Nature Search

Pathologist-like explainable AI for interpretable Gleason grading in prostate cancer

An inherently explainable AI trained on 1,015 expert-annotated prostate tissue images achieved strong Gleason pattern segmentation while providing interpretable outputs and addressing interobserver variability in pathology.

Gesa Mittmann
Sara Laiouar-Pedari
Titus J. Brinker
ResearchOpen Access08 Oct 2025
Nature Communications

Volume: 16, P: 1-17
Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer’s pathology

Native state proteomics of PV interneurons revealed unique molecular features of high translational and metabolic activity, and enrichment of Alzheimer’s risk genes. Early amyloid pathology exerted unique effects on mitochondria, mTOR signaling and neurotransmission in PV neurons.

Prateek Kumar
Annie M. Goettemoeller
Srikant Rangaraju
ResearchOpen Access01 Apr 2024
Nature Communications

Volume: 15, P: 1-26
Global, regional and national burden of dietary iron deficiency from 1990 to 2021: a Global Burden of Disease study

Systematic analysis from the Global Burden of Disease study reported that, despite global improvements from 1990 to 2021, dietary iron deficiency-associated disease burden remains high in women, children and residents in low socio-demographic index countries.

Sooji Lee
Yejun Son
Nicholas. J. Kassebaum
Research22 Apr 2025
Nature Medicine

Volume: 31, P: 1809-1829
Predicting opioid consumption after surgical discharge: a multinational derivation and validation study using a foundation model

Chris Varghese
Luke Peters
Caroline Reinke
ResearchOpen Access26 Aug 2025
npj Digital Medicine

Volume: 8, P: 1-16
Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems

Third-generation sequencing can reveal information beyond the simple sequence of bases, but fulfilling this potential requires complex reference sets for training. Here, the authors present an approach to generate these reference sets and present various use cases for such multidimensional sequencing.

Serena S. David
Brendan A. Pacheco
William A. Flavahan
ResearchOpen Access01 Jul 2025
Nature Communications

Volume: 16, P: 1-15
Global estimates on the number of people blind or visually impaired by age-related macular degeneration: a meta-analysis from 2000 to 2020

João M. Furtado
Jost B. Jonas
Rupert R. A. Bourne
ResearchOpen Access04 Jul 2024
Eye

Volume: 38, P: 2070-2082
Next-generation characterization of the Cancer Cell Line Encyclopedia

The original Cancer Cell Line Encyclopedia (CCLE) is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data.

Mahmoud Ghandi
Franklin W. Huang
William R. Sellers
Research08 May 2019
Nature

Volume: 569, P: 503-508
New insights into the genetic etiology of Alzheimer’s disease and related dementias

Meta-analysis of genome-wide association studies on Alzheimer’s disease and related dementias identifies new loci and enables generation of a new genetic risk score associated with the risk of future Alzheimer’s disease and dementia.

Céline Bellenguez
Fahri Küçükali
Jean-Charles Lambert
ResearchOpen Access04 Apr 2022
Nature Genetics

Volume: 54, P: 412-436
Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4⁺ and PDPN⁺ CAFs to clinical outcome

Scherz-Shouval and colleagues characterize the dynamic changes in cancer-associated fibroblast subpopulations during breast cancer progression. They find that the ratio of S100A4⁺ and PDPN⁺ CAF subsets is associated with clinical outcome.

Gil Friedman
Oshrat Levi-Galibov
Ruth Scherz-Shouval
Research29 Jun 2020
Nature Cancer

Volume: 1, P: 692-708
Shared and distinct transcriptomic cell types across neocortical areas

Single-cell transcriptomics of more than 20,000 cells from two functionally distinct areas of the mouse neocortex identifies 133 transcriptomic types, and provides a foundation for understanding the diversity of cortical cell types.

Bosiljka Tasic
Zizhen Yao
Hongkui Zeng
Research31 Oct 2018
Nature

Volume: 563, P: 72-78
Overcoming adaptive resistance to anti-VEGF therapy by targeting CD5L

The efficacy of antiangiogenic therapy in the clinic is often limited by the emergence of resistance. Here, the authors show that in ovarian cancer anti-VEGF inhibitors induce the overexpression of CD5L in endothelial cells through hypoxia-driven PPARy activation and that blocking CD5L can overcome resistance.

Christopher J. LaFargue
Paola Amero
Anil K. Sood
ResearchOpen Access26 Apr 2023
Nature Communications

Volume: 14, P: 1-18
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture

Whole-genome sequence analysis identifies five independent risk loci for Lewy body dementia and demonstrates overlapping genetic architecture with Alzheimer’s and Parkinson’s diseases.

Ruth Chia
Marya S. Sabir
Sonja W. Scholz
Research15 Feb 2021
Nature Genetics

Volume: 53, P: 294-303
Genomic–transcriptomic evolution in lung cancer and metastasis

Computational and machine-learning approaches that integrate genomic and transcriptomic variation from paired primary and metastatic non-small cell lung cancer samples from the TRACERx cohort reveal the role of transcriptional events in tumour evolution.

Carlos Martínez-Ruiz
James R. M. Black
Nicholas McGranahan
ResearchOpen Access12 Apr 2023
Nature

Volume: 616, P: 543-552
Acid-sensing ion channels contribute to synaptic transmission and inhibit cocaine-evoked plasticity

Exposure to psychostimulants such as cocaine induces synaptic plasticity within the nucleus accumbens (NAc) and alters behavior. Here the authors find a new role for the acid-sensing channel 1A (ASIC1A) in excitatory transmission and plasticity within the NAc that contributes to cocaine-induced learning and self-administration.

Collin J Kreple
Yuan Lu
John A Wemmie
Research22 Jun 2014
Nature Neuroscience

Volume: 17, P: 1083-1091
International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

Primary biliary cirrhosis is an autoimmune liver disease with poor therapeutic options. Here Cordell et al. a perform meta-analysis of European genome-wide association studies identifying six novel risk loci and a number of potential therapeutic pathways.

Heather J. Cordell
Younghun Han
Katherine A. Siminovitch
ResearchOpen Access22 Sept 2015
Nature Communications

Volume: 6, P: 1-11
Global estimates on the number of people blind or visually impaired by Uncorrected Refractive Error: a meta-analysis from 2000 to 2020

Julie-Anne Little
Nathan G. Congdon
Rupert Bourne
ResearchOpen Access04 Jul 2024
Eye

Volume: 38, P: 2083-2101
Assessing the clinical utility of cancer genomic and proteomic data across tumor types

For several cancer types analyzed by The Cancer Genome Atlas project, predictions of patient survival were not substantially improved by using common data mining approaches to combine traditional clinical variables with molecular profiling data.

Yuan Yuan
Eliezer M Van Allen
Han Liang
Research22 Jun 2014
Nature Biotechnology

Volume: 32, P: 644-652
Global estimates on the number of people blind or visually impaired by cataract: a meta-analysis from 2000 to 2020

Konrad Pesudovs
Van Charles Lansingh
Jaimie D. Steinmetz
ResearchOpen Access09 Mar 2024
Eye

Volume: 38, P: 2156-2172
Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and variable sgRNA activity. Applying CERES to new genome-scale CRISPR–Cas9 essentiality screen data from 342 cancer cell lines and other published data sets shows that CERES decreases false-positive results and provides consistent estimates of sgRNA activity.

Robin M Meyers
Jordan G Bryan
Aviad Tsherniak
Research30 Oct 2017
Nature Genetics

Volume: 49, P: 1779-1784
The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset

Using a zebrafish model of melanoma, this study has searched for genes that can cooperate with mutated BRAF, a frequent oncogenic event in human melanomas. It is found that SETDB1 can accelerate melanoma formation in fish and resides in a region frequently amplified in human melanomas. SETDB1, a histone methylating enzyme, is also frequently overexpressed in human melanomas and functions at least in part by regulating the expression of HOX genes.

Craig J. Ceol
Yariv Houvras
Leonard I. Zon
Research23 Mar 2011
Nature

Volume: 471, P: 513-517
Global estimates on the number of people blind or visually impaired by glaucoma: A meta-analysis from 2000 to 2020

Rupert R. A. Bourne
Jost B. Jonas
Jaimie D. Steinmetz
ResearchOpen Access02 Apr 2024
Eye

Volume: 38, P: 2036-2046
Global estimates on the number of people blind or visually impaired by diabetic retinopathy: a meta-analysis from 2000 to 2020

Katie Curran
Tunde Peto
Peng Zheng
ResearchOpen Access27 Jun 2024
Eye

Volume: 38, P: 2047-2057
Erratum: Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Glenn S Cowley
Barbara A Weir
William C Hahn
Amendments and Corrections11 Nov 2014
Scientific Data

Volume: 1, P: 1
The United States COVID-19 Forecast Hub dataset

Estee Y. Cramer
Yuxin Huang
Nicholas G. Reich
ResearchOpen Access01 Aug 2022
Scientific Data

Volume: 9, P: 1-15
Publisher Correction: Global estimates on the number of people blind or visually impaired by cataract: a meta-analysis from 2000 to 2020

Konrad Pesudovs
Van Charles Lansingh
Jaimie D. Steinmetz
Amendments and CorrectionsOpen Access16 Jul 2024
Eye

Volume: 38, P: 2229-2231
Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Glenn S Cowley
Barbara A Weir
William C Hahn
ResearchOpen Access30 Sept 2014
Scientific Data

Volume: 1, P: 1-12
Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study

Arezou A. Ghazani
Nelly M. Oliver
Nikhil Wagle
Research26 Jan 2017
Genetics in Medicine

Volume: 19, P: 787-795
A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins

Evanthia Mantzouki
James Campbell
Bastiaan W. Ibelings
ResearchOpen Access23 Oct 2018
Scientific Data

Volume: 5, P: 1-13
COVID-19 vaccines: where we stand and challenges ahead

Guido Forni
Alberto Mantovani
Paolo Vineis
Reviews21 Jan 2021
Cell Death & Differentiation

Volume: 28, P: 626-639

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