SLDR: a computational technique to identify novel genetic regulatory relationships

We developed a new computational technique called S tep-L evel D ifferential R esponse (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same ...

Authors: Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie and Jake Y Chen

Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response

The analysis of gene expression has played an important role in medical and bioinformatics research. Although it is known that a large number of samples is needed to determine the patterns of gene expression a...

Authors: Nam S Vo and Vinhthuy Phan

Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing

Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. However, the scientific discovery offered by NGS also include...

Authors: Michael A Bauer, Shweta S Chavan, Erich A Peterson, Christoph J Heuck and Donald J Johann Jr

Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists

Endocrine disrupting chemicals (EDCs) are exogenous compounds that interfere with the endocrine system of vertebrates, often through direct or indirect interactions with nuclear receptor proteins. Estrogen rec...

Authors: Hui Wen Ng, Wenqian Zhang, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong and Huixiao Hong

Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data

Extracted ion chromatogram (EIC) extraction and chromatographic peak detection are two important processing procedures in liquid chromatography/mass spectrometry (LC/MS)-based metabolomics data analysis. Most ...

Authors: Wenchao Zhang and Patrick X Zhao

Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population

Due to a significant decline in the costs associated with next-generation sequencing, it has become possible to decipher the genetic architecture of a population by sequencing a large number of individuals to ...

Authors: Wenqian Zhang, Joe Meehan, Zhenqiang Su, Hui Wen Ng, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong and Huixiao Hong

Trends in the production of scientific data analysis resources

As the amount of scientific data grows, peer-reviewed Scientific Data Analysis Resources (SDARs) such as published software programs, databases and web servers have had a strong impact on the productivity of s...

Authors: Jason Hennessey, Constantin Georgescu and Jonathan D Wren

Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group

The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organ...

Authors: Inimary T Toby, Jonah Widmer and David W Dyer

Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis

Tumors are heterogeneous in composition. They are composed of cancer cells proper, along with stromal elements that collectively form a microenvironment, all of which are necessary to nurture the malignant pro...

Authors: Erich A Peterson, Shweta S Chavan, Michael A Bauer, Christoph J Heuck and Donald J Johann Jr

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data

While next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an e...

Authors: Yan Peng, Andrew S Maxwell, Natalie D Barker, Jennifer G Laird, Alan J Kennedy, Nan Wang, Chaoyang Zhang and Ping Gong

Topic modeling for cluster analysis of large biological and medical datasets

The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, fo...

Authors: Weizhong Zhao, Wen Zou and James J Chen

Haystack, a web-based tool for metabolomics research

Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multipl...

Authors: Stephen C Grace, Stephen Embry and Heng Luo

Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches

Every year pathogenic organisms cause billions of dollars' worth damage to crops and livestock. In agriculture, study of plant-microbe interactions is demanding a special attention to develop management strate...

Authors: Sitanshu S Sahu, Tyler Weirick and Rakesh Kaundal

Improving protein fold recognition by random forest

Recognizing the correct structural fold among known template protein structures for a target protein (i.e. fold recognition) is essential for template-based protein structure modeling. Since the fold recogniti...

Authors: Taeho Jo and Jianlin Cheng

LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches

Laccases (E.C. 1.10.3.2) are multi-copper oxidases that have gained importance in many industries such as biofuels, pulp production, textile dye bleaching, bioremediation, and food production. Their usefulness...

Authors: Tyler Weirick, Sitanshu S Sahu, Ramamurthy Mahalingam and Rakesh Kaundal

XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry

Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of...

Authors: Mihir Jaiswal, Nathaniel Mark Crabtree, Michael A Bauer, Roger Hall, Kevin D Raney and Boris L Zybailov

Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D Wren, Mikhail G Dozmorov, Dennis Burian, Andy Perkins, Chaoyang Zhang, Peter Hoyt and Rakesh Kaundal