Exaggerated false positives by popular differential expression methods when analyzing human population samples

Y Li, X Ge, F Peng, W Li, JJ Li - Genome biology, 2022 - Springer
When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …

TIMER2. 0 for analysis of tumor-infiltrating immune cells

T Li, J Fu, Z Zeng, D Cohen, J Li, Q Chen… - Nucleic acids …, 2020 - academic.oup.com
Tumor progression and the efficacy of immunotherapy are strongly influenced by the
composition and abundance of immune cells in the tumor microenvironment. Due to the …

COSMIC: a curated database of somatic variants and clinical data for cancer

Z Sondka, NB Dhir, D Carvalho-Silva… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer. sanger.
ac. uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in …

[HTML][HTML] Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence

A Holzinger, M Dehmer, F Emmert-Streib, R Cucchiara… - Information …, 2022 - Elsevier
Medical artificial intelligence (AI) systems have been remarkably successful, even
outperforming human performance at certain tasks. There is no doubt that AI is important to …

Benchmarking self-supervised learning on diverse pathology datasets

M Kang, H Song, S Park, D Yoo… - Proceedings of the …, 2023 - openaccess.thecvf.com
Computational pathology can lead to saving human lives, but models are annotation hungry
and pathology images are notoriously expensive to annotate. Self-supervised learning has …

Fast and scalable search of whole-slide images via self-supervised deep learning

C Chen, MY Lu, DFK Williamson, TY Chen… - Nature Biomedical …, 2022 - nature.com
The adoption of digital pathology has enabled the curation of large repositories of gigapixel
whole-slide images (WSIs). Computationally identifying WSIs with similar morphologic …

Mutations and mechanisms of WNT pathway tumour suppressors in cancer

JM Bugter, N Fenderico, MM Maurice - Nature Reviews Cancer, 2021 - nature.com
Mutation-induced activation of WNT–β-catenin signalling is a frequent driver event in human
cancer. Sustained WNT–β-catenin pathway activation endows cancer cells with sustained …

Multi-omics data integration, interpretation, and its application

I Subramanian, S Verma, S Kumar… - … and biology insights, 2020 - journals.sagepub.com
To study complex biological processes holistically, it is imperative to take an integrative
approach that combines multi-omics data to highlight the interrelationships of the involved …

Vision Transformers in medical computer vision—A contemplative retrospection

A Parvaiz, MA Khalid, R Zafar, H Ameer, M Ali… - … Applications of Artificial …, 2023 - Elsevier
Abstract Vision Transformers (ViTs), with the magnificent potential to unravel the information
contained within images, have evolved as one of the most contemporary and dominant …

Machine learning for precision medicine

SJ MacEachern, ND Forkert - Genome, 2021 - cdnsciencepub.com
Precision medicine is an emerging approach to clinical research and patient care that
focuses on understanding and treating disease by integrating multi-modal or multi-omics …