Publications related to GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Collimation simulations for the FCC-ee

Tatiana Pieloni, Giovanni Iadarola, Milica Rakic, Bruce Roderik, Guillaume Clément Broggi, Félix Simon Carlier

The collimation system of the Future Circular Collider, operating with leptons (FCC-ee), must protect not only the experiments against backgrounds, but also the machine itself from beam losses. With a 17.8 MJ stored energy of the electron and positron beam ...

Iop Publishing Ltd2024

Development and clinical validation of computational imaging biomarkers for neurodegenerative diseases

Veronica Lily Ravano

Neurodegenerative and neuroinflammatory disorders often involve complex pathophysiological mechanisms that are â to this date â only partially understood. A more comprehensive understanding of those microstructural processes and their characterization ...

EPFL2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

From low-rank retractions to dynamical low-rank approximation and back

Daniel Kressner, Axel Elie Joseph Séguin, Gianluca Ceruti

In algorithms for solving optimization problems constrained to a smooth manifold, retractions are a well-established tool to ensure that the iterates stay on the manifold. More recently, it has been demonstrated that retractions are a useful concept for ot ...

Springer2024

SC-TPTP: An Extension of the TPTP Derivation Format for Sequent-Based Calculus

Simon Guilloud

Motivated by the transfer of proofs between proof systems, and in particular from first order automated theorem provers (ATPs) to interactive theorem provers (ITPs), we specify an extension of the TPTP derivation text format to describe proofs in first-ord ...

2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Yimon Aye, Chloé Rogg

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

WILEY-V C H VERLAG GMBH2023