Publication

An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments

Publications associées (31)

Modeling, analysis, and design of complex biological networks

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Marius Alexandru Botos Rogozsan

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Nature Portfolio2023

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Sebastian Maerkl, Michael Andrew Crone, Hon Ming Andrew Yip, Evan James Olson, Shiyu Cheng

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

National Academy of Sciences2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Judith Franziska Kribelbauer, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Hybrid Quadratic Programming - Pullback Bundle Dynamical Systems Control

Aude Billard, Bernardo Fichera

Dynamical System (DS)-based closed-loop control is a simple and effective way to generate reactive motion policies that well generalize to the robotic workspace, while retaining stability guarantees. Lately the formalism has been expanded in order to handl ...

SPRINGER INTERNATIONAL PUBLISHING AG2023

Low-Rank Tensor Approximations for Solving Multimarginal Optimal Transport Problems\ast

Daniel Kressner, Christoph Max Strössner

By the addition of entropic regularization, multimarginal optimal transport problems can be trans-formed into tensor scaling problems, which can be solved numerically using the multimarginal Sinkhorn algorithm. The main computational bottleneck of this alg ...

SIAM PUBLICATIONS2023

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

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Mounir Driss Mensi, Sandrine Gerber, Lucas Mayoraz, Perrine Agnes Edith Robin, Alireza Kavand

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

2023

Accelerated deep self-supervised ptycho-laminography for three-dimensional nanoscale imaging of integrated circuits

Manuel Guizar Sicairos, Yi Jiang

Three-dimensional inspection of nanostructures such as integrated circuits is important for security and reliability assurance. Two scanning operations are required: ptychographic to recover the complex transmissivity of the specimen, and rotation of the s ...

2023