Laboratory of Biological Network Characterization

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Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Investigating the dynamic activities of protein expression and signaling in living organisms is a crucial focus of intense research aimed at elucidating the processes that underlie disease progression and improving treatments and drug development. Resolvin ...

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

Transcription factor binding to a single binding site on DNA and its functional consequence in a promoter context are beginning to be relatively well understood. However, binding to clusters of sites has yet to be characterized in depth, and the functional ...

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fa ...

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional co ...

Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is a ...

In phenylketonuria, absence or malfunction of the phenylalanine hydroxylase enzyme results in toxic accumulation of phenylalanine in the body. An injectable recombinant enzyme therapy was recently approved and has the potential to improve the quality of li ...

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding ...

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduce ...

Laboratory of Biological Network Characterization

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Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

Chromatin modules and their implication in genomic organization and gene regulation

Statistical learning quantifies transposable element-mediated cis-regulation

Label-free plasmonic microarray for multiplexed analysis of cells and tumor organoids

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Systematic analysis of biomolecular binding reactions using microfluidic systems

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities

Induction of a chromatin boundary in vivo upon insertion of a tad border

Toward a mechanistic understanding of variable chromatin modules

Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platforms

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Circadian dynamics of RNA localisation in the mammalian liver

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors