Open Science

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Open code

Code repository associated with the FedECA article.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

A Vision Transformer Large pretrained with Dinov2 self-supervised method on PANCAN-XL.

A self-supervised learning model for histopathology trained with iBOT.

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huggingface.co/owkin

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github.com/owkin

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AI moonshot to accelerate open science in Glioblastoma

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We are seeking innovative lab facilities for wet-lab validation of our GBM targets and computing partners to revolutionize Glioblastoma patient care.

Open-access publications and preprints

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FedPyDESeq2: a federated framework for bulk RNA-seq differential expression analysis

Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity

Phikon-v2, A large and public feature extractor for biomarker prediction

Alexandre Filiot

A deep learning-based multiscale integration of spatial omics with tumor morphology.

Benoit Schmauch

Deep learning uncovers histological patterns of YAP1/TEAD activity related to disease aggressiveness in cancer patients

Benoit Schmauch

Robust Evaluation of Deep Learning-based Representation Methods for Survival and Gene Essentiality Prediction on Bulk RNA-seq Data

Nature Scientific Reports

Subgroup analysis methods for time-to-event outcomes in heterogeneous randomized controlled trials

Valentine Perrin

Combining a deep learning model with clinical data better predicts hepatocellular carcinoma behavior following surgery

Benoit Schmauch

Journal of Pathology Informatics

FedECA: A Federated External Control Arm Method for Causal Inference with Time-To-Event Data in Distributed Settings

Jean du Terrail

Validation of MSIntuit as an AI-based pre-screening tool for MSI detection from colorectal cancer histology slides

Charlie Saillard

Nature Communications

PyDESeq2: a python package for bulk RNA-seq differential expression analysis

Scaling Self-Supervised Learning for Histopathology with Masked Image Modeling

Alexandre Filiot