Publications related to Efficient use of accessibility in microRNA target prediction

Related publications (30)

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

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

Christina Ernst

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

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

Koopman-based Data-driven Robust Control of Nonlinear Systems Using Integral Quadratic Constraints

Alireza Karimi, Mert Eyuboglu

This paper introduces a novel method for data-driven robust control of nonlinear systems based on the Koopman operator, utilizing Integral Quadratic Constraints (IQCs). The Koopman operator theory facilitates the linear representation of nonlinear system d ...

2024

Soliton gas: Theory, numerics, and experiments

Andrey Gelash

The concept of soliton gas was introduced in 1971 by Zakharov as an infinite collection of weakly interacting solitons in the framework of Korteweg-de Vries (KdV) equation. In this theoretical construction of a diluted (rarefied) soliton gas, solitons with ...

Amer Physical Soc2024

Mean value theorems for collections of lattices with a prescribed group of symmetries

Nihar Prakash Gargava

Euclidean lattices are mathematical objects of increasing interest in the fields of cryptography and error-correcting codes. This doctoral thesis is a study on high-dimensional lattices with the motivation to understand how efficient they are in terms of b ...

EPFL2024

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

Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approa ...

Amer Chemical Soc2024

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

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

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Price Discrimination with Robust Beliefs

Thomas Alois Weber, Jun Han

This paper considers the problem of second-degree price discrimination when the type distribution is unknown or imperfectly specified by means of an ambiguity set. As robustness measure we use a performance index, equivalent to relative regret, which quant ...

Elsevier2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Degradation of EEG microstates patterns in subjective cognitive decline and mild cognitive impairment: Early biomarkers along the Alzheimer's Disease continuum?

Silvestro Micera

Alzheimer's disease (AD) pathological changes may begin up to decades earlier than the appearance of the first symptoms of cognitive decline. Subjective cognitive decline (SCD) could be the first pre-clinical sign of possible AD, which might be followed by ...

ELSEVIER SCI LTD2023

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

Antenna-coupled infrared nanospectroscopy of intramolecular vibrational interaction

Hatice Altug, Aurélian Michel John-Herpin

Many photonic and electronic molecular properties, as well as chemical and biochemical reactivities are controlled by fast intramolecular vibrational energy redistribution (IVR). This fundamental ultrafast process limits coherence time in applications from ...

National Academy of Sciences2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Solids that are also liquids: elastic tensors of superionic materials

Nicola Marzari, Tommaso Chiarotti, Giuliana Materzanini

Superionics are fascinating materials displaying both solid- and liquid-like characteristics: as solids, they respond elastically to shear stress; as liquids, they display fast-ion diffusion at normal conditions. In addition to such scientific interest, su ...

NATURE PORTFOLIO2023

Whole-genome doubling drives oncogenic loss of chromatin segregation

Juan Diaz Miyar, Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Ruxandra-Andreea Lambuta

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

NATURE PORTFOLIO2023

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Christof Holliger, Julien Maillard

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

Society for General Microbiology2023