Publications associées à Nuclear Receptor Rev-erb Alpha (Nr1d1) Functions in Concert with Nr2e3 to Regulate Transcriptional Networks in the Retina

Neuroprotection in the Retina: From Preventing Inflammatory Cell Death to Promoting Vascular Stability in the Central Nervous System

Glaucoma is one of the leading causes of irreversible blindness worldwide. Glaucoma is defined clinically as the presence of optic nerve head (ONH) degeneration and progressive loss of retinal ganglion cells (RGCs). Intra-ocular pressure (IOP) has been con ...

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

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

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

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

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

Anti-miR-873-5p improves alcohol-related liver disease by enhancing hepatic deacetylation via SIRT1

Kristina Schoonjans, Petar Petrov

Background & Aims: Current therapies for the treatment of alcohol-related liver disease (ALD) have proven largely ineffective. Patients relapse and the disease progresses even after liver transplantation. Altered epigenetic mechanisms are characteristic of ...

Elsevier2024

Colloidal self-assembly of soft neural interfaces from injectable photovoltaic microdevices

Mahmut Selman Sakar, Murat Kaynak, Zhangjun Huang, Haiyan Jia

Biomimetic retinas with a wide field of view and high resolution are in demand for neuroprosthetics and robot vision. Conventional neural prostheses are manufactured outside the application area and implanted as a complete device using invasive surgery. He ...

2023

Neuronal migration prevents spatial competition in retinal morphogenesis

Martin Weigert

The concomitant occurrence of tissue growth and organization is a hallmark of organismal development(1-3). This often means that proliferating and differentiating cells are found at the same time in a continuously changing tissue environment. How cells ada ...

NATURE PORTFOLIO2023

Statistical physics of periodic biological processes

Lorenzo Talamanca

Earth rotation around its axis imposes a 24-hour rhythmicity to all life on the planet. Rather than passively responding to these periodic changes, nature has given us an internal timekeeper, the circadian clock, to anticipate to our advantage the fluctuat ...

EPFL2023

Influence of macular pigment on the sensitivity to discomfort glare from daylight

Marilyne Andersen, Jan Wienold, Sneha Jain

Understanding the factors that influence the human perception of glare is necessary to properly address glare risks in buildings and achieve comfortable visual environments, especially in the workplace. Yet large inter-individual variabilities in glare per ...

Nature Research2023

Statistical learning quantifies transposable element-mediated cis-regulation

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

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

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Judith Franziska Kribelbauer, 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

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

Felix Naef, Cédric Gobet, Lorenzo Talamanca

The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an a ...

American Association for the Advancement of Science2023

Exploring the role of transcriptional and post-transcriptional processes in mRNA co-expression

Benjamin Joao Clément Antonin Hadrien Martin

Co-expression of two or more genes at the single-cell level is usually associated with functional co-regulation. While mRNA co-expression-measured as the correlation in mRNA levels-can be influenced by both transcriptional and post-transcriptional events, ...

Wiley2023

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

The circadian clock time tunes axonal regeneration

Thomas Haynes Hutson

Nerve injuries cause permanent neurological disability due to limited axonal regeneration. Injury-dependent and-independent mechanisms have provided important insight into neuronal regeneration, however, common denominators underpinning regeneration remain ...

Cell Press2023

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

Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling

Felix Naef, Nicholas Edward Phillips

Wearable biosensors and smartphone applications can measure physiological variables over multiple days in free-living conditions. We measure food and drink ingestion, glucose dynamics, physical activity, heart rate (HR), and heart rate variability (HRV) in ...

CELL PRESS2023