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RECOMB
2015
Springer
3 years 7 days ago
A Symmetric Length-Aware Enrichment Test
Young et al. [14] showed that due to gene length bias the popular Fisher Exact Test should not be used to study the association between a group of differentially expressed (DE) ge...
David Manescu, Uri Keich
RECOMB
2015
Springer
3 years 7 days ago
CRISPR Detection from Short Reads Using Partial Overlap Graphs
Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against pha...
Ilan Ben-Bassat, Benny Chor
RECOMB
2015
Springer
3 years 7 days ago
Learning Microbial Interaction Networks from Metagenomic Count Data
Many microbes associate with higher eukaryotes and impact their vitality. In order to engineer microbiomes for host benefit, we must understand the rules of community assembly and...
Surojit Biswas, Meredith McDonald, Derek S. Lundbe...
RECOMB
2015
Springer
3 years 7 days ago
Locating a Tree in a Phylogenetic Network in Quadratic Time
A fundamental problem in the study of phylogenetic networks is how to determine whether a phylogenetic network displays a phylogenetic tree or not. We develop a quadratic-time alg...
Philippe Gambette, Andreas D. M. Gunawan, Anthony ...
RECOMB
2015
Springer
3 years 7 days ago
HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data
Identifying phase information is biomedically important due to the association of complex haplotype effects, such as compound heterozygosity, with disease. As recent next-generat...
Emily Berger, Deniz Yörükoglu, Bonnie Be...
RECOMB
2012
Springer
6 years 6 months ago
A Model for Biased Fractionation after Whole Genome Duplication
Background: Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion...
David Sankoff, Chunfang Zheng, Baoyong Wang
RECOMB
2012
Springer
6 years 6 months ago
Reconstructing Boolean Models of Signaling
Abstract. Since the first emergence of protein-protein interaction networks, more than a decade ago, they have been viewed as static scaffolds of the signaling-regulatory events ...
Roded Sharan, Richard M. Karp
RECOMB
2012
Springer
6 years 6 months ago
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising
We develop a novel and general approach to estimating the accuracy of protein multiple sequence alignments without knowledge of a reference alignment, and use our approach to addre...
Dan F. DeBlasio, Travis J. Wheeler, John D. Kececi...
RECOMB
2012
Springer
6 years 6 months ago
Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
Abstract. Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution where genetic material is transferred between two more or less distantly related organisms. It ...
Sebastien Roch, Sagi Snir
RECOMB
2012
Springer
6 years 6 months ago
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
Signaling networks are essential for cells to control processes such as growth and response to stimuli. Although many “omic” data sources are available to probe signaling pathw...
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani...
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