrtomycetes 10.1111/j.1365-2958.2009.06841.x
Mobility and persistence of methane in groundwater in a controlled-release field experiment 10.1038/ngeo2919
Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities 10.1073/pnas.1722325115
An improved medium for the anaerobic growth of Paracoccus denitrificans Pd1222 10.3389/fmicb.2014.00018
Predicting microbial nitrogen pathways from basic principles 10.1111/j.1462-2920.2011.02450.x
Enrichment of anammox from activated sludge and its application in the CANON process 10.1007/s00248-004-0186-4
Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria 10.1042/BST0340174
Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: Cell plan, glycogen storage, and localization of cytochrome c proteins 10.1128/JB.01449-07
Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge 10.1007/s00253-011-3361-9
Linearly concatenated cyclobutane lipids form a dense bacterial membrane 10.1038/nature01128
Anammox bacteria disguised as denitrifiers: Nitrate reduction to dinitrogen gas via nitrite and ammonium 10.1111/j.1462-2920.2006.01183.x
Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation 10.1016/S0723-2020(00)80050-8
Continuous cultivation and thermodynamic aspects of niche definition in the nitrogen cycle 10.1016/B978-0-12-381294-0.00002-X
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations 10.1111/1462-2920.13895
Physiological role of the respiratory quinol oxidase in the anaerobic nitrite-reducing methanotroph 'candidatus methylomirabilis oxyfera' 10.1099/mic.0.045187-0
Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox) 10.1111/j.1742-4658.2005.04842.x
Anaerobic ammonium oxidation by anammox bacteria in the Black Sea 10.1038/nature01472
The anaerobic oxidation of ammonium 10.1016/S0168-6445(98)00023-0
Rapid recovery of cyanobacterial pigments in desiccated biological soil crusts following addition of 10.1371/journal.pone.0112372
Impacts of chemical gradients on microbial community structur 10.1038/ismej.2016.175
Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities 10.3389/fmicb.2015.01461
Erratum to "Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam" [Water Research 41 (2007) 18] (DOI:10.1016/j.watres.2007.03.044) 10.1016/j.watres.2009.09.051
Application, eco-physiology and biodiversity of anaerobic ammonium-oxidizing bacteria 10.1007/s11157-004-7247-5
Adaptation of a freshwater anammox population to high salinity wastewater 10.1016/j.jbiotec.2006.05.012
A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera' 10.1042/BST0390243
Cell compartmentalisation in planctomycetes: Novel types of structural organisation for the bacterial cell 10.1007/s002030100280
Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam 10.1016/j.watres.2007.03.044
Sacha van Hijum
van Hijum Sacha
ORCID: 0000-0003-0741-2991
Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11. 10.3389/fmicb.2018.02418
Integrating glycomics and genomics uncovers SLC10A7 as essential factor for bone mineralization by regulating post-Golgi protein transport and glycosylation. 10.1093/hmg/ddy213
The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease. 10.1093/cid/ciy417
Primary cilia-regulated transcriptome in the renal collecting duct. 10.1096/fj.201701228r
Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. 10.1186/s40168-017-0395-y
Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis". 10.1128/CMR.00082-17
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. 10.1128/CMR.00016-17
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. 10.7717/peerj.3698
Gut microbiome in ADHD and its relation to neural reward anticipation. 10.1371/journal.pone.0183509
The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease 10.1101/169722
Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. 10.1186/s40168-017-0278-2
Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. 10.1164/rccm.201605-1042OC
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine 10.7287/peerj.preprints.2918
Draft Genome Sequences of 24 Lactococcus lactis Strains. 10.1128/genomeA.01737-16
Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains. 10.1128/genomeA.01739-16
Advances and perspectives in computational prediction of microbial gene essentiality. 10.1093/bfgp/elv063
Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. 10.1038/srep42808
Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. 10.1128/mBio.01984-16
Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis. 10.1371/journal.pone.0167944
Reply to Meisel et al. 10.1016/j.jid.2016.11.013
An In vitro Model for Bacterial Growth on Human Stratum Corneum. 10.2340/00015555-2401
Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin. 10.1016/j.jaci.2016.09.017
Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5. 10.1128/genomeA.01090-16
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). 10.1186/s40793-016-0172-8
Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats. 10.1111/1462-2920.13455
Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening. 10.1016/j.ijfoodmicro.2016.03.027
Nomadic Lifestyle of Lactobacillus plantarum Revealed by Comparative Genomics of 54 strains Isolated from Different Niches 10.1101/043117
Draft Genome Sequence of Lactobacillus plantarum SF2A35B. 10.1128/genomeA.01638-15
Resequencing of the Lactobacillus plantarum Strain WJL Genome. 10.1128/genomeA.01382-15
Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland. 10.1128/genomeA.01377-15
Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877. 10.1128/genomeA.01370-15
The post-vaccine microevolution of invasive Streptococcus pneumoniae. 10.1038/srep14952
Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice. 10.1093/carcin/bgv120
Microbial bioinformatics for food safety and production. 10.1093/bib/bbv034
Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. 10.1371/journal.pone.0127036
Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU. 10.3389/fmicb.2015.00422
CiVi: circular genome visualization with unique features to analyze sequence elements. 10.1093/bioinformatics/btv249
Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine. 10.1128/genomeA.00097-15
The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. 10.1186/2049-2618-2-44
Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology. 10.1186/1471-2164-15-1106
From microbial gene essentiality to novel antimicrobial drug targets. 10.1186/1471-2164-15-958
Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness. 10.1186/s12934-014-0148-6
Degenerate target sites mediate rapid primed CRISPR adaptation. 10.1073/pnas.1400071111
Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains. 10.1016/j.plasmid.2014.01.002
Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. 10.1371/journal.pone.0085625
Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress. 10.1128/AEM.03434-13
Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract. 10.1002/biot.201200259
Multifactorial diversity sustains microbial community stability. 10.1038/ismej.2013.108
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. 10.1371/journal.pone.0063523
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. 10.1093/bfgp/elt008
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods. 10.1186/1471-2180-13-68
Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. 10.1371/journal.pone.0059239
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. 10.1186/1471-2334-13-110
Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer. 10.1016/j.bpg.2013.03.008
A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children. 10.1186/1471-2164-14-74
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. 10.1128/genomeA.00119-12
Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes. 10.1186/1471-2164-14-7
Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen. 10.1128/JB.01831-12
Microbiome dynamics of human epidermis following skin barrier disruption. 10.1186/gb-2012-13-11-r101
Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1. 10.1371/journal.pone.0045097
Application of state-of-art sequencing technologies to indigenous food fermentations. 10.1016/j.copbio.2012.08.004
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. 10.1371/journal.pone.0043012
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? 10.1093/bib/bbs034
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. 10.1186/1471-2164-13-170
Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730). 10.1128/JB.00141-12
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. 10.1128/JB.06275-11
Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. 10.1099/mic.0.055434-0
Characterization of the global impact of low temperature gas plasma on vegetative microorganisms. 10.1002/pmic.201000637
FACIL: Fast and Accurate Genetic Code Inference and Logo. 10.1093/bioinformatics/btr316
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. 10.1111/j.1751-7915.2011.00247.x
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. 10.1128/AEM.02283-10
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. 10.1128/AEM.01122-10
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. 10.1093/bioinformatics/btq535
Genome (re-)annotation and open-source annotation pipelines. 10.1111/j.1751-7915.2010.00191.x
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. 10.1186/1471-2164-11-299
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. 10.1128/JB.00121-10
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. 10.1128/JB.00276-10
PanCGHweb: a web tool for genotype calling in pangenome CGH data. 10.1093/bioinformatics/btq103
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. 10.1128/MMBR.00037-08
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. 10.1093/bioinformatics/btp013
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. 10.1186/1471-2105-9-535
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. 10.1093/bioinformatics/btn588
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. 10.1186/1471-2164-9-495
Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons. 10.1128/AEM.00117-08
The relative value of operon predictions. 10.1093/bib/bbn019
Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. 10.1186/1471-2105-9-93
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. 10.1093/bioinformatics/btl658
Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media. 10.1021/bp0602294
BAGEL: a web-based bacteriocin genome mining tool. 10.1093/nar/gkl237
Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. 10.1074/jbc.m601661200
Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance. 10.1128/AAC.50.5.1753-1761.2006
SIMAGE: simulation of DNA-microarray gene expression data. 10.1186/1471-2105-7-205
Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria. 10.1128/MMBR.70.1.157-176.2006
Comparative and functional genomics of lactococci. 10.1016/j.femsre.2005.04.004
The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element. 10.1074/jbc.m502349200
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. 10.1093/nar/gki356
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. 10.1128/JB.187.11.3752-3761.2005
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. 10.1186/1471-2164-6-77
Saturation and quantization reduction in microarray experiments using two scans at different sensitivities. 10.2202/1544-6115.1057
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. 10.1093/bioinformatics/bth206
PreP: gene expression data pre-processing. 10.1093/bioinformatics/btg318
Projector: automatic contig mapping for gap closure purposes. 10.1093/nar/gng144
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. 10.1093/bioinformatics/btg203
Transcriptome analysis and related databases of Lactococcus lactis. 10.1023/a:1020691801251