Comparison of computational methods for the identification of topologically associating domains
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The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...
Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...
Geometric properties of lattice quantum gravity in two dimensions are studied numerically via Monte Carlo on Euclidean Dynamical Triangulations. A new computational method is proposed to simulate gravity coupled with fermions, which allows the study of int ...
We propose a framework for the construction of 4D scientific models for cities of the past. It leverages both the use of computational methods for bootstrapping, and a collaborative interface for visualisation and edition. This permits to continuously enri ...
While the idea of technology as a driving force of history and society has been extensively studied in the history of the Industrial Revolutions, little attention has been paid to the social perception of those technologies. This thesis focuses on the disc ...
This journal club by Elisa Oricchio highlights two studies published in 2012, which used chromatin conformation capture methods to detect the formation of self-interacting chromatin regions, known as topologically associating domains (TADs). ...
An assembly refers to a collection of parts joined together to achieve a specific form and/or functionality. Assemblies make it possible to fabricate large and complex objects with several small and simple parts. Such parts can be assembled and disassemble ...
We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...
Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...