Romain Fernand Pietro Groux

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Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the necessary information that the organism will ever need, from its development to a mature individual to environment specific resp ...

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

We present SPar-K (Signal Partitioning with K-means), a method to search for archetypical chromatin architectures by partitioning a set of genomic regions characterized by chromatin signal profiles around ChIP-seq peaks and other kinds of functional sites. ...

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Romain Fernand Pietro Groux

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Computational study of transcription factor binding sites

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

SPar-K: a method to partition NGS signal data

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

SMiLE-seq identifies binding motifs of single and dimeric transcription factors