Publications associées à Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

Publications associées (47)

Abstract 4588: Cell states and resistance in colorectal cancer: What can we learn from patient-derived organoids?

Colorectal cancer (CRC) is among the three most commonly diagnosed cancers and one of the major causes of cancer-related morbidity and mortality. Despite the discovery of several predictive biomarkers, the 5-year survival rate for metastatic CRC is 15%. A ...

American Association for Cancer Research (AACR)2025

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, 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

Machine learning-enabled estimation of cardiac output from peripheral waveforms is independent of blood pressure measurement location in an in silico population

Ramin Mohammadi, Nikolaos Stergiopoulos, Georgios Rovas, Lydia Aslanidou, Sokratis Anagnostopoulos

Monitoring of cardiac output (CO) is a mainstay of hemodynamic management in the acutely or critically ill patient. Invasive determination of CO using thermodilution, albeit regarded as the gold standard, is cumbersome and bears risks inherent to catheteri ...

2025

Exploration and modulation of mechanical cues for enhanced cancer immunotherapy

Armand Kurum

The advent of immunotherapy, such as immune checkpoint blockade (ICB) and adoptive transfer of cytotoxic lymphocytes, has transformed the clinical care of cancer. However, a significant proportion of patients are resistant to immunotherapy or experience re ...

EPFL2024

Enhancing skin lesion classification: a CNN approach with human baseline comparison

Zaffar Ahmed Shaikh

This study presents an augmented hybrid approach for improving the diagnosis of malignant skin lesions by combining convolutional neural network (CNN) predictions with selective human interventions based on prediction confidence. The algorithm retains high ...

PeerJ2025

Development of cysteine cathepsin inhibitors combined with cell type-specific delivery for the treatment of B-cell lymphoma and solid tumors

Aaron Simone Petruzzella

Cysteine cathepsins proteases are enzymes that play essential physiological roles, but their activity is also associated to different aspects of cancer progression and to the development of other diseases. Therefore, cysteine cathepsins are relevant and pr ...

EPFL2024

On the added value of sequential deep learning for the upscaling of evapotranspiration

Devis Tuia

Estimating ecosystem-atmosphere fluxes such as evapotranspiration (ET) in a robust manner and at a global scale remains a challenge. Methods based on machine learning (ML) have shown promising results in achieving such upscaling, providing a complementary ...

2025

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Philippe Schwaller, Jeff Guo

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Amer Chemical Soc2024

Nanomotion-Based Drug Sensitivity Prediction in Ovarian and Colon Cancer Cell Lines Using Machine Learning

Sandor Kasas, María Inés Villalba

Cancer drug resistance remains a critical challenge in oncology, demanding rapid and reliable diagnostic tools to assess tumor cell susceptibility to treatment. This study presents a nanomotion-based drug susceptibility testing (DST) approach, integrating ...

American Chemical Society (ACS)2025

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

A Study on Quantum Graph Neural Networks Applied to Molecular Physics

Su Yeon Chang

This paper introduces a novel architecture for Quantum Graph Neural Networks, which is significantly different from previous approaches found in the literature. The proposed approach produces similar outcomes with respect to previous models but with fewer ...

IOP Publishing Ltd2025

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

Retrieval of Surface Solar Radiation through Implicit Albedo Recovery from Temporal Context

Michael Lehning, Devis Tuia, Yael Frischholz

To retrieve Surface Solar Radiation (SSR) from satellite images, a baseline reflectance of the observed ground in clear-sky conditions, also called background reflectance, is necessary to distinguish atmospheric absorption and scattering effects from surfa ...

2025

Next-Generation Modeling of Cancer Using Organoids

Wouter Richard Karthaus, Jillian Rose Love

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Cold Spring Harbor Lab Press, Publications Dept2024

Integer Linear Programming for Unsupervised Training Set Selection in Molecular Machine Learning

Anne-Clémence Corminboeuf, Friedrich Eisenbrand, Rubén Laplaza Solanas, Puck Elisabeth van Gerwen, Ksenia Briling, Jan Weinreich, Matthieu Nicolas Haeberle

Integer linear programming (ILP) is an elegant approach to solve linear optimization problems, naturally described using integer decision variables. Within the context of physics-inspired machine learning (ML) applied to chemistry, we demonstrate the relev ...

IOP Publishing Ltd2025

Cyclic Peptides for Drug Development

Christian Heinis, Alexander Lund Nielsen, Xinjian Ji

Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years ...

Wiley-VCH Verlag GmbH2024

Adapting Fine-Grained Cross-View Localization to Areas Without Fine Ground Truth

Zimin Xia

Given a ground-level query image and a geo-referenced aerial image that covers the query’s local surroundings, fine-grained cross-view localization aims to estimate the location of the ground camera inside the aerial image. Recent works have focused on dev ...

Springer Science and Business Media Deutschland GmbH2025

Characterization of the gut-bone marrow axis through bile acid signaling

Alejandro Alonso Calleja

Communication between the intestine and other organs such as the lungs, brain or bones is mediated by several metabolites, like short-chain fatty acids or bile acids, that relay information about nutritional and microbiota status. Bile acids are endogenous ...

EPFL2024

Neural Garment Modeling

Ren Li

The digitization of 3D deformable objects remains a significant challenge in computer graphics and vision, particularly in the accurate modeling of garments. Garments exhibit complex shape variability, non-rigid deformations, and frequent self-occlusion, m ...

EPFL2025

Bioengineering functional organoid models across scales

Tania Hübscher

The last two decades have seen the development of organoid models for many different tissues and organs. Organoids are three-dimensional organ-mimetics derived from stem or progenitor cells comprising various specialized cell types, resembling the architec ...

EPFL2024