A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic varian...

Authors: Quan Chen and Fengzhu Sun

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing

MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount ...

Authors: Chih-Hung Chou, Feng-Mao Lin, Min-Te Chou, Sheng-Da Hsu, Tzu-Hao Chang, Shun-Long Weng, Sirjana Shrestha, Chiung-Chih Hsiao, Jui-Hung Hung and Hsien-Da Huang

Expanding the boundaries of local similarity analysis

Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic i...

Authors: W Evan Durno, Niels W Hanson, Kishori M Konwar and Steven J Hallam

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previ...

Authors: Zhen Gao, Ruizhe Zhao and Jianhua Ruan

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild so...

Authors: Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu and Henry T Nguyen

FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action

Yeast deletion-mutant collections have been successfully used to infer the mode-of-action of drugs especially by profiling chemical-genetic and genetic-genetic interactions on a genome-wide scale. Although ten...

Authors: Minho Lee, Sangjo Han, Hyeshik Chang, Youn-Sig Kwak, David M Weller and Dongsup Kim

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (mul...

Authors: Sergey I Nikolenko, Anton I Korobeynikov and Max A Alekseyev

Genome reassembly with high-throughput sequencing data

Recent studies in genomics have highlighted the significance of structural variation in determining individual variation. Current methods for identifying structural variation, however, are predominantly focuse...

Authors: Nathaniel Parrish, Benjamin Sudakov and Eleazar Eskin

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information

The cost of RNA-Seq has been decreasing over the last few years. Despite this, experiments with four or less biological replicates are still quite common. Estimating the variances of gene expression estimates ...

Authors: Ellis Patrick, Michael Buckley, David Ming Lin and Yee Hwa Yang

Sum of parts is greater than the whole: inference of common genetic history of populations

Reconstructability of population history, from genetic information of extant individuals, is studied under a simulation setting. We do not address the issue of accuracy of the reconstruction algorithms: we ass...

Authors: Filippo Utro, Marc Pybus and Laxmi Parida

A probabilistic method for identifying rare variants underlying complex traits

Identifying the genetic variants that contribute to disease susceptibilities is important both for developing methodologies and for studying complex diseases in molecular biology. It has been demonstrated that...

Authors: Jiayin Wang, Zhongmeng Zhao, Zhi Cao, Aiyuan Yang and Jin Zhang

Unraveling overlapping deletions by agglomerative clustering

Structural variations in human genomes, such as deletions, play an important role in cancer development. Next-Generation Sequencing technologies have been central in providing ways to detect such variations. M...

Authors: Roland Wittler

Accelerating read mapping with FastHASH

With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next...

Authors: Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu and Can Alkan

Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis

One challenge in applying bioinformatic tools to clinical or biological data is high number of features that might be provided to the learning algorithm without any prior knowledge on which ones should be used...

Authors: Habil Zare, Gholamreza Haffari, Arvind Gupta and Ryan R Brinkman

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation

Gene duplication, followed by functional evolution of duplicate genes, is a primary engine of evolutionary innovation. In turn, gene expression evolution is a critical component of overall functional evolution...

Authors: Jia Zeng and Sridhar Hannenhalli

Erratum to: Unraveling overlapping deletions by agglomerative clustering

Authors: Roland Wittler