Publications associées à Using phylogenetic relationships to improve the inference of transcriptional regulatory networks

Publications associées (18)

Dual Isotope Analysis Reveals Phylogenetic Patterns and Novel Insights Into Methoxy Group Synthesis of Structural Biomolecules in Leaf and Woody Plant Tissues

Stable carbon and hydrogen isotopes of wood methoxy groups (δ2Hmeth, δ13Cmeth), mainly sourced by structural biomolecules like lignin and pectin, provide important insights into climatic, hydrological and physiological conditions. This study systematically ...

Wiley2025

A modular toolbox for the optogenetic deactivation of transcription

Matteo Fiumara, Johannes Gräff, Davide Martino Coda

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered inducti ...

OXFORD UNIV PRESS2025

Tango: Extracting Higher-Order Feedback through State Inference

Mathias Josef Payer

Fuzzing is the de facto standard for automated testing. However, while coverage-guided fuzzing excels at code discovery, its effectiveness falters when applied to complex systems. One such class entails persistent targets whose behavior depends on the stat ...

Association for Computing Machinery2024

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

David Michael Suter, Natalya Katanayeva, Haitham Ahmed Shaban Ahmed, Armelle Inge Marie Eleonore Tollenaere

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

National Academy of Sciences2024

Mechanism of Chromatin Ubiquitination by PRC1 on the Single-Molecule Level

Alexandra Teslenko

Multicellular eukaryotic organisms contain identical genetic information within each cell, stored within the nucleus as chromatin fibers. The regulation of gene expression allows cell-type-specific temporal and spatial gene activation or repression despite ...

EPFL2024

Aligning random graphs with a sub-tree similarity message-passing algorithm

Lenka Zdeborová, Giovanni Piccioli

The problem of aligning Erdos-Renyi random graphs is a noisy, average-case version of the graph isomorphism problem, in which a pair of correlated random graphs is observed through a random permutation of their vertices. We study a polynomial time message- ...

IOP Publishing Ltd2022

Essential role of Cp190 in physical and regulatory boundary formation

Nicolas Jean Philippe Guex, Christian Iseli, Julien Dorier

Boundaries in animal genomes delimit contact domains with enhanced internal contact frequencies and have debated functions in limiting regulatory cross-talk between domains and guiding enhancers to target promoters. Most mammalian boundaries form by stalli ...

2022

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

Didier Trono, Bart Deplancke, Priscilla Turelli, Christian Axel Wandall Thorball, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Charlène Mireille Raymonde Raclot, Delphine Yvette L Grun, Christopher James Playfoot

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influen ...

2020

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

Riccardo Dainese

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

EPFL2019

Analysis of the S. pombe Meiotic Proteome Reveals a Switch from Anabolic to Catabolic Processes and Extensive Post-transcriptional Regulation

Viesturs Simanis, Marc Moniatte, Romain Hamelin, Florence Armand, Andrea Krapp, Lucien Fabrice Krapp, Diego Chiappe

Meiotic progression in S. pombe is regulated by stage-specific gene expression and translation, changes in RNA stability, expression of anti-sense transcripts, and targeted proteolysis of regulatory proteins. We have used SILAC labeling to examine the rela ...

2019

Efficient Learning from Comparisons

Lucas Maystre

Humans are comparison machines: comparing and choosing an item among a set of alternatives (such as objects or concepts) is arguably one of the most natural ways for us to express our preferences and opinions. In many applications, the analysis of data con ...

EPFL2018

Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation

Stewart Cole, Claudia Sala, Andrej Benjak, Anthony Vocat, Gaëlle Séraphine Kolly, Andréanne Lupien, Nina Theres Odermatt

A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the histone-like nucleoid-structuring protein, is one of these NAPs and protects Escherichia coli from foreign gene expression. Though lacking a ...

American Society for Microbiology2017

What are the Odds? Probabilistic programming in Scala

Tiark Rompf, Nada Amin, Sandro Stucki, Manohar Jonnalagedda

Probabilistic programming is a powerful high-level paradigm for probabilistic modeling and inference. We present Odds, a small domain-specific language (DSL) for probabilistic programming, embedded in Scala. Odds provides first-class support for random var ...

ACM2013

Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone

Joao Emanuel Felipe Gerhard

Identifying the structure and dynamics of synaptic interactions between neurons is the first step to understanding neural network dynamics. The presence of synaptic connections is traditionally inferred through the use of targeted stimulation and paired re ...

Public Library of Science2013

Cellular Heterogeneity During Embryonic Stem Cell Differentiation to Epiblast Stem Cells Is Revealed by the ShcD/RaLP Adaptor Protein

Daniel Constam, Anja Dietze

The Shc family of adaptor proteins are crucial mediators of a plethora of receptors such as the tyrosine kinase receptors, cytokine receptors, and integrins that drive signaling pathways governing proliferation, differentiation, and migration. Here, we rep ...

Wiley-Blackwell2012

Transcriptional Regulatory Networks across Species : Evolution, Inference, and Refinement

Xiuwei Zhang

The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...

EPFL2011

Exploiting Binary Abstractions in Deciphering Gene Interactions

Giovanni De Micheli, Abhishek Garg

We consider computationally reconstructing gene regulatory networks on top of the binary abstraction of gene expression state information. Unlike previous Boolean network approaches, the proposed method does not handle noisy gene expression values directly ...

2006

Engineered Streptomyces quorum-sensing components enable inducible siRNA-mediated translation control in mammalian cells and adjustable transcription control in mice

Florian Maria Wurm

BACKGROUND: Recent advances in functional genomics, gene therapy, tissue engineering, drug discovery and biopharmaceuticals production have been fostered by precise small-molecule-mediated fine-tuning of desired transgenes. METHODS: Capitalizing on well-ev ...

2005