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RECOMB
2009
Springer
16 years 7 months ago
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted seconda...
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
RECOMB
2009
Springer
16 years 7 months ago
Shared Peptides in Mass Spectrometry Based Protein Quantification
In analyzing the proteome using mass spectrometry, the mass values help identify the molecules, and the intensities help quantify them, relative to their abundance in other sample...
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Sh...
RECOMB
2009
Springer
16 years 7 months ago
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Collective behavior involving distally separate regions in a protein is known to widely affect its function. In this paper, we present an online approach to study and characterize ...
Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnik...
RECOMB
2008
Springer
16 years 6 months ago
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes
The transcriptional regulatory sequences in metazoan genomes often consist of multiple cis-regulatory modules (CRMs). Each CRM contains locally enriched occurrences of binding site...
Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Sel...
RECOMB
2008
Springer
16 years 6 months ago
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins
Abstract. In engineering protein variants by constructing and screening combinatorial libraries of chimeric proteins, two complementary and competing goals are desired: the new pro...
Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg