ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact protein-DNA binding sites from ChIP-enriched sequencing data. State-of-the-art heuristic, exhaust...

Chromatin immunoprecipitation (ChIP) followed by microarray-based (ChIP-Chip) or next-generation sequencing-based (ChIP-Seq) analysis has been established as a powerful and widely used method to investigate DNA-protein interactions relative to a genomic location in vivo. Here, we present a ChIP-Chip protocol, which utilizes an alternative, easier amplification protocol and when using high-quali...

Epigenetic studies increasingly require analysis of a small number of cells that are of one specific type and derived from patients or animals. In this report, we demonstrate a simple microfluidic device that integrates sonication and immunoprecipitation (IP) for epigenetic assays, such as chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). By incorporating an u...

Retina Implants have the purpose to restore visual perception in blind patients suffering from retinitis pigmentosa (RP) and eventually also age-related macular degeneration (AMD). Electrical stimulation of the remaining retinal nerve fibre layers leads to visual sensations (phosphenes) [1, 2]. Our retina implant consisting of a light sensitive CMOS chip (1,500 pixels) and 16 separate direct st...

A one-dimensional, visual tracking chip has been implemented using neuromorphic, analog VLSI techniques to model selective visual attention in the control of saccadic and smooth pursuit eye movements. The chip incorporates focal-plane processing to compute image saliency and to select a target feature for tracking. The target position and direction of motion are reported as the target moves acr...

Patients and methods 34 patients were selected on clinical grounds by members of the French reference center for autoinflammatory diseases (CeReMAI). 9 of them were considered positive control samples as they had previously known variants (by Sanger sequencing) and were run in parallel for methodological validation. A custom panel of 108kb was designed to capture the genomic regions of interest...

Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for the analysis of ChIP-Chip experiments. The growing popularity of ChIP-seq spurred the development o...

UNLABELLED We present a fast, versatile and adaptive-multiscale algorithm for analyzing a wide-variety of DNA microarray data. Its primary application is in normalization of array data as well as subsequent identification of 'enriched targets', e.g. differentially expressed genes in expression profiling arrays and enriched sites in ChIP-on-chip experimental data. We show how to accommodate the ...

We have developed the first fully integrated microfluidic system for DNA sequencing-by-synthesis. Using this chip and fluorescence detection, we have reliably sequenced up to 4 consecutive bps. The described sequencer can be integrated with other microfluidic components on the same chip to produce true lab-on-a-chip technology. The surface chemistry that was designed to anchor the DNA to elasto...

This document describes the BCRANK R package. BCRANK[1] is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be app...