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Single-Cell Lipidomics by LC-MS Interlaboratory Study Reveals the Impact of X-ray Irradiation on a Pancreatic Cancer Cell Line and Its Bystanders
Kyle D. G. Saunders ; Johanna von Gerichten ; Rahul Deshpande ; et al.
Anal Chem
Saunders, K D G, von Gerichten, J, Deshpande, R, Spick, M, Bird, S, Schettino, G, Bolland, H, Whetton, A, Velliou, E & Bailey, M J 2025, 'Single-Cell Lipidomics by LC-MS Interlaboratory Study Reveals the Impact of X-ray Irradiation on a Pancreatic Cancer Cell Line and Its Bystanders', Analytical Chemistry, vol. 97, no. 25, pp. 13532-13541. https://doi.org/10.1021/acs.analchem.5c02010

Benchmarking scRNA-seq copy number variation callers
Katharina T. Schmid ; Aikaterini Symeonidi ; Dmytro Hlushchenko ; et al.
Nat Commun

Single-cell transcriptome combined with genetic tracing reveals a roadmap of fibrosis formation during proliferative vitreoretinopathy
Mengyu Liao ; Zhisheng Ye ; Yumeng Zhao ; et al.
Proc Natl Acad Sci U S A
Liao, M, Ye, Z, Zhao, Y, Nan, J, Liu, Y, Yao, X, Yang, T, Guo, J, Jin, X, Zhang, H, You, C, Xu, H, Yu, J, Chen, Y, Wang, X & Yan, H 2025, 'Single-cell transcriptome combined with genetic tracing reveals a roadmap of fibrosis formation during proliferative vitreoretinopathy', Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 37, e2424487122. https://doi.org/10.1073/pnas.2424487122

Single-cell lipidomics: performance evaluation across four liquid chromatography mass spectrometry (LC-MS) systems
Johanna von Gerichten ; Kyle D. G. Saunders ; Matt Spick ; et al.
Analyst
von Gerichten, J, Saunders, K D G, Spick, M & Bailey, M J 2025, 'Single-cell lipidomics : performance evaluation across four liquid chromatography mass spectrometry (LC-MS) systems', Analyst, vol. 150, no. 20, pp. 4525-4534. https://doi.org/10.1039/d5an00851d

Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
Frederic B Bastian ; Alessandro Brandulas Cammarata ; Sara Carsanaro ; et al.
Nucleic Acids Res
Nucleic acids research, vol. 53, no. D1, pp. D878-D885

Antagonism between H3K27me3 and genome–lamina association drives atypical spatial genome organization in the totipotent embryo
Isabel Guerreiro ; Franka J. Rang ; Yumiko K. Kawamura ; et al.
Nat Genet
Nature Genetics, 56, pp. 2228-2237

Identification of malignant cells in single-cell transcriptomics data
Andreatta, Massimo ; Garnica Caparros, Josep ; Carmona, Santiago
Commun Biol

Beyond the nuclear border: single-cell analysis of in situ sequenced human brain tissue using cellular features: single-cell analysis of in situ sequenced human brain tissue using cellular features
Janssen M. Kotah ; Thomas Rust ; Hilmar R. J. van Weering ; et al.
Commun Biol

Single-cell signaling network profiling during redox stress reveals dynamic redox regulation in immune cells
Yi-Chuan Wang ; Ping-Hsun Wu ; Wen-Chieh Ting ; et al.
Nat Commun
Nature communications, vol. 16, no. 1, pp. 5600

A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics
Shi, Mengnan ; Méar, Loren ; Karlsson, Max ; et al.
Genome Biol
Genome Biology, Vol 26, Iss 1, Pp 1-21 (2025)
Shi, M, Méar, L, Karlsson, M, Álvez, M B, Digre, A, Schutten, R, Katona, B, Vuu, J, Lindström, E, Hikmet, F, Jin, H, Yuan, M, Li, X, Yang, H, Song, X, Sjöstedt, E, Edfors, F, Oksvold, P, von Feilitzen, K, Zwahlen, M, Forsberg, M, Johansson, F, Mulder, J, Hökfelt, T, Luo, Y, Butler, L, Zhong, W, Mardinoglu, A, Sivertsson, Å, Ponten, F, Fagerberg, L, Lindskog, C, Uhlén, M & Zhang, C 2025, 'A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics', Genome Biology, vol. 26, 152. https://doi.org/10.1186/s13059-025-03616-4
Shi, M, Méar, L, Karlsson, M, Álvez, M B, Digre, A, Schutten, R, Katona, B, Vuu, J, Lindström, E, Hikmet, F, Jin, H, Yuan, M, Li, X, Yang, H, Song, X, Sjöstedt, E, Edfors, F, Oksvold, P, von Feilitzen, K, Zwahlen, M, Forsberg, M, Johansson, F, Mulder, J, Hökfelt, T, Luo, Y, Butler, L, Zhong, W, Mardinoglu, A, Sivertsson, Å, Ponten, F, Fagerberg, L, Lindskog, C, Uhlén, M & Zhang, C 2025, 'A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics', Genome Biology, vol. 26, no. 1, 152, pp. 152. https://doi.org/10.1186/s13059-025-03616-4

Single-Cell Transcriptomic Profiling of Cholangiocyte Organoids Derived from Bile Ducts of Primary Sclerosing Cholangitis Patients
Frank, Anna Katharina ; Chung, Brian K. ; De Novales, Miguel Larraz Lopez ; et al.
Dig Dis Sci
Digestive Diseases and Sciences

Quantifying DNA replication speeds in single cells by scEdU-seq
Jeroen van den Berg ; Vincent van Batenburg ; Christoph Geisenberger ; et al.
Nat Methods

Human autoimmunity at single cell resolution in aplastic anemia before and after effective immunotherapy
Zhijie Wu ; Shouguo Gao ; Xingmin Feng ; et al.
Nat Commun
Nature Communications, Vol 16, Iss 1, Pp 1-21 (2025)
Wu, Z, Gao, S, Feng, X, Li, H, Sompairac, N, Jamshidi, S, Choy, D, Reis, R A D, Gao, Q, Kajigaya, S, Alemu, L, Raffo, D Q, Groarke, E M, Kordasti, S, Patel, B A & Young, N S 2025, ' Human autoimmunity at single cell resolution in aplastic anemia before and after effective immunotherapy ', Nature Communications, vol. 16, no. 1, 5048 . https://doi.org/10.1038/s41467-025-60213-6

Droplet-based Cytotoxicity Assay to Assess Chimeric Antigen Receptor T cells at the Single-cell Level
Ismetova Usheva, Zelvera ; Petersen, David Leander ; Barington, Torben ; et al.
Journal of Visualized Experiments.

Multimodal Nanoplasmonic and Fluorescence Imaging for Simultaneous Monitoring of Single‐Cell Secretory and Intracellular Dynamics
Saeid Ansaryan ; Yung‐Cheng Chiang ; Yen‐Cheng Liu ; et al.
Adv Sci (Weinh)
Advanced Science, Vol 12, Iss 16, Pp n/a-n/a (2025)
Advanced science, vol. 12, no. 16, pp. e2415808

Building and analyzing metacells in single-cell genomics data
Mariia Bilous ; Léonard Hérault ; Aurélie AG Gabriel ; et al.
Mol Syst Biol
Molecular Systems Biology, Vol 20, Iss 7, Pp 744-766 (2024)
Molecular systems biology, vol. 20, no. 7, pp. 744-766

Multiplexed Lectin-PAINT super-resolution microscopy enables cell glycotyping
Marrit M. E. Tholen ; Roger Riera ; Cristina Izquierdo-Lozano ; et al.
Commun Biol
Communications Biology, Vol 8, Iss 1, Pp 1-12 (2025)

tagtango: an application to compare single-cell annotations
Bernat Bramon Mora ; Helen Lindsay ; Antonin Thiébaut ; et al.
Bioinformatics
Bioinformatics, vol. 41, no. 2

A spheroid whole mount drug testing pipeline with machine-learning based image analysis identifies cell-type specific differences in drug efficacy on a single-cell level
Vitacolonna, Mario ; Bruch, Roman ; Schneider, Richard ; et al.
BMC Cancer
BMC Cancer, Vol 24, Iss 1, Pp 1-23 (2024)
BMC Cancer, 24 (1), Art.-Nr.: 1542

Transcriptional linkage analysis with in vivo AAV-Perturb-seq
Santinha, Antonio J. ; Klingler, Esther ; Kuhn, Maria ; et al.
Nature
Nature, 622 (7982)