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1.  OpenHelix: bioinformatics education outside of a different box 
Briefings in Bioinformatics  2010;11(6):598-609.
The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.
PMCID: PMC2984537  PMID: 20798181
bioinformatics education; training and learning; outreach; genomics; data management; computational biology resources
2.  Identification of attenuation and antitermination regulation in prokaryotes 
Genome Biology  2002;3(6):preprint0003.1-preprint0003.60.
The prediction of genes with attenuation or antitermination regulation is reported. The method is based on known characteristics of upstream sequences of regulated genes. We analyzed 26 complete genomes and are thus able to give a more complete picture of attenuation regulation in prokaryotes.
Many operons of biochemical pathways in bacterial genomes are regulated by processes called attenuation and antitermination. Though the specific mechanism can be quite different, attenuation and antitermination in these operons have in common the termination of transcription by a RNA 'terminator' fold upstream of the first gene in the operon. In the past, detecting regulation by attenuation or antitermination has often been a long process of experimental trial and error, on a case by case basis. We report here the prediction of over 290 upstream regions of genes with attenuation or antitermination regulation structures in the completed genomes of Bacillis subtilis and Escherichia coli for which extensive experimental studies have been done on attenuation and antitermination regulation. These predictions are based on a computational method devised from characteristics of known terminator fold candidates and benchmark regions of entire genomes. We extend this methodology to 24 additional complete genomes and are thus able to give a more complete picture of attenuation and antitermination regulation in bacteria.
PMCID: PMC4071262

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