Publications associées à InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Collimation simulations for the FCC-ee

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

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

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

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

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

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

Scalable Logic Rewriting Using Don’t Cares

Giovanni De Micheli, Alessandro Tempia Calvino

Logic rewriting is a powerful optimization technique that replaces small sections of a Boolean network with better implementations. Typically, exact synthesis is used to compute optimum replacement on-the-fly, with possible support for Boolean don't cares. ...

2024

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

Chloé Rogg, Yimon Aye

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

Numerical tools for burning plasmas

Laurent Villard, Alberto Bottino, Jonathan Graves, Ben McMillan, Emmanuel Lanti, Emanuele Poli, Xiao Wang, Baruch Rofman

The software stack under development within a European coordinated effort on tools for burning plasma modelling is presented. The project is organised as a Task (TSVV Task 10) under the new E-TASC initiative (Litaudon et al 2022 Plasma Phys. Control. Fusio ...

IOP Publishing Ltd2023

Media Coverage of 3D Visual Tools Used in Urban Participatory Planning

Jens Ingensand, Thibaud Nicolas Chassin

The opportunities provided by adopting digitally-generated visual tools in urban participatory planning are compelling. These visual tools can promote interactions between authorities and citizens and among citizens. However, the urban participatory practi ...

IGI GLOBAL2023

Understanding Revision Behavior in Adaptive Writing Support Systems for Education

Tanja Christina Käser Jacober, Paola Mejia Domenzain, Luca Mouchel, Thiemo Wambsganss

Revision behavior in adaptive writing support systems is an important and relatively new area of research that can improve the design and effectiveness of these tools, and promote students' self-regulated learning (SRL). Understanding how these tools are u ...

Zenodo2023

Digital Intervention for Collaborative and Human-Centered Activities in Design-Based Learning Scenarios

Denis Gillet, Isabelle Barbara Marie-Hélène Cardia

Training science and engineering students to become responsible citizens and professionals requires novel and creative pedagogical approaches, such as design thinking. This concept relies on processes and tools to develop creativity and problem-solving ski ...

IEEE2023

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Cédric Terrier, Daniel Alexander Florez Orrego, Michel Lopez, Meire Ellen Gorete Ribeiro Domingos

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

Assessing the readiness of municipalities for digital process innovation

Mert Duygan

Pre-adoption phases of innovation are understudied in the innovation literature. This article addresses preadoption phases of innovation by running a prospective analysis. We assess the readiness of municipalities for the adoption of a digital tool that br ...

ELSEVIER SCI LTD2023

Evaluation of teachers’ orchestration tools usage in robotic classrooms

Pierre Dillenbourg, Sina Shahmoradi, Barbara Bruno, Aditi Kothiyal

Teachers’ self-efficacy in managing classrooms is an important consideration when it comes to bringing educational robots to classrooms. Orchestration tools support teachers by providing awareness indicators of students’ progress as well as levers to contr ...

2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Development of a Robotic Microsurgeon for Embryonic Research

Ece Özelçi

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

EPFL2023