Publications associées à Identifying gene function and module connections by the integration of multispecies expression compendia

Publications associées (34)

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

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

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

Squalene Depletion in Skin Following Human Exposure to Ozone under Controlled Chamber Conditions

Shen Yang

A major component of human skin oil is squalene, a highly unsaturated hydrocarbon that protects the skin from atmospheric oxidants. Skin oil, and thus squalene, is continuously replenished on the skin surface. Squalene is also quickly consumed through reac ...

Amer Chemical Soc2024

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

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

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Nagammal Neelagandan

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

Amer Assoc Advancement Science2024

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

Two-particle Bose-Einstein correlations and their Lévy parameters in PbPb collisions at √sNN=5.02 TeV

Jian Wang, Matthias Finger, Qian Wang, Yiming Li, João Miguel das Neves Duarte, Matthias Wolf, Varun Sharma, Yi Zhang, Tian Cheng, Yixing Chen, Alexis Kalogeropoulos, Ioannis Papadopoulos, Hua Zhang, Siyuan Wang, Xin Chen, Michele Bianco, Sebastiana Gianì, Sun Hee Kim, Davide Di Croce, Jian Zhao, Rakesh Chawla, Jan Steggemann, Konstantin Androsov, Anna Mascellani, Federica Legger, Matteo Galli, Gabriele Grosso

Two -particle Bose-Einstein momentum correlation functions are studied for charged-hadron pairs in lead -lead collisions at a center -of -mass energy per nucleon pair of .'/sNN = 5.02 TeV. The data sample, containing 4.27 x 109 minimum bias events correspo ...

Amer Physical Soc2024

Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Stefano Coda, Stephan Brunner, Oleg Krutkin, Samuele Mazzi, Umesh Kumar, Mackenzie Peter-Fulford Van Rossem

Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...

IOP Publishing Ltd2024

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Moritz Hofer

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

EPFL2024

Sparse autoregressive neural networks for classical spin systems

Giuseppe Carleo, Dian Wu, Indaco Biazzo

Efficient sampling and approximation of Boltzmann distributions involving large sets of binary variables, or spins, are pivotal in diverse scientific fields even beyond physics. Recent advances in generative neural networks have significantly impacted this ...

Iop Publishing Ltd2024

High-performance deep spiking neural networks with 0.3 spikes per neuron

Wulfram Gerstner, Stanislaw Andrzej Wozniak, Guillaume Emmanuel Fernand Bellec, Ana Stanojevic, Angeliki Pantazi

Communication by rare, binary spikes is a key factor for the energy efficiency of biological brains. However, it is harder to train biologically-inspired spiking neural networks than artificial neural networks. This is puzzling given that theoretical resul ...

Springer Science and Business Media LLC2024

Stable parameterization of continuous and piecewise-linear functions

Michaël Unser, Alexis Marie Frederic Goujon, Joaquim Gonçalves Garcia Barreto Campos

Rectified-linear-unit (ReLU) neural networks, which play a prominent role in deep learning, generate continuous and piecewise-linear (CPWL) functions. While they provide a powerful parametric representation, the mapping between the parameter and function s ...

2023

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

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

Debates on the dorsomedial prefrontal/dorsal anterior cingulate cortex: insights for future research

Nicolas Clairis

The dorsomedial prefrontal cortex/dorsal anterior cingulate cortex (dmPFC/dACC) is a brain area subject to many theories and debates over its function(s). Even its precise anatomical borders are subject to much controversy. In the past decades, the dmPFC/d ...

Oxford Univ Press2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Maria del Carmen Sandi Perez

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

PERGAMON-ELSEVIER SCIENCE LTD2023

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Michael Andrew Crone, Evan James Olson, Sebastian Maerkl, Shiyu Cheng, Hon Ming Andrew Yip

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

National Academy of Sciences2023

Algebraic twists of GL(2) automorphic forms

Vignesh Arumugam Nadarajan

In this thesis we consider the problem of estimating the correlation of Hecke eigenvalues of GL2 automorphic forms with a class of functions of algebraic origin defined over finite fields called trace functions. The class of trace functions is vast and inc ...

EPFL2023