Publications related to Evaluating synteny for improved comparative studies

Related publications (30)

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

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

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

Extensions of Peer Prediction Incentive Mechanisms

Adam Julian Richardson

As large, data-driven artificial intelligence models become ubiquitous, guaranteeing high data quality is imperative for constructing models. Crowdsourcing, community sensing, and data filtering have long been the standard approaches to guaranteeing or imp ...

EPFL2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

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

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

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ana Marija Jaksic

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

Ultrahigh-quality-factor micro- and nanomechanical resonators using dissipation dilution

Tobias Kippenberg, Nils Johan Engelsen, Alberto Beccari

Mechanical resonators are widely used in sensors, transducers and optomechanical systems, where mechanical dissipation sets the ultimate limit to performance. Over the past 15 years, the quality factors in strained mechanical resonators have increased by f ...

Nature Portfolio2024

Room-temperature quantum optomechanics using an ultralow noise cavity

Tobias Kippenberg, Nils Johan Engelsen, Alberto Beccari, Guanhao Huang

At room temperature, mechanical motion driven by the quantum backaction of light has been observed only in pioneering experiments in which an optical restoring force controls the oscillator stiffness1,2. For solid-state mechanical resonators in which oscil ...

Nature Portfolio2024

Data-driven statistical optimization of a groundwater monitoring network

Andrea Rinaldo

We propose a comparative study of three different methods aimed at optimizing existing groundwater monitoring networks. Monitoring piezometric heads in subsurface porous formations is crucial at regional scales to properly characterize the relevant subsurf ...

Elsevier2024

A state-of-the-art, systematic review of indoor environmental quality studies in work-from-home settings

Giorgia Chinazzo, Sarah Wael Ahmed Crosby

The COVID-19 pandemic has led to a significant increase in working from home worldwide, making the workfrom-home (WFH) setting a crucial context for studying the influence of indoor environmental quality (IEQ) on workers' well-being and productivity. A nar ...

Pergamon-Elsevier Science Ltd2024

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

A Practical Influence Approximation for Privacy-Preserving Data Filtering in Federated Learning

Boi Faltings, Panayiotis Danassis, Ljubomir Rokvic

Federated Learning by nature is susceptible to low-quality, corrupted, or even malicious data that can severely degrade the quality of the learned model. Traditional techniques for data valuation cannot be applied as the data is never revealed. We present ...

2023

Blue Brain Nexus: An open, secure, scalable system for knowledge graph management and data-driven science

Henry Markram, Henry Genet, Alejandra Garcia Rojas Martinez, Sean Lewis Hill, Huanxiang Lu, Mohameth François Sy, Samuel Claude Kerrien, Michaël Fernand Paul Dupont, Silvia Rosario Jimenez Tejeda, Bogdan Roman, Ian Lavriushev, Anna-Kristin Kaufmann, Didac Montero Mendez, Wojciech Adam Wajerowicz, Pierre-Alexandre Fonta, Kenneth William Pirman, Julien Antonin Machon, Jonathan Raël Lurie, Dhanesh Neela Mana, Natalia Stafeeva, Alexander Désiré Ulbrich, Carolina Johanna Elisabeth Lindqvist

Modern data-driven science often consists of iterative cycles of data discovery, acquisition, preparation, analysis, model building and validation leading to knowledge discovery as well as dissemination at scale. The unique challenges of building and simul ...

2023

incentive Mechanism Design for Responsible Data Governance: A Large-Scale Field Experiment

Boi Faltings, Naman Goel

A crucial building block of responsible artificial intelligence is responsible data governance, including data collection. Its importance is also underlined in the latest EU regulations. The data should be of high quality, foremost correct and representati ...

2023

Dynamism in the context of views out: A literature review

Marilyne Andersen, Caroline Karmann, Yunjoung Cho

Previous studies have shown that access to a satisfactory view to the outside with sufficient daylight is essential for building occupants' health and well-being. It has also been suggested that certain features of visual content improve view-out quality, ...

2023

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Christel Sybille Hassler

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at l ...

SPRINGERNATURE2023

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

On the Performance of Subjective Visual Quality Assessment Protocols for Nearly Visually Lossless Image Compression

Touradj Ebrahimi, Davi Nachtigall Lazzarotto, Michela Testolina

The past decades have witnessed rapid growth in imaging as a major form of communication between individuals. Due to recent advances in capture, storage, delivery and display technologies, consumers demand improved perceptual quality while requiring reduce ...

2023

Host-Pathogen Interactions Through the Genomic Lens

Zhi Ming Xu

Hosts and pathogens are involved in a long-standing evolutionary arms race characterized by successive rounds of evolution. Specifically, while hosts evolve resistance against infections, pathogens adapt to re-establish virulence. Since the signatures of t ...

EPFL2023