Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

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Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Traditional martial arts are treasures of humanity's knowledge and critical carriers of sociocultural memories throughout history. However, such treasured practices have encountered various challenges in knowledge transmission and now feature many entries ...

One-dimensional materials have gained much attention in the last decades: from carbon nanotubes to ultrathin nanowires to few-atom atomic chains, these can all display unique electronic properties and great potential for next-generation applications. Exfol ...

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

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 ...

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

Telomeres are the nucleoprotein structures at the ends of linear chromosomes. Telomeres are transcribed into long non-coding Telomeric Repeat-Containing RNA (TERRA), whose functions rely on its ability to associate with telomeric chromatin. The conserved T ...

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

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The dynamic genetic determinants of increased transcriptional divergence in spermatids

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Opportunities and challenges in design and optimization of protein function

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Formaldehyde regulates one-carbon metabolism and epigenetics

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Ontology-based Knowledge Representation for Traditional Martial Arts

Searching for the Thinnest Metallic Wire

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Chromatin modules and their implication in genomic organization and gene regulation

Landscapes of DNA Mechanics and Genomes

The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase(+) cells and telomeric recombination in ALT(+) cells

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Generative power of a protein language model trained on multiple sequence alignments

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring