Publications related to Deep learning approaches for conformational flexibility and switching properties in protein design

Predicting protein interactions using geometric deep learning on protein surfaces

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 Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

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

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

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

Anthony Marchand

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

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Computational drug development for membrane protein targets

Henning Paul-Julius Stahlberg, Pierre Vogel, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Felix Naef, Pierre Vandergheynst, Cédric Gobet, Mohan Vamsi Nallapareddy, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Niloufar Sharif

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

Elsevier Sci Ltd2024

Deep learning approach for identification of H II regions during reionization in 21-cm observations - II. Foreground contamination

Michele Bianco, Jean-Paul Richard Kneib, Emma Elizabeth Tolley, Tianyue Chen

The upcoming Square Kilometre Array Observatory will produce images of neutral hydrogen distribution during the epoch of reionization by observing the corresponding 21-cm signal. However, the 21-cm signal will be subject to instrumental limitations such as ...

Oxford Univ Press2024

Predicting the long-term collective behaviour of fish pairs with deep learning

Francesco Mondada, Alexandre Massoud Alahi, Vaios Papaspyros

Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social in ...

2024

Understanding generalization and robustness in modern deep learning

Maksym Andriushchenko

In this thesis, we study two closely related directions: robustness and generalization in modern deep learning. Deep learning models based on empirical risk minimization are known to be often non-robust to small, worst-case perturbations known as adversari ...

EPFL2024

Multi-temporal forest monitoring in the Swiss Alps with knowledge-guided deep learning

Devis Tuia, Thiên-Anh Claris Nguyen, Marc Conrad Russwurm, Gaston Jean Lenczner

Monitoring forests, in particular their response to climate and land use change, requires studying long time scales. While efficient deep learning methods have been developed to process short time series of satellite imagery, leveraging long time series of ...

Elsevier Science Inc2024

Glenohumeral joint force prediction with deep learning

Dominique Pioletti, Alexandre Terrier, Philippe Büchler, Patrick Goetti

Deep learning models (DLM) are efficient replacements for computationally intensive optimization techniques. Musculoskeletal models (MSM) typically involve resource-intensive optimization processes for determining joint and muscle forces. Consequently, DLM ...

Elsevier Sci Ltd2024

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot, Ling Hai

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic, Ziang Li

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Portfolio2024

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (1/6)

Jean-Philippe Thiran, Roser Vinals Terres

This dataset contains a collection of ultrafast ultrasound acquisitions from nine volunteers and the CIRS 054G phantom. For a comprehensive understanding of the dataset, please refer to the paper: Viñals, R.; Thiran, J.-P. A KL Divergence-Based Loss for In ...

Zenodo2024

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (2/6)

Jean-Philippe Thiran, Roser Vinals Terres

This dataset contains a collection of ultrafast ultrasound acquisitions from nine volunteers and the CIRS 054G phantom. For a comprehensive understanding of the dataset, please refer to the paper: Viñals, R.; Thiran, J.-P. A KL Divergence-Based Loss for In ...

EPFL Infoscience2024

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (3/6)

Jean-Philippe Thiran, Roser Vinals Terres

This dataset contains a collection of ultrafast ultrasound acquisitions from nine volunteers and the CIRS 054G phantom. For a comprehensive understanding of the dataset, please refer to the paper: Viñals, R.; Thiran, J.-P. A KL Divergence-Based Loss for In ...

Zenodo2024