NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine.

Authors: Wang, Aoyi¹ (AUTHOR), Peng, Haoyang¹ (AUTHOR), Wang, Yingdong¹ (AUTHOR), Zhang, Haoran¹ (AUTHOR), Cheng, Caiping¹ (AUTHOR), Zhao, Jinzhong¹ (AUTHOR), Zhang, Wuxia¹ (AUTHOR), Chen, Jianxin² (AUTHOR), Li, Peng¹ (AUTHOR)

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

Subject Terms: Chinese medicine, Gene expression profiling, Herbal medicine, Drug target, Biological networks

Deep learning in integrating spatial transcriptomics with other modalities.

Authors: Luo, Jiajian¹ (AUTHOR), Fu, Jiye¹ (AUTHOR), Lu, Zuhong¹ (AUTHOR), Tu, Jing¹ (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: Transcriptomes, Gene expression profiling, RNA sequencing, Multiomics, Chromatin

Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation.

Authors: Xu, Yongjie^1,2 (AUTHOR), Zang, Zelin^1,2 (AUTHOR), Hu, Bozhen^1,2 (AUTHOR), Yuan, Yue² (AUTHOR), Tan, Cheng^1,2 (AUTHOR), Xia, Jun^1,2 (AUTHOR), Li, Stan Z² (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-14. 14p.

Subject Terms: Gene expression profiling, Data augmentation, Laplacian matrices, RNA sequencing, Cell differentiation

Picroside II Inhibits Glycolysis and Migration in HepG2 Cells.

Authors: Lei, Xia^1,2,3 (AUTHOR), Yang, Si-Cheng^1,2 (AUTHOR), Peng, Kang-Bo^1,2,3 (AUTHOR), Wang, Meng-Fan^1,2,3 (AUTHOR), Wu, He-Zhen^1,2,3 (AUTHOR) 1397@hbtcm.edu.cn, Yang, Yan-Fang^1,2,3 (AUTHOR) 1397@hbtcm.edu.cn

Source: Pharmacognosy Magazine. Mar2025, Vol. 21 Issue 1, p192-206. 15p.

Subject Terms: *SURFACE plasmon resonance, *GENE expression profiling, *CARRIER proteins, *GLUCOSE metabolism, *DATABASES

Fascia-derived stem cells enhance fat graft retention by promoting vascularization through the HMOX1-HIF-1α pathway.

Authors: Chen, Guo¹ (AUTHOR) chenguo857@163.com, Long, Jie^1,2 (AUTHOR) longjie719@126.com, Zhang, Yuge¹ (AUTHOR) zhangyuge1109@163.com, Zhou, Xuhua¹ (AUTHOR) choul7100@gmail.com, Gao, Botao¹ (AUTHOR) liangzaichongchongchong@hotmail.com, Qin, Zijin^1,3 (AUTHOR) collarqin@gmail.com, Zhu, Yuhan¹ (AUTHOR) zhuyuhan3364@163.com, Song, Binyu¹ (AUTHOR) sby2023@126.com, Cui, Ziwei¹ (AUTHOR) Czwei0209@163.com, liu, Zhangzi¹ (AUTHOR) lzz10086110@163.com, Xu, Man¹ (AUTHOR) 13289277779@163.com, Yu, Zhou¹ (AUTHOR) yz20080512@163.com, Song, Baoqiang¹ (AUTHOR) songbq2012@163.com, Zhang, Ziang¹ (AUTHOR) zhang_ziang@hotmail.com

Source: Stem Cell Research & Therapy. 2/25/2025, Vol. 16 Issue 1, p1-21. 21p.

Subject Terms: *LIFE sciences, *GENE expression profiling, *GENE expression, *STEM cells, *ADIPOSE tissues

Genome-wide KAS-Seq mapping of leukocytes in ischemia-reperfusion model reveals IL7R as a potential therapeutic target for ischemia-reperfusion injury.

Authors: Zhang, Lei^1,2 (AUTHOR), Duolikun, Maimaitiyasen³ (AUTHOR), Chen, Hangyu^1,2 (AUTHOR), Wang, Zihao⁴ (AUTHOR), Li, Xuehui⁵ (AUTHOR), Xiao, Hong³ (AUTHOR), Dong, Yuchao⁴ (AUTHOR), Chen, Haoyu⁶ (AUTHOR), Liu, Fengyong⁷ (AUTHOR), Fan, Shiyong⁴ (AUTHOR) fansy@bmi.ac.cn, Lin, Jian^1,2,3,8 (AUTHOR) linjian@pku.edu.cn, Chen, Long^1,2 (AUTHOR) lcchenlong@163.com

Source: Scientific Reports. 2/20/2025, Vol. 15 Issue 1, p1-15. 15p.

Subject Terms: *GENE expression profiling, *DRUG target, *GENE expression, *REPERFUSION injury, *INTERLEUKIN-7, *REPERFUSION, *MYOCARDIAL reperfusion

Alterations in Methionine Cycle and Wnt/MAPK Signaling Associated with HMBi-Induced Cashmere Growth in Goats.

Authors: Xi, Minjie¹ (AUTHOR), Jiang, Jiali¹ (AUTHOR), Wang, Bo¹ (AUTHOR), Wang, Yihan¹ (AUTHOR), Di, Meiqi¹ (AUTHOR), Cong, Yuyan¹ (AUTHOR), Zhang, Ruiyang¹ (AUTHOR) zhangruiyang@syau.edu.cn

Source: International Journal of Molecular Sciences. Feb2025, Vol. 26 Issue 4, p1663. 18p.

Subject Terms: *PHYSIOLOGY, *GENE expression profiling, *WNT signal transduction, *CELL differentiation, *BETAINE, *CYCLIN-dependent kinases

Characterization of G2/M checkpoint classifier for personalized treatment in uterine corpus endometrial carcinoma.

Authors: Liu, Yiming¹ (AUTHOR) 1343z00@163.com, Wang, Yusi² (AUTHOR) wangyusi@hrbmu.edu.cn, Tan, Shu¹ (AUTHOR) tanshu2599@126.com, Shi, Xiaochen¹ (AUTHOR) 1342363509@qq.com, Wen, Jinglin¹ (AUTHOR) wenjinglin1995@163.com, Chen, Dejia¹ (AUTHOR) dejiachen@outlook.com, Zhao, Yue¹ (AUTHOR) 2654137350@qq.com, Pan, Wenjing³ (AUTHOR) pwj0129@163.com, Jia, Zhaoyang³ (AUTHOR) jzy_1013@163.com, Lu, Chunru⁴ (AUTHOR) 64579401@qq.com, Lou, Ge¹ (AUTHOR) louge@ems.hrbmu.edu.cn

Source: Cancer Cell International. 2/7/2025, Vol. 25 Issue 1, p1-22. 22p.

Subject Terms: *ARTIFICIAL neural networks, *GENE expression profiling, *ENDOMETRIAL cancer, *DRUG analysis, *DRUG resistance

Inter- and Transgenerational Effects of In Ovo Stimulation with Bioactive Compounds on Cecal Tonsils and Cecal Mucosa Transcriptomes in a Chicken Model.

Authors: Ibrahim, Mariam^1,2 (AUTHOR) miriam.ibrahim@pbs.edu.pl, Bednarczyk, Marek³ (AUTHOR), Stadnicka, Katarzyna¹ (AUTHOR) katarzyna.stadnicka@cm.umk.pl, Grochowska, Ewa¹ (AUTHOR) ewa.grochowska@cm.umk.pl

Source: International Journal of Molecular Sciences. Feb2025, Vol. 26 Issue 3, p1174. 29p.

Subject Terms: *GENE expression profiling, *EMBRYOLOGY, *GENE expression, *CHICKENS, *SYNBIOTICS

Covariate-adjusted construction of gene regulatory networks using a combination of generalized linear model and penalized maximum likelihood.

Authors: Chatrabgoun, Omid^1,2 (AUTHOR) ad8337@coventry.ac.uk, Daneshkhah, Alireza³ (AUTHOR), Torkaman, Parisa² (AUTHOR), Johnston, Mark¹ (AUTHOR), Sohrabi Safa, Nader⁴ (AUTHOR), Kashif Bashir, Ali⁴ (AUTHOR)

Source: PLoS ONE. 1/29/2025, Vol. 20 Issue 1, p1-18. 18p.

Subject Terms: *GENE expression, *GENE expression profiling, *SPARSE matrices, *MACHINE learning, *GENES

Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data.

Authors: Cheng, Jinming^1,2 (AUTHOR), Jin, Xinyi^1,2 (AUTHOR), Smyth, Gordon K.^1,3 (AUTHOR) smyth@wehi.edu.au, Chen, Yunshun^1,2,4 (AUTHOR) yuchen@wehi.edu.au

Source: BMC Bioinformatics. 1/20/2025, Vol. 26 Issue 1, p1-15. 15p.

Subject Terms: *GENE expression profiling, *TRANSCRIPTOMES, *RNA sequencing, *LIFE sciences, *BREAST cancer

Improving Replication in Endometrial Omics: Understanding the Influence of the Menstrual Cycle.

Authors: Chung, Jessica^1,2 (AUTHOR) jchung@unimelb.edu.au, Rogers, Peter Adrian¹ (AUTHOR) parogers@unimelb.edu.au

Source: International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 2, p857. 19p.

Subject Terms: *MENSTRUAL cycle, *GENE expression profiling, *REPRODUCIBLE research, *GENE expression, *ENDOMETRIOSIS, *ENDOMETRIUM

Exploring the role of ELOVLs family in lung adenocarcinoma based on bioinformatic analysis and experimental validation.

Authors: Wang, Zihan¹ (AUTHOR), Cui, Wenjing^2,3 (AUTHOR), Liang, Long¹ (AUTHOR), Qu, Jingge¹ (AUTHOR), Pei, Yuqiang¹ (AUTHOR), Li, Danyang¹ (AUTHOR), Luo, Ying¹ (AUTHOR), Zhang, Yue¹ (AUTHOR), Qiu, Yifan⁴ (AUTHOR), Sun, Yongchang¹ (AUTHOR) suny@bjmu.edu.cn

Source: BMC Cancer. 1/10/2025, Vol. 25 Issue 1, p1-17. 17p.

Subject Terms: *METABOLIC reprogramming, *GENE expression profiling, *GENE expression, *FATTY acids, *POLYMERASE chain reaction

Comprehensive analysis of the expression and prognostic value of ARMCs in pancreatic adenocarcinoma.

Authors: Zhuo, Guanxiang^1,2 (AUTHOR), Lin, Shengzhai^1,3 (AUTHOR), Yuan, Fei^1,3 (AUTHOR), Zheng, Qiaoling⁴ (AUTHOR), Guo, Yinpin^1,3 (AUTHOR), Wang, Zuwei⁵ (AUTHOR), Hu, Jianfei⁵ (AUTHOR), Yao, Meihong⁴ (AUTHOR), Zhong, Fuxiu⁶ (AUTHOR), Chen, Shi^5,7 (AUTHOR) wawljwalj@163.com, Chen, Yanling^1,3 (AUTHOR) drchenyl@126.com, Chen, Huixing^1,3 (AUTHOR) chenhuixing@163.com

Source: BMC Cancer. 1/7/2025, Vol. 25 Issue 1, p1-18. 18p.

Subject Terms: *GENE expression profiling, *TUMOR markers, *DATABASES, *MISSENSE mutation, *SURVIVAL rate

SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning.

Authors: Liu, Wei¹ (AUTHOR), Wang, Bo¹ (AUTHOR), Bai, Yuting¹ (AUTHOR), Liang, Xiao¹ (AUTHOR), Xue, Li¹ (AUTHOR), Luo, Jiawei¹ (AUTHOR) luojiawei@hnu.edu.cn

Source: Briefings in Bioinformatics. Nov2024, Vol. 25 Issue 6, p1-12. 12p.

Subject Terms: Transcriptomes, Gene expression profiling, Deep learning, Supervised learning, Neighborhoods, Heterogeneity

scDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information.

Authors: Zhao, Liuyang¹ (AUTHOR), Jiang, Landu² (AUTHOR), Xie, Yufeng³ (AUTHOR), Huang, JianHao³ (AUTHOR), Xie, Haoran⁴ (AUTHOR), Tian, Jun^5,6 (AUTHOR) tianj@sustech.edu.cn, Zhang, Dian¹ (AUTHOR) tianj@sustech.edu.cn

Source: Briefings in Bioinformatics. Nov2024, Vol. 25 Issue 6, p1-11. 11p.

Subject Terms: Gene expression profiling, RNA sequencing, Deep learning, Transfer of training, Knowledge transfer

CDHu40: a novel marker gene set of neuroendocrine prostate cancer.

Authors: Liu, Sheng¹ (AUTHOR), Nam, Hye Seung² (AUTHOR), Zeng, Ziyu³ (AUTHOR), Deng, Xuehong² (AUTHOR), Pashaei, Elnaz¹ (AUTHOR), Zang, Yong⁴ (AUTHOR), Yang, Lei⁵ (AUTHOR), Li, Chenglong⁶ (AUTHOR), Huang, Jiaoti⁷ (AUTHOR), Wendt, Michael K^8,9 (AUTHOR), Lu, Xin^3,10 (AUTHOR), Huang, Rong² (AUTHOR), Wan, Jun^1,10,11 (AUTHOR) junwan@iu.edu

Source: Briefings in Bioinformatics. Nov2024, Vol. 25 Issue 6, p1-12. 12p.

Subject Terms: Castration-resistant prostate cancer, Gene expression profiling, Survival rate, Prostate-specific antigen, Prostate cancer

Identification of the shared gene signatures in retinoblastoma and osteosarcoma by machine learning.

Authors: Ye, Rongjie^1,2 (AUTHOR), Yuan, Quan³ (AUTHOR), You, Wenkang^1,2 (AUTHOR), Huang, Yukai⁴ (AUTHOR), Lin, Zhangdian^1,2 (AUTHOR), Tang, Haifeng^1,2 (AUTHOR) 2289325268@qq.com, Zeng, Rongdong^1,2 (AUTHOR) zrd201295@fjmu.edu.cn

Source: Scientific Reports. 12/28/2024, Vol. 14 Issue 1, p1-14. 14p.

Subject Terms: *DISEASE risk factors, *GENE expression profiling, *GENE expression, *GENE regulatory networks, *OVERALL survival, *MACHINE learning

A stable combination of non-stable genes outperforms standard reference genes for RT-qPCR data normalization.

Authors: Djari, Anis¹ (AUTHOR), Madignier, Guillaume^1,2 (AUTHOR), Chervin, Christian¹ (AUTHOR), van der Rest, Benoît¹ (AUTHOR), Giovannoni, James J.^3,4 (AUTHOR), Bouzayen, Mondher¹ (AUTHOR), Maza, Elie¹ (AUTHOR) Elie.Maza@toulouse-inp.fr

Source: Scientific Reports. 12/28/2024, Vol. 14 Issue 1, p1-14. 14p.

Subject Terms: *GENE expression profiling, *GENE expression, *NUCLEOTIDE sequencing, *LIFE sciences, *DATABASES

Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53.

Authors: Wertheim, Kenneth Y.^1,2,3,4 (AUTHOR), Chisholm, Robert² (AUTHOR), Richmond, Paul² (AUTHOR), Walker, Dawn^1,2 (AUTHOR) d.c.walker@sheffield.ac.uk

Source: PLoS Computational Biology. 12/23/2024, Vol. 20 Issue 12, p1-44. 44p.

Subject Terms: *GENE expression profiling, *TECHNOLOGICAL innovations, *DIGITAL twin, *P53 protein, *TUMOR microenvironment