BlastR-fast and accurate database searches for non-coding RNAs

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Decentralized learning (DL) is an emerging approach that enables nodes to collaboratively train a machine learning model without sharing raw data. In many application domains, such as healthcare, this approach faces challenges due to the high level of hete ...

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, ...

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 ...

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) pr ...

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the abil ...

In this paper, we quantify weak protein-protein interactions in solution using cross-interaction chromatography (CIC) and surface plasmon resonance (SPR) and demonstrate that they can be modulated by the addition of millimolar concentrations of free amino ...

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 ...

We recently identified a novel ribonuclease in Bacillus subtilis called Rae1 that cleaves mRNAs in a translation-dependent manner. Rae1 is a member of the NYN/PIN family of ribonucleases and is highly conserved in the Firmicutes, the Cyanobacteria and the ...

Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...

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 ...

Bicyclic peptides are an attractive molecule format for the development of therapeutics and research tools. Our laboratory is specialized on the development of bicyclic peptide ligands by phage display. In brief, libraries of randompeptides each containing ...

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 ...

It has recently been speculated that long-time average quantities of hyperchaotic dissipative systems may be approximated by weighted sums over unstable invariant tori embedded in the attractor, analogous to equivalent sums over periodic orbits, which are ...

The complex mechanisms involved in cellular processes have been increasingly understood this past century and the central role of the DNA molecule has been recognized. The base pair sequence along a DNA fragment is observed not only to encode the genomic i ...

Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex ins ...

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 ...

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

For more than a century, it has been recognized that our genetic inheritance and our environment interact to shape who we are and how we act (nature vs. nurture ), and the study of genetics has allowed us to explain why traits can vary dramatically betwee ...

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...

BlastR-fast and accurate database searches for non-coding RNAs

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Fair Decentralized Learning

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Toward a mechanistic understanding of variable chromatin modules

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution

Modulating Weak Protein-Protein Cross-Interactions by the Addition of Free Amino Acids at Millimolar Concentrations

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

Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

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

Screening of structurally diverse bicyclic peptide libraries by phage display

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

Predicting chaotic statistics with unstable invariant tori

On the statistical physics of chains and rods, with application to multi-scale sequence-dependent DNA modelling

First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host

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

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

A Systems Approach to Identify Genetic and Environmental Regulators of Metabolism

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes