Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays

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Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Climate changes influence lake hydrodynamics and radiation levels and thus may affect the fate and transport of waterborne pathogens in lakes. This study examines the impact of climate change on the fate, transport, and associated risks of four waterborne ...

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 ...

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 ...

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 evolution of the 3D morphology is at the center of many relevant biological processes ranging from cellular differentiation to cancer invasion and metastasis. Microscopy techniques, such as electron microscopy (EM), super-resolution (SR) optical micros ...

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 ...

DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...

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 ...

Biologically inspired solid-state nanopores are artificial openings or apertures in thin membranes similar to natural protein ion channels in a lipid bilayer of cell membranes. In solid-state nanopores, a thin insulating membrane with single or multiple po ...

Upon recognition of aberrantly located DNA, the innate immune sensor cyclic GMP-AMP synthase (cGAS) activates stimulator of IFN genes (STING)/IFN regulatory factor (IRF)3-driven antiviral responses. In this study, we characterized the ability of a specific ...

SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. De ...

Colorectal cancer (CRC) is one of the deadliest cancers worldwide. Despite extensive research in the field, new therapies targeting CRC are in urgent need. CRC is a highly heterogeneous disease with high levels of intra- and inter-patient heterogeneity. Ca ...

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outco ...

Using an unbiased high-throughput microRNA (miRNA)-silencing screen combined with functional readouts for mitochondrial oxidative capacity in C2C12 myocytes, we previously identified 19 miRNAs as putative regulators of skeletal muscle mitochondrial metabol ...

Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and ...

Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome ofM. lepraewas first described and subsequently ...

Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays

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Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Waterborne Virus Transport and Risk Assessment in Lake Geneva Under Climate Change

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

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

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

Time-Resolved Scanning Ion Conductance Microscopy and Single-Molecule Spectroscopy

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

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

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

2D MoS2 Nanopores: Wafer-scale Fabrication and Monolayer Stability for Long-term Single-Molecule Sensing

A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913

Host genomics of SARS-CoV-2 infection

Intestinal stem cells differentiation and its application in cancer therapy

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

MicroRNA-204-5p modulates mitochondrial biogenesis in C2C12 myotubes and associates with oxidative capacity in humans

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

Genomic Characterization of Mycobacterium lepraeto Explore Transmission Patterns Identifies New Subtype in Bangladesh