On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

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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 ...

Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription ...

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 basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members(1). Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-on ...

Background: Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performance computational tools. Despite the ...

The ratio of nuclear content to cytoplasmic volume (N/C ratio) is a key regulator driving the maternal-to -zy-gotic transition in most animal embryos. Altering this ratio often impacts zygotic genome activation and de-regulates the timing and outcome of em ...

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 ...

Metal plasticity is an inherently multiscale phenomenon due to the complex long-range field of atomistic dislocations that are the primary mechanism for plastic deformation in metals. Atomistic/Continuum (A/C) coupling methods are computationally efficient ...

The need for reproducible, credible, multiscale biological modeling has led to the development of standardized simulation platforms, such as the widely-used NEURON environment for computational neuroscience. Developing and maintaining NEURON over several d ...

Imaging technologies drive discovery in cell biology. Innovations in microscopy hardware, imaging methods and computational analysis of large-scale, complex datasets can increase imaging resolution, definition and allow access to new biology. We asked expe ...

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

The objective of meta-learning is to exploit knowledge obtained from observed tasks to improve adaptation to unseen tasks. Meta-learners are able to generalize better when they are trained with a larger number of observed tasks and with a larger amount of ...

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

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

Context transcription factors establish cooperative environments and mediate enhancer communication

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

Cooperation between bHLH transcription factors and histones for DNA access

lifex-fiber: an open tool for myofibers generation in cardiac computational models

The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica

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

Lattice Green's function method for Atomistic/Continuum coupling

Modernizing the NEURON Simulator for Sustainability, Portability, and Performance

Imaging cell biology

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Dif-MAML: Decentralized Multi-Agent Meta-Learning

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples