Abstract | Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. Abstract | 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 Author Affiliations 1 School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui, P R China 2 Key Laboratory of Tea Biochemistry & Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P R China 3 Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA For all author emails, please log on.
BMC Genomics 2013, 14:823 doi:10.1186/1471-2164-14-823 Published: 23 November 2013 Abstract Background Pear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Results Conclusion close Sign up to receive new article alerts from BMC Genomics. BMC Structural Biology | Full text | 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).
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. To study the framework accuracy, we use two datasets of sequences which have previously established secondary structures. Accuracy Figure 13. Figure 14. Table 1. Table 2. Figure 15. Abstract | 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.
T. Road, Kolkata, 700108, India 2 Machine Intelligence Unit, Indian Statistical Institute, 203, B. For all author emails, please log on. BMC Bioinformatics 2013, 14:266 doi:10.1186/1471-2105-14-266 Published: 4 September 2013 Abstract Background The miRNAs, a class of short approximately 22‐nucleotide non‐coding RNAs, often act post‐transcriptionally to inhibit mRNA expression. Results In this regard, a new miRNA selection algorithm, called μHEM, is presented based on rough hypercuboid approach. Conclusions Keywords: MicroRNA; Feature selection; Rough hypercuboid; Bootstrap error; Support vector machine close Sign up to receive new article alerts from BMC Bioinformatics. Abstract | The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci.
Abstract | Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. Journal of Molecular Signaling | Abstract | Direct RNA sequencing mediated identification of mRNA localized in protrusions of human MDA-MB-231 metastatic breast cancer cells. Abstract | 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 Author Affiliations Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China For all author emails, please log on. Genome Biology 2013, 14:R92 doi:10.1186/gb-2013-14-8-r92 Published: 30 August 2013 Abstract Background mRNA degradation is a critical factor in determining mRNA abundance and enables rapid adjustment of gene expression in response to environmental stress.
Results Here, we perform a global study of uncapped mRNAs, via parallel analysis of RNA ends (PARE), under cold stress in Brachypodium distachyon. Conclusion To our knowledge, this is the first global analysis of mRNA degradation under environmental stress conditions in Brachypodium distachyon. Keywords: mRNA stability; decapping; cold stress; PARE; Brachypodium distachyon close Sign up to receive new article alerts from Genome Biology. Abstract | 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 . BMC Genomics 2013, 14 :589 doi:10.1186/1471-2164-14-589 Published: 29 August 2013 Abstract (provisional) Background Qualitative alterations or abnormal expression of microRNAs (miRNAs) in colon cancer have mainly been demonstrated in primary tumors.
Results Most changes in miRNA and gene expression levels had already manifested in the primary tumors while these levels were almost stably maintained in the subsequent primary tumor-to-metastasis transition. Conclusions Using a large dataset of CRC miRNA and gene expression profiles, we describe the interplay of miRNA groups in regulating gene expression, which in turn affects modulated pathways that are important for tumor development. Abstract | 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 Author Affiliations 1 Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia 2 School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia 3 Ramaciotti Centre for Gene Function Analysis, The University of New South Wales, Sydney 2052, NSW, Australia For all author emails, please log on.
BMC Genomics 2013, 14:585 doi:10.1186/1471-2164-14-585 Published: 28 August 2013 Abstract Background In spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of Campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. Results Conclusion Keywords: close. Abstract | 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.
BMC Genomics 2013, 14:586 doi:10.1186/1471-2164-14-586 Published: 28 August 2013 Abstract Background A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Results We focus on two structures in the honey bee (the sting gland and digestive tract) both contained within one larger structure, the whole abdomen. Conclusions Many RNA-seq studies currently use composite extractions, and even whole insect extractions, when tissue and structure specific extractions are possible. Keywords: RNA-seq; Tissue specificity; Genomics close. Abstract | 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 1 Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China 2 University of Chinese Academy of Sciences, Beijing 100049, China For all author emails, please log on. BMC Genomics 2013, 14:582 doi:10.1186/1471-2164-14-582 Published: 28 August 2013 Abstract Background Cotton bollworm (Helicoverpa armigera) and oriental tobacco budworm (Helicoverpa assulta) are noctuid sibling species.
Results According to the gene annotation results, we identified 83 and 68 olfaction related transcripts from H. armigera and H. assulta, respectively. Conclusions This study supplied some differentially expressed genes affecting host selection and adaptation between the two sibling species. Keywords: close. Abstract | Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data. Abstract | 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 Author Affiliations 1 Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada 2 Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada For all author emails, please log on. BMC Genomics 2013, 14:578 doi:10.1186/1471-2164-14-578 Published: 28 August 2013 Abstract Background The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions.
Results Conclusion Keywords: close Sign up to receive new article alerts from BMC Genomics. Aquatic Biosystems | Abstract | 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 3 Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA 4 EDIMAR, Fundación La Salle, Margarita, Venezuela 5 University of Maryland, College Park, Maryland, USA For all author emails, please log on.
Aquatic Biosystems 2013, 9:17 doi:10.1186/2046-9063-9-17 Published: 28 August 2013 Abstract Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Results Conclusions Keywords: close. Abstract | 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.
BMC Bioinformatics 2013, 14:262 doi:10.1186/1471-2105-14-262 Published: 27 August 2013 Abstract Background RNA-seq, a massive parallel-sequencing-based transcriptome profiling method, provides digital data in the form of aligned sequence read counts. Results We developed a novel nonparametric empirical Bayesian-based approach (NPEBseq) to model the RNA-seq data. Conclusions NPEBseq can successfully detect differential expression between different conditions not only at gene level but also at exon level from RNA-seq datasets.
Close Sign up to receive new article alerts from BMC Bioinformatics. Learning the language of post-transcriptional gene regulation. Abstract | 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 Author Affiliations Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India For all author emails, please log on.
BMC Genomics 2013, 14:572 doi:10.1186/1471-2164-14-572 Published: 23 August 2013 Abstract Background The origin, evolution and speciation of the lion, has been subject of interest, debate and study. Results The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Conclusion This work presents first report on complete mitogenome of Panthera leo persica. Keywords: Asiatic lion; Big cats; Panthera leo persica; Mitogenome; Ion torrent; Phylogeny; Evolution; Felidae; Divergence time close. Abstract | A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. Abstract | The root transcriptome for North American ginseng assembled and profiled across seasonal development. Abstract | De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Biotechnology | Abstract | 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 Author Affiliations Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85, Uppsala, Sweden For all author emails, please log on. BMC Biotechnology 2013, 13:66 doi:10.1186/1472-6750-13-66 Published: 19 August 2013 Abstract Background With increasing biobanking of biological samples, methods for large scale extraction of nucleic acids are in demand. Results 864 fresh-frozen human normal and tumor tissue samples from breast and colon were serially extracted in batches of 96 samples. Conclusions The technology described here enables the processing of many tissue samples simultaneously with a high quality product and a time and cost reduction for the user. Keywords: Nucleic acid extraction; Cancer; Open automation; Sample preparation; Tissue biobanking close Sign up to receive new article alerts from BMC Biotechnology.
Abstract | 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 Author Affiliations 1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China 2 Beijing Genomics Institute-Shenzhen (BGI-Shenzhen), Chinese Academy of Sciences, Shenzhen 518083, China 3 Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK For all author emails, please log on.
BMC Genomics 2013, 14:560 doi:10.1186/1471-2164-14-560 Published: 16 August 2013 Abstract Background The grain aphid (Sitobion avenae F.) is a major agricultural pest which causes significant yield losses of wheat in China, Europe and North America annually. Results Conclusions Keywords: close Sign up to receive new article alerts from BMC Genomics. Abstract | 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 Author Affiliations Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada For all author emails, please log on.
BMC Genomics 2013, 14:558 doi:10.1186/1471-2164-14-558 Published: 16 August 2013 Abstract Background Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Results Using a comparative RNA sequencing analysis of three divergent model streptomycetes (S. coelicolor, S. avermitilis and S. venezuelae), we discovered hundreds of novel cis-antisense RNAs and intergenic small RNAs (sRNAs).
Convergent un translated overlapping RNAs. Conclusions Keywords: close Sign up to receive new article alerts from BMC Genomics. Abstract | De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. Abstract | Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. Abstract | Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. Abstract | Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. Abstract | Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. Abstract | Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome. Biotechnology for Biofuels | Abstract | RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium.
Abstract | 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. 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. Journal of Experimental & Clinical Cancer Research | Abstract | Blood RNA biomarker panel detects both left- and right-sided colorectal neoplasms: a case--control study. 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. Abstract | Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns. 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. BMC Infectious Diseases | Abstract | 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. Abstract | NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. Abstract | 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. Abstract | Comparing somatic mutation-callers: Beyond Venn diagrams. Abstract | Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Abstract | FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. Abstract | 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. Abstract | HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. Full text | RNAalifold: improved consensus structure prediction for RNA alignments.
Abstract | 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. BMC Microbiology | Abstract | The role of the RNA chaperone Hfq in Haemophilus influenzae pathogenesis. BioMed Central | The Open Access Publisher. A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases.
Full text | 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. Abstract | Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. Abstract | Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools.