Publications associées à Transcribing meetings with the AMIDA systems

Publications associées (34)

Nongenetic evolution of the tumor: from challenges to new therapeutic opportunities

The ability of cancer cells to change and adapt poses a critical challenge to identifying curative solutions. Tumor evolution has been extensively studied from a genetic perspective, to guide clinicians in selecting the most appropriate therapeutic option ...

WILEY2024

Mean value theorems for collections of lattices with a prescribed group of symmetries

Nihar Prakash Gargava

Euclidean lattices are mathematical objects of increasing interest in the fields of cryptography and error-correcting codes. This doctoral thesis is a study on high-dimensional lattices with the motivation to understand how efficient they are in terms of b ...

EPFL2024

Koopman-based Data-driven Robust Control of Nonlinear Systems Using Integral Quadratic Constraints

Alireza Karimi, Mert Eyuboglu

This paper introduces a novel method for data-driven robust control of nonlinear systems based on the Koopman operator, utilizing Integral Quadratic Constraints (IQCs). The Koopman operator theory facilitates the linear representation of nonlinear system d ...

2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

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

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

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Denis Duboule, Lucille Delisle, Alexandre Gauthier Aurèle Mayran, Hocine Rekaik, Célia Corinne Renée Bochaton

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

NATURE PORTFOLIO2023

Comparing end-tidal CO2, respiration volume per time (RVT), and average gray matter signal for mapping cerebrovascular reactivity amplitude and delay with breath-hold task BOLD fMRI

Stefano Moia

Cerebrovascular reactivity (CVR), defined as the cerebral blood flow response to a vasoactive stimulus, is an imaging biomarker with demonstrated utility in a range of diseases and in typical development and aging processes. A robust and widely implemented ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2023

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

Whole-genome doubling drives oncogenic loss of chromatin segregation

Juan Diaz Miyar, Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Ruxandra-Andreea Lambuta

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

NATURE PORTFOLIO2023

4M: Massively Multimodal Masked Modeling

David Mizrahi, Amir Roshan Zamir, Shuqing Teresa Yeo, Oguzhan Fatih Kar, Roman Christian Bachmann

Current machine learning models for vision are often highly specialized and limited to a single modality and task. In contrast, recent large language models exhibit a wide range of capabilities, hinting at a possibility for similarly versatile models in co ...

Neural Information Processing Systems (Nips)2023

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

Learning V1 Simple Cells with Vector Representation of Local Content and Matrix Representation of Local Motion

Yufan Ren

This paper proposes a representational model for image pairs such as consecutive video frames that are related by local pixel displacements, in the hope that the model may shed light on motion perception in primary visual cortex (V1). The model couples the ...

ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE2022

Algebra and geometry of link homology Lecture notes from the IHES 2021 Summer School

Oscar Salomon Kivinen

These notes cover the lectures of the first named author at 2021 IHES Summer School on "Enumerative Geometry, Physics and Representation Theory" with additional details and references. They cover the definition of Khovanov-Rozansky triply graded homology, ...

WILEY2022

A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819

Didier Trono, Gabriela Ecco

Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase reg ...

2022

Coxeter Combinatorics For Sum Formulas In The Representation Theory Of Algebraic Groups

Jonathan Gruber

Let G be a simple algebraic group over an algebraically closed field F of characteristic p >= h, the Coxeter number of G. We observe an easy 'recursion formula' for computing the Jantzen sum formula of a Weyl module with p-regular highest weight. We also d ...

AMER MATHEMATICAL SOC2022

From Undercomplete to Sparse Overcomplete Autoencoders to Improve LF-MMI Speech Recognition

Hervé Bourlard, Selen Hande Kabil

Starting from a strong Lattice-Free Maximum Mutual Information (LF-MMI) baseline system, we explore different autoencoder configurations to enhance Mel-Frequency Cepstral Coefficients (MFCC) features. Autoencoders are expected to generate new MFCC features ...

ISCA-INT SPEECH COMMUNICATION ASSOC2022

Epigenetic memory aids: Synaptic and molecular effects of HDAC inhibition that support memory formation

Allison Marie Burns

Learning and memory rely on synaptic communication in which intracellular signals are transported to the nucleus to stimulate transcriptional activation. Memory induced transcriptional increases are accompanied by alterations to the epigenetic landscape an ...

EPFL2022

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections

Didier Trono, Julien Paul André Pontis

The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, ...

Nature Portfolio2022