Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

MCBIOS 2008 was held February 23–24, 2008 in Oklahoma City, Oklahoma at the Cox Convention Center in Bricktown. It was the best attended in the series of MCBIOS conferences (140 registrants) with the most participation (68 posters submitted). Informative and engaging keynote talks were delivered by Dr. Bruce Roe and Dr. Edward Dougherty. The full agenda is online at http://www.okbios.org. Student poster award winners were: Vinay Ravindrakumar of University of Arkansas for Medical Sciences (1st place), Quan Shi of Little Rock Central High School (2nd) and Brian Roux of the University of New Orleans (UNO) (3rd), with honorary mentions going to Murat Eren of UNO and Prashanti Manda of Mississippi State University (MSU). Student talk winners were: Daniel Quest of the University of Nebraska Medical Center (1st place), Nan Wang of MSU (2nd), and William Sanders of MSU (3rd).

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[2]  Taewon Lee,et al.  Testing for treatment effects on gene ontology , 2008, BMC Bioinformatics.

[3]  Weida Tong,et al.  Very Important Pool (VIP) genes – an application for microarray-based molecular signatures , 2008, BMC Bioinformatics.

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[10]  Iftekhar Amin,et al.  Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions , 2007, BMC Bioinformatics.

[11]  Chaoyang Zhang,et al.  Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks , 2007, BMC Bioinformatics.

[12]  Hesham H. Ali,et al.  MTAP: The Motif Tool Assessment Platform , 2008, BMC Bioinformatics.

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[17]  Matthew Landry,et al.  Analysis of nanopore detector measurements using Machine-Learning methods, with application to single-molecule kinetic analysis , 2007, BMC Bioinformatics.

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[19]  Stephen Winters-Hilt,et al.  The α-Hemolysin nanopore transduction detector – single-molecule binding studies and immunological screening of antibodies and aptamers , 2007, BMC Bioinformatics.

[20]  Lei Zhou,et al.  BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences , 2007, Bioinform..

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[22]  Tao Chen,et al.  Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats , 2007, BMC Bioinformatics.

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[24]  Andrey A. Ptitsyn,et al.  Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway , 2007, BMC Bioinformatics.

[25]  Iftekhar Amin,et al.  Preliminary nanopore cheminformatics analysis of aptamer-target binding strength , 2007, BMC Bioinformatics.

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[29]  Dong Xu,et al.  Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate , 2008, BMC Bioinformatics.

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[31]  Luonan Chen,et al.  Inferring transcriptional regulatory networks from high-throughput data , 2007, Bioinform..

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[35]  Jake Yue Chen,et al.  ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining , 2008, BMC Bioinformatics.

[36]  Stephen Winters-Hilt,et al.  Hybrid MM/SVM structural sensors for stochastic sequential data , 2008, BMC Bioinformatics.

[37]  Joo Chuan Tong,et al.  Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage , 2008, BMC Bioinformatics.

[38]  Bindu Nanduri,et al.  Prediction of peptides observable by mass spectrometry applied at the experimental set level , 2007, BMC Bioinformatics.

[39]  Andrey A. Ptitsyn.  Comprehensive analysis of circadian periodic pattern in plant transcriptome , 2008, BMC Bioinformatics.

[40]  Rasiah Loganantharaj,et al.  Towards validating the hypothesis of phylogenetic profiling , 2007, BMC Bioinformatics.

[41]  Jean-Loup Faulon,et al.  Boolean dynamics of genetic regulatory networks inferred from microarray time series data , 2007, Bioinform..

[42]  Mutlu Mete,et al.  Automatic delineation of malignancy in histopathological head and neck slides , 2007, BMC Bioinformatics.

[43]  H. K. Dai,et al.  A survey of DNA motif finding algorithms , 2007, BMC Bioinformatics.

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[46]  Dan Schonfeld,et al.  Time-dependent ARMA modeling of genomic sequences , 2008, BMC Bioinformatics.

[47]  Laura K. Schnackenberg,et al.  Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis , 2007, BMC Bioinformatics.

[48]  George Hripcsak,et al.  Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial study. , 2008, Journal of the American Medical Informatics Association : JAMIA.

[49]  Kai Wang,et al.  Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks , 2007, ISMB/ECCB.

[50]  Jonathan D. Wren,et al.  Clustering microarray-derived gene lists through implicit literature relationships , 2007, Bioinform..

[51]  Ute Baumann,et al.  A framework for gene expression analysis , 2007, Bioinform..

[52]  Alexander G. Churbanov,et al.  Clustering ionic flow blockade toggles with a Mixture of HMMs , 2008, BMC Bioinformatics.

[53]  Mikhail G. Dozmorov,et al.  From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells , 2008, BMC Bioinformatics.

[54]  Stephen Winters-Hilt,et al.  A novel, fast, HMM-with-Duration implementation – for application with a new, pattern recognition informed, nanopore detector , 2007, BMC Bioinformatics.

[55]  Xiaowei Xu,et al.  A structural approach for finding functional modules from large biological networks , 2008, BMC Bioinformatics.

[56]  Yang Huang,et al.  A novel hybrid approach to automated negation detection in clinical radiology reports. , 2007, Journal of the American Medical Informatics Association : JAMIA.

[57]  Hongfang Liu,et al.  Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging , 2006, J. Am. Medical Informatics Assoc..

[58]  Xujing Wang,et al.  TAPPA: topological analysis of pathway phenotype association , 2007, Bioinform..

[59]  Sean R. Davis,et al.  GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor , 2007, Bioinform..

[60]  Mikhail G. Dozmorov,et al.  Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis , 2007, BMC Bioinformatics.

[61]  Cory B. Giles,et al.  Large-scale directional relationship extraction and resolution , 2008, BMC Bioinformatics.

[62]  Stephen Winters-Hilt,et al.  SVM clustering , 2007, BMC Bioinformatics.

[63]  Nan Wang,et al.  ProtQuant: a tool for the label-free quantification of MudPIT proteomics data , 2007, BMC Bioinformatics.

[64]  Tao Han,et al.  Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples , 2008, BMC Bioinformatics.

[65]  Shipra Agrawal,et al.  CREMOFAC - a database of chromatin remodeling factors , 2006, Bioinform..

[66]  Tao Chen,et al.  Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver , 2007, BMC Bioinformatics.

[67]  Yuanyuan Ding,et al.  Robust clustering in high dimensional data using statistical depths , 2007, BMC Bioinformatics.

[68]  Kai Li,et al.  Exploring the functional landscape of gene expression: directed search of large microarray compendia , 2007, Bioinform..

[69]  João Ricardo Sato,et al.  Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method , 2007, Bioinform..

[70]  Ge Gao,et al.  DPTF: a database of poplar transcription factors , 2007, Bioinform..

[71]  Eytan Domany,et al.  STOP: searching for transcription factor motifs using gene expression , 2007, Bioinform..

[72]  Alexander J. Hartemink,et al.  Informative priors based on transcription factor structural class improve de novo motif discovery , 2006, ISMB.

[73]  Peter Szolovits,et al.  Evaluating the state-of-the-art in automatic de-identification. , 2007, Journal of the American Medical Informatics Association : JAMIA.

[74]  Arun Rawat,et al.  Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data , 2008, BMC Bioinformatics.

[75]  John J. Thaden,et al.  An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks , 2008, BMC Bioinformatics.

[76]  Joshua S. Yuan,et al.  Statistical tools for transgene copy number estimation based on real-time PCR , 2007, BMC Bioinformatics.

[77]  Peter J Bentley,et al.  Methods for improving simulations of biological systems: systemic computation and fractal proteins , 2009, Journal of The Royal Society Interface.

[78]  Carl Baribault,et al.  Duration learning for analysis of nanopore ionic current blockades , 2007, BMC Bioinformatics.

[79]  Zhiwen Yu,et al.  Graph-based consensus clustering for class discovery from gene expression data , 2007, Bioinform..

[80]  Arnoldo Frigessi,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm305 Gene expression Predicting survival from microarray data—a comparative study , 2022 .

[81]  Joaquín Dopazo,et al.  Functional profiling of microarray experiments using text-mining derived bioentities , 2007, Bioinform..

[82]  Iftekhar Amin,et al.  Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding , 2007, BMC Bioinformatics.

[83]  Andrey A. Ptitsyn,et al.  Systems biology approach to identification of biomarkers for metastatic progression in cancer , 2008, BMC Bioinformatics.