Publications associées à CleanEx: new data extraction and merging tools based on MeSH term annotation

Publications associées (33)

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

Integrating very high resolution environmental proxies in genotype-environment association studies

Stéphane Joost, Kevin Leempoel, Annie Sandrine Guillaume

Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics ...

Wiley2024

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

Maria Brbic

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 Publishing Group2024

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

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

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

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

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

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

ms3: A parser for MuseScore files, serving as data factory for annotated music corpora

Martin Alois Rohrmeier, Johannes Hentschel

The Python library ms3 makes scores (symbolic representations of music) operational for computational approaches by representing their contents as sets of tabular files. Music scores represent relations between sounding events by graphical means. The Free ...

2023

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Maria Brbic

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We c ...

American Association for the Advancement of Science2023

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

Digital reconstruction of the mammalian spinal cord: from anatomical reference volume to cell type atlas of the mouse spinal cord

Ihor Kuras

The spinal cord is an elongated nervous structure that together with the brain forms the central nervous system. It relays sensory and motor information between the brain and the body, thus controlling most somatic and autonomic body functions. In recent y ...

EPFL2023

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

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Evaristo Jose Planet Letschert, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Marius Alexandru Botos Rogozsan

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Nature Portfolio2023

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

Silja Michelle Placzek

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

EPFL2023

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Sandrine Gerber, Mounir Driss Mensi, Perrine Agnes Edith Robin, Lucas Mayoraz, Alireza Kavand

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

2023