Chemical approach for the study of the 'kissing complex' of Moloney murine leukaemia Virus

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Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

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 ...

Background Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic c ...

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginn ...

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 ...

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) al ...

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

Transformers have been proven a successful model for a variety of tasks in sequence modeling. However, computing the attention matrix, which is their key component, has quadratic complexity with respect to the sequence length, thus making them prohibitivel ...

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...

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 ...

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

The intrinsic high entropy metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collatera ...

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 ...

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA ...

Chemical approach for the study of the 'kissing complex' of Moloney murine leukaemia Virus

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Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Recycling of Polymerase Chain Reaction (PCR) Kits

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

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Impact of phylogeny on structural contact inference from protein sequence data

De novo designed proteins: a study in engineering novel folds and functions

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Fast Transformers with Clustered Attention

Statistical physics of interacting proteins: Impact of dataset size and quality assessed in synthetic sequences

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

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

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

Circadian dynamics of RNA localisation in the mammalian liver

On the relevance of quality score metadata in genomic sequence data for omics applications

Electronic and structural dynamics in DNA single strands