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

Related publications (43)

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

OXFORD UNIV PRESS2025

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

Julien Dorier

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 ...

Cold Spring Harbor Laboratory2025

Spectroscopy of two-dimensional interacting lattice electrons using symmetry-aware neural backflow transformations

Giuseppe Carleo, Jannes Willy E. Nys, Imelda Romero

Neural networks have shown to be a powerful tool to represent the ground state of quantum many-body systems, including fermionic systems. However, efficiently integrating lattice symmetries into neural representations remains a significant challenge. In th ...

NATURE PORTFOLIO2025

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

Giorgia Benegiamo

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 ...

2025

Learning to Reason with Neural Networks: Principles and Methods

Aryo Lotfi Jandaghi

This thesis focuses on understanding and improving the reasoning capabilities of neural networks. It develops theoretical results and empirical analyses to uncover reasoning potential and limitations, leveraging these insights to guide the design of improv ...

EPFL2025

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Computational design of complex protein folds and soluble analogs of membrane proteins

Casper Alexander Goverde

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

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

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Search for Pair Production of Heavy Particles Decaying to a Top Quark and a Gluon in the Lepton Plus Jets Final State in Proton-proton Collisions at √s=13 Tev

Jan Steggemann, Anna Mascellani, Joanna Malgorzata Wanczyk

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton-proton collisions at a center-of-mass energy of 13 TeV ...

SPRINGER2025

Plasma state monitoring and disruption characterization using multimodal VAEs

Giulio Romanelli, Olivier Sauter, Alessandro Pau, Yoeri Renier Johannes Poels, Cristina Venturini

When a plasma disrupts in a tokamak, significant heat and electromagnetic loads are deposited onto the surrounding device components. These forces scale with plasma current and magnetic field strength, making disruptions one of the key challenges for futur ...

IOP Publishing Ltd2025

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

The effect of hydration and dynamics on the mass density of single proteins

Lucas Sebastian Powell-Rudden

The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses molecular dynamics sim ...

2025

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Deep learning–based detection of generalized convulsive seizures using a wrist‐worn accelerometer

David Atienza Alonso, Jonathan Dan, Antoine Jérôme Spahr

Objective To develop and validate a wrist‐worn accelerometer‐based, deep‐learning tunable algorithm for the automated detection of generalized or bilateral convulsive seizures (CSs) to be integrated with off‐the‐shelf smartwatches. Methods We conducted a ...

Wiley2025

Modelleyen: Continual Learning and Planning via Structured Modelling of Environment Dynamics

Boi Faltings, Zeki Doruk Erden

The current machine learning paradigm relies on continuous representations and fixed neural network architectures to approximate environmental structures, leading to challenges with continual learning, internal structure design, and goal-directed behavior ...

Springer Science and Business Media Deutschland GmbH2025

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

K-space physics-informed neural network (k-PINN) for compressed spectral mapping and efficient inversion of vibrations in thin composite laminates

Olga Fink

The vibrational response of structural components carries valuable information about their underlying mechanical properties, health status and operational conditions. This underscores the need for the development of efficient physics-based inversion algori ...

Elsevier BV2025

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

Mario Paolone, Vladimir Sovljanski

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 ...

2024

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Paolo Pegolo

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Amer Chemical Soc2024