BMC Bioinformatics Journal

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An improved algorithm for flux variability analysis.. 23:550. 2022
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data.. 21:562. 2020
Compositional zero-inflated network estimation for microbiome data.. 21:581. 2020
Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles.. 20:725. 2019
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression.. 20:603-603:1. 2019
Optimal clustering with missing values.. 20:321. 2019
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).. 20:316. 2019
Local edge-enhanced active contour for accurate skin lesion border detection.. 20:91. 2019
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.. 19:450-450:1. 2018
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models.. 19:80. 2018
A Bayesian approach to determine the composition of heterogeneous cancer tissue.. 19:90. 2018
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).. 19:69. 2018
Simulating variance heterogeneity in quantitative genome wide association studies.. 19:72. 2018
Bayesian graphical models for computational network biology.. 19:63. 2018
Phage spanins: diversity, topological dynamics and gene convergence.. 19:326. 2018
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors.. 18:552. 2017
Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm.. 18:328-328. 2017
Towards targeted combinatorial therapy design for the treatment of castration-resistant prostate cancer.. 18:134. 2017
An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data.. 18:94. 2017
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.. 18:519. 2017
CUFID-query: accurate network querying through random walk based network flow estimation.. 18:500. 2017
Effective computational detection of piRNAs using n-gram models and support vector machine.. 18:517. 2017
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).. 18:159. 2017
Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images.. 17:367. 2016
Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach.. 17:357. 2016
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model.. 17:395. 2016
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network.. 17:351. 2016
Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides.. 16 Suppl 13:S12. 2015
Dynamical modeling of uncertain interaction-based genomic networks.. 16 Suppl 13:S3. 2015
Efficient experimental design for uncertainty reduction in gene regulatory networks.. 16 Suppl 13:S2. 2015
Density-based parallel skin lesion border detection with webCL.. 16 Suppl 13:S5. 2015
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain.. 16:147. 2015
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks.. 16:410. 2015
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.. 15:401. 2014
Automated identification of cell-type-specific genes in the mouse brain by image computing of expression patterns.. 15:209. 2014
A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis.. 14:372. 2013
Image-level and group-level models for Drosophila gene expression pattern annotation.. 14:350. 2013
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data.. 14:303-303. 2013
Modeling the next generation sequencing sample processing pipeline for the purposes of classification.. 14:307. 2013
Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering.. 14:222. 2013
Normalization and missing value imputation for label-free LC-MS analysis.. 13 Suppl 16:S5. 2012
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses.. 13 Suppl 15:S8. 2012
Guest editors' introduction.. 13 Suppl 10:S1. 2012
Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval.. 13:107. 2012
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.. 13:253. 2012
An improved border detection in dermoscopy images for density based clustering.. 12 Suppl 10:S12. 2011
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores.. 12 Suppl 10:S6. 2011
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.. 12 Suppl 10:S5. 2011
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty.. 12 Suppl 10:S9. 2011
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.. 12 Suppl 10:S1. 2011
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception.. 12 Suppl 1:S19. 2011
HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.. 12 Suppl 1:S43. 2011
Gene set analysis for longitudinal gene expression data.. 12:273. 2011
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data.. 11 Suppl 9:S12. 2010
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum.. 11 Suppl 6:S12. 2010
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network.. 11 Suppl 6:S8. 2010
BPDA - a Bayesian peptide detection algorithm for mass spectrometry.. 11:490. 2010
Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach.. 11:13-13. 2010
Automatic identification of angiogenesis in double stained images of liver tissue.. 10 Suppl 11:S13. 2009
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. 10. 2009
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.. 10 Suppl 11:S3. 2009
Novel software package for cross-platform transcriptome analysis (CPTRA).. 10 Suppl 11:S16. 2009
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 10. 2009
A bag-of-words approach for Drosophila gene expression pattern annotation.. 10:119. 2009
Ontology driven integration platform for clinical and translational research.. 10 Suppl 2:S2. 2009
Bayesian modeling of ChIP-chip data using latent variables.. 10:352. 2009
Identifying significant temporal variation in time course microarray data without replicates.. 10:96. 2009
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.. 10:332. 2009
Sample entropy analysis of cervical neoplasia gene-expression signatures.. 10:66. 2009
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures.. 9:398. 2008
A structural approach for finding functional modules from large biological networks.. 9 Suppl 9:S19. 2008
An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks.. 9 Suppl 9:S15. 2008
Adaptive diffusion kernel learning from biological networks for protein function prediction.. 9:162. 2008
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.. 9:320. 2008
Automatic delineation of malignancy in histopathological head and neck slides.. 8 Suppl 7:S17. 2007
PeanutMap: an online genome database for comparative molecular maps of peanut.. 7:375. 2006
Noise-injected neural networks show promise for use on small-sample expression data.. 7:274. 2006
The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci.. 7:283. 2006
MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.. 6:64-64.
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis. 2012