Publication

Landscapes of DNA Mechanics and Genomes

Related publications (29)

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

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

Seeking the new, learning from the unexpected: Computational models of surprise and novelty in the brain

Alireza Modirshanechi

Human babies have a natural desire to interact with new toys and objects, through which they learn how the world around them works, e.g., that glass shatters when dropped, but a rubber ball does not. When their predictions are proven incorrect, such as whe ...

EPFL2024

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

Frustrated magnets in the limit of infinite dimensions: Dynamics and disorder-free glass transition

Achille Mauri

We study the statistical mechanics and the equilibrium dynamics of a system of classical Heisenberg spins with frustrated interactions on a d -dimensional simple hypercubic lattice, in the limit of infinite dimensionality d -> infinity . In the analysis we ...

Amer Physical Soc2024

CONTROL OF HYPERBOLIC AND PARABOLIC EQUATIONS ON NETWORKS AND SINGULAR LIMITS

Nicola De Nitti

vanishing viscosity, networks. This work has received funding from the Alexander von Humboldt-Professorship program, the Transregio 154 Project "Mathematical Modelling, Simulation and Optimization Using the Example of Gas Networks" of the DFG, the grant PI ...

Amer Inst Mathematical Sciences-Aims2024

Interpret3C: Interpretable Student Clustering Through Individualized Feature Selection

Julian Thomas Blackwell, Tanja Christina Käser Jacober, Paola Mejia Domenzain, Vinitra Swamy, Isadora Alves de Salles

Clustering in education, particularly in large-scale online environments like MOOCs, is essential for understanding and adapting to diverse student needs. However, the effectiveness of clustering depends on its interpretability, which becomes challenging w ...

2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

Planning urban proximities: An empirical analysis of how residential preferences conflict with the urban morphologies and residential practices

Vincent Kaufmann, Luca Giovanni Pattaroni, Marc-Edouard Baptiste Grégoire Schultheiss

Urban proximity planning is foreseen as a solution to foster a “sustainable” city, including economic viability, environmental soundness and social inclusivity. This paper focuses on the inclusivity aspects by questioning the adoption of urban proximities: ...

2024

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

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

Zhidian Zhang

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 ...

EPFL2024

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

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

Chromosome organization shapes replisome dynamics in Caulobacter crescentus

Suliana Manley, Laurent Casini, Chen Zhang

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial specie ...

Nature Portfolio2024

Holography and localization of information in quantum gravity

Kyriakos Papadodimas, Alexandre Mathieu Frédéric Belin

Within the AdS/CFT correspondence, we identify a class of CFT operators which represent diff-invariant and approximately local observables in the gravitational dual. Provided that the bulk state breaks all asymptotic symmetries, we show that these operator ...

Springer Nature2024

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

On Speed and Advantage : Results in Information Velocity and Monitoring Problems

Reka Inovan

Information theory has allowed us to determine the fundamental limit of various communication and algorithmic problems, e.g., the channel coding problem, the compression problem, and the hypothesis testing problem. In this work, we revisit the assumptions ...

EPFL2024

Control of nuclear envelope dynamics during acute ER stress by LINC complexes disassembly and selective, asymmetric autophagy of the outer nuclear membrane

Maurizio Molinari

The endoplasmic reticulum (ER) extends to the outer (ONM) and the inner (INM) nuclear membrane forming the nuclear envelope (NE) that delimits the nucleoplasm containing the cell genome. Unfolded protein responses (UPRs) and reticulophagy responses increas ...

Taylor & Francis Inc2024