Nature Search

A pathology foundation model for cancer diagnosis and prognosis prediction

A study describes the development of a generalizable foundation machine learning framework to extract pathology imaging features for cancer diagnosis and prognosis prediction.

Xiyue Wang
Junhan Zhao
Kun-Hsing Yu
Research04 Sept 2024
Nature

Volume: 634, P: 970-978
KDM6A epigenetically regulates subtype plasticity in small cell lung cancer

Duplaquet, Li et al. identify and characterize KDM6A as an epigenetic regulator that impacts chromatin accessibility to modulate ASCL1-to-NEUROD1 subtype switching in small cell lung cancer.

Leslie Duplaquet
Yixiang Li
Matthew G. Oser
Research17 Aug 2023
Nature Cell Biology

Volume: 25, P: 1346-1358
HPV RNA CISH score identifies two prognostic groups in a p16 positive oropharyngeal squamous cell carcinoma population

Jérémy Augustin
Marion Mandavit
Cécile Badoual
Research20 Jun 2018
Modern Pathology

Volume: 31, P: 1645-1652
Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

The epigenomic landscape of renal cell carcinoma (RCC) remains to be explored. Here, integrative epigenomic analysis of primary human RCC samples and RCC GWAS risk SNPs identifies transcription-factor specific subtypes and enrichment of risk variants in allelically-imbalanced peaks.

Amin H. Nassar
Sarah Abou Alaiwi
Matthew L. Freedman
ResearchOpen Access21 Jan 2023
Nature Communications

Volume: 14, P: 1-16
Regulation of neuroendocrine plasticity by the RNA-binding protein ZFP36L1

LSD1 inhibition blocks the neuroendocrine phenotype of some small cell lung cancers (SCLCs). Here, a genome-wide CRISPR/Cas9 LSD1 inhibitor resistance screen identifies the mRNA-binding protein ZFP36L1 as a gene repressed by LSD1 that when restored inhibits SCLC neuroendocrine differentiation.

Hsiao-Yun Chen
Yavuz T. Durmaz
Matthew G. Oser
ResearchOpen Access25 Aug 2022
Nature Communications

Volume: 13, P: 1-22
Machine learning derived retinal pigment score from ophthalmic imaging shows ethnicity is not biology

Here authors show that machine learning derives the degree of background retinal pigmentation with more nuance than self-described ethnicity. Retinal pigment scores are associated with genes linked to melanin and may improve algorithmic fairness.

Anand E. Rajesh
Abraham Olvera-Barrios
Yalin Zheng
ResearchOpen Access02 Jan 2025
Nature Communications

Volume: 16, P: 1-14
A foundation model for generalizable disease detection from retinal images

RETFound, a foundation model for retinal images that learns generalizable representations from unlabelled images, is trained on 1.6 million unlabelled images by self-supervised learning and then adapted to disease detection tasks with explicit labels.

Yukun Zhou
Mark A. Chia
Pearse A. Keane
ResearchOpen Access13 Sept 2023
Nature

Volume: 622, P: 156-163
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Primary open-angle glaucoma (POAG) is highly heritable, yet not well understood from a genetic perspective. Here, the authors perform a meta-analysis of genome-wide association studies in 34,179 POAG cases, identifying 44 previously unreported risk loci and mapping effects across multiple ethnicities.

Puya Gharahkhani
Eric Jorgenson
Janey L. Wiggs
ResearchOpen Access24 Feb 2021
Nature Communications

Volume: 12, P: 1-16
Clinical assessment of the miR-34, miR-200, ZEB1 and SNAIL EMT regulation hub underlines the differential prognostic value of EMT miRs to drive mesenchymal transition and prognosis in resected NSCLC

Simon Garinet
Audrey Didelot
Helene Blons
Research12 Oct 2021
British Journal of Cancer

Volume: 125, P: 1544-1551
MET alterations in biphasic squamoid alveolar papillary renal cell carcinomas and clinicopathological features

Thomas Denize
Pierre Alexandre Just
Virginie Verkarre
Research07 Aug 2020
Modern Pathology

Volume: 34, P: 647-659
Convolutional neural network-based classification of glaucoma using optic radiation tissue properties

Kruper et al. investigate the impact of glaucoma on brain tissue by comparing MRI data from 856 people with glaucoma to matched controls without glaucoma. They find that neural networks using tissue properties from visual brain connections more accurately detect glaucoma than those trained on non-visual brain connections.

John Kruper
Adam Richie-Halford
Yalin Zheng
ResearchOpen Access11 Apr 2024
Communications Medicine

Volume: 4, P: 1-10
Impact of the COVID-19 pandemic on the research activities of UK ophthalmologists

H. D. J. Hogg
L. Low
J. S. Rahi
ResearchOpen Access31 Oct 2022
Eye

Volume: 37, P: 2089-2094
Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

The International Glaucoma Genetics Consortium reports a genome-wide association study meta-analysis of optic disc parameters relevant to primary open-angle glaucoma. They identify two novel variants in PPP1R36-PLEKHG3 and SERPINE3 by multi-trait analysis in European-ancestry cohorts that were replicated in independent Asian cohorts.

Pieter W. M. Bonnemaijer
Elisabeth M. van Leeuwen
Cornelia M. van Duijn
ResearchOpen Access27 Nov 2019
Communications Biology

Volume: 2, P: 1-12

Search

A pathology foundation model for cancer diagnosis and prognosis prediction

KDM6A epigenetically regulates subtype plasticity in small cell lung cancer

HPV RNA CISH score identifies two prognostic groups in a p16 positive oropharyngeal squamous cell carcinoma population

Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

Regulation of neuroendocrine plasticity by the RNA-binding protein ZFP36L1

Machine learning derived retinal pigment score from ophthalmic imaging shows ethnicity is not biology

A foundation model for generalizable disease detection from retinal images

Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Clinical assessment of the miR-34, miR-200, ZEB1 and SNAIL EMT regulation hub underlines the differential prognostic value of EMT miRs to drive mesenchymal transition and prognosis in resected NSCLC

MET alterations in biphasic squamoid alveolar papillary renal cell carcinomas and clinicopathological features

Convolutional neural network-based classification of glaucoma using optic radiation tissue properties

Impact of the COVID-19 pandemic on the research activities of UK ophthalmologists

Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

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