Publications associées à Improving inference of transcriptional regulatory networks based on network evolutionary models

Publications associées (38)

OPTIMAL TRANSPORT-INSPIRED DEEP LEARNING FRAMEWORK FOR SLOW-DECAYING KOLMOGOROV \bfitn-WIDTH PROBLEMS: EXPLOITING SINKHORN LOSS AND WASSERSTEIN KERNEL

Reduced-order models (ROMs) are widely used in scientific computing to tackle high-dimensional systems. However, traditional ROM methods may only partially capture the intrinsic geometric characteristics of the data. These characteristics encompass the und ...

2025

High-dimensional learning of narrow neural networks

Hugo Chao Cui

Recent years have been marked with the fast-pace diversification and increasing ubiquity of machine learning (ML) applications. Yet, a firm theoretical understanding of the surprising efficiency of neural networks (NNs) to learn from high-dimensional data ...

2025

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

Improving Lipschitz-Constrained Neural Networks by Learning Activation Functions

Michaël Unser, Dimitris Perdios, Alexis Marie Frederic Goujon, Pakshal Narendra Bohra, Sebastian Jonas Neumayer, Stanislas Ducotterd

Lipschitz-constrained neural networks have several advantages over unconstrained ones and can be applied to a variety of problems, making them a topic of attention in the deep learning community. Unfortunately, it has been shown both theoretically and empi ...

2024

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Wigner kernels: Body-ordered equivariant machine learning without a basis

Michele Ceriotti, Sergey Pozdnyakov, Filippo Bigi

Machine-learning models based on a point-cloud representation of a physical object are ubiquitous in scientific applications and particularly well-suited to the atomic-scale description of molecules and materials. Among the many different approaches that h ...

AIP Publishing2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Didier Trono, Evaristo Jose Planet Letschert

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 ...

2024

Predicting electronic screening for fast Koopmans spectral functional calculations

Nicola Marzari

Koopmans spectral functionals are a powerful extension of Kohn-Sham density-functional theory (DFT) that enables the prediction of spectral properties with state-of-the-art accuracy. The success of these functionals relies on capturing the effects of elect ...

2024

ConGeo: Robust Cross-View Geo-Localization Across Ground View Variations

Devis Tuia, Antoine Bosselut, Javiera Francisca Castillo Navarro, Syrielle Mathilde Marie Montariol, Li Mi

Cross-view geo-localization aims at localizing a ground-level query image by matching it to its corresponding geo-referenced aerial view. In real-world scenarios, the task requires accommodating diverse ground images captured by users with varying orientat ...

Springer Cham2024

Optimizing Dynamic Aperture Studies with Active Learning

Tatiana Pieloni, Mike Seidel, Davide Di Croce, Ekaterina Krymova

Dynamic aperture is an important concept for the study of non-linear beam dynamics in circular accelerators. It describes the extent of the phase-space region where a particle's motion remains bounded over a given number of turns. Understanding the feature ...

Iop Publishing Ltd2024

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Nagammal Neelagandan

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

Amer Assoc Advancement Science2024

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

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 ...

ROYAL SOC2023

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Evaristo Jose Planet Letschert, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Fast Parallel Algorithms for Enumeration of Simple, Temporal, and Hop-constrained Cycles

Paolo Ienne, Kubilay Atasu, Jovan Blanusa

Cycles are one of the fundamental subgraph patterns and being able to enumerate them in graphs enables important applications in a wide variety of fields, including finance, biology, chemistry, and network science. However, to enable cycle enumeration in r ...

Assoc Computing Machinery2023

Fast Parallel Algorithms for Enumeration of Simple, Temporal, and Hop-Constrained Cycles

Paolo Ienne, Kubilay Atasu, Jovan Blanusa

Finding cycles in directed graphs enables important applications in various domains such as finance, biology, chemistry, and network science. However, as the size of graph datasets continues to grow, it becomes increasingly difficult to discover cycles wit ...

arXiv2023

Chromatin modules and their implication in genomic organization and gene regulation

Judith Franziska Kribelbauer, Bart Deplancke, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023