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Benchmarking cell type and gene set annotation by large language models with AnnDictionary

Cell type labelling in single-cell datasets remains a major bottleneck. Here, the authors present AnnDictionary, an open-source toolkit that enables atlas-scale analysis and provides the first benchmark of LLMs for de novo cell type annotation from marker genes, showing high accuracy at low cost.

George Crowley
Robert C. Jones
Stephen R. Quake
ResearchOpen Access28 Oct 2025
Nature Communications

Volume: 16, P: 1-14
Phylogenomics and the rise of the angiosperms

Phylogenomic analysis of 7,923 angiosperm species using a standardized set of 353 nuclear genes produced an angiosperm tree of life dated with 200 fossil calibrations, providing key insights into evolutionary relationships and diversification.

Alexandre R. Zuntini
Tom Carruthers
William J. Baker
ResearchOpen Access24 Apr 2024
Nature

Volume: 629, P: 843-850
Structural insight into small molecule action on Frizzleds

WNT-Frizzled (FZD) signaling plays a critical role in embryonic development, tissue homeostasis and human disease but no small molecule drugs targeting FZD with distinct efficacy have emerged so far. Here, authors identify the Smoothened agonist SAG1.3 as a partial agonist for FZD6 with limited subtype selectivity.

Paweł Kozielewicz
Ainoleena Turku
Gunnar Schulte
ResearchOpen Access21 Jan 2020
Nature Communications

Volume: 11, P: 1-16
Cholesterol lowering depletes atherosclerotic lesions of smooth muscle cell-derived fibromyocytes and chondromyocytes

Carramolino et al. show that fibromyocytes and chondromyocytes are selectively depleted, while cap cells are maintained, in regressing mouse plaques.

Laura Carramolino
Julián Albarrán-Juárez
Jacob F. Bentzon
Research19 Jan 2024
Nature Cardiovascular Research

Volume: 3, P: 203-220
Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer

Fibroblast heterogeneity is a prominent but poorly understood feature of solid tumours. Here three major fibroblast subpopulations in non-small cell lung cancer are identified and characterised through single cell RNA-sequencing, multiplexed immunohistochemistry and digital cytometry.

Christopher J. Hanley
Sara Waise
Gareth J. Thomas
ResearchOpen Access31 Jan 2023
Nature Communications

Volume: 14, P: 1-18
Identification of growth stage-specific watering thresholds for drought screening in Solanum aethiopicum Shum

Mildred Julian Nakanwagi
Godfrey Sseremba
Elizabeth Balyejusa Kizito
ResearchOpen Access21 Jan 2020
Scientific Reports

Volume: 10, P: 1-11
Modelling of immune infiltration in prostate cancer treated with HDR-brachytherapy using Raman spectroscopy and machine learning

Sandra N. Popescu
Kirsty Milligan
Andrew Jirasek
ResearchOpen Access16 Oct 2025
Scientific Reports

Volume: 15, P: 1-16
Autophagy in metazoans: cell survival in the land of plenty

Julian J. Lum
Ralph J. DeBerardinis
Craig B. Thompson
Reviews13 May 2005
Nature Reviews Molecular Cell Biology

Volume: 6, P: 439-448
CD8 + T cell infiltration is associated with improved survival and negatively correlates with hypoxia in clear cell ovarian cancer

Nancy Guo
Aijun Yang
Julian J. Lum
ResearchOpen Access21 Apr 2023
Scientific Reports

Volume: 13, P: 1-10
Metabolic engineering for optimized CAR-T cell therapy

The immunosuppressive metabolic tumour microenvironment in solid tumours limits the antitumour activity of cell-based immunotherapy. In this Perspective, McPhedran et al. propose a framework to overcome this issue by engineering metabolic networks in T cells to enhance chimeric antigen receptor T cell efficiency

Sarah J. McPhedran
Gillian A. Carleton
Julian J. Lum
Reviews22 Feb 2024
Nature Metabolism

Volume: 6, P: 396-408
Minimizing the risk of reporting false positives in large-scale RNAi screens

Large-scale RNA interference (RNAi)-based analyses, very much as other 'omic' approaches, have inherent rates of false positives and negatives. The variability in the standards of care applied to validate results from these studies, if left unchecked, could eventually begin to undermine the credibility of RNAi as a powerful functional approach. This Commentary is an invitation to an open discussion started among various users of RNAi to set forth accepted standards that would insure the quality and accuracy of information in the large datasets coming out of genome-scale screens. Please visit methagora to view and post comments on this article

Christophe J Echeverri
Philip A Beachy
René Bernards
Comments & Opinion01 Oct 2006
Nature Methods

Volume: 3, P: 777-779
Raman spectroscopy identifies radiation response in human non-small cell lung cancer xenografts

Samantha J. Harder
Martin Isabelle
Andrew Jirasek
ResearchOpen Access17 Feb 2016
Scientific Reports

Volume: 6, P: 1-10
TREM-1 activation is a potential key regulator in driving severe pathogenesis of enterovirus A71 infection

Siti Naqiah Amrun
Jeslin J. L. Tan
Lisa F. P. Ng
ResearchOpen Access02 Mar 2020
Scientific Reports

Volume: 10, P: 1-13
Raman spectroscopy and convolutional neural networks for monitoring biochemical radiation response in breast tumour xenografts

Alejandra M. Fuentes
Apurva Narayan
Andrew Jirasek
ResearchOpen Access27 Jan 2023
Scientific Reports

Volume: 13, P: 1-12
Transdiagnostic subgroups of cognitive impairment in early affective and psychotic illness

Julian Wenzel
Luzie Badde
Henrik Rohner
ResearchOpen Access22 Sept 2023
Neuropsychopharmacology

Volume: 49, P: 573-583
Principles of reproducible metabolite profiling of enriched lymphocytes in tumors and ascites from human ovarian cancer

Identifying metabolites in cells of the tumor microenvironment is an area of intense study. This protocol describes specimen collection, enrichment of human immune cell populations and analysis by flow cytometry and LC–MS.

Marisa K. Kilgour
Sarah MacPherson
Julian J. Lum
Protocols19 Aug 2022
Nature Protocols

Volume: 17, P: 2668-2698
Prediction of disease progression indicators in prostate cancer patients receiving HDR-brachytherapy using Raman spectroscopy and semi-supervised learning: a pilot study

Kirsty Milligan
Xinchen Deng
Andrew Jirasek
ResearchOpen Access06 Sept 2022
Scientific Reports

Volume: 12, P: 1-13
Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells

Kirsty Milligan
Xinchen Deng
Andrew Jirasek
ResearchOpen Access16 Feb 2021
Scientific Reports

Volume: 11, P: 1-11

Search

Benchmarking cell type and gene set annotation by large language models with AnnDictionary

Phylogenomics and the rise of the angiosperms

Structural insight into small molecule action on Frizzleds

Cholesterol lowering depletes atherosclerotic lesions of smooth muscle cell-derived fibromyocytes and chondromyocytes

Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer

Identification of growth stage-specific watering thresholds for drought screening in Solanum aethiopicum Shum

Modelling of immune infiltration in prostate cancer treated with HDR-brachytherapy using Raman spectroscopy and machine learning

Autophagy in metazoans: cell survival in the land of plenty

CD8 + T cell infiltration is associated with improved survival and negatively correlates with hypoxia in clear cell ovarian cancer

Metabolic engineering for optimized CAR-T cell therapy

Minimizing the risk of reporting false positives in large-scale RNAi screens

Raman spectroscopy identifies radiation response in human non-small cell lung cancer xenografts

TREM-1 activation is a potential key regulator in driving severe pathogenesis of enterovirus A71 infection

Raman spectroscopy and convolutional neural networks for monitoring biochemical radiation response in breast tumour xenografts

Transdiagnostic subgroups of cognitive impairment in early affective and psychotic illness

Principles of reproducible metabolite profiling of enriched lymphocytes in tumors and ascites from human ovarian cancer

Prediction of disease progression indicators in prostate cancer patients receiving HDR-brachytherapy using Raman spectroscopy and semi-supervised learning: a pilot study

Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells

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