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

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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, ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

The evolution of airborne mapping witnesses the introduction of hybrid lidar-camera systems to enhance data collection, i.e. to obtain simultaneously high-density point-cloud and texture. Yet, the common adjustment of both optical data streams is a nontriv ...

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

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

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

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

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

Learning to Reason with Neural Networks: Principles and Methods

Predicting protein interactions using geometric deep learning on protein surfaces

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

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

Plasma state monitoring and disruption characterization using multimodal VAEs

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

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

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

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

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

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

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

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

On the Perspectives of Image-to-Lidar Constraints in Dynamic Network Optimisation