RNAseq Google Scholar Results 1 - 40 of 40 6/2/10
RNA-seq: from technology to biologybahlerlab.info [PDF]
S Marguerat, J Bähler - Cellular and Molecular Life Sciences, 2010 - Springer
Abstract Next-generation sequencing technologies are now being exploited not only to analyse
static genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although
these powerful and rapidly evolving technologies have only been available for a couple ...
RNA-Seq: a method for comprehensive transcriptome analysis.
U Nagalakshmi, K Waern, M Snyder - Current protocols in …, 2010 - ncbi.nlm.nih.gov
A recently developed technique called RNA Sequencing (RNA-Seq) uses massively parallel
sequencing to allow transcriptome analyses of genomes at a far higher resolution than is available
with Sanger sequencing- and microarray-based methods. In the RNA-Seq method, ...
[HTML] … Statistical Method for the Detection of Alternative Splicing Using RNA-Seqnih.gov [HTML]
L Wang, Y Xi, J Yu, L Dong, L Yen, W Li - 2010 - ncbi.nlm.nih.gov
Deep sequencing of transcriptome (RNA-seq) provides unprecedented opportunity to interrogate
plausible mRNA splicing patterns by mapping RNA-seq reads to exon junctions (thereafter junction
reads). In most previous studies, exon junctions were detected by using the quantitative ...
FRT-seq: amplification-free, strand-specific transcriptome sequencing
L Mamanova, RM Andrews, KD James, EM … - Nature Methods, 2010 - nature.com
... Here we report an RNA-seq approach for the Illumina Genome Analyzer in which reverse
transcription takes place on the flowcell surface ('FRT-seq'; Supplementary Fig. 1,
Supplementary Table 1 and Online Methods). ... Standard RNA-seq libraries. ...
Defining transcribed regions using RNA-seq
BT Wilhelm, S Marguerat, I Goodhead, J Bähler - Nature Protocols, 2010 - nature.com
Next-generation sequencing technologies are revolutionizing genomics research. It is now possible
to generate gigabase pairs of DNA sequence within a week without time-consuming cloning
or massive infrastructure. This technology has recently been applied to the development ...
edgeR: a Bioconductor package for differential expression analysis of digital gene …nih.gov [HTML]
MD Robinson, DJ McCarthy, GK Smyth - Bioinformatics, 2010 - Oxford Univ Press
... Although initially developed for serial analysis of gene expression (SAGE), the methods and
software should be equally applicable to emerging technologies such as RNA-seq (Li et
al., 2008; Marioni et al., 2008) giving rise to digital expression data. ...
Leveraging skewed transcript abundance by RNA-Seq to increase the genomic …vanderbilt.edu [PDF]
… , M Johnston, JT Tossberg, A Rokas - Proceedings of the …, 2010 - National Acad Sciences
Assembling the tree of life is a major goal of biology, but progress has been hindered by the
difficulty and expense of obtaining the orthologous DNA required for accurate and fully resolved
phylogenies. Next-generation DNA sequencing technologies promise to accelerate ...
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 updatenih.gov [HTML]
M Gilsdorf, T Horn, Z Arziman, O Pelz, E … - Nucleic Acids …, 2010 - Oxford Univ Press
... the human genome. The new version also facilitates the integration with other
genomic data sets and contains expression profiling (RNA-Seq) data for several
cell lines commonly used in RNAi experiments. INTRODUCTION. ...
[PDF] Sex-specific and lineage-specific alternative splicing in primatesuchicago.edu [PDF]
Y Gilad - 2010 - stephenslab.uchicago.edu
... was previously possible. Specifically, we used RNA-seq to study transcript levels
in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three
males and three females from each species. Our approach ...
[PDF] 39-End Sequencing for Expression Quantification (3SEQ) from Archival …stanford.edu [PDF]
AH Beck, Z Weng, DM Witten, S Zhu, JW Foley, IOL Ng - 2010 - med.stanford.edu
... Page 2. to sequence human genomes [37,38], study the genome wide binding of transcription
factors [39,40] and nucleosomes [41], characterize genome methylation patterns [42], and have
been recently applied to the sequencing of transcriptomes (RNA-Seq) [35,36,43–45]. ...
BamView: Viewing mapped read alignment data in the context of the reference …
T Carver, U Bohme, TD Otto, J Parkhill, M … - Bioinformatics, 2010 - Oxford Univ Press
... when embedded in Artemis, is that it allows annotation to be changed based on manually inspect-
ing data from transcriptome sequencing experiments (RNAseq, Otto et ... The BAM view is displaying
RNA- Seq Solexa reads from the early ring stage in the life cycle of P. falciparum ...
Alternative splicing: global insights
M Hallegger, M Llorian, CWJ Smith - FEBS Journal, 2010 - interscience.wiley.com
... ac.uk. *These authors contributed equally to this work. Copyright Journal compilation ©
2010 Federation of European Biochemical Societies. KEYWORDS. alternative splicing •
microarray • RNA-Seq. ABSTRACT. Following the ...
[HTML] Identification of Potential Therapeutic Targets for Burkholderia …nih.gov [HTML]
DR Yoder-Himes, KT Konstantinidis, JM Tiedje - 2010 - ncbi.nlm.nih.gov
... Comparison to Previous Transcriptomic Studies. A previous study examined the transcriptomic
response via Illumina sequencing of cDNA (RNA-seq) from two closely related B. cenocepacia
strains, AU1054 (an epidemic strain from CF patients) and HI2424, under the same ...
WormBase: a comprehensive resource for nematode researchnih.gov [HTML]
TW Harris, I Antoshechkin, T Bieri, D … - Nucleic Acids …, 2010 - Oxford Univ Press
... These changes include 127 new C. elegans genes and 443 new C. elegans isoforms.
Most of these changes have been based either on RNA-Seq transcript data (from 454
or Illumina sequencing) or on comparative gene analysis. ...
Cross-mapping and the identification of editing sites in mature microRNAs in high- …
MJL de Hoon, RJ Taft, T Hashimoto, M … - Genome …, 2010 - genome.cshlp.org
... assignment of RNAs to genome loci. Similar strategies have been developed pre- viously
for mapping short sequences obtained from CAGE and RNA-seq (Jurka 2000; Faulkner
et al. 2008). Alignment errors preferentially occur near ...
[HTML] Translog, a web browser for studying the expression divergence of …biomedcentral.com [HTML]
X Dong, A Akalin, Y Sharma, B Lenhard - BMC Bioinformatics, 2010 - biomedcentral.com
... The increasing volume of available transcriptome data such as CAGE[19] and RNA-seq [20] for
different developmental stages and tissues for different species can be harnessed to understand
the mechanisms of spatiotemporal expression changes of genes that share a (not so ...
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell …
RD Morin, NA Johnson, TM Severson, AJ Mungall, J … - Nature Genetics, 2010 - nature.com
... Biotechniques 45, 81–94 (2008). | Article | PubMed | ChemPort |; Mortazavi, A., Williams, BA,
McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by
RNA-Seq. Nat. Methods 5, 621–628 (2008). | Article | PubMed | ChemPort |; Ley, TJ et al. ...
Small RNA Diversity in Plants and its Impact in Development
C Lelandais-Briere, C Sorin, M Declerck, A … - Current …, 2010 - ingentaconnect.com
... The number of MPSS signatures obtained from rice mRNAs were proportional to gene expression
[60] and, in yeast, the so- called RNA-Seq which subjects fragmented complementary DNAs to
high-throughput sequencing gave even more accurate results than qRT-PCR [78 ...
Genome variation discovery with high-throughput sequencing data
AV Dalca, M Brudno - Briefings in Bioinformatics, 2010 - Oxford Univ Press
... novel genomes (de novo sequencing) [4–7], resequence individuals when a reference genome
exists (variation discovery) [8, 9], sequence messenger and noncoding RNA to discover novel
transcripts and quantify their expression levels in various tissues (RNA-Seq) [10, 11 ...
Endometrial biopsy: a valuable clinical and research tool in bovine reproduction
A Chapwanya, KG Meade, F Narciandi, P Stanley, JF … - Theriogenology, 2010 - Elsevier
Consensus miRNA expression profiles derived from interplatform normalization of …
R Bargaje, M Hariharan, V Scaria, B Pillai - RNA, 2010 - rnajournal.cshlp.org
... The platforms include bead-based study and microarray platforms developed by
different laboratories. Small RNA cloning and RNA-seq studies were not included,
since there are very few studies using these techniques. Each ...
L Wang, Z Feng, X Wang, X Wang, X Zhang - Bioinformatics, 2010 - portal.acm.org
... Summary: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major
quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify
differentially expressed genes or isoforms for RNA-seq data from different samples. ...
Identification of genes differentially expressed during interaction of resistant and …biomedcentral.com [PDF]
A Baldo, JL Norelli, RE Farrell, C Basset, HS … - BMC Plant …, 2010 - biomedcentral.com
... that can be detected. With the development of an apple genome sequence [32], short-read, high-
throughput sequencing technologies such as (RNa-seq 454 technology) should allow greater
coverage of the apple transcriptome following E. amylovora infection in future studies. ...
Novel clinicogenome network modeling for revolutionizing genotypephenotype- …
DH Roukos - Expert Review of Molecular Diagnostics, 2010 - ingentaconnect.com
... Full-genome sequencing or more targeted discovery of point mutations, copy-number changes
and rearrangements; • 'RNA-seq', analogous to expressed sequence tags (ESTs) or serial analysis
of gene expression (SAGE), and small RNA sequencing for microRNA profiling. ...
ENCODE whole-genome data in the UCSC Genome Browsernih.gov [HTML]
KR Rosenbloom, TR Dreszer, M Pheasant, … - Nucleic Acids …, 2010 - Oxford Univ Press
... tracks include chromatin immunoprecipitation experiments for transcription factor binding and
histone modification; maps of open chromatin, chromatin interactions, and DNA methylation;
transcriptome profiling of whole cell and cellular compartments by RNA-seq and microarray ...
[PDF] A minimum of two distinct heritable factors are required to explain correlation …wehi.edu.au [PDF]
JF Markham, CJ Wellard, ED Hawkins, KR … - Journal of the Royal …, 2010 - wehi.edu.au
Page 1. 1 A minimum of two distinct heritable factors are required to explain correlation
structures in proliferating lymphocytes. John F. Markham 1 , Cameron J. Wellard 2 ,
Edwin D. Hawkins 3 , Ken R. Duffy 4 , Philip D. Hodgkin ...
[HTML] 3′-End Sequencing for Expression Quantification (3SEQ) from Archival …nih.gov [HTML]
AH Beck, Z Weng, DM Witten, S Zhu, JW Foley, P … - 2010 - ncbi.nlm.nih.gov
... been used to sequence human genomes [37], [38], study the genome wide binding of transcription
factors [39], [40] and nucleosomes [41], characterize genome methylation patterns [42], and have
been recently applied to the sequencing of transcriptomes (RNA-Seq) [35], [36 ...
A single-base resolution map of an archaeal transcriptome171.66.122.45 [HTML]
O Wurtzel, R Sapra, F Chen, Y Zhu, BA … - Genome …, 2010 - genome.cshlp.org
... The resulting pellet was washed with 70% ethanol, air-dried, and resuspended in 40 μL of dH
2 O. cDNA preparation. 5′-end RNA-seq. ... Whole-transcript RNA-seq. Ten micrograms of total
RNA was treated with RQ1 RNase-free DNase in a final volume of 50 μL. ...
Methods and compositions of treating a flaviviridae family viral infection
S Einav, JS Glenn, W Yang, H Dvory-sobol, IC Choong, … - 2010 - freepatentsonline.com
Briefly described, embodiments of this disclosure include compounds,
pharmaceutical compositions, methods of treating a host infected with a
virus from the Flaviviridae family of viruses, methods of i.
RNA processing and its regulation: global insights into biological networks
DD Licatalosi, RB Darnell - Nature Reviews Genetics, 2010 - nature.com
... RNA–seq (or next- generation RNA sequencing) (Box 1) takes advantage of the power of
new single-molecule sequencing methods 59, 60 that can currently produce billions of
nucleotides of sequence in a matter of days for several thousand dollars. ...
The role of Hfq in bacterial pathogens
Y Chao, J Vogel - Current Opinion in Microbiology, 2010 - Elsevier
... RNomics and deep sequencing (RNA-seq) approaches discovered the small RNA and mRNA
targets of Hfq, and indicated that this protein might impact on the expression of up to 20% of all
genes in some organisms, including genes of type 3 secretion systems. ...
De novo prediction of structured RNAs from genomic sequences
J Gorodkin, IL Hofacker, E Torarinsson, Z Yao, JH … - Trends in …, 2010 - Elsevier
... The comparative approach is important for an additional reason. Over the next few years, we
expect that emerging technology such as high-throughput sequencing of RNA (RNAseq [11])
will reveal the transcriptomes of many organisms with unprecedented depth and precision. ...
A Genomic Approach to Human Autoimmune Diseases
V Pascual, D Chaussabel, J … - Annual Review of …, 2010 - Annual Reviews
Page 1. ANRV406-IY28-20 ARI 24 December 2009 0:58 R EVIEW S I N A DVA N C
E A Genomic Approach to Human Autoimmune Diseases Virginia Pascual,1 Damien
Chaussabel,1 and Jacques Banchereau1,2 1Baylor Institute ...
Genomics of medulloblastoma: from Giemsa-banding to next-generation …
PA Northcott, JT Rutka, MD Taylor - Journal of Neurosurgery: Pediatrics, 2010 - dx.doi.org
[PDF] Systems medicine for a next-generation of biomarkers and drugs: Changing …gastricbreastcancer.com [PDF]
DH Roukos - Gastric & Breast Cancer, 2010 - gastricbreastcancer.com
... This technology allows three major fields of application: • Full-genome sequencing or more
targeted discovery of point mutations, copy-number changes and rearrangements; • 'RNA-seq',
analogous to expressed sequence tags (ESTs) or serial analysis of gene expression ...
Integrating multiple genome annotation databases improves the interpretation of …biomedcentral.com [PDF]
J Yin, S McLoughlin, IB Jeffery, A Glaviano, B … - BMC …, 2010 - biomedcentral.com
... This approach could easily be applied to other species and gene expression measurement
platforms such as exon microarrays or RNA seq. Methods Data sources Zebrafish
transcriptome cross reference files were downloaded from Ensembl (Zv7, ...
ARH: predicting splice variants from genome-wide data with modified entropy
A Rasche, R Herwig - Bioinformatics, 2010 - Oxford Univ Press
... expression. The exon arrays point to a deeper transcription pattern in terms of
splicing. Similar expression variability is found in RNA-Seq data (data not shown).
ARH has been shown to cope with variable exon expression. ...
The Evolution of Gene Regulatory Interactions
DA Garfield, GA Wray - BioScience, 2010 - Univ California Press
... Developmental Biology 329: 410–421. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: A
revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57–63. Weedon MN, et al.
2008. Genome-wide association analysis identifies 20 loci that influence adult height. ...
[PDF] The Evolution of Gene Regulatory Interactionseurekalert.org [PDF]
GA WRAY, DA GARFIELD - BioScience, 2010 - eurekalert.org
Page 1. The idea that changes in gene regulation can play an important role in
evolution is not new. In an influential article published in 1975, Mary-Claire King
and Allan Wilson argued that because the sequence and function ...
Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and …
G He, X Zhu, AA Elling, L Chen, X Wang, L … - The Plant Cell …, 2010 - Am Soc Plant Biol
Page 1. Global Epigenetic and Transcriptional Trends among Two Rice Subspecies
and Their Reciprocal Hybrids W Guangming He,a,b,c,1 Xiaopeng Zhu,d,1 Axel A.
Elling,c,1 Liangbi Chen,e Xiangfeng Wang,a,c Lan Guo,a ...
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