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More than 100 thousand public datasets
posted on Jan 15, 2022
public data

SysFate takes the head of NGS-QC database
posted on Sep 01, 2018
SysFate takes the head of NGS-QC database
In Sept. 2018 the new team SysFate, founded by Marco Mendoza, takes the head of the maintenance and further developments of the NGS-QC database

H Gronemeyer at the College de France (May 9, 2017)
posted on May 24, 2017
Click to see video
H Gronemeyer discussed at the College de France the "Systems Biology of Retinoid Action" on May 9, 2017.

H Gronemeyer at the Colloque Annuel Institut Universitaire de France (May 17-19, 2017)
posted on May 24, 2017

H Gronemeyer gave at the Colloque Annuel Institut Universitaire de France (May 17-19, 2017), which was about "(A)Symmetries", a talk entitled "(A)Symmetries in biological systems and the underlying gene-regulatory principles". A video will be soon available.

Epimetheus, a genome-wide quantile-based multi-profile normaliz

posted on May 16, 2017
BMC Bioinformatics. 2017 May 12;18(1):259. doi: 10.1186/s12859-017-1655-3.
Background: Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today’s challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations. Critically, the most preferred Chromatin ImmunoPrecipitation-Sequencing (ChIP-Seq) is inherently prone to significant variability between assays, which poses significant challenge on comparative studies. One challenge concerns data normalization to adjust sequencing depth variation.

Results: Currently existing tools either apply linear scaling corrections and/or are restricted to specific genomic regions, which can be prone to biases. To overcome these restrictions without any external biases, we developed Epimetheus, a genome-wide quantile-based multi-profile normalization tool for histone modification data and related datasets.

Conclusions: Epimetheus has been successfully used to normalize epigenomics data in previous studies on X inactivation in breast cancer and in integrative studies of neuronal cell fate acquisition and tumorigenic transformation; Epimetheus is freely available to the scientific community.

Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neur
posted on Sep 26, 2016
Genome Research 20 September 2016
Cell lineages, which shape the body architecture and specify cell functions, derive from the integration of a plethora of cell intrinsic and extrinsic signals. These signals trigger a multiplicity of decisions at several levels to modulate the activity of dynamic gene regulatory networks (GRNs), which ensure both general and cell-specific functions within a given lineage, thereby establishing cell fates. Significant knowledge about these events and the involved key drivers comes from homogeneous cell differentiation models. Even a single chemical trigger, such as the morphogen all-trans retinoic acid (RA), can induce the complex network of gene-regulatory decisions that matures a stem/precursor cell to a particular step within a given lineage. Here we have dissected the GRNs involved in the RA-induced neuronal or endodermal cell fate specification by integrating dynamic RXRA binding, chromatin accessibility, epigenetic promoter epigenetic status and the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. Our data reveal how RA induces a network of transcription factors (TFs), which direct the temporal organization of cognate GRNs, thereby driving neuronal/endodermal cell fate specification. Modeling signal transduction propagation using the reconstructed GRNs indicated critical TFs for neuronal cell fate specification, which were confirmed by CRISPR/Cas9-mediated genome editing. Overall, this study demonstrates that a systems view of cell fate specification combined with computational signal transduction models provides the necessary insight in cellular plasticity for cell fate engineering. The present integrated approach can be used to monitor the in vitro capacity of (engineered) cells/tissues to establish cell lineages for regenerative medicine.

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factor
posted on Sep 26, 2016
Genome Medicine 19 May 2016
BACKGROUND: Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which coordinate the deregulation of gene networks during cell transformation are largely unknown.

METHODS: We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. We applied a systems biology approach by combining transcriptome and epigenome data for each step during transformation and integrated transcription factor-target gene associations in order to reconstruct the gene regulatory networks that are at the basis of the transformation process.

RESULTS: We identified 142 transcription factors and 24 chromatin remodelers/modifiers (CRMs) which are preferentially associated with specific co-expression pathways that originate from deregulated gene programming during tumorigenesis. These transcription factors are involved in the regulation of divers processes, including cell differentiation, the immune response, and the establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes which are not only co-regulated but also functionally related. Decortication of transcription factor targets enabled us to define potential key regulators of cell transformation which are engaged in RNA metabolism and chromatin remodeling.

CONCLUSIONS: We reconstructed gene regulatory networks that reveal the alterations occurring during human cellular tumorigenesis. Using these networks we predicted and validated several transcription factors as key players for the establishment of tumorigenic traits of transformed cells. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of the gene regulatory network that is altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

LOGIQA: a database dedicated to long-range genome interactions quality assessment
posted on May 17, 2016
BMC Genomics 16 May 2016
Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets. We have developed LOGIQA (, a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment. Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions. LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.

A protocol for the use of the NGS-QC Generator database
posted on May 01, 2016
NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

 2016;1418:243-65. doi: 10.1007/978-1-4939-3578-9_13.


The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators ( ) for >21,000 publicly available datasets.

F1000Research Article describing the NGS-QC Antibody certification system!!!
posted on Jan 15, 2016
ChIP-seq antibody certification

We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq). This certification comprises a standardized ChIP procedure and the attribution of a numerical quality control indicator (QCi) to biological replicate experiments. The QCi computation is based on a universally applicable quality assessment that quantitates the global deviation of randomly sampled subsets of ChIP-seq dataset with the original genome-aligned sequence reads. Comparison with a QCi database for >28,000 ChIP-seq assays were used to attribute quality grades (ranging from ‘AAA’ to ‘DDD’) to a given dataset. In the present report we used the numerical QC system to assess the factors influencing the quality of ChIP-seq assays, including the nature of the target, the sequencing depth and the commercial source of the antibody.  We have used this approach specifically to certify mono and polyclonal antibodies obtained from Active Motif directed against the histone modification marks H3K4me3, H3K27ac and H3K9ac for ChIP-seq. The antibodies received the grades AAA to BBC ( We propose to attribute such quantitative grading of all antibodies attributed with the label “ChIP-seq grade”.

NGS-QC database highlighted on the EMBO encounters news letter
posted on Nov 20, 2015
Quality control system and QC database for functional genomics

A free tool to improve data quality and the value of results obtained from data mining and integration

Gifu/Japan Retinoids meeting
posted on Oct 21, 2015
Marco Mendoza and Hinrich Gronemeyer provided an overview of the new developments performed around the NGS-QC Generator project
Marco Mendoza and Hinrich Gronemeyer provided an overview of the new developments performed around the NGS-QC Generator project

posted on Oct 14, 2014
Hinrich Gronemeyer has been ranked by ScienceWatch of Thomson Reuters among the world's most influential scientific minds 2014

Swiss German Galaxy Tour 2014
posted on Sep 04, 2014
Marco Mendoza presented the NGS-QC Generator tool at the 2nd Swiss Galaxy Workshop.

New Opinion Article in Genomics Data
posted on Aug 14, 2014
Assessing Quality Standards for ChIP-seq and related Massive parallel sequencing-generated datasets

Massive parallel DNA sequencing combined with chromatin immunoprecipitation and a large variety of DNA/RNA-enrichment methodologies are at the origin of data resources of major importance. Indeed these resources, available for multiple genomes, represent the most comprehensive catalogue of (i) cell, development and signal transduction-specified patterns of binding sites for transcription factors ('cistromes') and for transcription and chromatin modifying machineries, (ii) the patterns of specific local post-translational modifications of histones and DNA ('epigenome') or of regulatory chromatin binding factors. In addition, (iii) the resources specifying chromatin structure alterations are emerging. Importantly, these types of "omics" datasets populate increasingly public repositories and provide highly valuable resources for the exploration of general principles of cell function in a multi-dimensional genome-transcriptome-epigenome-chromatin structure context. However, data mining is critically dependent on the data quality, an issue that, surprisingly, is still largely ignored by scientists and well-financed consortia, data repositories and scientific journals. So what determines the quality of ChIP-seq experiments and the datasets generated therefrom and what refrains scientists from associating quality criteria to their data? In this 'opinion' we trace the various parameters that influence the quality of this type of datasets, as well as the computational efforts that were made until now to qualify them. Moreover, we describe a universal quality control (QC) certification approach that provides a quality rating for ChIP-seq and enrichment-related assays. The corresponding QC tool and a regularly updated database, from which at present the quality parameters of more than 8,000 data sets can be retrieved, are freely accessible at

NGS Symposium 2014
posted on Jul 11, 2014
Hinrich Gronemeyer presented the NGS-QC system at the NGS Symposium in the Max Planck Institute in Freiburg on July 11, 2014

FASEB Retinoids meeting
posted on May 14, 2014
Itasca Illinois; June 1-6, 2014
H. Gronemeyer and M.Mendoza have been invited to give a talk at the FASEB SRC: FASEB 2nd International Conference on Retinoids

Welcome to NGS-QC portal
posted on Apr 17, 2014

As you certainly know datasets obtained by enrichment-based technologies coupled to massive parallel sequencing (ChIP-seq, DNase-seq, FAIRE-seq, GRO-seq, MeDIP-seq, MRE-seq, …) can vary significantly, even in cases where for example the same cell types and antibodies are used for ChIP-seq. The complexity of these assays, differences in conditions (crosslinking, chromatin shearing, …) and variation in experimenter manipulation are aspects that contribute to these apparent variation. Our proprietary NGS-QC system represents the first universal solution for assessing quality descriptors for such kind of datasets, covers the largest collection of certified publicly available datasets and is freely available to the academic community. We are working further to develop this tool and expand the database to ultimately harbour all enrichment-based NGS profiles, such that the scientific community may count with a comprehensive resource of quality certified datasets. Furthermore, the NGS-QC Generator tool allows you to assess the quality of your own generated datasets, thus to decide at an early time point to continue the analysis or optimize conditions. The NGS-QC report can also help you to choose a sequencing depth to use to obtain a certain quality level. We invite all users to share their experience in using these tools, as well as your thoughts concerning the necessity of having quality descriptors for ChIP-seq and enrichment-related datasets, through this dedicated community forum.

ISMB 2014
posted on Apr 17, 2014

Marco A. Mendoza presented the NGS-QC tool at the Regulatory Genomics Special Interest Group (RegGenSIG) ISMB 2014; Boston.

Assessing Quality Standards for ChIP-seq and related Massive parallel sequencing-generated datasets

Frontiers in Genomics and Epigenetics
posted on Apr 17, 2014
M. Mendoza presented the NGS-QC concept at the Centre de Regulacio Genomica (CRG) Barcelona-Spain; 23rd May 2013

A quality control system for profiles obtained by ChIP sequencing

CRG Core Facilities Technology Symposium

ALPHY/PhyloSIB 2014
posted on Apr 17, 2014
M. Mendoza presented the NGS-QC concept at the Swiss-French meeting on Bioinformatics and Evolutionary Genomics Geneva Switzerland; 4-5 February 2014
A quality control system for profiles obtained by ChIP sequencing

Training on Galaxy:
posted on Apr 17, 2014
How to efficiently use the NGS-QC tool available through the customised Galaxy instance
Strasbourg France; 05 December 2013
Considering that the democratisation of the use of massive parallel sequencing applications is already taking place, we believe that the access to methodologies for assessing the quality of generated NGS profiles might follow this trend. For this reason, the NGS-QC Generator has been released as part of a customized instance of the web-based platform Galaxy. As part of a training on Galaxy organised by the IGBMC, we (i) Introduced the attendants to the use of NGS-QC Generator for the quality assessment of any NGS-generated datasets; (ii) illustrated the quality descriptors assessed for given datasets and compare them with those available in our publicly available QC database and (iii) provided some tips for the use of the NGS-QC database as a comprehensive resource for selecting optimal conditions for performing new NGS-assays.