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Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd) Research article Min Xie1†, Ying Huang1†, Yanping Zhang1, Xin Wang1, Hua Yang2, Oliver Yu2, Wenhao Dai3 and Congbing Fang12* * Corresponding author: Congbing Fang fcb_ah@ahau.edu.cn † Equal contributors.

Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd)

Enhancement of Accuracy and Efficiency for RNA Secondary Structure Prediction by Sequence Segmentation and MapReduce. Datasets and hardware platform For the study of both accuracy and performance, we plug seven RNA secondary structure prediction programs into our framework for both the chunk-based predictions and the predictions of the same sequences without chunking (the whole sequence is taken).

Enhancement of Accuracy and Efficiency for RNA Secondary Structure Prediction by Sequence Segmentation and MapReduce

Five of the programs, IPknot [24], pknotsRG [25], HotKnots [3], NUPACK [26], PKNOTS [8] can predict both stem-loops and pseudoknots. The remaining two programs, UNAFOLD [27] and RNAfold [28], can predict stem-loops only. We consider both the centered (C) and optimized (O) chunking methods and compare them against the naïve regular method (R) as a reference. We also consider a wide range of parameter settings with maximum chunk length c from 60 to 150 bases, minimum stem length L from 3 to 8, and maximum gap length G from 0 to 8. µHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix. Research article Sushmita Paul12 and Pradipta Maji12* * Corresponding author: Pradipta Maji pmaji@isical.ac.in Author Affiliations 1 Biomedical Imaging and Bioinformatics Lab, Indian Statistical Institute, 203, B.

µHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix

T. The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. Direct RNA sequencing mediated identification of mRNA localized in protrusions of human MDA-MB-231 metastatic breast cancer cells. BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles. A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon.

Research Jingyu Zhang, Zhiwei Mao and Kang Chong* * Corresponding author: Kang Chong chongk@ibcas.ac.cn.

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon

Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis. Research article Silvia Pizzini , Andrea Bisognin , Susanna Mandruzzato , Marta Biasiolo , Arianna Facciolli , Lisa Perilli , Elisabetta Rossi , Giovanni Esposito , Massimo Rugge , Pierluigi Pilati , Simone Mocellin , Donato Nitti , Stefania Bortoluzzi and Paola Zanovello For all author emails, please log on .

Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis

Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association. Research article Nandan P Deshpande1†, Nadeem O Kaakoush2†, Marc R Wilkins123 and Hazel M Mitchell2* * Corresponding author: Hazel M Mitchell H.Mitchell@unsw.edu.au † Equal contributors.

Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions. Research article Brian R Johnson1*, Joel Atallah1 and David C Plachetzki2 * Corresponding author: Brian R Johnson brnjohnson@ucdavis.edu Author Affiliations 1 Department of Entomology, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA 2 Department of Ecology and Evolution, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA For all author emails, please log on.

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions

Identification of differential expression genes associated with host selection and adaptation between two sibling insect species by transcriptional profile analysis. Research article Haichao Li12, Hao Zhang12, Ruobing Guan12 and Xuexia Miao1* * Corresponding author: Xuexia Miao xxm@sippe.ac.cn Author Affiliations.

Identification of differential expression genes associated with host selection and adaptation between two sibling insect species by transcriptional profile analysis

Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data. RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. Research article Marc J Champigny1, Wilson WL Sung1, Vasile Catana1, Rupa Salwan1, Peter S Summers1, Susan A Dudley1, Nicholas J Provart2, Robin K Cameron1, G Brian Golding1 and Elizabeth A Weretilnyk1* * Corresponding author: Elizabeth A Weretilnyk weretil@mcmaster.ca.

RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments. Research Lorelei Bozo-Hurtado1, M Alexandra García-Amado2, Andrei Chistoserdov3, Ramon Varela4, J Jesus Narvaez4, Rita Colwell5 and Paula Suárez1* * Corresponding author: Paula Suárez pulisuarez@gmail.com Author Affiliations 1 Departamento de Biología de Organismos, Universidad Simón Bolívar, Caracas, Venezuela 2 Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. Software Yingtao Bi and Ramana V Davuluri* * Corresponding author: Ramana V Davuluri rdavuluri@wistar.org Author Affiliations Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, 19104 Philadelphia, PA, USA For all author emails, please log on.

Learning the language of post-transcriptional gene regulation. Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera. Research article Snehal B Bagatharia*, Madhvi N Joshi, Rohan V Pandya, Aanal S Pandit, Riddhi P Patel, Shivangi M Desai, Anu Sharma, Omkar Panchal, Falguni P Jasmani and Akshay K Saxena * Corresponding author: Snehal B Bagatharia snehalbagatharia@hotmail.com. A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. The root transcriptome for North American ginseng assembled and profiled across seasonal development.

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. Automated serial extraction of DNA and RNA from biobanked tissue specimens. Research article Lucy Mathot, Monica Wallin and Tobias Sjöblom* * Corresponding author: Tobias Sjöblom tobias.sjoblom@igp.uu.se. Identifying potential RNAi targets in grain aphid (Sitobion avenae F.) based on transcriptome profiling of its alimentary canal after feeding on wheat plants. Research article Min Zhang1†, Yuwen Zhou2†, Hui Wang1, Huw Dylan Jones3, Qiang Gao2, Dahai Wang1, Youzhi Ma1* and Lanqin Xia1* * Corresponding authors: Youzhi Ma mayouzhi@caas.cn - Lanqin Xia xialanqin@caas.cn † Equal contributors. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. Research article Matthew J Moody, Rachel A Young, Stephanie E Jones and Marie A Elliot* * Corresponding author: Marie A Elliot melliot@mcmaster.ca.

De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA.

Research article. Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome. RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium. Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling. Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness.

Research article. DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Genome-wide identification, molecular cloning, expression profiling and posttranscriptional regulation analysis of the Argonaute gene family in Salvia miltiorrhiza, an emerging model medicinal plant. Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing. Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa) The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. An integrated hierarchical Bayesian approach to normalizing left-censored microRNA microarray data.

REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. Blood RNA biomarker panel detects both left- and right-sided colorectal neoplasms: a case. GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-Seq data. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns. Methodology article. Deep brain stimulation modulates nonsense-mediated RNA decay in Parkinson's patients leukocytes. Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq.

MicroRNAome profiling in benign and malignant neurofibromatosis type 1-associated nerve sheath tumors: evidences of PTEN pathway alterations in early NF1 tumorigenesis. Analysis and annotation of the hexaploid oat seed transcriptome. A stable CC-chemokine receptor (CCR)-5 tropic virus is correlated with the persistence of HIV RNA at less than 2.5 copies in successfully treated naive subjects. NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. TCC: an R package for comparing tag count data with robust normalization strategies. KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella. RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping.

Impact of heat shock transcription factor 1 on global gene expression profiles in cells which induce either cytoprotective or pro-apoptotic response following hyperthermia. Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates. Comparing somatic mutation-callers: Beyond Venn diagrams. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes. Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization. HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. RNAalifold: improved consensus structure prediction for RNA alignments. Deconvolution of gene expression from cell populations across the C. elegans lineage. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.

Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis) A special bioinformatics challenge for DNA Day – open to all. BioMed Central blogs network. The role of the RNA chaperone Hfq in Haemophilus influenzae pathogenesis. The Open Access Publisher. A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases. RNAalifold: improved consensus structure prediction for RNA alignments. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. Transposable elements reveal a stem cell specific class of long noncoding RNAs. Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools.