Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D Wren, Yuriy Gusev, Raphael D Isokpehi, Daniel Berleant, Ulisses Braga-Neto, Dawn Wilkins and Susan Bridges

Facilitating functional annotation of chicken microarray data

Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest...

Authors: Teresia J Buza, Ranjit Kumar, Cathy R Gresham, Shane C Burgess and Fiona M McCarthy

Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modificati...

Authors: Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L Reichel, Nathan R Stewart, Ryan D Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W Sykes, Jason N Burris, Joseph J Bozell, Max Zong-Ming Cheng…

Threshold selection in gene co-expression networks using spectral graph theory techniques

Gene co-expression networks are often constructed by computing some measure of similarity between expression levels of gene transcripts and subsequently applying a high-pass filter to remove all but the most l...

Authors: Andy D Perkins and Michael A Langston

HPD: an online integrated human pathway database enabling systems biology studies

Pathway-oriented experimental and computational studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gen...

Authors: Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty and Jake Y Chen

Computational analysis of gene expression space associated with metastatic cancer

Prostate carcinoma is among the most common types of cancer affecting hundreds of thousands people every year. Once the metastatic form of prostate carcinoma is documented, the majority of patients die from th...

Authors: Andrey Ptitsyn

Exploratory visual analysis of conserved domains on multiple sequence alignments

Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. Thi...

Authors: TJ Jankun-Kelly, Andrew D Lindeman and Susan M Bridges

Structural and functional-annotation of an equine whole genome oligoarray

The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for ...

Authors: Lauren A Bright, Shane C Burgess, Bhanu Chowdhary, Cyprianna E Swiderski and Fiona M McCarthy

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data

The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray results. Gene annotation ...

Authors: Bart HJ van den Berg, Chamali Thanthiriwatte, Prashanti Manda and Susan M Bridges

Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes

Nanomaterials are being manufactured on a commercial scale for use in medical, diagnostic, energy, component and communications industries. However, concerns over the safety of engineered nanomaterials have su...

Authors: Amin Zollanvari, Mary Jane Cunningham, Ulisses Braga-Neto and Edward R Dougherty

Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants

Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological ...

Authors: Natàlia Garcia-Reyero, Ira R Adelman, Dalma Martinović, Li Liu and Nancy D Denslow

Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles

Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platfor...

Authors: Zhiguang Li, Zhenqiang Su, Zhining Wen, Leming Shi and Tao Chen

Automatic identification of angiogenesis in double stained images of liver tissue

To grow beyond certain size and reach oxygen and other essential nutrients, solid tumors trigger angiogenesis (neovascularization) by secreting various growth factors. Based on this fact, several researches pr...

Authors: Mutlu Mete, Leah Hennings, Horace J Spencer and Umit Topaloglu

NATbox: a network analysis toolbox in R

There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as ...

Authors: Shweta S Chavan, Michael A Bauer, Marco Scutari and Radhakrishnan Nagarajan

Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM)

Understanding the relationship between the protein sequence and the 3D structure is a major research area in bioinformatics. The prediction of complete protein tertiary structure based only on sequence informa...

Authors: Bernard Chen and Matthew Johnson

Novel software package for cross-platform transcriptome analysis (CPTRA)

Next-generation sequencing techniques enable several novel transcriptome profiling approaches. Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performa...

Authors: Xin Zhou, Zhen Su, R Douglas Sammons, Yanhui Peng, Patrick J Tranel, C Neal Stewart Jr and Joshua S Yuan

An automated proteomic data analysis workflow for mass spectrometry

Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be i...

Authors: Ken Pendarvis, Ranjit Kumar, Shane C Burgess and Bindu Nanduri

PathBinder – text empirics and automatic extraction of biomolecular interactions

The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful prope...

Authors: Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao and Eve Syrkin Wurtele

Graph ranking for exploratory gene data analysis

Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of a...

Authors: Cuilan Gao, Xin Dang, Yixin Chen and Dawn Wilkins

Integrating phenotype and gene expression data for predicting gene function

This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both ...

Authors: Brandon M Malone, Andy D Perkins and Susan M Bridges