Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference

Introduction The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS’2011) was held in College Station, Texas on April 1-2, 2011. The Conference General Chair was Ulisses Braga-Neto, the MCBIOS President for the 2010-2011 term, from Texas A&M University. There were nearly 200 registrants and 140 abstracts were submitted, divided into 48 oral presentation abstracts and 92 poster session abstracts. In addition, participants attended talks by very distinguished Keynote speakers. Joan W. Bennett, from Rutgers University and Member of the National Academy of Science, presented the talk “Chromosomal Composition and Computational Competence;” Donald Geman, from The Johns Hopkins University and co-inventor of the Gibbs Sampler and Random Forest Classifiers, lectured on “Measuring Network Regulation and Differential Expression by Rank Conservation;” while John Weinstein, Chair of the Department of Bioinformatics and Computational Biology at the University of Texas M.D. Anderson Cancer Center, talked on “Personalizing Cancer Medicine in the Era of Next-Generation Sequencing: Omics and Informatics.” The conference also benefited from invited dinner and lunch speakers, who gave informal, highly informative and entertaining talks. Edward R. Dougherty, from Texas A&M University and Director of Computational Biology at the Translational Genomics Institute, asked the audience “Is Biological Science Delightful?” whereas Ernesto Marques, from the Center for Vaccine Research at the University of Pittsburgh, gave the talk “Activation of the Complement System in Dengue Infection: Opportunities for Computational Modeling.” Participants also had the opportunity to attend handson workshops on NCBI tools, presented by Peter Cooper from NCBI/NIH, and on protein evolution, presented by Hugh Nicholas and Troy Wymore, from the Pittsburgh Supercomputing Center. The winners of conference awards were: Best Oral Presentations (students): First place: Suzanne Matthews, Texas A&M University Second place (3-way tie): Lori Dalton, Texas A&M University Second place: Shelton Griffith, Oak Ridge National Lab Second place: Winston Haynes, Hendrix College Best Oral Presentations (Post-Doctoral fellows): Yan Li, NCTR Fan Zhang, IUPUI Best Poster (Computation): First place: Tianchuan Du, Southern University Second place: Christopher Cathey, Jackson State University Third place: Ralph Crosby, Texas A&M University Best Poster (Biology): First place: Awantika Singh, UALR/UAMS Second place: Mohammed Shahrokh Esfahani, Texas A&M University Third place: Fang-Han Hsu, Texas A&M University MCBIOS Outstanding Service Award: Dr. Jonathan D. Wren, Oklahoma Medical Research Foundation * Correspondence: jdwren@gmail.com Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation; 825 N.E. 13th Street, Oklahoma City, OK 73104-5005, USA Full list of author information is available at the end of the article Wren et al. BMC Bioinformatics 2011, 12(Suppl 10):S1 http://www.biomedcentral.com/1471-2105/12/S10/S1

[1]  Michael D. McMullen,et al.  IView: introgression library visualization and query tool , 2010, BMC Bioinformatics.

[2]  Mikhail G. Dozmorov,et al.  Predicting gene ontology from a global meta-analysis of 1-color microarray experiments , 2011, BMC Bioinformatics.

[3]  Weida Tong,et al.  Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project , 2011, BMC Bioinformatics.

[4]  James M. Watt,et al.  Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213 , 2012, BMC Bioinformatics.

[5]  Yuan Liu,et al.  Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer , 2017, BMC Bioinformatics.

[6]  Shuju Bai,et al.  Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate , 2010, BMC Bioinformatics.

[7]  Edward R. Dougherty,et al.  Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty , 2011, BMC Bioinformatics.

[8]  James J. Chen,et al.  An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays , 2010, BMC Bioinformatics.

[9]  Andrey A. Ptitsyn,et al.  Computational workflow for analysis of gain and loss of genes in distantly related genomes , 2012, BMC Bioinformatics.

[10]  Zang-Hee Cho,et al.  Validation of an arterial tortuosity measure with application to hypertension collection of clinical hypertensive patients , 2011, BMC Bioinformatics.

[11]  Sanmin Liu,et al.  Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses , 2012, BMC Bioinformatics.

[12]  Eric Morales,et al.  The NTD Nanoscope: potential applications and implementations , 2011, BMC Bioinformatics.

[13]  Mohsen Sharifi,et al.  Development of models for predicting Torsade de Pointes cardiac arrhythmias using perceptron neural networks , 2017, BMC Bioinformatics.

[14]  Preetam Ghosh,et al.  First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA , 2011, BMC Bioinformatics.

[15]  J. R. Daum,et al.  Ska3 Is Required for Spindle Checkpoint Silencing and the Maintenance of Chromosome Cohesion in Mitosis , 2009, Current Biology.

[16]  Changhe Yuan,et al.  Empirical evaluation of scoring functions for Bayesian network model selection , 2012, BMC Bioinformatics.

[17]  Quang Tran,et al.  Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities , 2017, BMC Bioinformatics.

[18]  Zhen Su,et al.  Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis , 2012, BMC Bioinformatics.

[19]  Mary Yang,et al.  Identification and characterization of conserved lncRNAs in human and rat brain , 2017, BMC Bioinformatics.

[20]  Chaoyang Zhang,et al.  Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks , 2010, BMC Bioinformatics.

[21]  Aleksandra Markovets,et al.  Analysis of cancer metabolism with high-throughput technologies , 2011, BMC Bioinformatics.

[22]  Zhen Su,et al.  Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization , 2012, BMC Bioinformatics.

[23]  Bindu Nanduri,et al.  HPIDB - a unified resource for host-pathogen interactions , 2010, BMC Bioinformatics.

[24]  Nicholas Petrick,et al.  Scaling bioinformatics applications on HPC , 2017, BMC Bioinformatics.

[25]  Mutlu Mete,et al.  Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images , 2010, BMC Bioinformatics.

[26]  Edward R. Dougherty,et al.  Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network , 2010, BMC Bioinformatics.

[27]  Edward R. Dougherty,et al.  Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors , 2017, BMC Bioinformatics.

[28]  Teresa W. Haynes,et al.  A predictive model for secondary RNA structure using graph theory and a neural network , 2010, BMC Bioinformatics.

[29]  Fan Zhang,et al.  HOMER: a human organ-specific molecular electronic repository , 2011, BMC Bioinformatics.

[30]  Xiaoning Qian,et al.  Effective computational detection of piRNAs using n-gram models and support vector machine , 2017, BMC Bioinformatics.

[31]  Shelton D. Griffith,et al.  Scenario driven data modelling: a method for integrating diverse sources of data and data streams , 2011, BMC Bioinformatics.

[32]  Weida Tong,et al.  Two new ArrayTrack libraries for personalized biomedical research , 2010, BMC Bioinformatics.

[33]  Samuel A. Smits,et al.  Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective , 2010, BMC Bioinformatics.

[34]  T. J. Jankun-Kelly,et al.  GOModeler- A tool for hypothesis-testing of functional genomics datasets , 2010, BMC Bioinformatics.

[35]  Fan Zhang,et al.  IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis , 2012, BMC Bioinformatics.

[36]  Michael W. Berry,et al.  Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization) , 2010, BMC Bioinformatics.

[37]  Bindu Nanduri,et al.  Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences , 2010, BMC Bioinformatics.

[38]  Arun Rawat,et al.  Quail Genomics: a knowledgebase for Northern bobwhite , 2010, BMC Bioinformatics.

[39]  Karl F. MacDorman,et al.  PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries , 2012, BMC Bioinformatics.

[40]  Diane J. Cook,et al.  BirdsEyeView (BEV): graphical overviews of experimental data , 2012, BMC Bioinformatics.

[41]  Yongsheng Bai,et al.  Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data , 2017, BMC Bioinformatics.

[42]  Mikhail G. Dozmorov,et al.  High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses , 2011, BMC Bioinformatics.

[43]  Tibor Pechan,et al.  Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide , 2012, BMC Bioinformatics.

[44]  Jun Huan,et al.  Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism , 2010, BMC Bioinformatics.

[45]  Lei Xu,et al.  The EDKB: an established knowledge base for endocrine disrupting chemicals , 2010, BMC Bioinformatics.

[46]  Xiaoning Qian,et al.  Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores , 2011, BMC Bioinformatics.

[47]  Xiaowei Xu,et al.  Constructing a robust protein-protein interaction network by integrating multiple public databases , 2011, BMC Bioinformatics.

[48]  Fan Zhang,et al.  PEPPI: a peptidomic database of human protein isoforms for proteomics experiments , 2010, BMC Bioinformatics.

[49]  Cyriac Kandoth,et al.  A framework for automated enrichment of functionally significant inverted repeats in whole genomes , 2010, BMC Bioinformatics.

[50]  Xiaoning Qian,et al.  CUFID-query: accurate network querying through random walk based network flow estimation , 2017, BMC Bioinformatics.

[51]  Intawat Nookaew,et al.  dBBQs : dataBase of Bacterial Quality scores , 2017 .

[52]  Tansel Halic,et al.  Texture based skin lesion abruptness quantification to detect malignancy , 2017, BMC Bioinformatics.

[53]  Lantao Liu,et al.  Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum , 2010, BMC Bioinformatics.

[54]  Ying Li,et al.  RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags , 2011, BMC Bioinformatics.

[55]  Zhen Su,et al.  Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function , 2010, BMC Bioinformatics.

[56]  Ying Wang,et al.  Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens , 2011, BMC Bioinformatics.

[57]  Preetam Ghosh,et al.  Dynamics of protofibril elongation and association involved in Aβ42 peptide aggregation in Alzheimer’s disease , 2010, BMC Bioinformatics.

[58]  Coskun Bayrak,et al.  Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR) surgery , 2010, BMC Bioinformatics.

[59]  Mutlu Mete,et al.  An improved border detection in dermoscopy images for density based clustering , 2011, BMC Bioinformatics.

[60]  Edward R. Dougherty,et al.  A CoD-based stationary control policy for intervening in large gene regulatory networks , 2011, BMC Bioinformatics.

[61]  Charles Bland,et al.  Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks , 2010, BMC Bioinformatics.

[62]  Susan M. Bridges,et al.  Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize , 2010, BMC Bioinformatics.

[63]  Jake Yue Chen,et al.  Repositioning drugs by targeting network modules: a Parkinson’s disease case study , 2017, BMC Bioinformatics.

[64]  Intawat Nookaew,et al.  Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? , 2017, BMC Bioinformatics.

[65]  Michael W. Berry,et al.  Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets , 2011, BMC Bioinformatics.

[66]  Preetam Ghosh,et al.  A Modified Stokes-Einstein Equation for A Beta Aggregation , 2016 .

[67]  Yixin Chen,et al.  Implementation of multiple-instance learning in drug activity prediction , 2012, BMC Bioinformatics.

[68]  Ruchi Verma,et al.  A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins , 2012, BMC Bioinformatics.

[69]  Suzanne J. Matthews,et al.  An efficient and extensible approach for compressing phylogenetic trees , 2011, BMC Bioinformatics.

[70]  Charles Wang,et al.  Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples , 2010, BMC Bioinformatics.

[71]  Jonathan D. Wren,et al.  A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide , 2009, Bioinform..

[72]  Daniel Quest,et al.  Next generation models for storage and representation of microbial biological annotation , 2010, BMC Bioinformatics.

[73]  Xiaowei Xu,et al.  Investigating drug repositioning opportunities in FDA drug labels through topic modeling , 2012, BMC Bioinformatics.

[74]  Chaoyang Zhang,et al.  Deep learning architectures for multi-label classification of intelligent health risk prediction , 2017, BMC Bioinformatics.

[75]  Mutlu Mete,et al.  Lesion detection in demoscopy images with novel density-based and active contour approaches , 2010, BMC Bioinformatics.

[76]  Yixin Chen,et al.  Leveraging domain information to restructure biological prediction , 2011, BMC Bioinformatics.

[77]  Cory B. Giles,et al.  ALE: automated label extraction from GEO metadata , 2017, BMC Bioinformatics.

[78]  Ulrich Melcher,et al.  Assessing constancy of substitution rates in viruses over evolutionary time , 2010, BMC Bioinformatics.

[79]  Xiaowei Xu,et al.  Mining FDA drug labels using an unsupervised learning technique - topic modeling , 2011, BMC Bioinformatics.