iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

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Publications associées (29)

Molecular reconstruction and simulation of the Neuron-Glia-Vasculature system

Polina Shichkova

The outstanding information processing capacity of the brain relies on numerous molecular mechanisms. It is an extremely energy-expensive function, which involves specialization and collaboration of different cell types. A common framework to study the com ...

EPFL2023

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

Technology Mapping Using Multi-output Library Cells

Giovanni De Micheli, Alessandro Tempia Calvino

Technology mapping transforms a technology-independent representation into a technology-dependent one given a library of cells. Even if technology libraries contain multi-output cells, state-of-the-art techniques fully exploit single-output cells only. Mul ...

2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Denis Duboule, Guillaume Andrey, Christopher Chase Bolt, Lucille Delisle, Aurélie Hintermann

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

Nature Portfolio2022

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

Didier Trono, Shaoline Sheppard, Evaristo Jose Planet Letschert, Christopher James Playfoot

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional co ...

2022

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Nina Vesel

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022

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