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» Binding as sets of scopes
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ENTCS
2007
151views more  ENTCS 2007»
15 years 8 days ago
Coalgebraic Modal Logic Beyond Sets
Polyadic coalgebraic modal logic is studied in the setting of locally presentable categories. It is shown that under certain assumptions, accessible functors admit expressive logi...
Bartek Klin
BMCBI
2004
88views more  BMCBI 2004»
15 years 5 days ago
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
Background: This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more g...
Saurabh Sinha, Mathieu Blanchette, Martin Tompa
RECOMB
2006
Springer
16 years 18 days ago
Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence
Abstract. We describe and empirically evaluate machine learning methods for the prediction of zinc binding sites from protein sequences. We start by observing that a data set consi...
Sauro Menchetti, Andrea Passerini, Paolo Frasconi,...
NIPS
2008
15 years 1 months ago
Predicting the Geometry of Metal Binding Sites from Protein Sequence
Metal binding is important for the structural and functional characterization of proteins. Previous prediction efforts have only focused on bonding state, i.e. deciding which prot...
Paolo Frasconi, Andrea Passerini
CSL
2004
Springer
15 years 5 months ago
A Dependent Type Theory with Names and Binding
We consider the problem of providing formal support for working tract syntax involving variable binders. Gabbay and Pitts have shown in their work on Fraenkel-Mostowski (FM) set th...
Ulrich Schöpp, Ian Stark