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Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

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Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: Combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

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Modeling gene expression control using Omes Law

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Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes

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Identifying genetic regulatory variants that affect transcription factor activity

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Modelling Transcriptional Regulation with a Mixture of Factor Analyzers and Variational Bayesian Expectation Maximization

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SVMotif: A Machine Learning Motif Algorithm

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A Biophysical Model for Identifying Splicing Regulatory Elements and Their Interactions

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Sequence information gain based motif analysis

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Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters

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Statistical Methods for Inference of Genetic Networks and Regulatory Modules

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Epigenetic regulation of cis-regulatory elements and transcription factors during development

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Learning Hidden Markov Models for Regression using Path Aggregation

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The EM Algorithm and the Rise of Computational Biology

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MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs

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iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species

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Polynomial and RBF Kernels as Marker Selection Tools-A Breast Cancer Case Study

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Modeling Cooperative Gene Regulation Using Fast Orthogonal Search

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Statistical Methods in Bioinformatics

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Machine learning for multimodality genomic signal processing

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Sequence Motifs in Ranked Expression Data

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Hormonal crosstalk during the reproductive stage of Coffea arabica: interactions among gibberellin, abscisic acid, and ethylene

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An overview of recent developments in genomics and associated statistical methods

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Identifying Regulatory Sites Using Neighborhood Species

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Grid Methodology for Identifying Co-Regulated Genes and Transcription Factor Binding Sites

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A PARALLEL SCHEME FOR COMPARING TRANSCRIPTION FACTOR BINDING SITES MATRICES

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Screening and Clustering of Sparse Regressions with Finite Non-Gaussian Mixtures

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Bioinformatic identification of novel putative photoreceptor specific cis-elements

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Modelling and identification of transcription-factor binding motifs in human chondrogenesis

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Validating a Threshold-Based Boolean Model of Regulatory Networks on a Biological Organism

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Beyond the Gene List: Exploring Transcriptomics Data in Search for Gene Function, Trait Mechanisms and Genetic Architecture

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Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation

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Hypothesis testing in finite mixture of regressions: Sparsity and model selection uncertainty

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Integrating biological information into the statistical analysis and design of microarray experiments

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c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

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SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing

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Statistical methods for joint data mining of gene expression and DNA sequence database

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Model the Relationship Between Gene Expression and TFBSs Using a Simplified Neural Network with Bayesian Variable Selection

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Towards ubiquitous bio-information computing: data protocols, middleware, and Web services for heterogeneous biological information integration and retrieval

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Discovering Transcriptional Regulatory Rules from Gene Expression and TF-DNA Binding Data by Decision Tree Learning

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A continuous-index Bayesian hidden Markov model for prediction of nucleosome positioning in genomic DNA

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A simple yet powerful test for assessing goodness‐of‐fit of high‐dimensional linear models

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Quantifying the tissue-specific regulatory information within enhancer DNA sequences

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Shared transcription factors contribute to distinct cell fates

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Transcription Factor Binding Site Identification by Phylogenetic Footprinting

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Statistical Approaches to Use a Model Organism for Regulatory Sequences Annotation of Newly Sequenced Species

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Computational approaches, databases and tools for in silico motif discovery

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Identifying Transcription Regulatory Elements in the Human and Mouse Genomes Using Tissue-specific Gene Expression Profiles

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DNA regulatory motif selection based on support vector machine (SVM) and its application in microarray experiment of Kashin-Beck disease

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Componentwise variable selection in finite mixture regression

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Measures of Uncertainty for Shrinkage Model Selection

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Extracting sequence features to predict protein–DNA interactions: a comparative study

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The identification of functional motifs in temporal gene expression analysis

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Inferring Transcription Factor interactions using a novel HV-SVM classifier

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Prediction of Gene Expression Levels and the Role of Cis-Acting Elements in Age-Related Cataract by Applying a Promoter-Based Modeling Approach

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Mining Regulatory Elements in the Plasmodium falciparum Genome Using Gene Expression Data

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Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates

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Variable selection procedures from multiple testing

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The LASSO path as a feature importance proxy

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Motif Location Prediction by Divide and Conquer

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PeakRegressor Identifies Composite Sequence Motifs Responsible for STAT1 Binding Sites and Their Potential rSNPs

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Combining Replicates and Nearby Species Data: A Bayesian Approach

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A Sequential Rejection Testing Method for High-Dimensional Regression with Correlated Variables

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Mining Low-Variance Biclusters to Discover Coregulation Modules in Sequencing Datasets

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Prioritize Transcription Factor Binding Sites for Multiple Co-Expressed Gene Sets Based on Lasso Multinomial Regression Models

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Modelling Transcriptional Regulation with a Mixture of Factor Analyzers and Variational Bayesian Expectation Maximization

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XPRIME: A Method Incorporating Expert Prior Information into Motif Exploration

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Inferring Genetic Regulatory Interactions with Bayesian Logic-Based Model

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Robust Semiparametric Regression Estimation Using Targeted Maximum Likelihood with Application to Biomarker Discovery and Epidemiology

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Sequence Pattern Discovery with Applications to Understanding Gene Regulation and Vaccine Design

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From DNA Motifs to Gene Networks: A Review of Physical Interaction Models

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Computational Molecular Biology of Genome Expression and Regulation

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Functional in Silico Analysis of Gene Regulatory Polymorphism

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Bayesian Variable Selection for Gene Expression Modeling With Regulatory Motif Binding Sites in Neuroinflammatory Events

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Including transcription factor information in the superparamagnetic clustering of microarray data

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Node harvest: simple and interpretable regression and classicationPreprint

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Integrative Modeling and Analysis of High-throughput Biological Data

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SArKS: de novo discovery of gene expression regulatory motifs and domains by suffix array kernel smoothingPreprint

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Sparse regression and marginal testing using cluster prototypesPreprint

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Emergence de structures modulaires dans les régulations des systèmes biologiques : théorie et applications à Bacillus subtilis

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Predictive Models of Gene Regulation

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High-dimensional regression problems with special structure

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Algorithms for String Pattern Discovery

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Nucleic Acid and Protein Sequence Analysis and Bioinformatics

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Targeting Differentially Co-regulated Genes by Multiobjective and Multimodal Optimization

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Statistical Network Analysis for Biological Systems and Pathways

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A Vocabulon Study of E.Coli Regulatory Sites with Feedback to Expression Array Analysis

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Improving Thermodynamic Models of Transcription by Combining ChIP and Expression Measurements of Synthetic Promoters

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Motifs, binding, and expression : computational studies of transcriptional regulation

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High‐Throughput Technologies and Functional Genomics

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Statistical Learning and Modeling of TF-DNA Binding

Jiang, B., & Liu, J. S. (2011) · Springer eBooks · doi:10.1007/978-3-642-16345-6_3

PlasmoTFBM: An Intelligent Queriable Database for Predicted Transcription Factor Binding Motifs in Plasmodium falciparum

Yang, C., Zeng, E., Mathee, K., & Narasimhan, G. (2007) · Springer eBooks · doi:10.1007/978-0-387-34569-7_9

UBIC2 — TOWARDS UBIQUITOUS BIO-INFORMATION COMPUTING: DATA PROTOCOLS, MIDDLEWARE, AND WEB SERVICES FOR HETEROGENEOUS BIOLOGICAL INFORMATION INTEGRATION AND RETRIEVAL

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A METHODOLOGY FOR MOTIF DISCOVERY EMPLOYING ITERATED CLUSTER RE-ASSIGNMENT

Abul, O., Drabløs, F., & Sandve, G. K. (2006) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1142/9781860947575_0032

Analysis of Cis-acting Regulatory Motifs Involved in Alternative Splicing

Zhao, S. (2009) · NCSU Libraries Repository (North Carolina State University Libraries)

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

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MotifScorer: using a compendium of microarrays to identify regulatory motifs

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Regulatory element detection using correlation with expression

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Development of Software Facilities to Characterize Regulatory Binding Motifs and Application to Streptococcaceae

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Detecting Transcriptional cis-Regulation from Gene Expression Data

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