Publications associées à Lossy compression of quality scores in differential gene expression: A first assessment and impact analysis

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

Touradj Ebrahimi, Davi Nachtigall Lazzarotto, Michela Testolina

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

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

Bart Deplancke, Daniel Migliozzi, Hüseyin Baris Atakan, Mustafa Demir, Riccardo Dainese, Daniel Alpern, Dariia Gudkova, Gilles Weder

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

Stimulus-responsive assembly of nonviral nucleocapsids

Angela Steinauer

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

Nature Portfolio2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic, Ziang Li

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Portfolio2024

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

Alex Russell Lederer

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 ...

EPFL2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

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 ...

Nature Portfolio2024

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

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

SPEEDING UP KRYLOV SUBSPACE METHODS FOR COMPUTING f(A)b VIA RANDOMIZATION

Daniel Kressner, Alice Cortinovis

This work is concerned with the computation of the action of a matrix function f(A), such as the matrix exponential or the matrix square root, on a vector b. For a general matrix A, this can be done by computing the compression of A onto a suitable Krylov ...

Siam Publications2024

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

Hui Huang, Nils Rädecker

Objectives The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat str ...

BMC2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Early-life vitamin A treatment rescues neonatal infection-induced durably impaired tolerogenic properties of celiac lymph nodes

Jörn Pezoldt

Gut -draining mesenteric and celiac lymph nodes (mLNs and celLNs) critically contribute to peripheral tolerance toward food and microbial antigens by supporting the de novo induction of regulatory T cells (Tregs). These tolerogenic properties of mLNs and c ...

Cell Press2024

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

Touradj Ebrahimi, Vlad Hosu, Davi Nachtigall Lazzarotto, Michela Testolina

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

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

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

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

Touradj Ebrahimi, Evgeniy Upenik, Michela Testolina

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

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

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Didier Trono, Julien Léonard Duc, Christina Ernst

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

2023

Communication-efficient distributed training of machine learning models

Thijs Vogels

In this thesis, we explore techniques for addressing the communication bottleneck in data-parallel distributed training of deep learning models. We investigate algorithms that either reduce the size of the messages that are exchanged between workers, or th ...

EPFL2023