Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
S. A. F. T. van Hijum
M. H. Medema
O. P. Kuipers
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
antiSMASH
10.1007/978-1-4899-7478-5_703
Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters
10.1007/978-1-62703-122-6_2
Synthetic Biology in Streptomyces Bacteria
10.1016/b978-0-12-385075-1.00021-4
Computational approaches to natural product discovery
10.1038/nchembio.1884
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
10.1038/nrmicro2478
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
10.1371/journal.pcbi.1004016
Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
10.1016/j.febslet.2011.06.014
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
10.1371/journal.pone.0051511
The future of industrial antibiotic production: From random mutagenesis to synthetic biology
10.4161/bbug.2.4.16114
Metabolomics methods for the synthetic biology of secondary metabolism
10.1016/j.febslet.2012.02.008
Computational tools for the synthetic design of biochemical pathways
10.1038/nrmicro2717
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
10.1186/1471-2164-11-299
Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
10.1111/j.1751-7915.2010.00226.x
Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea
10.1111/j.1462-2920.2008.01724.x
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters
10.1016/j.cell.2014.06.034
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
10.1371/journal.pcbi.1003822
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
10.1093/nar/gkv437
Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice
10.1016/j.copbio.2013.03.006
Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block
10.1021/sb500368w
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers
10.1093/nar/gkt449
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
10.1093/nar/gkr466
The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways
10.1093/gbe/evq013
MS/MS networking guided analysis of molecule and gene cluster families
10.1073/pnas.1303471110
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
10.1093/molbev/mst025
Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii
10.1128/jb.02132-12
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
10.1093/nar/gkr323
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
10.1128/mmbr.00037-08
Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
10.1186/s12864-015-2154-4
Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66
10.1021/acschembio.5b00801
Computational strategies for genome-based natural product discovery and engineering in fungi
10.1016/j.fgb.2016.01.006
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
10.1093/nar/gkw960
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
10.1038/nmicrobiol.2016.197
Editorial: Synthetic biology and bioinformatics
10.1039/c6np90031c
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1093/nar/gkx305
Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus
10.1186/s12864-017-3966-1
Mining prokaryotes for antimicrobial compounds: from diversity to function
10.1093/femsre/fux014
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
10.1093/bib/bbx146
Standardization for natural product synthetic biology
10.1039/c6np00030d
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways
10.1039/c6np00035e
Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin
10.1128/genomea.00453-17
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
10.1093/bioinformatics/btx400
Collaborating with Undergraduates To Contribute to Biochemistry Community Resources
10.1021/acs.biochem.7b00872
Road MAPs to engineer host microbiomes.
10.1016/j.mib.2017.11.023
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.
10.1111/1462-2920.13927
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
10.1073/pnas.1705567114
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
10.1093/nar/gkx319
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.
10.1016/j.fgb.2016.01.012
Exploration and exploitation of the environment for novel specialized metabolites.
10.1016/j.copbio.2018.01.017
Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
10.1128/mSystems.00182-17
Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.
10.1016/j.chembiol.2018.02.008
HEx: A heterologous expression platform for the discovery of fungal natural products.
10.1126/sciadv.aar5459
luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria.
10.1128/msystems.00208-17
A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
10.1021/jacs.7b13292
Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.
10.3389/fmicb.2018.01158
Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.
10.1038/s41396-018-0186-x
Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH.
10.1007/978-1-4939-7874-8_15
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences
10.1186/s40793-018-0318-y
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters
10.1093/nar/gky1060
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1101/463620
Mining bacterial genomes to reveal secret synergy
10.1074/jbc.H118.006669
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
10.1038/s42003-019-0333-6
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
10.1186/s13104-019-4222-3
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
10.1093/nar/gkz310
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs
10.1101/gr.243477.118
Genome Mining Approaches to Bacterial Natural Product Discovery
10.1016/b978-0-12-409547-2.14627-x
Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines
10.1039/C9NP00021F
PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1101/083535
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.
10.3389/fpls.2019.00846
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
10.1126/science.aaw9285
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
10.1093/nar/gkz882
A metabolic pathway for bile acid dehydroxylation by the gut microbiome
10.1101/758557
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines
10.1101/669291
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology
10.1038/s41564-019-0588-1
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1101/856955
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae
10.1111/nph.16338
Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat
10.1098/rspb.2019.2527
Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota
10.1101/2020.03.06.976126
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
10.1101/2020.03.14.992123
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota
10.1099/mgen.0.000373
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
10.1093/nar/gkaa374
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products
10.1101/2020.05.19.104752
Ecology and genomics of Actinobacteria: new concepts for natural product discovery
10.1038/s41579-020-0379-y
The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-0993-2
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1074/jbc.RA120.013528
Microbial natural product databases: moving forward in the multi-omics era
10.1039/D0NP00053A
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01228-1
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
10.1128/mSystems.00267-20
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01271-y
BiG-FAM: the biosynthetic gene cluster families database
10.1093/nar/gkaa812
Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic assembly lines
10.1093/bioinformatics/btaa595
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes
10.1093/nar/gkaa978
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
10.1038/s41598-020-77723-6
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
10.1371/journal.pbio.3001026
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
10.1093/gigascience/giaa154
The year 2020 in natural product bioinformatics: an overview of the latest tools and databases
10.1039/D0NP00090F
Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis
10.1101/2021.02.11.430889
A systematic analysis of metabolic pathways in the human gut microbiota
10.1101/2021.02.25.432841
Omics-based strategies to discover novel classes of RiPP natural products
10.1016/j.copbio.2020.12.008
Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria
10.1038/s41467-021-21163-x
The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range
10.3389/fbioe.2021.623701
Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques
10.1101/2021.01.20.427441
Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes
10.3389/fmicb.2020.574053
A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo
10.21203/rs.3.rs-126949/v1
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
10.1016/j.chembiol.2020.11.009
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters
10.1101/2020.11.08.370601
antiSMASH 6.0: improving cluster detection and comparison capabilities
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The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
10.1093/nar/gkab353
Mining genomes to illuminate the specialized chemistry of life
10.1038/s41576-021-00363-7
Dominant drivers of the human plasma metabolome
10.21203/rs.3.rs-688716/v1
A global survey of specialized metabolic diversity encoded in bacterial genomes
10.1101/2021.08.11.455920
cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters
10.1093/bioadv/vbab016
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.
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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.
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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
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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.
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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.
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Degenerate target sites mediate rapid primed CRISPR adaptation.
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Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains.
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Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress.
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Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress.
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Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract.
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Multifactorial diversity sustains microbial community stability.
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Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.
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Explaining microbial phenotypes on a genomic scale: GWAS for microbes.
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Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.
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Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.
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Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.
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Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.
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A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children.
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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.
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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.
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Application of state-of-art sequencing technologies to indigenous food fermentations.
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Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?
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PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
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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.
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Characterization of the global impact of low temperature gas plasma on vegetative microorganisms.
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FACIL: Fast and Accurate Genetic Code Inference and Logo.
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Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.
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Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.
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Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus.
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SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
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Genome (re-)annotation and open-source annotation pipelines.
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A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
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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.
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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.
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Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons.
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The relative value of operon predictions.
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Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons.
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FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.
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Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.
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BAGEL: a web-based bacteriocin genome mining tool.
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Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae.
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Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance.
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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.
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Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
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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.
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Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
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PreP: gene expression data pre-processing.
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Projector: automatic contig mapping for gap closure purposes.
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UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.
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Transcriptome analysis and related databases of Lactococcus lactis.
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