Search Results - "CZI Cell Science Program"

CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.

Authors: Abdulla S Aevermann B Assis P et al.

Corporate Authors: Abdulla S Aevermann B Assis P et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D886-D900.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution.

Authors: Pearce, James D. Simmonds, Sara E. Mahmoudabadi, Gita et al.

Source: Science. 7/2/2026, Vol. 393 Issue 6806, p1-11. 11p.

scHilda: Hierarchical Integration of LLM with KG database for single cell type annotation.

Authors: Li, Yilang Sun, Yidi Geng, Aoyun et al.

Source: PLoS Computational Biology. 5/11/2026, Vol. 22 Issue 5, p1-19. 19p.

Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease.

Authors: Zhang, Lai-Ying Allen, Peter C. Lutzky, Viviana P. et al.

Source: PLoS ONE. 4/29/2026, Vol. 21 Issue 4, p1-18. 18p.

Autophagy Activators Normalize Aberrant Tau Proteostasis and Rescue Synapses in Human Familial Alzheimer's Disease iPSC‐Derived Cortical Organoids.

Authors: Labra, Sergio R. Compher, Jadon Prabhavalkar, Akhil et al.

Source: Advanced Science. 3/23/2026, Vol. 13 Issue 17, p1-29. 29p.

Autonomous biomedical research with an artificial intelligence agent.

Authors: Huang, Kexin Zhang, Serena Wang, Hanchen et al.

Source: Science. Jul2026, p1.

ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization.

Authors: Jagadesan, Sankarasubramanian Guda, Chittibabu

Source: PLoS Computational Biology. 11/13/2025, Vol. 21 Issue 11, p1-19. 19p.

Inferring pathway activity from single-cell and spatial transcriptomics data with PaaSc.

Authors: Liao, Xiqi Hong, Yuyang Feng, Yan et al.

Source: PLoS Computational Biology. 11/10/2025, Vol. 21 Issue 11, p1-22. 22p.

Transformative advances in single-cell omics: a comprehensive review of foundation models, multimodal integration and computational ecosystems.

Authors: Yiu, Taylor Chen, Bin Wang, Haoyu et al.

Source: Journal of Translational Medicine. 10/27/2025, Vol. 23 Issue 1, p1-18. 18p.

RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing.

Authors: Bouirdene, Sophiane G. Gotty, Simon Leclercq, Mickaël et al.

Source: Scientific Reports. 8/24/2025, Vol. 15 Issue 1, p1-9. 9p.

scCompass: An Integrated Multi‐Species scRNA‐seq Database for AI‐Ready.

Authors: Wang, Pengfei Liu, Wenhao Wang, Jiajia et al.

Source: Advanced Science. Jul2025, Vol. 12 Issue 25, p1-16. 16p.

CD2AP at the junction of nephropathy and Alzheimer's disease.

Authors: Vandal, Milene Janmaleki, Mohsen Rea, Isabel et al.

Source: Molecular Neurodegeneration. 6/4/2025, Vol. 20 Issue 1, p1-22. 22p.

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.

Authors: Jogani, Saiyam Pol, Anand Santosh Prajapati, Mayur et al.

Source: Briefings in Bioinformatics. May2025, Vol. 26 Issue 3, p1-12. 12p.

A multidisciplinary approach towards modeling of a virtual human lung.

Authors: Lam, Timothy Quach, Henry T. Hall, Lauren et al.

Source: NPJ Systems Biology & Applications. 4/18/2025, Vol. 11 Issue 1, p1-8. 8p.

Digital evolution: Novo Nordisk's shift to ontology-based data management.

Authors: Tan, Shawn Zheng Kai Baksi, Shounak Bjerregaard, Thomas Gade et al.

Source: Journal of Biomedical Semantics. 3/22/2025, Vol. 16 Issue 1, p1-11. 11p.

The transcriptomic landscape of monosomy X (45,X) during early human fetal and placental development.

Authors: Suntharalingham, Jenifer P. del Valle, Ignacio Buonocore, Federica et al.

Source: Communications Biology. 2/16/2025, Vol. 8 Issue 1, p1-19. 19p.

Cell-specific priors rescue differential gene expression in spatial spot-based technologies.

Authors: Nahman, Ornit Few-Cooper, Timothy J Shen-Orr, Shai S

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-12. 12p.

STHELAR, a multi-tissue dataset linking spatial transcriptomics and histology for cell type annotation.

Authors: Giraud-Sauveur F Blampey Q Benkirane H et al.

Source: Scientific data [Sci Data] 2026 Mar 12; Vol. 13 (1). Date of Electronic Publication: 2026 Mar 12.

Publication Type: Journal Article; Dataset

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN: 2052-4463 (Electronic) Linking ISSN: 20524463 NLM ISO Abbreviation: Sci Data Subsets: MEDLINE

A single-cell cell-of-origin audit of the lncRNA RMST: bulk expression under-represents its broad neural expression and over-attributes a liver biomarker.

Authors: Tani H; Department of Health Pharmacy, Yokohama University of Pharmacy, 601 Matano, Totsuka, Yokohama, Kanagawa, 245-0066, Japan. hidenori.tani@yok.hamayaku.ac.jp.

Source: Functional & integrative genomics [Funct Integr Genomics] 2026 Jul 29; Vol. 26 (1). Date of Electronic Publication: 2026 Jul 29.

Publication Type: Journal Article

Journal Info: Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE

Universal cell embedding provides a foundation model for cell biology.

Authors: Rosen Y Roohani Y Agrawal A et al.

Corporate Authors: Rosen Y Roohani Y Agrawal A et al.

Source: Nature [Nature] 2026 Jul 08. Date of Electronic Publication: 2026 Jul 08.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE