Publications related to Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Related publications (38)

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

2025

Estimation of Stiffness Maps in Deforming Cells Through Optical Flow With Bounded Curvature

Michaël Unser

The stiffness of cells and of their nuclei is a biomarker of several pathological conditions. Current measurement methods rely on invasive physical probes that yield one or two stiffness values for the whole cell. However, the internal distribution of cell ...

Institute of Electrical and Electronics Engineers2025

Antagonism as a Foraging Strategy in Microbial Communities

Martin Ackermann, Lucas Pierre Antoine Paoli

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

AMER ASSOC ADVANCEMENT SCIENCE2025

SaliencyMix plus : Noise-Minimized Image Mixing Method With Saliency Map in Data Augmentation

Zhixiong Jin

Data augmentation is vital in deep learning for enhancing model robustness by artificially expanding training datasets. However, advanced methods like CutMix blend images and assign labels based on pixel ratios, often introducing label noise by neglecting ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2025

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Anaïs Betsabeh Haget, Maria Boulougouri

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

OXFORD UNIV PRESS2025

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

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

From roots to canopy: Unraveling the influence of species diversity on tree water relations under warmer and drier climates

Eugénie Isabelle Mas

The worsening of drought events with rising air temperature alters tree water relations causing severe hydraulic impairments and widespread forest mortality. Mixing tree species with contrasting hydraulic traits could reduce forest vulnerability to extreme ...

EPFL2024

Generation of LOD4 models for buildings towards the automated 3D modeling of BIMs and digital twins

Katrin Beyer, Frédéric Kaplan, Bryan German Pantoja Rosero, Alexander Michael Rusnak

An image-based methodology is presented for the automatic generation of geometric building models at LOD4, incorporating both interior and exterior geometrical information. Existing approaches often focus on simplified geometries for either exteriors or in ...

Elsevier BV2024

Tandem catalysis enables chlorine-containing waste as chlorination reagents

Paul Joseph Dyson, Xinbang Wu, Mingyang Liu

Chlorinated compounds are ubiquitous. However, accumulation of chlorine-containing waste has a negative impact on human health and the environment due to the inapplicability of common disposal methods, such as landfill and incineration. Here we report a su ...

Nature Portfolio2024

Tree diversity reduces variability in sapling survival under drought

Jingjing Liang, Charlotte Grossiord

Enhancing tree diversity may be important to fostering resilience to drought-related climate extremes. So far, little attention has been given to whether tree diversity can increase the survival of trees and reduce its variability in young forest plantatio ...

Wiley2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

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

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

Invasive palms have more efficient and prolonged CO2 assimilation compared to native sub-Mediterranean vegetation

Charlotte Grossiord, Christoph Bachofen, Janisse Deluigi, Thibaut Michel Georges Juillard

In sub-Mediterranean ecosystems, shade-tolerant broadleaf evergreens, especially the invasive Trachycarpus fortunei, are spreading uncontrollably in the forest understorey, impeding the regeneration of the native deciduous woody vegetation. Most invasive s ...

Elsevier2024

Horner-Wadsworth-Emmons olefination for bioconjugation

Yimon Aye

Through site-specific generation of intermediary reactive aldehydes, Horner-Wadsworth-Emmons olefination can now deliver selective functionalization of stable recombinant proteins and monoclonal antibodies, whilst preserving protein integrity. ...

Springernature2024

Organ-specific biotransformation in salmonids: Insight into intrinsic enzyme activity and biotransformation of three micropollutants

Kristin Schirmer

Aquatic ecosystems continue to be threatened by chemical pollution. To what extent organisms are able to cope with chemical exposure depends on their ability to display mechanisms of defense across different organs. Among these mechanisms, biotransformatio ...

Elsevier2024

Multilingual Contrastive Decoding via Language-Agnostic Layers Skipping

Chris Wendler

Decoding by contrasting layers (DoLa), is designed to improve the generation quality of large language models (LLMs) by contrasting the prediction probabilities between an early exit output (amateur logits) and the final output (expert logits).However, we ...

Association for Computational Linguistics (ACL)2024

Next-Generation Modeling of Cancer Using Organoids

Wouter Richard Karthaus, Jillian Rose Love

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Cold Spring Harbor Lab Press, Publications Dept2024

On the selection and effectiveness of pseudo-absences for species distribution modeling with deep learning

Devis Tuia, Benjamin Alexander Kellenberger, Nina Marion Aurélia Van Tiel, Lloyd Haydn Hughes, Robin Adrien Zbinden

Species distribution modeling is a highly versatile tool for understanding the intricate relationship between environmental conditions and species occurrences. However, the available data often lacks information on confirmed species absence and is limited ...

Elsevier2024