Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters [PDF]
, 2019 Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic ...
Blin, Kai +3 more
core +12 more sources
Data Mining of the Coffee Rust Genome [PDF]
, 2012 The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed.
Alvaro Gaitan +5 more
core +2 more sources
Reference Based Genome Compression [PDF]
, 2012 DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot ...
Chern, Bobbie +5 more
core +2 more sources
Strain prioritization and genome mining for enediyne natural products [PDF]
, 2016 The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date.
Ben Shen +18 more
core +2 more sources
Predicting Combinatorial Binding of Transcription Factors to Regulatory Elements in the Human Genome by Association Rule Mining [PDF]
, 2007 Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cisregulatory elements have been well studied, the combinations of transcription
Iyer, Vishwanath R. +3 more
core +2 more sources
PROPHECY—a database for high-resolution phenomics [PDF]
, 2004 The rapid recent evolution of the field phenomics—the genome-wide study of gene dispensability by quantitative analysis of phenotypes—has resulted in an increasing demand for new data analysis and visualization tools.
Blomberg, Anders +6 more
core +2 more sources
Expanding the set of rhodococcal Baeyer–Villiger monooxygenases by high-throughput cloning, expression and substrate screening [PDF]
, 2012 To expand the available set of Baeyer–Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1.
A Alfieri +38 more
core +4 more sources
Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels [PDF]
, 2015 The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species.
Carniel, Elisabeth +13 more
core +1 more source
Mining microbial genomes for new natural products and biosynthetic pathways [PDF]
, 2008 Analyses of microbial genome sequences have revealed numerous examples of ‘cryptic’ or ‘orphan’ biosynthetic gene clusters, with the potential to direct the production of novel, structurally complex natural products.
Austin +67 more
core +2 more sources
Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes [PDF]
, 2016 We are indebted with Marnix Medema, Paul Straight and Sean Rovito, for useful discussions and critical reading of the manuscript, as well as with Alicia Chagolla and Yolanda Rodriguez of the MS Service of Unidad Irapuato, Cinvestav, and Araceli Fernandez
Barona-Gomez, Francisco +7 more
core +1 more source