scCADE: A Superior Tool for Predicting Perturbation Responses in Single-Cell Gene Expression Using Contrastive Learning and Attention Mechanisms

Authors: Ou, Jingfeng, Li, Jiawei, Xia, Zhiliang, Dai, Shurui, Ding, Yulian, Guo, Yan, Jiang, Limin, Tang, Jijun

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :441-444 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Tcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses

Authors: Lucie Janeckova, Monika Stastna, Dusan Hrckulak, Linda Berkova, Jan Kubovciak, Jakub Onhajzer, Vitezslav Kriz, Stela Dostalikova, Tereza Mullerova, Katerina Vecerkova, Marketa Tenglerova, Stepan Coufal, Klara Kostovcikova, Richard S. Blumberg, Dominik Filipp, Konrad Basler, Tomas Valenta, Michal Kolar, Vladimir Korinek

Source: Stem Cell Research & Therapy, Vol 16, Iss 1, Pp 1-29 (2025)

Subject Terms: Antimicrobial peptides, Paneth cells, Intestinal cell lineage, Colorectal cancer, Intestinal crypt, Single-cell transcriptomics, Medicine (General), R5-920, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/1757-6512

Access URL: https://doaj.org/article/877eaf9e704245aa887f3c1e13127953

Single-cell RNA sequencing and spatial transcriptomics reveal the heterogeneity and intercellular communication of cancer-associated fibroblasts in gastric cancer

Authors: Xijie Zhang, Bo Ren, Bo Liu, Rui Wang, Sen Li, Yuzhou Zhao, Wence Zhou

Source: Journal of Translational Medicine, Vol 23, Iss 1, Pp 1-14 (2025)

Subject Terms: Gastric cancer, Cancer-associated fibroblasts, Single-cell transcriptomics, Cell–cell interactions, Tumor microenvironment, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/a1fa4af80be7407b82b0934ee304ff1c

Identification of potential drug targets for pelvic organ prolapse using a proteome-wide Mendelian randomization approach

Authors: Ziwei Xie, Yuxin Feng, Yue He, Yingying Lin, Xiaohong Wang

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-13 (2025)

Subject Terms: Pelvic organ prolapse, Plasma proteomics, Mendelian randomization, Single-cell transcriptomics, Molecular docking, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/0dbd667431554055b82a8d9766ff98a3

Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data

Authors: Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone

Source: Molecular Systems Biology, Vol 21, Iss 3, Pp 214-230 (2025)

Subject Terms: Gene Regulatory Network Inference, Prior Knowledge, Single-cell Transcriptomics, Single-cell Multiomics, Graph Learning, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/6aee50edcff5460bb98791439556ea64

Decoding SFRP2 progenitors in sustaining tooth growth at single-cell resolution

Authors: Tianyuan Zhao, Qing Zhong, Zewen Sun, Xiaoyi Yu, Tianmeng Sun, Zhengwen An

Source: Stem Cell Research & Therapy, Vol 16, Iss 1, Pp 1-17 (2025)

Subject Terms: Single-cell transcriptomics, SFRP2, Dental pulp stem cells, Tissue growth, Evolution, Medicine (General), R5-920, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/1757-6512

Access URL: https://doaj.org/article/e6cbc8f98ab742048ef85c5523764414

Single-cell and spatial omics: exploring hypothalamic heterogeneity

Authors: Muhammad Junaid, Eun Jeong Lee, Su Bin Lim

Source: Neural Regeneration Research, Vol 20, Iss 6, Pp 1525-1540 (2025)

Subject Terms: cellular diversity, hypothalamus, multi-omics, single-cell transcriptomics, spatial transcriptomics, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://journals.lww.com/10.4103/NRR.NRR-D-24-00231; https://doaj.org/toc/1673-5374; https://doaj.org/toc/1876-7958

Access URL: https://doaj.org/article/7d5ef5f803f443d182676eb9666aadd2

High order expression dependencies finely resolve cryptic states and subtypes in single cell data

Authors: Abel Jansma, Yuelin Yao, Jareth Wolfe, Luigi Del Debbio, Sjoerd V Beentjes, Chris P Ponting, Ava Khamseh

Source: Molecular Systems Biology, Vol 21, Iss 2, Pp 173-207 (2025)

Subject Terms: Higher-order Gene Expression Dependencies, Single-cell Transcriptomics, Structure Learning, Cell State, Cell Cycle Phases, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/64c51b07beb44a51a910a6e990929ced

Integrative multi-omics analysis reveals the role of toll-like receptor signaling in pancreatic cancer

Authors: Jie Peng, Jiaao Sun, Youfeng Yu, Qihang Yuan, Yong Zhang

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-19 (2025)

Subject Terms: Pancreatic cancer, Toll-like receptor signal, Machine learning, Single-cell transcriptomics, Immune microenvironment, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/a30291ea5c8e4a78ac34417da8423e84

From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades – a personal perspective

Authors: Ann-Christine Syvänen

Source: Upsala Journal of Medical Sciences, Vol 129, Pp 1-20 (2024)

Subject Terms: genomics, genetics, snp genotyping, polymerase chain reaction, microarrays, next generation sequencing, epigenomics, systemic lupus erythematosus, acute lymphoblastic leukemia, finnish disease heritage, whole genome sequencing, single cell transcriptomics, Medicine

File Description: electronic resource

Relation: https://ujms.net/index.php/ujms/article/view/11134/18464; https://doaj.org/toc/0300-9734; https://doaj.org/toc/2000-1967

Access URL: https://doaj.org/article/7e951e155e574f7e982761dd2d909d41

Single-cell multi-omics in the study of digestive system cancers

Authors: Shuang Zhou, Nanfei Lin, Liying Yu, Xiaoshan Su, Zhenlong Liu, Xiaowan Yu, Hongzhi Gao, Shu Lin, Yiming Zeng

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 431-445 (2024)

Subject Terms: Digestive system cancer, Single-cell sequencing (SCS), Heterogeneity, Tumor microenvironment (TME), Single-cell omics, Single-cell transcriptomics (ST), Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023004816; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/d011d875492847e59ece547666389729

Single-cell transcriptomics reveals over-activated reactive oxygen species pathway in hepatocytes in the development of hepatocellular carcinoma

Authors: Xiaoping Wang, Penghui Li, Huicong Ji, Zhenzhen Xu, Huiwu Xing

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-12 (2024)

Subject Terms: Single-cell transcriptomics, Hepatocellular carcinoma, Reactive oxygen species pathway, GPX4+ HCC hepatocytes, CellChat, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/80794edc38204c37a559a51922c51c3d

Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma

Authors: Jason C. Klein, Lei Wang, Douglas Strand, Chewlan Lastufka, Gregory A. Hosler, Gary C. Hon

Source: Molecular Cancer, Vol 23, Iss 1, Pp 1-6 (2024)

Subject Terms: Sarcoma, Prognosis, Biomarker, Single-cell transcriptomics, Spatial transcriptomics, Collagen, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/1476-4598

Access URL: https://doaj.org/article/8e5780871a3c4ef2a2a8af13c6227cf8

Deciphering the Oncogenic Landscape of Hepatocytes Through Integrated Single‐Nucleus and Bulk RNA‐Seq of Hepatocellular Carcinoma

Authors: Huanhou Su, Xuewen Zhou, Guanchuan Lin, Chaochao Luo, Wei Meng, Cui Lv, Yuting Chen, Zebin Wen, Xu Li, Yongzhang Wu, Changtai Xiao, Jian Yang, Jiameng Lu, Xingguang Luo, Yan Chen, Paul KH Tam, Chuanjiang Li, Haitao Sun, Xinghua Pan

Source: Advanced Science, Vol 12, Iss 14, Pp n/a-n/a (2025)

Subject Terms: hepatocellular carcinoma classification, hepatocyte subtype, metabolic pathway, quantile distribution model, single‐cell transcriptomics, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/ab3dd8421be04dfdb9ce77f8722e7dc6

Single-cell and spatial transcriptomic analysis reveals tumor cell heterogeneity and underlying molecular program in colorectal cancer

Authors: Teng Wang, Zhaoming Chen, Wang Wang, Heng Wang, Shenglong Li

Source: Frontiers in Immunology, Vol 16 (2025)

Subject Terms: colorectal cancer, tumor heterogeneity, prognosis, therapy, single-cell transcriptomics, spatial transcriptomics, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1556386/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/5a7054b7a0414ca19cd367869aedf772

Unveiling SSR4: a promising biomarker in esophageal squamous cell carcinoma

Authors: Jiaqi Zhang, Fang Jia, Chuqiao Li, Shunzhe Song, Aixia Gong

Source: Frontiers in Immunology, Vol 16 (2025)

Subject Terms: esophageal squamous cell carcinoma, SSR4, biomarker, single-cell transcriptomics, immune cells, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1544154/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/89be9b8b25504d4180ec58b353b9c0de

Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies

Authors: Jorge Blanco Mendana, Margaret Donovan, Lindsey Gengelbach O'Brien, Benjamin Auch, John Garbe, Daryl M Gohl

Source: eLife, Vol 12 (2025)

Subject Terms: next-generation sequencing, single-cell transcriptomics, genetic barcoding, behavior, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/88334; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/9b68712cd2c24723b0e991a6296479d3

A Study on the Inflammatory Response of the Brain in Neurosyphilis

Authors: Qiyu Zhang, Jie Ma, Jia Zhou, Hanlin Zhang, Mansheng Li, Huizi Gong, Yujie Wang, Heyi Zheng, Jun Li, Ling Leng

Source: Advanced Science, Vol 12, Iss 5, Pp n/a-n/a (2025)

Subject Terms: blood‒brain barrier, inflammation‐mediated brain injury, neurosyphilis, proteomics, single‐cell transcriptomics, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/904e867bfffb482ab20ffbcddf524306

Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes

Authors: Yidi Sun, Zhuoyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui, Quan Zou, Zilong Zhang

Source: Journal of Translational Medicine, Vol 22, Iss 1, Pp 1-15 (2024)

Subject Terms: Single-cell transcriptomics, T cells, DCIS, IDC, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/b704410050554544ab053325177da360

Deciphering STAT3’s negative regulation of LHPP in ESCC progression through single-cell transcriptomics analysis

Authors: Yurao Chen, Zemao Zheng, Luoshai Wang, Ronghuai Chen, Ming He, Xiang Zhao, Liyan Jin, Juan Yao

Source: Molecular Medicine, Vol 30, Iss 1, Pp 1-15 (2024)

Subject Terms: ESCC, Single-cell transcriptomics, Tumor microenvironment, STAT3, LHPP, Therapeutics. Pharmacology, RM1-950, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/1528-3658

Access URL: https://doaj.org/article/a3911e18c4ba43239ca32aa69894d971