Publications related to Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

Related publications (31)

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

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

Subjective performance evaluation of bitrate allocation strategies for MPEG and JPEG Pleno point cloud compression

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

The recent rise in interest in point clouds as an imaging modality has motivated standardization groups such as JPEG and MPEG to launch activities aiming at developing compression standards for point clouds. Lossy compression usually introduces visual arti ...

Springer2024

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

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

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Jaspreet Singh Saini

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Amer Soc Microbiology2024

Electromagnetic Radiation of Implantable Antennas

Mingxiang Gao

In the development of implantable bioelectronics, the establishment of efficient wireless RF links between implants and external nodes is crucial, providing substantial contributions to the advancement of medical diagnosis, therapies, and basic science. Im ...

EPFL2024

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

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

Time vs. Truth: Age-Distortion Tradeoffs and Strategies for Distributed Inference

Yunus Inan

In 1948, Claude Shannon laid the foundations of information theory, which grew out of a study to find the ultimate limits of source compression, and of reliable communication. Since then, information theory has proved itself not only as a quest to find the ...

EPFL2023

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

JPEG AIC-3 Dataset: Towards Defining the High Quality to Nearly Visually Lossless Quality Range

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

Visual data play a crucial role in modern society, and the rate at which images and videos are acquired, stored, and exchanged every day is rapidly increasing. Image compression is the key technology that enables storing and sharing of visual content in an ...

2023

Evaluating the effect of sparse convolutions on point cloud compression

Touradj Ebrahimi, Davi Nachtigall Lazzarotto

The use of point clouds as an imaging modality has been rapidly growing, motivating research on compression methods to enable efficient transmission and storage for many applications. While compression standards relying on conven- tional techniques such as ...

2023

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

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

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

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

On the assessment of high-quality images: advances on the JPEG AIC-3 activity

Touradj Ebrahimi, Michela Testolina, Evgeniy Upenik

Recent advances in image compression have made it both possible and desirable for image quality to approach the visually lossless range. However, the most commonly used subjective visual quality assessment protocols, e.g. those reported in ITU-T Rec. BT.50 ...

2023

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

Evaluation of the impact of lossy compression on event camera-based computer vision tasks

Touradj Ebrahimi, Davi Nachtigall Lazzarotto, Bowen Huang

In the field of image acquisition, Dynamic Vision Sensors (DVS) present an innovative methodology, capturing only the variations in pixel brightness instead of absolute values and thereby revealing unique features. Given that the primary deployment of DVS ...

2023

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

Shafranov shift correction to the Furth-Yoshikawa scaling of tokamak adiabatic compression

Olivier Sauter

In 1970, Furth and Yoshikawa (1970 Phys. Fluids 13 2593-6) introduced the scalings of adiabatic plasma compression. Basically, if the shape of the external plasma boundary and the aspect ratio are preserved during the compression, then the density, kinetic ...

2023