Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
Marnix H. Medema Yared Paalvast Don D. Nguyen Alexey Melnik Pieter C. Dorrestein Eriko Takano Rainer Breitling Paul P. Gardner
Eriko Takano
Takano Eriko
ORCID: 0000-0002-6791-3256
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Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
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Breitling Rainer
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LC-MS metabolomics from study design to data-analysis-using a versatile pathogen as a test case 10.5936/csbj.201301002
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models 10.1371/journal.pone.0051511
Selection of a highly invasive neuroblastoma cell population through long-term human cytomegalovirus infection 10.1038/oncsis.2012.10
Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation 10.1021/ac3018795
Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS 10.1021/pr300083x
Metabolomics methods for the synthetic biology of secondary metabolism 10.1016/j.febslet.2012.02.008
Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets 10.1007/s11306-011-0341-0
msCompare: A framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies 10.1074/mcp.M111.015974
Human neuroblastoma cells with acquired resistance to the p53 activator RITA retain functional p53 and sensitivity to other p53 activating agents 10.1038/cddis.2012.35
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Computational tools for the synthetic design of biochemical pathways 10.1038/nrmicro2717
Dynamic modelling under uncertainty: The case of trypanosoma brucei energy metabolism 10.1371/journal.pcbi.1002352
Adaptation of cancer cells from different entities to the MDM2 inhibitor nutlin-3 results in the emergence of p53-mutated multi-drug-resistant cancer cells 10.1038/cddis.2011.129
Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2) 10.1002/pmic.201100254
Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: Improved metabolite identification by retention time prediction 10.1021/ac2021823
Exploring the metabolic state of microorganisms using metabolomics 10.4155/bio.11.248
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor 10.1186/1756-0500-4-325
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Synthetic biology in streptomyces bacteria 10.1016/B978-0-12-385075-100021-4
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Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus 10.1111/j.1751-7915.2010.00226.x
Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2) 10.1111/j.1751-7915.2010.00232.x
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms 10.1038/nrmicro2478
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Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples 10.1021/pr1006944
Metabolomics to unveil and understand phenotypic diversity between pathogen populations 10.1371/journal.pntd.0000904
Towards an unbiased metabolic profiling of protozoan parasites: Optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis 10.1007/s00216-010-4139-0
The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways 10.1093/gbe/evq013
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Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans 10.1534/genetics.110.119677
The silicon trypanosome 10.1017/S0031182010000466
The potential of metabolomics for Leishmania research in the post-genomics era 10.1017/S0031182009992022
Metabolomic systems biology of trypanosomes 10.1017/S003118201000017X
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior 10.1186/1752-0509-4-81
Biomodel engineering - From structure to behavior 10.1007/978-3-642-11712-1_1
Metabolomic characterization of the salt stress response in streptomyces coelicolor 10.1128/AEM.01992-09
Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor 10.1186/1471-2164-11-202
Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply 10.1093/mp/ssq012
Genome-based phylogenetic analysis of Streptomyces and its relatives 10.1016/j.ympev.2009.11.019
Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines 10.1016/j.bcp.2009.08.013
The dynamic architecture of the metabolic switch in Streptomyces coelicolor 10.1186/1471-2164-11-10
Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms 10.1002/emmm.200900051
Expression quantitative trait loci are highly sensitive to cellular differentiation state 10.1371/journal.pgen.1000692
Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells 10.1186/1476-4598-8-80
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Probabilistic assignment of formulas to mass peaks in metabolomics experiments 10.1093/bioinformatics/btn642
Robust signaling networks of the adipose secretome 10.1016/j.tem.2008.08.006
Simple data-reduction method for high-resolution LC - MS data in metabolomics 10.4155/bio.09.146
Increasing the mass accuracy of high-resolution LC-MS data using background ions - A case study on the LTQ-Orbitrap 10.1002/pmic.200800314
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Greased hedgehogs: New links between hedgehog signaling and cholesterol metabolism 10.1002/bies.20663
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A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat 10.1186/1471-2105-8-132
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Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data 10.1007/s11306-006-0029-z
Network theory to understand microarray studies of complex diseases 10.2174/156652406778195044
A lock-and-key model for protein-protein interactions 10.1093/bioinformatics/btl338
Biological microarray interpretation: The rules of engagement 10.1016/j.bbaexp.2006.06.003
Interspecies comparison of gene structure and computational analysis of gene regulation of 17beta-hydroxysteroid dehydrogenase type 1 10.1016/j.mce.2005.10.014
Regulation of ubiquitin-binding proteins by monoubiquitination 10.1038/ncb1354
Current challenges in quantitative modeling of epidermal growth factor signaling 10.1016/j.febslet.2005.10.034
Feature selection and the class imbalance problem in predicting protein function from sequence 10.2165/00822942-200594030-00004
Biological master games: Using biologists' reasoning to guide algorithm development for integrated functional genomics 10.1089/omi.2005.9.225
Rank-based methods as a non-parametric alternative of the t-statistic for the analysis of biological microarray data 10.1142/S0219720005001442
GeneRank: Using search engine technology for the analysis of microarray experiments 10.1186/1471-2105-6-233
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The potassium-dependent transcriptome of arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling 10.1104/pp.104.046482
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Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments 10.1186/1471-2105-5-34
Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor 10.1186/1471-2431-4-5
Closing the gap: Identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis 10.1210/me.2002-0436
Isopentenyl-diphosphate isomerases in human and mouse: Evolutionary analysis of a mammalian gene duplication 10.1007/s00239-003-2476-8
Embryonic expression of cholesterogenic genes is restricted to distinct domains and colocalizes with apoptotic regions in mice 10.1016/S0169-328X(03)00094-9
A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment 10.1194/jlr.R200010-JLR200
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Phytoestrogens inhibit human 17β-hydroxysteroid dehydrogenase type 5 10.1016/S0303-7207(00)00422-6
17β-hydroxysteroid dehydrogenase type 7 - An ancient 3-ketosteroid reductase of cholesterogenesis 10.1016/S0303-7207(00)00416-0
Evolution of 17β-HSD type 4, a multifunctional protein of β-oxidation 10.1016/S0303-7207(00)00415-9
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Determination of cDNA, gene structure and chromosomal localization of the novel human 17β-hydroxysteroid dehydrogenase type 7 10.1016/S0014-5793(99)01366-6
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. 10.1093/nar/gkv437
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. 10.1093/bioinformatics/btv072
A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments. 10.1186/PREACCEPT-1857144210135244
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Computational modelling of kinase signalling cascades. 10.1007/978-1-60761-795-2_22
Feature selection and the class imbalance problem in predicting protein function from sequence. 10.2165/00822942-200504030-00004
Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family. 10.1093/oxfordjournals.molbev.a003761
Synthetic Biology of Antibiotic Production 10.1002/3527600906.mcb.20120052
Transactions on Computational Systems Biology XII 10.1007/978-3-642-11712-1
Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering 10.3390/computation1020027
The future of industrial antibiotic production: From random mutagenesis to synthetic biology 10.4161/bbug.2.4.16114
Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning 10.1007/978-3-540-77226-2_89
Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning 10.1007/978-3-540-77226-2_88
Bacterial Microcompartments: Biomaterials for Synthetic Biology-Based Compartmentalization Strategies 10.1021/acsbiomaterials.5b00059
Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans 10.1371/journal.pgen.0020222.eor
Towards synthesis of monoterpenes and derivatives using synthetic biology 10.1016/j.cbpa.2016.06.002
Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology 10.1016/j.tibtech.2016.12.008
Rational cell culture optimization enhances experimental reproducibility in cancer cells 10.1101/167148
Selenzyme: Enzyme selection tool for pathway design 10.1101/188979
Butyrolactone signalling circuits for synthetic biology 10.1016/j.cbpa.2015.06.024
Synthetic biology of natural products 10.1101/cshperspect.a023994
Advanced LC-MS applications for identification and quantification of the metabolome 10.2217/9781910419441.fseb2013.14.55
Re Genotyper: Detecting mislabeled samples in genetic data 10.1371/journal.pone.0171324
East meets west: On the true identity of cheiracanthium rupestre and xysticus albomaculatus (Arachnida: Araneae: Eutichuridae, Thomisidae) | Anmerkung zur wahren identität von cheiracanthium rupestre und xysticus albomaculatus (Arachnida: Araneae: Eutichuridae, Thomisidae) 10.5431/aramit5208
Phantom spiders 2: More notes on dubious spider species from Europe | Phantomspinnen 2: Weitere bemerkungen zu zweifelhaften spinnenarten aus Europa 10.5431/aramit5209
CodonGenie: Optimised ambiguous codon design tools 10.7717/peerj-cs.120
Public DNA barcoding data resolve the status of the genus Arboricaria (araneae: Gnaphosidae) | Öffentliche DNA-barcode-daten klären den Status der gattung arboricaria 10.5431/aramit5405
Bioinformatics for the synthetic biology of natural products: Integrating across the Design-Build-Test cycle 10.1039/c6np00018e
biochem4j: Integrated and extensible biochemical knowledge through graph databases 10.1371/journal.pone.0179130
SYNBIOCHEM - A SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals 10.1042/BST20160009
Phantom spiders: Notes on dubious spider species from Europe | Zusammenfassung. Phantomspinnen: Bemerkungen zu zweifelhaften spinnenarten aus Europa 10.5431/aramit5010
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification 10.1093/nar/gkx319
LC–MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes 10.1007/s11306-015-0827-2
A transatlantic perspective on 20 emerging issues in biological engineering 10.7554/eLife.30247
CodonGenie: optimised ambiguous codon design tools 10.7287/peerj.preprints.2797v1
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Rational cell culture optimization enhances experimental reproducibility in cancer cells 10.1038/s41598-018-21050-4
Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins 10.1128/mBio.02118-17
Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor 10.1021/acssynbio.7b00425
Mobilising ion mobility mass spectrometry for metabolomics 10.1039/C8AN00902C
Defining informative priors for ensemble modeling in systems biology 10.1038/s41596-018-0056-z
The “Three Cs” of Novel Antibiotic Discovery and Production through Synthetic Biology: Biosynthetic Gene Clusters, Heterologous Chassis, and Synthetic Microbial Consortia 10.1002/adbi.201800064
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters 10.1038/s42003-019-0333-6
SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli 10.1021/acssynbio.8b00399
Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships 10.1021/acs.analchem.9b02354
Bioengineering horizon scan 2020 10.7554/eLife.54489
Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling 10.1371/journal.pcbi.1008039
Host Systems for the Production of Recombinant Spider Silk 10.1016/j.tibtech.2020.09.007
Towards engineering and production of artificial spider silk using tools of synthetic biology 10.1049/enb.2019.0017
Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146 10.1016/j.jbiosc.2021.01.002
A completely resolved phylogenetic tree of British spiders 10.1101/2021.03.12.434792
Blood, Sweat and Tears: Extraterrestrial Regolith Biocomposites with in Vivo Binders 10.26434/chemrxiv.14769369.v1
Blood, Sweat and Tears: Extraterrestrial Regolith Biocomposites with in Vivo Binders 10.26434/chemrxiv.14769369
Blood, sweat, and tears: extraterrestrial regolith biocomposites with in vivo binders 10.1016/j.mtbio.2021.100136