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RECOMB
2008
Springer
9 years 6 months ago
Reconstructing the Evolutionary History of Complex Human Gene Clusters
Abstract. Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human geno...
Adam C. Siepel, Eric D. Green, Giltae Song, Tom&aa...
RECOMB
2008
Springer
9 years 6 months ago
Locating Multiple Gene Duplications through Reconciled Trees
We introduce the first exact and efficient algorithm for Guig?o et al.'s problem that, given a collection of rooted, binary gene trees and a rooted, binary species tree, deter...
J. Gordon Burleigh, Mukul S. Bansal, André ...
RECOMB
2008
Springer
9 years 6 months ago
Computation of Median Gene Clusters
Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e. sets of g...
Sebastian Böcker, Katharina Jahn, Julia Mixta...
RECOMB
2008
Springer
9 years 6 months ago
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles
We present a method for identifying connected gene subnetworks significantly enriched for genes that are dysregulated in specimens of a disease. These subnetworks provide a signat...
Igor Ulitsky, Richard M. Karp, Ron Shamir
RECOMB
2008
Springer
9 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
9 years 6 months ago
Accounting for Non-genetic Factors Improves the Power of eQTL Studies
Abstract. The recent availability of large scale data sets profiling single nucleotide polymorphisms (SNPs) and gene expression across different human populations, has directed muc...
Oliver Stegle, Anitha Kannan, Richard Durbin, John...
RECOMB
2008
Springer
9 years 6 months ago
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads
Next Generation Sequencing (NGS) technologies are capable of reading millions of short DNA sequences both quickly and cheaply. While these technologies are already being used for r...
Paul Medvedev, Michael Brudno
CHI
2004
ACM
9 years 6 months ago
Computational Biology and Language
Madhavi Ganapathiraju, Narayanas Balakrishnan, Raj...
RECOMB
2009
Springer
9 years 7 months ago
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
Abstract. Understanding the regulatory mechanisms that are responsible for an organism's response to environmental changes is an important question in molecular biology. A fir...
Oliver Stegle, Katherine J. Denby, David L. Wild, ...
RECOMB
2009
Springer
9 years 7 months ago
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
The availability of high density single nucleotide polymorphisms (SNPs) data has made genome-wide association study computationally challenging. Twolocus epistasis (gene-gene inter...
Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wa...
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