A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
Lotte Witjes
Rik Kooke
Justin J. J. van der Hooft
Ric C. H. de Vos
Joost J. B. Keurentjes
Marnix H. Medema
Harm Nijveen
BMC Research Notes, 2019-4-2
Justin van der Hooft
van der Hooft Justin
/ Justin J.J. van der Hooft
ORCID: 0000-0002-9340-5511
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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
10.1093/nar/gkab335
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
Harm Nijveen
Nijveen Harm
ORCID: 0000-0002-9167-4945
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.
10.1186/1471-2164-15-250
Birth, Death, and Diversification of Mobile Promoters in Prokaryotes
10.1534/genetics.114.162883
Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis
10.1093/jxb/eru378
Understanding and identifying amino acid repeats
10.1093/bib/bbt003
Discovery of T Cell Epitopes Implementing HLA-Peptidomics into a Reverse Immunology Approach
10.4049/jimmunol.1202351
Obituary: In memory of Jack Leunissen
10.1093/bib/bbt036
QualitySNPng: a user-friendly SNP detection and visualization tool
10.1093/nar/gkt333
The Human Leukocyte Antigen-presented Ligandome of B Lymphocytes
10.1074/mcp.M112.024810
Promoter propagation in prokaryotes
10.1093/nar/gks787
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
10.1093/nar/gkr1019
HSPVdb-the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
10.1007/s00251-010-0497-1
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
10.1093/bioinformatics/btq435
Constraint-based probabilistic learning of metabolic pathways from tomato volatiles
10.1007/s11306-009-0166-2
ProGMap: an integrated annotation resource for protein orthology
10.1093/nar/gkp462
Benchmarking protein classification algorithms via supervised cross-validation
10.1016/j.jbbm.2007.05.011
Primer3Plus, an enhanced web interface to Primer3
10.1093/nar/gkm306
TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure
10.1093/nar/gkl171
Regulatory elements in the rat βB2-crystallin promoter
10.1006/exer.2001.1077
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
10.1093/bioinformatics/btv479
CyLineUp: A Cytoscape app for visualizing data in network small multiples
10.12688/f1000research.8402.1
Promoter reuse in prokaryotes
10.4161/mge.23195
Learning from Co-expression Networks: Possibilities and Challenges
10.3389/fpls.2016.00444
Mutations in the RET proto-oncogene in sporadic medullary thyroid carcinomas
10.1016/0165-4608(94)90338-7
Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control
10.1093/pcp/pcx164
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population
10.3389/fgene.2017.00201
AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana
10.1111/tpj.13457
A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds
10.1007/s00425-015-2283-7
Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways
10.1093/pcp/pcv207
Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds
10.1016/j.gdata.2015.06.003
Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature
10.1186/s41073-016-0008-5
GeneNetwork: framework for web-based genetics
10.21105/joss.00025
Elucidating and mining the Tulipa and Lilium transcriptomes
10.1007/s11103-016-0508-1
Molecular regulation of temperature-dependent floral induction in Tulipa gesneriana
10.1104/pp.16.01758
Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans
10.1371/journal.pone.0161102
A footprint of desiccation tolerance in the genome of Xerophyta viscosa
10.1038/nplants.2017.38
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
10.1186/s13104-019-4222-3
Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans hawaiian strain CB4856
10.1534/genetics.115.175950
A multi-parent recombinant inbred line population of C. Elegans allows identification of novel QTLs for complex life history traits
10.1186/s12915-019-0642-8
Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds
10.1111/jipb.12788
