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Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes. Research article Michele Perazzolli1*, Marco Moretto1, Paolo Fontana1, Alberto Ferrarini2, Riccardo Velasco1, Claudio Moser1, Massimo Delledonne2 and Ilaria Pertot1 * Corresponding author: Michele Perazzolli michele.perazzolli@fmach.it Author Affiliations 1 IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all’Adige (TN), Italy 2 Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134, Verona, Italy For all author emails, please log on.

BMC Genomics 2012, 13:660 doi:10.1186/1471-2164-13-660 Published: 22 November 2012 Abstract Background Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine and is commonly controlled by fungicide treatments. Results More than 14.8 million paired-end reads were obtained for each biological replicate of T39-treated and control leaf samples collected before and 24 h after P. viticola inoculation.

Conclusions Keywords: close. BMC Genomics | Full text | Computational RNomics of Drosophilids. We report here on a computational screen for structured RNA motifs in Drosophilids based on 12-species Pecan alignments provided by the Consortium. The detected RNAz hits are either (parts of) independently transcribed non-coding RNAs with evolutionarily conserved secondary structures, or they are structured elements that are parts of coding transcripts such as SECIS or IRE elements. Sensitivity and Specificity Overall, 42 482 RNAz hits corresponding to roughly 5 Mb in the D. melanogaster genome show evidence of evolutionarily conserved RNA secondary structure. About 20% of these overlap existing annotation. The 16 377 loci of the high confidence set covers approximately 2.1 Mb of DNA, see Tab. 1.

Table 1. In total, 336 hits correspond to known non-coding RNAs according to at least one source of annotation (FlyBase: 316; BLAST against miRBase: 79; BLAST against Noncode: 44; BLAST against Rfam: 222; tRNAscan: 159). Table 2. Figure 1. Genomic Distribution Additional file 1. Figure 2. Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis. Research article Jiajie Sun1, Mijie Li1, Zhuanjian Li1, Jing Xue1, Xianyong Lan1, Chunlei Zhang2, Chuzhao Lei1 and Hong Chen1* * Corresponding author: Hong Chen chenhong1212@263.net Author Affiliations 1 College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China 2 Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China For all author emails, please log on.

BMC Genomics 2013, 14:42 doi:10.1186/1471-2164-14-42 Published: 18 January 2013 Abstract Background MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Results Total RNAs from the Chinese Qinchuan bovine longissimus thoracis at fetal and adult stages were used to construct small RNA libraries for Solexa SBS technology sequencing. Conclusions Keywords: close. Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome. BMC Plant Biology | Abstract | Expression of geminiviral AC2 RNA silencing suppressor changes sugar and jasmonate responsive gene expression in transgenic tobacco plants. Research article Arto J Soitamo*, Balaji Jada and Kirsi Lehto * Corresponding author: Arto J Soitamo artsoi@utu.fi Author Affiliations Department of Biochemistry and Food Chemistry, Laboratory of Molecular Plant Biology, University of Turku, Vesilinnantie 5, LTII, 2.floor, Turku, 20014, Finland For all author emails, please log on.

BMC Plant Biology 2012, 12:204 doi:10.1186/1471-2229-12-204 Published: 7 November 2012 Abstract Background RNA-silencing is a conserved gene regulation and surveillance machinery, which in plants, is also used as major defence mechanism against viruses. Results Expression of AC2 RSS in transgenic tobacco plants induced clear phenotypic changes both in leaves and in flowers. Conclusions AC2 RSS in transgenic tobacco plants interferes with the silencing machinery. Close Sign up to receive new article alerts from BMC Plant Biology. BioMed Central blogs network. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. Biology Direct. Abstract | Bioinformatics clouds for big data manipulation. Synthetic “poop” as a treatment for C. Difficile published in new journal Microbiome.

A new treatment for superbug Clostridium difficile is published today in the launch issue of Microbiome. Canadian researchers have developed a “super-probiotic”, a synthetic stool called the RePOOPulate, as an alternative to stool transplantation. The RePOOPulate is composed of 33 different bacterial strains isolated from the stool of a healthy 41 year old female at the University of Guelph. The bacteria were purified on agar plates, identified by rRNA sequencing and then pooled together in fixed ratios to form the RePOOPulate. A pilot study was conducted at Kingston General Hospital, Canada, where the RePOOPulate probiotic was inoculated into two female patients in their 70s, both of whom had severe C. difficile infection and had not responded to antibiotics. C. difficile infection causes many gastrointestinal problems, including severe diarrhea, and often leads to outbreaks in hospitals and long-term care facilities.

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. Research article Muktak Aklujkar1*, Shelley A Haveman1, Raymond DiDonato1, Olga Chertkov2, Cliff S Han2, Miriam L Land3, Peter Brown1 and Derek R Lovley1 * Corresponding author: Muktak Aklujkar muktak@microbio.umass.edu Author Affiliations 1 University of Massachusetts Amherst, Amherst, MA, 01003, USA 2 Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA 3 Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA For all author emails, please log on.

BMC Genomics 2012, 13:690 doi:10.1186/1471-2164-13-690 Published: 10 December 2012 Abstract Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically.

Results Conclusions Keywords: Pelobacter; Genome; Metabolism; Physiology; Geobacter; 2,3-butanediol close. Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. Research article Esteban Marcellin1†, Tim R Mercer1†, Cuauhtemoc Licona-Cassani1, Robin W Palfreyman1, Marcel E Dinger2, Jennifer A Steen1, John S Mattick2 and Lars K Nielsen1* * Corresponding author: Lars K Nielsen lars.nielsen@uq.edu.au † Equal contributors Author Affiliations 1 Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld, 4072, Australia 2 Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, 4067, Australia For all author emails, please log on.

BMC Genomics 2013, 14:15 doi:10.1186/1471-2164-14-15 Published: 16 January 2013 Abstract Background Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Results We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. Conclusions Keywords: RNA-sequencing; actinobacteria; Saccharopolyspora erythraea; Erythromycin; Metabolic switch close. Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome.

Research article Cai Chen1 and Ralf Bundschuh123* * Corresponding author: Ralf Bundschuh bundschuh@mps.ohio-state.edu Author Affiliations 1 Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA 2 Departments of Physics and Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA 3 Center for RNA Biology, The Ohio State University, Columbus, OH, USA For all author emails, please log on. BMC Genomics 2012, 13:616 doi:10.1186/1471-2164-13-616 Published: 13 November 2012 Abstract Background The genomic information which is transcribed into the primary RNA can be altered by RNA editing at the transcriptional or post-transcriptional level, which provides an effective way to create transcript diversity in an organism. Results We apply different computational tools that are capable of identifying indel differences between RNA reads and the matching reference genome and we initially find hundreds of such indel candidates.

Conclusions Keywords: close. Comparative genomics and transcriptomics of trait-gene association. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses. Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. Abstract | Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. Abstract | A Computational model for compressed sensing RNAi cellular screening. BioMed Central | The Open Access Publisher. De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

Research article Musa A Hassan1, Mariane B Melo1, Brian Haas2, Kirk D C Jensen1 and Jeroen P J Saeij1* * Corresponding author: Jeroen P J Saeij jsaeij@mit.edu Author Affiliations 1 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 2 Genome Annotation Research and Development, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA For all author emails, please log on. BMC Genomics 2012, 13:696 doi:10.1186/1471-2164-13-696 Published: 12 December 2012 Abstract Background Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons.

Results We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. Conclusion Keywords: Toxoplasma; RNA-seq; Trinity; LincRNA; Alternative splicing; Transcriptome close. Silence | Abstract | Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression. Research article Crystal Sweetman1, Darren CJ Wong1, Christopher M Ford1 and Damian P Drew12* * Corresponding author: Damian P Drew damian.drew@adelaide.edu.au Author Affiliations 1 Wine Science and Business, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, 5064, Australia 2 Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, 1871, Denmark For all author emails, please log on.

BMC Genomics 2012, 13:691 doi:10.1186/1471-2164-13-691 Published: 11 December 2012 Abstract Background Vitis vinifera berry development is characterised by an initial phase where the fruit is small, hard and acidic, followed by a lag phase known as veraison. Results A total of 162 million 100-base pair reads were generated from pooled Vitis vinifera (cv. Conclusions In this study we report the global transcriptional profile of Shiraz grapes at key stages of development.

Keywords: close. Abstract | FUSIM: a software tool for simulating fusion transcripts. Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. Widespread promoter-mediated coordination of transcription and mRNA degradation. De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.

Research article Luca Venturini†, Alberto Ferrarini†, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Silvia Dal Santo, Andrea Minio, Genny Buson, Paola Tononi, Elisa Debora Zago, Gianpiero Zamperin, Diana Bellin, Mario Pezzotti and Massimo Delledonne* BMC Genomics 2013, 14:41 doi:10.1186/1471-2164-14-41 Published: 18 January 2013 Abstract Background Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. Results We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. Conclusions The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations.

Keywords: close Sign up to receive new article alerts from BMC Genomics. Biogeography of the ecosystems of the healthy human body. The complex transcriptional landscape of the anucleate human platelet. Abstract | Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq. Research article Chad E Niederhuth123, O Rahul Patharkar123 and John C Walker123* * Corresponding author: John C Walker WalkerJ@missouri.edu Author Affiliations 1 Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA 2 Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA 3 Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA For all author emails, please log on.

BMC Genomics 2013, 14:37 doi:10.1186/1471-2164-14-37 Published: 17 January 2013 Abstract Background Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals. Results Using RNA-Seq, we compare the transcriptomes of wild-type and hae hsl2 stage 15 flowers, using the floral receptacle which is enriched for abscission zone cells. 2034 genes were differentially expressed with a False Discovery Rate adjusted p < 0.05, of which 349 had two fold or greater change in expression. Conclusion close. Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum.

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity. Methodology article Katie S Viljoen and Jonathan M Blackburn* * Corresponding author: Jonathan M Blackburn jonathan.blackburn@uct.ac.za Author Affiliations Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa For all author emails, please log on.

BMC Genomics 2013, 14:14 doi:10.1186/1471-2164-14-14 Published: 16 January 2013 Abstract Background RNA and microarray quality assessment form an integral part of gene expression analysis and, although methods such as the RNA integrity number (RIN) algorithm reliably asses RNA integrity, the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation requires further investigation. Results Conclusions Keywords: Gene expression profiling; Microarray; RNA quality; RNA integrity number; Quality control; ComBat; Surrogate variable analysis; Non-biological experimental variance close. Abstract | FUSIM: a software tool for simulating fusion transcripts.

BMC International Health and Human Rights | Abstract | In the face of war: examining sexual vulnerabilities of Acholi adolescent girls living in displacement camps in conflict-affected Northern Uganda. An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells. Research article Seungyoon Nam12*, Xinghua Long23, ChangHyuk Kwon1, Sun Kim4 and Kenneth P Nephew2 * Corresponding author: Seungyoon Nam seungyoon.nam@ncc.re.kr Author Affiliations 1 Cancer Genomics Branch, National Cancer Center, Goyang-si, Gyeonggi-do, 410-769, Korea 2 Department of Cellular and Integrative Physiology, Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA 3 Zhongnan Hospital, Wuhan University, Wuhan, 430071, China 4 Department of Computer Science and Engineering, Bioinformatics Institute, Seoul National University, Seoul, 151-742, Korea For all author emails, please log on.

BMC Genomics 2012, 13:732 doi:10.1186/1471-2164-13-732 Published: 27 December 2012 Abstract Background A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs) into interpretable functional networks. Results Conclusions Keywords: Bioinformatics; miRNA; Network; Breast cancer; Antiestrogen resistance close. Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. Abstract | HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Research Federico A Santoni12*, Jessica Guerra2 and Jeremy Luban23* * Corresponding authors: Federico A Santoni federico.santoni@unige.ch - Jeremy Luban jeremy.luban@umassmed.edu Author Affiliations 1 Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, Geneva, CH-1211, Switzerland 2 Department of Microbiology and Molecular Medicine, University of Geneva, 1211, Geneva 4, Switzerland 3 Program in Molecular Medicine and Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 373 Plantation Street, Biotech 2, Suite 319, Worcester, MA, 01605, USA For all author emails, please log on.

Retrovirology 2012, 9:111 doi:10.1186/1742-4690-9-111 Published: 20 December 2012 Abstract Background Certain post-translational modifications to histones, including H3K4me3, as well as binding sites for the transcription factor STAT1, predict the site of integration of exogenous gamma-retroviruses with great accuracy and cell-type specificity. Results close. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. Abstract | RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi.

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice. Abstract | HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. Identification of 3[prime] gene ends using transcriptional and genomic conservation across vertebrates. The prediction of the porcine pre-microRNAs in genome-wide based on support vector machine (SVM) and homology searching. Insights into the regulation of human CNV-miRNAs from the view of their target genes. Expression profiles of microRNAs from lactating and non-lactating bovine mammary glands and identification of miRNA related to lactation.

Full text | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? Abstract | Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. The ADAR protein family.

Transposable elements reveal a stem cell specific class of long noncoding RNAs. Transcriptomic analysis of 'Suli' pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq. Genome Biology. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. Employing machine learning for reliable miRNA target identification in plants. Abstract | miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases.

Abstract | Predicting RNA-Protein Interactions Using Only Sequence Information. BMC Cancer | Abstract | RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls. BMC Evolutionary Biology | Abstract | Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias. RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. RNA-Seq Quantification of the Human Small Airway Epithelium Transcriptome. Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella-induced microRNAs in human monocytes.

RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA. Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons. BMC Medicine | Abstract | Targeting the epidermal growth factor receptor in non-small cell lung cancer cells: the effect of combining RNA interference with tyrosine kinase inhibitors or cetuximab. Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.

Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics | Full text | CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications. Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis. Single cell transcriptomics of neighboring hyphae of Aspergillus niger. PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data. Abstract | GSVA: gene set variation analysis for microarray and RNA-Seq data. Genome Biology | 2012 Special Issue: "Epigenomics" Breast Cancer Research | Abstract | Small interfering RNA library screen identified polo-like kinase-1 (PLK1) as a potential therapeutic target for breast cancer that uniquely eliminates tumour-initiating cells. CCS | Abstract | Efficient RNA interference in patients' acute lymphoblastic leukemia cells amplified as xenografts in mice.

Abstract | The concept of RNA-assisted protein folding: the role of tRNA. Abstract | Analysis of Energy-based Algorithms for RNA Secondary Structure Prediction. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. A comparative analysis of DNA methylation across human embryonic stem cell lines.

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. A comparative analysis of DNA methylation across human embryonic stem cell lines. Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast.

Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage. Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy.