High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions:http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000916
Semi-supervised recursively partitioned mixture models for identifying cancer subtypeshttp://bioinformatics.oxfordjournals.org/content/early/2010/08/15/bioinformatics.btq470.full.pdf+html
PROFESS: a PROtein Function, Evolution, Structure and Sequence database: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911846/
The advantage of the ‘answering queries using views’ approach to the database integration problem is that it reduces the integration problem to two steps: (i) building wrappers of the source databases, thereby providing simple ‘views’, and (ii) applying standard database queries on the views. Thus, implementing wrappers enables a robust query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. This will allow the user to move beyond simple text-based queries. Therefore, the PROFESS (PROtein Function, Evolution, Structure and Sequence) database uses wrappers to assist in the structural, functional and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing.
eggNOG http://eggnog.embl.de/
evolutionary genealogy of genes: Non-supervised Orthologous Groups
multiple structural alignment program, MAMMOTH-mult
http://ub.cbm.uam.es/mammoth/mult/
PROFESS
http://bionmr-c1.unl.edu/
Edit distance eg. kitten -> sitting has 3 character changes needed, useful for autocomplete
http://en.wikipedia.org/wiki/Levenshtein_distance
SPA: Short peptide analyzer of intrinsic disorder status of short peptides
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900848/?tool=pubmed
Biological Insights of Transcription Factor through Analyzing ChIP-Seq Data
Kaida Ning, 2009
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