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

Chattez avec Graph Search

Posez n’importe quelle question sur les cours, conférences, exercices, recherches, actualités, etc. de l’EPFL ou essayez les exemples de questions ci-dessous.

AVERTISSEMENT : Le chatbot Graph n'est pas programmé pour fournir des réponses explicites ou catégoriques à vos questions. Il transforme plutôt vos questions en demandes API qui sont distribuées aux différents services informatiques officiellement administrés par l'EPFL. Son but est uniquement de collecter et de recommander des références pertinentes à des contenus que vous pouvez explorer pour vous aider à répondre à vos questions.

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

Regulatory elements, such as enhancers and silencers, control transcription by establishing physical proximity to target gene promoters. Neurons in flies and mammals exhibit long-range three-dimensional genome contacts, proposed to connect genes with dista ...

Understanding how interacting particles approach thermal equilibrium is a major challenge of quantum simulators(1,2). Unlocking the full potential of such systems towards this goal requires flexible initial state preparation, precise time evolution and ext ...

Electrochemical Impedance Spectroscopy (EIS) and Equivalent Circuit Models (ECMs) are widely used to characterize the impedance and estimate parameters of electrochemical systems such as batteries. We use a generic ECM with ten parameters grouped to model ...

The self-assembly of molecular components into organized nanomaterials is a fundamental process observed in nature, crucial for various biological functions. Gaining a deepened understanding of the underlying self-assembly principles provides valuable insi ...

Why biological quality-control systems fail is often mysterious. Specifically, checkpoints such as the DNA damage checkpoint or the spindle assembly checkpoint are overriden after prolonged arrests allowing cells to continue dividing despite the continued ...

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 ...

Personalized ranking methods are at the core of many systems that learn to produce recommendations from user feedbacks. Their primary objective is to identify relevant items from very large vocabularies and to assist users in discovering new content. These ...

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 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 ...

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Context: Exploring the design space is an important process in a design task. In this study, we considered design space exploration for the learners in vocational education and training (VET). The goal of the study was to investigate how they explore the d ...

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted ...

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

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 ...

The nucleoprotein filament (NPF) is the fundamental element of homologous recombination (HR), a major mechanism for the repair of double-strand DNA breaks in the cell. The NPF is made of the damaged DNA strand surrounded by recombinase proteins, and its se ...

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 ...

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and ...

Though the effect of the recently identified mitochondrial NAD(+) transporter SLC25A51 on glucose metabolism has been described, its contribution to other NAD(+)-dependent processes throughout the cell such as ADP-ribosylation remains elusive. Here, we rep ...

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

Chattez avec Graph Search

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons

Thermalization and criticality on an analogue-digital quantum simulator

On the use of Cramér-Rao Lower Bound for least-variance circuit parameters identification of Li-ion cells

Exploring the self-assembly of supramolecular crystals with DNA tiles

Principles of checkpoint override

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

Dynamic Personalized Ranking

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

Electronic and structural dynamics in DNA single strands

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

How Florist Apprentices Explore Bouquet Designs: Supporting Design Space Exploration for Vocational Students

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Structural and DNA binding properties of mycobacterial integration host factor mIHF

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

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

Structural transitions and mechanochemical coupling in the nucleoprotein filament explain homology selectivity and Rad51 protein cooperativity in cellular DNA repair

Landscapes of DNA Mechanics and Genomes

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD(+) levels