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All students should keep an eye on this page for updates and headlines in the main publications venues where computational genomics results are reported.

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Bioinformatics - recent issues Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data Shimmer: detection of genetic alterations in tumors using next-generation sequence data Predicting the functional consequences of cancer-associated amino acid substitutions An HMM-based algorithm for evaluating rates of receptor-ligand binding kinetics from thermal fluctuation data A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number A powerful and efficient set test for genetic markers that handles confounders Learning gene network structure from time laps cell imaging in RNAi Knock downs A multi-layer inference approach to reconstruct condition-specific genes and their regulation	BMC Bioinformatics - Latest Articles SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins Incorporating time-delays in S-System model for reverse engineering genetic networks Quantifying single nucleotide variant detection sensitivity in exome sequencing bioNerDS: exploring bioinformatics' database and software use through literature mining FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq Boosting forward-time population genetic simulators through genotype compression KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain Utilizing protein structure to identify non-random somatic mutations	Briefings in Bioinformatics - current issue Obituary: In memory of Jack Leunissen Joint analysis of miRNA and mRNA expression data A comparative analysis of biclustering algorithms for gene expression data A reversed framework for the identification of microRNA-target pairs in plants A statistical procedure to map high-order epistasis for complex traits Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes Automated glycopeptide analysis--review of current state and future directions Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data
Journal of Computational Biology - Table of Contents Catching the Genomic Wave in Oligonucleotide Single-Nucleotide Polymorphism Arrays by Modeling Sequence Binding An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids Exploiting Genome Structure in Association Analysis HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking Prediction of siRNA Potency Using Sparse Logistic Regression Biological Cluster Evaluation for Gene Function Prediction Data Structures for Parsimony Correlation and Biosequence Co-Evolution A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign On Contigs and Coverage CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data	IEEE/ACM Transactions on Computational Biology and Bioinformatics PrePrint: Utilizing Both Topological and Attribute Information for Protein Coplex Identification in PPI Networks PrePrint: FNphasing: A Novel Fast Heuristic Algorithm for Haplotype Phasing Based on Flow Network Model PrePrint: Operon Prediction using Chaos Embedded Particle Swarm Optimization PrePrint: Multivariate Hypergeometric Similarity Measure PrePrint: Biological Sequence Analysis with Multivariate String Kernels PrePrint: Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis PrePrint: Mining Featured Patterns of MiRNA Interaction based on Sequence and Structure Similarity PrePrint: Mining Quasi-Bicliques from HIV-1--Human Protein Interaction Network: A Multiobjective Biclustering Approach PrePrint: Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing IEEE/ACM Transactions on Computational Biology and Bioinformatics -