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ISBRA
2009
Springer
12 years 8 days ago
Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks
Identifying gene regulatory networks from high-throughput gene expression data is one of the most important goals of bioinformatics, but it remains difficult to define what makes a...
Peter Larsen, Yang Dai
ISBRA
2009
Springer
12 years 8 days ago
Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates
Identification of cis-regulatory motifs has long been a hotspot in the study of alternative splicing. We propose a two-step approach: we first identify k-mer seed motifs by testing...
Sihui Zhao, Jihye Kim, Steffen Heber
ISBRA
2009
Springer
12 years 8 days ago
Prediction of Contiguous Regions in the Amniote Ancestral Genome
Abstract. We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently seque...
Aïda Ouangraoua, Frédéric Boyer...
ISBRA
2009
Springer
12 years 8 days ago
Untangling Tanglegrams: Comparing Trees by Their Drawings
A tanglegram is a pair of trees on the same set of leaves with matching leaves in the two trees joined by an edge. Tanglegrams are widely used in biology – to compare evolutiona...
Balaji Venkatachalam, Jim Apple, Katherine St. Joh...
ISBRA
2009
Springer
12 years 8 days ago
Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression
There are many methods for assessing the quality of microarray data, but little guidance regarding what to do when defective data is identified. Depending on the scientific questio...
Brian E. Howard, Beate Sick, Steffen Heber
ISBRA
2009
Springer
12 years 8 days ago
Imputation-Based Local Ancestry Inference in Admixed Populations
Abstract. Accurate inference of local ancestry from whole-genome genetic variation data is critical for understanding the history of admixed human populations and detecting SNPs as...
Bogdan Pasaniuc, Justin Kennedy, Ion I. Mandoiu
ISBRA
2009
Springer
12 years 8 days ago
A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation
Abstract. DNA copy number is the number of replicates of a contiguous segment of DNA on the genome. Copy number alteration (CNA) is a genetic abnormality in which the number of the...
Matthew Hayes, Jing Li
ISBRA
2009
Springer
12 years 8 days ago
Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing
KIM, JIHYE. Mining of Cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing. (Under the direction of Steffen Heber). Alternative splicing (AS) is an important...
Jihye Kim, Sihui Zhao, Brian E. Howard, Steffen He...
ISBRA
2009
Springer
12 years 8 days ago
Mean Square Residue Biclustering with Missing Data and Row Inversions
Cheng and Church proposed a greedy deletion-addition algorithm to find a given number of k biclusters, whose mean squared residues (MSRs) are below certain thresholds and the miss...
Stefan Gremalschi, Gulsah Altun, Irina Astrovskaya...
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