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BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Related publications (25)

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Assessment of transcript reconstruction methods for RNA-seq

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcri ...

Nature Publishing Group2013

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The PyroTRF-ID bioinformatics methodology (http://bbcf.epfl.ch/PyroTRF-ID/) was developed to combine pyrosequencing and T-RFLP for describing microbial communities and identifying T-RFs by comparison of experimental and digital T-RFLP profiles obtained fro ...

2013

Identification of HMX1 target genes: A predictive promoter model approach

Purpose: A homozygous mutation in the H6 family homeobox 1 (HMX1) gene is responsible for a new oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration (MIM 612109). However, the HMX1 pathway rem ...

Molecular Vision2013

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, Jacques Rougemont, David Gregory Weissbrodt, Noam Shani, Lucas Sinclair

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microb ...

BioMed Central2012

PyroTRF-ID: a novel bioinformatics approach for the identification of terminal-restriction fragments using microbiome pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, Jacques Rougemont, David Gregory Weissbrodt, Noam Shani, Lucas Sinclair

Aim: In molecular microbial ecology, pyrosequencing is gradually supplanting classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for enhanced characterization of microbiome ...

2012

Regulation of gene expression is a carefully regulated phenomenon in the cell. “Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). Mammalian c ...

2012

Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster

Drosophila melanogaster is one of the most important genetic models and techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) are being employed extensively for deciphering the genetics basis of physiological functions. In RT-qPCR, ...

Elsevier2011

Heritable changes to the transcriptome that are independent to changes in the genome are defined as epigenetics. DNA methylation and posttranslational modifications of histones, such as acetylation/deacetylation and methylation/demethylation of lysine resi ...

Elsevier2010

BACKGROUND: Processing by gamma-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a div ...

Public Library of Science2009

Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR

Stewart Cole, Iain Old

BACKGROUND: Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can present a challenge because phi29 ...

2008