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

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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

Analysis of accretion disc structure and stability using open code for vertical structure

Pascale Jablonka

Detailed chemical abundances of very metal-poor (VMP; [Fe/H] < -2) stars are important for better understanding the first stars, early star formation, and chemical enrichment of galaxies. Big on-going and coming high-resolution spectroscopic surveys provid ...

OXFORD UNIV PRESS2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Pablo Gainza Cirauqui, Michael Bronstein, Zander Harteveld, Andreas Scheck, Sarah Wehrle, Anthony Marchand, Alexandra Krina Van Hall-Beauvais, Freyr Sverrisson

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

Compilation and Design Space Exploration of Dataflow Programs for Heterogeneous CPU-GPU Platforms

Aurélien François Gilbert Bloch

Today's continued increase in demand for processing power, despite the slowdown of Moore's law, has led to an increase in processor count, which has resulted in energy consumption and distribution problems. To address this, there is a growing trend toward ...

EPFL2023

The Replica Project: Co-Designing a Discovery Engine for Digital Art History

Isabella Di Lenardo

This article explains how the Replica project is a particular case of different professionals coming together to achieve the digitization of a historical photographic archive, intersecting complementary knowledge specific to normally unconnected communitie ...

2022

Digitised Newspapers – A New Eldorado for Historians? Reflections on Tools, Methods and Epistemology

Maud Ehrmann

The application of digital technologies to historical newspapers has changed the research landscape historians were used to. An Eldorado? Despite undeniable advantages, the new digital affordance of historical newspapers also transforms research practices ...

De Gruyter2022

Strategic Insights into Engineering Parameters Affecting Cell Type-Specific Uptake of DNA-Based Nanomaterials

Maartje Martina Cornelia Bastings, Alice Comberlato, Hugo José Rodriguez Franco, Marianna Mainardi Koga

DNA-based nanomaterials are gaining popularity as uniform and programmable bioengineering tools as a result of recent solutions to their weak stability under biological conditions. The DNA nanotechnology platform uniquely allows decoupling of engineering p ...

American Chemical Society2022

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Anne-Florence Raphaëlle Bitbol, Nicola Dietler

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

Public Library Science2022

Bringing Functional Context to Emerging Proximity-mapping Proteomics Tools

Yimon Aye

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current st ...

SWISS CHEMICAL SOC2022