HLA typing from RNA-Seq sequence reads. ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. 5[prime] tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. Research article Joseph M Dhahbi1*, Stephen R Spindler1, Hani Atamna2, Amy Yamakawa1, Dario Boffelli3, Patricia Mote1 and David IK Martin3 * Corresponding author: Joseph M Dhahbi jdhahbi@ucr.edu.
![5[prime] tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction](http://cdn.pearltrees.com/s/pic/th/concentrated-restriction-56848603)
Genome Medicine. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. Sixty years of genome biology. Phylogenomics of strongylocentrotid sea urchins. Research article Kord M Kober12* and Giacomo Bernardi1 * Corresponding author: Kord M Kober kord.kober@nursing.ucsf.edu Author Affiliations 1 Department of Ecology & Evolutionary Biology, University Of California Santa Cruz, Santa Cruz, CA, USA 2 Department of Physiological Nursing, University Of California San Francisco, San Francisco, CA, USA For all author emails, please log on.
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.
Quantifying variances in comparative RNA secondary structure prediction. Genome-wide association study of sleep in Drosophila melanogaster. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Gene promoters show chromosome-specificity and reveal chromosome territories in humans. Research article Paul Gagniuc1* and Constantin Ionescu-Tirgoviste2 * Corresponding author: Paul Gagniuc paul_gagniuc@acad.ro.
iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. 1 BGI Tech Solutions Co., Ltd, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China 2 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China 3 School of Life Science and Technology, University of Electronic Science and Technology of China, No.4, Section 2, North Jianshe Road, Chengdu 610054, China 4 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Panyu District, Guangzhou 510006, China.
Description of plant tRNA-derived RNA fragments (tRFs) associated with Argonaute and identification of their putative targets. Combined ChIP-Seq and transcriptome analysis identifies AP-1/JunD as a primary regulator of oxidative stress and IL-1beta synthesis in macrophages. The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus.
M-pick, a Modularity-based Method for OTU Picking of 16S rRNA Sequences. Puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis. Characterisation of the wheat (triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat. Research article Youko Oono1*, Fuminori Kobayashi1, Yoshihiro Kawahara1, Takayuki Yazawa12, Hirokazu Handa1, Takeshi Itoh1 and Takashi Matsumoto1 * Corresponding author: Youko Oono yoono@nias.affrc.go.jp.
Quantitation of cell-free DNA and RNA in plasma during tumor progression in rats. Research Dolores C García-Olmo1*, María G Picazo1, Inmaculada Toboso1, Ana I Asensio1 and Damián García-Olmo2 * Corresponding author: Dolores C García-Olmo doloresg@sescam.jccm.es Author Affiliations.
Circulating rotaviral RNA in children with rotavirus antigenemia. Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. Research article Liandong Yang12, Ming Zou12, Beide Fu12 and Shunping He1* * Corresponding author: Shunping He clad@ihb.ac.cn.
Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation. Research article Feng Xu12, Qian Liu12, Luying Chen12, Jiebin Kuang12, Thomas Walk1, Jinxiang Wang12* and Hong Liao12 * Corresponding author: Jinxiang Wang jinxwang@scau.edu.cn Author Affiliations 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, PR China.
Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. Research article Sudeep Perumbakkam1, William M Muir1, Alexis Black-Pyrkosz2, Ron Okimoto3 and Hans H Cheng2* * Corresponding author: Hans H Cheng hans.cheng@ars.usda.gov Author Affiliations.
Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia. Estimation of data-specific constitutive exons with RNA-Seq data. Methodology article Ellis Patrick12, Michael Buckley2 and Yee Hwa Yang1* * Corresponding author: Yee H Yang jean.yang@sydney.edu.au Author Affiliations 1 School of Mathematics and Statistics, University of Sydney, Sydney NSW 2006, Australia 2 CSIRO Mathematical & Information Sciences, Private Bag 33, Clayton South 3168, Australia For all author emails, please log on. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Research Jong Kyoung Kim and John C Marioni* * Corresponding author: John C Marioni marioni@ebi.ac.uk. Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. RNAalifold: improved consensus structure prediction for RNA alignments. Original RNAalifold The original RNAalifold approach combines a thermodynamic energy minimization [22] with a simple scoring model to assess evolutionary conservation. Both an energy minimization and a partition function version are implemented in the Vienna RNA package [4].
Energy minimization uses the following recursions: Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans. Research article Joel V Tamayo, Mahekta Gujar, Stuart J Macdonald and Erik A Lundquist* * Corresponding author: Erik A Lundquist erikl@ku.edu Author Affiliations. Characterization and differential expression of microRNAs in the ovaries of pregnant and non-pregnant goats (Capra hircus) Research article , , , , , , and Abstract (provisional) Background Ovarian follicular development and hormone secretion are complex and coordinated biological processes which will usually be altered during pregnancy. Ovarian function is tightly regulated by a multitude of genes, and also by some specific miRNAs.
Results. Global mapping of transcription start sites and promoter motifs in the symbiotic alpha-proteobacterium Sinorhizobium meliloti 1021. Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing. Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach. Research article Nathaniel K Jue†, Michael B Murphy†, Seth D Kasowitz, Sohaib M Qureshi, Craig J Obergfell, Sahar Elsisi, Robert J Foley, Rachel J O’Neill and Michael J O’Neill* * Corresponding author: Michael J O’Neill michael.oneill@uconn.edu † Equal contributors Author Affiliations.
Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax. Research article. HuntMi: an efficient and taxon-specific approach in pre-miRNA identification. Methodology article. Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing.
Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification. Research Daisuke Hayasaka*†, Kotaro Aoki† and Kouichi Morita * Corresponding author: Daisuke Hayasaka hayasaka@nagasaki-u.ac.jp † Equal contributors. Mast cells contribute to double-stranded RNA-induced augmentation of airway eosinophilia in a murine model of asthma. MicroRNAs and their putative targets in Brassica napus seed maturation.
Research article Daiqing Huang, Chushin Koh, J Allan Feurtado, Edward WT Tsang and Adrian J Cutler* MicroRNA miR-30 family regulates non-attachment growth of breast cancer cells. Comparative transcriptomics of early dipteran development. Mitochondrial genomes of two Sinochlora species (Orthoptera): novel genome rearrangements and recognition sequence of replication origin. A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.
Research Mario Looso1†, Jens Preussner1†, Konstantinos Sousounis3, Marc Bruckskotten1, Christian S Michel1, Ettore Lignelli1, Richard Reinhardt2, Sabrina Höffner1, Marcus Krüger1, Panagiotis A Tsonis3*, Thilo Borchardt1* and Thomas Braun1* * Corresponding authors: Panagiotis A Tsonis ptsonis1@udayton.edu - Thilo Borchardt Thilo.Borchardt@mpi-bn.mpg.de - Thomas Braun Thomas.Braun@mpi-bn.mpg.de † Equal contributors. Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFbeta3-knockout mice alleles: RNA-Seq analysis of TGFbeta3 Mice. Research article. MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood.
A highly expressed miR-101 isomiR is a functional silencing small RNA. Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element. Next generation sequencing of viral RNA genomes. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis. RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes. Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples. Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai.
Dynamic regulation of epigenomic landscapes during hematopoiesis. A systems-based approach to analyse the host response in murine lung macrophages challenged with respiratory syncytial virus. The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels. Efficient recovery of proteins from multiple source samples after trizol(R) or trizol(R)LS RNA extraction and long-term storage. A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) Estimate hidden dynamic profiles of siRNA effect on apoptosis.
Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneum. De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. Comparative genomics and functional study of lipid metabolic genes in Caenorhabditis elegans. Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. Inferring microRNA and transcription factor regulatory networks in heterogeneous data. A comparison of methods for differential expression analysis of RNA-seq data. Smoking decreases the response of human lung macrophages to double-stranded RNA by reducing TLR3 expression. Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayval[latin small letter dotless i]k.
RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks. Genome-wide co-expression analysis predicts protein kinases as important regulators ofphosphate deficiency-induced root hair remodeling in Arabidopsis. MGcV: the microbial genomic context viewer for comparative genome analysis. CRAC: an integrated approach to the analysis of RNA-seq reads. Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote.
Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. Differential expression analysis for paired RNA-seq data. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restriction. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts. The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq. Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach.
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. PASTA: splice junction identification from RNA-Sequencing data. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution.