Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways

[1]  A. Tramontano,et al.  Protein structure prediction and design. , 1998, Biotechnology annual review.

[2]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[3]  D. Gautheret,et al.  Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. , 2001, Journal of molecular biology.

[4]  Wentao Gao,et al.  UpGene: Application of a Web‐Based DNA Codon Optimization Algorithm , 2008, Biotechnology progress.

[5]  Enrique Merino,et al.  RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements , 2005, Nucleic Acids Res..

[6]  R. Reid,et al.  GeMS: an advanced software package for designing synthetic genes , 2005, Nucleic acids research.

[7]  Dieter Jahn,et al.  Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes , 2005, Bioinform..

[8]  Dieter Jahn,et al.  JCat: a novel tool to adapt codon usage of a target gene to its potential expression host , 2005, Nucleic Acids Res..

[9]  A. Helwak,et al.  High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells , 2006, PLoS biology.

[10]  M. Fischbach,et al.  Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. , 2006, Chemical reviews.

[11]  P. R. Jensen,et al.  Synthetic promoter libraries--tuning of gene expression. , 2006, Trends in biotechnology.

[12]  Santiago Garcia-Vallvé,et al.  Working toward a new NIOSH. , 1996, Nucleic Acids Res..

[13]  J. Zucko,et al.  ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures , 2008, Nucleic acids research.

[14]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[15]  Peter Man-Un Ung,et al.  Automated genome mining for natural products , 2009, BMC Bioinformatics.

[16]  Ed Zintel,et al.  Resources , 1998, IT Prof..

[17]  I. Hoof,et al.  CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. , 2009, Journal of biotechnology.

[18]  Christopher A. Voigt,et al.  Automated Design of Synthetic Ribosome Binding Sites to Precisely Control Protein Expression , 2009, Nature Biotechnology.

[19]  D. Haft,et al.  SMURF: Genomic mapping of fungal secondary metabolite clusters. , 2010, Fungal genetics and biology : FG & B.

[20]  R. Mitra,et al.  TATA is a modular component of synthetic promoters. , 2010, Genome research.

[21]  Gitanjali Yadav,et al.  SBSPKS: structure based sequence analysis of polyketide synthases , 2010, Nucleic Acids Res..

[22]  Anirban Mitra,et al.  WebGeSTer DB—a transcription terminator database , 2010, Nucleic Acids Res..

[23]  Sang-Kyu Jung,et al.  Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization , 2011, BMC Bioinformatics.

[24]  O. Kuipers,et al.  PePPER: a webserver for prediction of prokaryote promoter elements and regulons , 2012, BMC Genomics.

[25]  Scheila de Avila e Silva,et al.  BacPP: bacterial promoter prediction--a tool for accurate sigma-factor specific assignment in enterobacteria. , 2011, Journal of theoretical biology.

[26]  H. Salis.  The ribosome binding site calculator. , 2011, Methods in enzymology.

[27]  Kai Blin,et al.  NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity , 2011, Nucleic Acids Res..

[28]  M. Graf,et al.  Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression , 2011, PloS one.

[29]  Kai Blin,et al.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..

[30]  Shilin Chen,et al.  An introduction to the medicinal plant genome project , 2011, Frontiers of medicine.

[31]  J. Badger,et al.  The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity , 2012, PloS one.

[32]  Dong-Yup Lee,et al.  Computational codon optimization of synthetic gene for protein expression , 2012, BMC Systems Biology.

[33]  Huimin Zhao,et al.  Direct cloning of large genomic sequences , 2012, Nature Biotechnology.

[34]  José Luís Oliveira,et al.  Corrigendum: EuGene: maximizing synthetic gene design for heterologous expression , 2016, Bioinform..

[35]  P. G. Arnison,et al.  Erratum: Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature (Natural Product Reports (2013) 30 (108-160) DOI:10.1039/C2NP20085F) , 2013 .

[36]  Kai Blin,et al.  antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..

[37]  P. G. Arnison,et al.  Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. , 2013, Natural product reports.

[38]  Oscar P. Kuipers,et al.  BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides , 2013, Nucleic Acids Res..

[39]  Roger G. Linington,et al.  Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters , 2014, Cell.

[40]  M. Thaker,et al.  Antibiotic resistance–mediated isolation of scaffold-specific natural product producers , 2014, Nature Protocols.

[41]  H. Salis,et al.  Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites , 2013, Nucleic acids research.

[42]  S. Brady,et al.  eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes. , 2014, Chemistry & biology.

[43]  V. Mootha,et al.  Expansion of Biological Pathways Based on Evolutionary Inference , 2014, Cell.

[44]  Jinwen Wang,et al.  COStar: a D-star Lite-based dynamic search algorithm for codon optimization. , 2014, Journal of theoretical biology.

[45]  H. Salis,et al.  Efficient search, mapping, and optimization of multi‐protein genetic systems in diverse bacteria , 2014 .

[46]  Xiao Sun,et al.  Data access for the 1,000 Plants (1KP) project , 2014, GigaScience.

[47]  Dong-Yup Lee,et al.  Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design , 2014, Bioinform..

[48]  David H Burkhardt,et al.  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources , 2014, Cell.

[49]  B. Shen.  A New Golden Age of Natural Products Drug Discovery , 2015, Cell.

[50]  G. Challis,et al.  Discovery of microbial natural products by activation of silent biosynthetic gene clusters , 2015, Nature Reviews Microbiology.

[51]  D. Söll,et al.  Codon Bias as a Means to Fine-Tune Gene Expression. , 2015, Molecular cell.

[52]  Warren Lau,et al.  Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone , 2015, Science.

[53]  C. Smolke,et al.  Complete biosynthesis of opioids in yeast , 2015, Science.

[54]  Kai Blin,et al.  antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..

[55]  Nicole K Clay,et al.  A new cyanogenic metabolite in Arabidopsis required for inducible pathogen defense , 2015, Nature.

[56]  V. Hatzimanikatis,et al.  Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. , 2015, Current opinion in chemical biology.

[57]  B. Moore,et al.  Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. , 2015, ACS chemical biology.

[58]  Giovanna Ambrosini,et al.  The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools , 2014, Nucleic Acids Res..

[59]  O. Troyanskaya,et al.  Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.

[60]  A. Usobiaga,et al.  Evolution of the Cannabinoid and Terpene Content during the Growth of Cannabis sativa Plants from Different Chemotypes. , 2016, Journal of natural products.

[61]  Sven Panke,et al.  Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort , 2016, Nature Communications.

[62]  F. Barona-Gómez,et al.  Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes , 2016, bioRxiv.

[63]  S de Avila E Silva,et al.  BacPP: a web-based tool for Gram-negative bacterial promoter prediction. , 2016, Genetics and molecular research : GMR.

[64]  Klaas Vandepoele,et al.  CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool , 2016, Front. Plant Sci..

[65]  Christopher A. Voigt,et al.  Synthetic biology to access and expand nature's chemical diversity , 2016, Nature Reviews Microbiology.

[66]  D. Newman,et al.  Natural Products as Sources of New Drugs from 1981 to 2014. , 2016, Journal of natural products.

[67]  Lin Wang,et al.  A review of computational tools for design and reconstruction of metabolic pathways , 2017, Synthetic and systems biotechnology.

[68]  R. Bhattacharya,et al.  Natural products against Alzheimer's disease: Pharmaco-therapeutics and biotechnological interventions. , 2017, Biotechnology advances.

[69]  Kai Yu,et al.  Synthetic Gene Design Using Codon Optimization On-Line (COOL). , 2017, Methods in molecular biology.

[70]  Jian Tian,et al.  Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli , 2017, Scientific Reports.

[71]  Kai Blin,et al.  plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters , 2016, bioRxiv.

[72]  Michael A. Skinnider,et al.  PRISM 3: expanded prediction of natural product chemical structures from microbial genomes , 2017, Nucleic Acids Res..

[73]  Maximilian Ccjc Ebert,et al.  Computational tools for enzyme improvement: why everyone can - and should - use them. , 2017, Current opinion in chemical biology.

[74]  Bart Nijsse,et al.  Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms , 2017, PloS one.

[75]  Kai Blin,et al.  The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery , 2017, Nucleic Acids Res..

[76]  Kai Blin,et al.  antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification , 2017, Nucleic Acids Res..

[77]  Christopher J. Schwalen,et al.  A new genome-mining tool redefines the lasso peptide biosynthetic landscape , 2016, Nature chemical biology.

[78]  Renaud Vincentelli,et al.  A Novel Platform for High-Throughput Gene Synthesis to Maximize Recombinant Expression in Escherichia coli. , 2017, Methods in molecular biology.

[79]  Pablo Carbonell,et al.  RetroPath2.0: A retrosynthesis workflow for metabolic engineers. , 2018, Metabolic engineering.

[80]  Tyler W. H. Backman,et al.  ClusterCAD: a computational platform for type I modular polyketide synthase design , 2017, Nucleic Acids Res..

[81]  N. A. Jorge,et al.  Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools , 2018, Front. Genet..

[82]  M. Majewska,et al.  Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview. , 2018, Gene.

[83]  Jian Tian,et al.  Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts , 2018, International journal of molecular sciences.

[84]  Vikram Khipple Mulligan,et al.  De Novo Design of Bioactive Protein Switches , 2019, Nature.

[85]  T. Weber.  Engineering of cell factories for the production of natural products. , 2019, Natural product reports.

[86]  David Baker,et al.  Modular and tunable biological feedback control using a de novo protein switch , 2019, Nature.

[87]  Adrian T. Grzybowski,et al.  Complete biosynthesis of cannabinoids and their unnatural analogues in yeast , 2019, Nature.

[88]  S. Lee,et al.  antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline , 2019, Nucleic Acids Res..

[89]  Kai Blin,et al.  The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters , 2018, Nucleic Acids Res..

[90]  Brian Kuhlman,et al.  Advances in protein structure prediction and design , 2019, Nature Reviews Molecular Cell Biology.

[91]  A. Santini,et al.  Rewiring cellular metabolism for heterologous biosynthesis of Taxol , 2020, Natural product research.

[92]  F. Baquero,et al.  Defining and combating antibiotic resistance from One Health and Global Health perspectives , 2019, Nature Microbiology.

[93]  Kevin K. Yang,et al.  Machine-learning-guided directed evolution for protein engineering , 2018, Nature Methods.

[94]  A. Feliz,et al.  A Review of the Microbial Production of Bioactive Natural Products and Biologics , 2019, Front. Microbiol..

[95]  Timothy K Lu,et al.  A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS) , 2019, Nature Communications.

[96]  Saurabh Sinha,et al.  Towards a fully automated algorithm driven platform for biosystems design , 2019, Nature Communications.

[97]  F. Barona-Gómez,et al.  EvoMining reveals the origin and fate of natural product biosynthetic enzymes , 2018, bioRxiv.

[98]  Christina D. Smolke,et al.  Synthetic biology strategies for microbial biosynthesis of plant natural products , 2019, Nature Communications.

[99]  Luis V. Santana-Quintero,et al.  Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. , 2019, Journal of molecular biology.

[100]  Harald Schwalbe,et al.  "CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts. , 2019, Protein expression and purification.

[101]  C. Maranas,et al.  From directed evolution to computational enzyme engineering—A review , 2019, AIChE Journal.

[102]  Mohammad Alanjary,et al.  Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. , 2019, Natural product reports.

[103]  Roger G. Linington,et al.  MIBiG 2.0: a repository for biosynthetic gene clusters of known function , 2019, Nucleic Acids Res..