Publications related to The MIDI Degradation Toolkit: Symbolic Music Augmentation and Correction

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

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

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

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

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

On matching data and model in LF-MMI-based dysarthric speech recognition

Enno Hermann

In light of steady progress in machine learning, automatic speech recognition (ASR) is entering more and more areas of our daily life, but people with dysarthria and other speech pathologies are left behind. Their voices are underrepresented in the trainin ...

EPFL2023

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Sebastian Maerkl, Ragunathan Bava Ganesh

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

FRONTIERS MEDIA SA2022

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

Didier Trono, Helen Mary Rowe, 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

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors

Barbora Lavickova

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduce ...

EPFL2021

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Philipp Bucher, René Dreos

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy fol ...

NATURE PUBLISHING GROUP2019

Cell-free gene-regulatory network engineering with synthetic transcription factors

Sebastian Maerkl, Zoe Newell Swank, Nadanai Laohakunakorn

Gene-regulatory networks are ubiquitous in nature and critical for bottom-up engineering of synthetic networks. Transcriptional repression is a fundamental function that can be tuned at the level of DNA, protein, and cooperative protein-protein interaction ...

National Academy of Sciences2019

Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells

Onur Tidin

Cells live in ever-changing environments, thereby facing a variety of dynamic environmental signals. Environmental stimuli elicit intracellular responses through signaling pathways, which converge on transcriptional activation or repression of target genes ...

EPFL2018

Modeling and analysis of parts and devices of genetic regulation

Yves Berset

DNA encrypts the composition of the cellular material that is synthesized through transcription and translation. Never-theless, gene regulation mechanisms determine the final amount of transcribed and translated material. Transcription factors (TF) are a c ...

EPFL2018

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

Cédric Gobet

Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...

EPFL2018

A practical qPCR approach to detect TERRA, the elusive telomeric repeat-containing RNA

Joachim Lingner, Marianna Feretzaki

Telomeres, the heterochromatic structures that protect the ends of the chromosomes, are transcribed into a class of long non-coding RNAs, telomeric repeat-containing RNAs (TERRA), whose transcriptional regulation and functions are not well understood. The ...

2017

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous p ...

Royal Society of Chemistry2017

Rhythmic modulation of transcriptional burst frequency in circadian gene promoters

Damien Lionel Nicolas

Isogenic cells sharing a common environment present a large degree of heterogeneity in gene expression, and stochasticity inherent to transcription substantially participates in this cell-to-cell variability. Notably, a majority of mammalian genes are tran ...

EPFL2017

Parkin functionally interacts with PGC-1 proportional to to preserve mitochondria and protect dopaminergic neurons

Patrick Aebischer, Bernard Schneider, Graham Knott, Johan Auwerx, Darren Moore, Norman Lionel Moullan, Lu Zheng, Nathalie Marie Géraldine Bernard, Davide D'Amico

To understand the cause of Parkinson's disease (PD), it is important to determine the functional interactions between factors linked to the disease. Parkin is associated with autosomal recessive early-onset PD, and controls the transcription of PGC-1a, a m ...

Oxford University Press2017

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Felix Naef, Jonathan Aryeh Sobel, Guillaume Rey, Irina Krier, Nouria Hernandez, Bart Deplancke, Matteo Dal Peraro, Sunil Kumar Raghav, Frédéric Bruno Martin Gachon, Alexandra Styliani Kalantzi, Benjamin Dieter Weger

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

Public Library of Science2017

Eukaryotic transcription factor binding kinetics : a single-molecule and functional study

Andrea Callegari

Transcription represents a key regulatory step in gene expression and transcription factors (TFs) are the key molecular players of this process. TFs inhibit or promote the assembly of the transcriptional machinery by binding DNA and several co-factors. Whe ...

EPFL2016

Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids

Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Meltem Weger

Altered daily patterns of hormone action are suspected to contribute to metabolic disease. It is poorly understood how the adrenal glucocorticoid hormones contribute to the coordination of daily global patterns of transcription and metabolism. Here, we exa ...

Public Library Science2016

The effect of the functional interaction between PGC-1α and Parkin on mitochondrial quality control in Parkinson's disease

Lu Zheng

Although several genetic factors have been directly associated to Parkinsonâ s disease (PD), no single pathway has emerged to explain the etiology of this neurodegenerative disease. To further understand the cause of Parkinsonâ s disease (PD), it is ther ...

EPFL2016

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Felix Naef, Patrick Descombes, Cédric Gobet, Jingkui Wang, Florian Atger, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. Although rhythmic mRNA accumulation has been exte ...

National Academy of Sciences2015