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16 papers found.
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FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs

Motivation: Understanding exact structure of an individual’s haplotype plays a significant role in various fields of human genetics. Despite tremendous research effort in recent years, fast and accurate haplotype reconstruction remains as an active research topic, mainly owing to the computational challenges involved. Existing haplotype assembly algorithms focus primarily on...

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

Zhaojun Zhang 1 Wei Wang 0 0 Department of Computer Science, University of California , Los Angeles, CA, USA 1 Department of Computer Science, University of North Carolina at Chapel Hill , Chapel

A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

A change-point model for identifying 30UTR switching by next-generation RNA sequencing Wei Wang 1 Zhi Wei 1 Hongzhe Li 0 Associate Editor: Inanc Birol 0 Department of Biostatistics and Epidemiology

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

Motivation: PIWI-interacting RNAs (piRNAs), 23–36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial...

Normalization and noise reduction for single cell RNA-seq experiments

based on spike-in ERCC molecules. Availability and implementation: The software is implemented by R and the download version is available at Contact: wei-wang{at}

Graph-regularized dual Lasso for robust eQTL mapping

Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage...

Improved image alignment method in application to X-ray images and biological images

Ching-Wei Wang 1 Hsiang-Chou Chen 0 Associate Editor: Jonathan Wren 0 Graduate Institute of Applied Science and Technology, Honors College National Taiwan University of Science and Technology

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy

their biological roles. Contact: tingjunhou{at}; tjhou{at}; wei-wang{at} Supplementary information: Supplementary data are available at Bioinformatics online.

Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts

Motivation: We describe a statistical model to dissect the noise in transcriptional bursts in a developmental system. Results: We assume that, at any given moment of time, each copy of a native gene inside a cell can exist in either a bursting (active) or non-bursting (inactive) state. The experimentally measured total noise in the transcriptional states of a gene in a population...

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment

Motivation: RNA-seq techniques provide an unparalleled means for exploring a transcriptome with deep coverage and base pair level resolution. Various analysis tools have been developed to align and assemble RNA-seq data, such as the widely used TopHat/Cufflinks pipeline. A common observation is that a sizable fraction of the fragments/reads align to multiple locations of the...

STAR: an integrated solution to management and visualization of sequencing data

and Contact: wei-wang{at}

TEAM: efficient two-locus epistasis tests in human genome-wide association study

As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene–gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in...

Efficient genome ancestry inference in complex pedigrees with inbreeding

Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of...

seeQTL: a searchable database for human eQTLs

Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots. Availability and implementation: seeQTL is freely available for non-commercial use at...

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows

Motivation: Typical high-throughput genotyping techniques produce numerous missing calls that confound subsequent analyses, such as disease association studies. Common remedies for this problem include removing affected markers and/or samples or, otherwise, imputing the missing data. On small marker sets imputation is frequently based on a vote of the K-nearest-neighbor (KNN...

ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data

Summary: ArrayFusion annotates conventional CGH results and various types of microarray data from a range of platforms (cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip) and converts them into standard formats which can be visualized in genome browsers (Affymetrix™ Integrated Genome Browser and GBrowse in the HapMap Project). Converted files can then be imported...