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POPL
2006
ACM
16 years 7 months ago
A fixpoint calculus for local and global program flows
We define a new fixpoint modal logic, the visibly pushdown ?-calculus (VP-?), as an extension of the modal ?-calculus. The models of this logic are execution trees of structured p...
Rajeev Alur, Swarat Chaudhuri, P. Madhusudan
RECOMB
2005
Springer
16 years 7 months ago
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
Abstract. With ever increasing amount of available data on protein-protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discover...
Mehmet Koyutürk, Ananth Grama, Wojciech Szpan...
RECOMB
2005
Springer
16 years 7 months ago
Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences
Abstract. In order to guarantee that the optimal motif is found, traditional pattern-driven approaches perform an exhaustive search over all candidate motifs of length l. We develo...
Sing-Hoi Sze, Xiaoyan Zhao
RECOMB
2004
Springer
16 years 7 months ago
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response
We present a novel classification-based algorithm called GeneClass for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple orga...
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, ...
RECOMB
2001
Springer
16 years 7 months ago
Finding motifs using random projections
motif discovery problem abstracts the task of discovering short, conserved sites in genomic DNA. Pevzner and Sze recently described a precise combinatorial formulation of motif di...
Jeremy Buhler, Martin Tompa
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