Monthly Archives: January 2011

Jan-2011 Poll Results

What will ultimately have the bigger impact on future molecular diagnostics and drug development? Transcriptomics – Epigenetics, DNA/RNA editing, alternative splicing, microRNA regulation (79%, 99 Votes) Genomics – Genotype, GWAS, mutations / SNP, indels, copy number variation (21%, 26 Votes) ...

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Transcriptome Sequencing of Non-model Species

Eastern Diamondback Rattlesnake (Conus bullatus) Protozoan Parasite (Plasmodium falciparum) Périgord Black Truffle (Tuber melanosporum) Migratory Locust (Locusta migratoria) Mosquito (Anopheles funestus) Milkweed Bug (Oncopeltus fasciatus) Greenhouse Whitefly (Trialeurodes vaporariorum) Pigeon Pea (Cajanus Cajan) Buckwheat (Fagopyrum) Mungbean (Vigna radiata) Copepod (Tigriopus ...

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RNA-Seq and Rattlesnakes

Animal toxins represent a valuable source of pharmacologically active macromolecules, a unique system for studying molecular adaptation, and a powerful framework for examining structure-function relationships in proteins. Snake venoms in particular represent a tremendous opportunity to study a large, integrated ...

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A Look at the Future of RNA-Seq

from Genetic Engineering News- Third-Generation Sequencing Debuts by Vicki Glaser Helicos BioSciences In Helicos’ tSMS technology, labeled nucleotides are mixed with nucleic-acid templates immobilized on a flow cell. Detection of the fluorescent signals emitted as a result of each base ...

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RNA-Seq at AGBT

The 12th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 2-5, 2011. The AGBT meeting has become the most complete scientific forum for acquiring information about the latest advances in ...

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Transcriptomics to Fight Bed Bugs

Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its ...

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RNA-Seq Conference – Final Agenda

RNA-Seq Insights into the Active Genome Part of the X-Gen Congress and Expo March 14-18 San Diego, CA Transcriptomics underpins many fields of biological science. While RNA-Seq is perhaps the most complex NGS application, the determination of expression levels of ...

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Guide to analyzing RNA-seq data

Here is an excellent tutorial posted on the SEQanswers web forum by Matt Young. Guide to analyzing RNA-seq data – BioinfWiki.pdf Guide to analyzing RNA-seq data – BioinfWiki – Update 21-01-2011.pdf

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NEUMA – estimating mRNA abundances from RNA-Seq data

NEUMA (Normalization by Expected Uniquely Mappable Area) is a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. NEUMA, is based on effective length normalization using uniquely mappable areas of gene and ...

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Nice Review of Advances in RNA-Seq Data Analysis

from Nature Biotechnology Two methods for de novo transcriptome assembly of short reads were published this year from Lior Pachter and colleagues1 and from Aviv Regev and colleagues2. The transcriptome can be analyzed by sequencing cDNA reverse transcribed from RNA ...

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