Publications associées à Illumina

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Jia Yuan Jiang, Daniel Alpern, Antonio Carlos Alves Meireles Filho, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

National Academy of Sciences2020

Comparison of chitin‐induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains

Melanie Blokesch, Sandrine Stutzmann

The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits ...

2020

2D MoS2 nanopores: ionic current blockade height for clustering DNA events

Aleksandra Radenovic, Ke Liu

2D nanopores can be used to electrophoretically drive DNA molecules, which can in turn be identified through measurable electronic current blockades. In this work, we use experimental data from molybdenum disulfide nanopores threading DNA nucleotides and p ...

2019

The effect of different organic substrates on the microbial communities of aerobic granular wastewater treatment sludge

Aline Sondra Adler

Aerobic granular sludge (AGS) is a promising alternative wastewater treatment to the conven- tional activated sludge system, allowing space and energy savings. This process is particularly suited for biological phosphorus removal, avoiding use of coagulant ...

EPFL2019

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

Riccardo Dainese

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

EPFL2019

Insights from the Genome Sequence of Mycobacterium lepraemurium: Massive Gene Decay and Reductive Evolution

Stewart Cole, Andrej Benjak, Charlotte Avanzi

Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, My ...

Amer Soc Microbiology2017

From next-generation resequencing reads to a high-quality variant data set

Susanne Petra Pfeifer

Sequencing has revolutionized biology by permitting the analysis of genomic variation at an unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it accessible for a wide range of research topics. However, the produced data c ...

Nature Publishing Group2017

Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic

Stewart Cole, Pushpendra Singh

Background: Leprosy has afflicted humankind throughout history leaving evidence in both early texts and the archaeological record. In Britain, leprosy was widespread throughout the Middle Ages until its gradual and unexplained decline between the 14th and ...

Biomed Central Ltd2014

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Nouria Hernandez, Alisa Yurovsky

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifac ...

Oxford University Press2014

IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies-A Price Comparison with Sanger Sequencing

Tatiana Favez, Pascal Escher

The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the numb ...

Springer-Verlag Berlin2014

Application of High-Density DNA Resequencing Microarray for Detection and Characterization of Botulinum Neurotoxin-Producing Clostridia

Stewart Cole

Background: Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs) that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxi ...

Public Library of Science2013

Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays

Stewart Cole

We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy ...

Public Library of Science2010

MER41 repeat sequences contain inducible STAT1 binding sites

Philipp Bucher

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we ...

Public Library of Science2010

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

Stewart Cole, Jacques Rougemont, Pushpendra Singh, Philippe Busso, Alexandre Gattiker

Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained b ...

2009

Probabilistic base calling of Solexa sequencing data

Felix Naef, Jacques Rougemont, Christian Iseli, Arnaud Amzallag, Ioannis Xenarios

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008