Preface

Authors: Robert A Colvin and Jundong Liu

Reordering based integrative expression profiling for microarray classification

Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledge-supe...

Authors: Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey and Jake Y Chen

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data

RNA polymerase II (PolII) is essential in gene transcription and ChIP-seq experiments have been used to study PolII binding patterns over the entire genome. However, since PolII enriched regions in the genome ...

Authors: Zhi Han, Lu Tian, Thierry Pécot, Tim Huang, Raghu Machiraju and Kun Huang

Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain

The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated wi...

Authors: Jeremy W Prokop, Thomas C Leeper, Zhong-Hui Duan and Amy Milsted

THINK Back: KNowledge-based Interpretation of High Throughput data

Results of high throughput experiments can be challenging to interpret. Current approaches have relied on bulk processing the set of expression levels, in conjunction with easily obtained external evidence, su...

Authors: Fernando Farfán, Jun Ma, Maureen A Sartor, George Michailidis and Hosagrahar V Jagadish

Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery

The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural ele...

Authors: Franziska Jentzsch and Jennifer V Hines

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development ...

Authors: Juan Esquivel-Rodríguez and Daisuke Kihara

Constructing patch-based ligand-binding pocket database for predicting function of proteins

Many of solved tertiary structures of unknown functions do not have global sequence and structural similarities to proteins of known function. Often functional clues of unknown proteins can be obtained by pred...

Authors: Lee Sael and Daisuke Kihara

Convergence of genetic influences in comorbidity

Predisposition to complex diseases is explained in part by genetic variation, and complex diseases are frequently comorbid, consistent with pleiotropic genetic variation influencing comorbidity. Genome Wide As...

Authors: Richard C McEachin, Keerthi S Sannareddy, James D Cavalcoli, Alla Karnovsky, Jacqueline M Vink and Maureen A Sartor

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets

Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment ...

Authors: Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu and Geoffrey Fox

Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry

When flow cytometric data on mixtures of cell populations are collected from samples under different experimental conditions, computational methods are needed (a) to classify the samples into similar groups, a...

Authors: Ariful Azad, Saumyadipta Pyne and Alex Pothen

Fold change and p-value cutoffs significantly alter microarray interpretations

As context is important to gene expression, so is the preprocessing of microarray to transcriptomics. Microarray data suffers from several normalization and significance problems. Arbitrary fold change (FC) cu...

Authors: Mark R Dalman, Anthony Deeter, Gayathri Nimishakavi and Zhong-Hui Duan

Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data

Using gene co-expression analysis, researchers were able to predict clusters of genes with consistent functions that are relevant to cancer development and prognosis. We applied a weighted gene co-expression n...

Authors: Yang Xiang, Cun-Quan Zhang and Kun Huang

Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome

Retrotransposons are mobile DNA elements that spread through genomes via the action of element-encoded reverse transcriptases. They are ubiquitous constituents of most eukaryotic genomes, especially those of h...

Authors: Lauren S Mogil, Kamil Slowikowski and Howard M Laten