TRIAGE: an R package for regulatory gene analysis.

Authors: Zhao, Qiongyi¹ (AUTHOR), Shim, Woo Jun¹ (AUTHOR), Sun, Yuliangzi¹ (AUTHOR), Sinniah, Enakshi¹ (AUTHOR), Shen, Sophie¹ (AUTHOR), Boden, Mikael² (AUTHOR), Palpant, Nathan J¹ (AUTHOR)

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

Subject Terms: RNA sequencing, Gene regulatory networks, Gene expression, Regulator genes, Cell physiology

Online-adjusted evolutionary biclustering algorithm to identify significant modules in gene expression data.

Authors: Galindo-Hernández, Raúl¹ (AUTHOR), Rodríguez-Vázquez, Katya¹ (AUTHOR), Galán-Vásquez, Edgardo¹ (AUTHOR), Castellanos, Carlos Ignacio Hernández¹ (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-18. 18p.

Subject Terms: Gene regulatory networks, Gene expression, Evolutionary algorithms, Pearson correlation (Statistics), DNA

A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks.

Authors: Liu, Yong¹ (AUTHOR), Zhong, Le¹ (AUTHOR), Yan, Bin² (AUTHOR), Chen, Zhuobin³ (AUTHOR), Yu, Yanjia¹ (AUTHOR), Yu, Dan² (AUTHOR), Qin, Jing³ (AUTHOR), Wang, Junwen^2,4 (AUTHOR)

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

Subject Terms: Gene regulatory networks, Gene expression, Regulator genes, Gene expression profiling, Genetic transcription, Deep learning

BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction.

Authors: Tan, Yuejun^1,2 (AUTHOR), Xie, Linhai^3,4 (AUTHOR), Yang, Hong¹ (AUTHOR), Zhang, Qingyuan⁴ (AUTHOR), Luo, Jinyuan¹ (AUTHOR), Zhang, Yanchun² (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-10. 10p.

Subject Terms: Gene regulatory networks, Genetic regulation, Autoencoder, Biological neural networks, Data distribution

TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data.

Authors: Ma, Xin¹ (AUTHOR), Lin, Lijing² (AUTHOR), Zhao, Qian¹ (AUTHOR), Iqbal, Mudassar¹ (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-11. 11p.

Subject Terms: Gene regulatory networks, Matrix decomposition, Multiomics, Nonnegative matrices, Genetic regulation

The CGA1-SNAT regulatory module potentially contributes to cytokinin-mediated melatonin biosynthesis and drought tolerance in wheat.

Authors: Shamloo-Dashtpagerdi, Roohollah¹ (AUTHOR) shamloo.r@gmail.com, Lindlöf, Angelica² (AUTHOR) angelica.lindlof@his.se, Aliakbari, Massume³ (AUTHOR)

Source: BMC Plant Biology. 3/7/2025, Vol. 25 Issue 1, p1-13. 13p.

Subject Terms: *CROP science, *GENE regulatory networks, *GENETIC engineering, *AGRICULTURE, *LIFE sciences, *DROUGHT tolerance

Cross-validation for training and testing co-occurrence network inference algorithms: Cross-validation for training and testing co-occurrence network...: D. Agyapong et al.

Authors: Agyapong, Daniel¹ (AUTHOR) da2343@nau.edu, Propster, Jeffrey Ryan² (AUTHOR) Jeffrey.Propster@nau.edu, Marks, Jane² (AUTHOR) Jane.Marks@nau.edu, Hocking, Toby Dylan³ (AUTHOR) toby.dylan.hocking@usherbrooke.ca

Source: BMC Bioinformatics. 3/6/2025, Vol. 26 Issue 1, p1-24. 24p.

Subject Terms: *GENE regulatory networks, *BIODEGRADATION, *MICROBIAL ecology, *LIFE sciences, *HUMAN ecology

STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes.

Authors: Wang, Ran^1,2,3 (AUTHOR), Qian, Yan⁴ (AUTHOR), Guo, Xiaojing⁵ (AUTHOR), Song, Fangda⁶ (AUTHOR), Xiong, Zhiqiang¹ (AUTHOR), Cai, Shirong⁴ (AUTHOR), Bian, Xiuwu⁷ (AUTHOR), Wong, Man Hon³ (AUTHOR), Cao, Qin^8,9 (AUTHOR) qcao@cuhk.edu.hk, Cheng, Lixin⁵ (AUTHOR) easonlcheng@gmail.com, Lu, Gang^1,2,7,9 (AUTHOR) lugang@cuhk.edu.hk, Leung, Kwong Sak^3,7,10 (AUTHOR) ksleung@cse.cuhk.edu.hk

Source: Genome Medicine. 3/3/2025, Vol. 17 Issue 1, p1-23. 23p.

Subject Terms: *GENE regulatory networks, *CYTOLOGY, *LIFE sciences, *TRANSCRIPTOMES, *TUMOR microenvironment

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

Authors: Stock, Marco^1,2,3,4 (AUTHOR), Losert, Corinna^2,5 (AUTHOR), Zambon, Matteo^1,2,3 (AUTHOR), Popp, Niclas^1,2,3 (AUTHOR), Lubatti, Gabriele^1,2,3 (AUTHOR), Hörmanseder, Eva¹ (AUTHOR), Heinig, Matthias^2,5,6 (AUTHOR), Scialdone, Antonio^1,2,3 (AUTHOR) antonio.scialdone@helmholtz-munich.de

Source: Molecular Systems Biology. Mar2025, Vol. 21 Issue 3, p214-230. 17p.

Subject Terms: *GENE regulatory networks, *REGULATOR genes, *RNA sequencing, *TRANSCRIPTOMES, *PRIOR learning

Identification of key genes and signaling pathway in the pathogenesis of Huntington's disease via bioinformatics and next generation sequencing data analysis.

Authors: Vastrad, Basavaraj¹ (AUTHOR), Vastrad, Chanabasayya² (AUTHOR) channu.vastrad@gmail.com

Source: Egyptian Journal of Medical Human Genetics. 3/4/2025, Vol. 26 Issue 1, p1-71. 71p.

Subject Terms: *NUCLEOTIDE sequencing, *GENE regulatory networks, *HUNTINGTON disease, *RECEIVER operating characteristic curves, *GENE expression

The dynamic regulatory network of stamens and pistils in papaya.

Authors: Xiang, Tao^1,2 (AUTHOR), Zhu, Yating^1,2 (AUTHOR), Wang, Yang^1,2 (AUTHOR), Chen, Xi² (AUTHOR), Zhang, Zhibin² (AUTHOR), Lai, Juan² (AUTHOR), Zhou, Ping³ (AUTHOR), Ming, Ray² (AUTHOR), Yue, Jingjing² (AUTHOR) jingjingyue11@126.com

Source: BMC Plant Biology. 2/25/2025, Vol. 25 Issue 1, p1-23. 23p.

Subject Terms: *GENE regulatory networks, *SEX determination, *REGULATOR genes, *LIFE sciences, *MORPHOGENESIS, *GENETIC sex determination, *PAPAYA

Integrating QTL mapping with transcriptome analysis mined candidate genes of growth stages in castor (Ricinus communis L.).

Authors: Huang, Guanrong¹ (AUTHOR), Lu, Jiannong¹ (AUTHOR), Yin, Xuegui¹ (AUTHOR) yinxuegui@126.com, Zhang, Liuqin¹ (AUTHOR), Lin, Haihong¹ (AUTHOR), Zhang, Xiaoxiao¹ (AUTHOR), Liu, Chaoyu¹ (AUTHOR), Zuo, Jinying¹ (AUTHOR)

Source: BMC Genomics. 2/22/2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: *GENE expression, *GENE regulatory networks, *LIFE sciences, *CROP yields, *GENE mapping

Comprehensive bioinformatic analysis reveals prognostic significance and functional insights of candidate gene expression in colorectal cancer.

Authors: Ke, Tao-Wei¹ (AUTHOR), Chang, Sheng-Chi¹ (AUTHOR), Yeh, Chung-Min² (AUTHOR), Lin, Shu-Hui^2,3,4 (AUTHOR), Yeh, Kun-Tu^2,5 (AUTHOR) 10159@cch.org.tw

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

Subject Terms: *GENE regulatory networks, *GENE expression, *MEDICAL sciences, *CANCER cell proliferation, *GENE silencing

NPR1-like genes in Theobroma cacao: Evolutionary insights and potential in enhancing resistance to Phytophthora megakarya.

Authors: Rasheed, Muhammad Umar¹ (AUTHOR), Malik, Aiman¹ (AUTHOR), Haider, Muhammad Zeshan² (AUTHOR), Sami, Adnan² (AUTHOR), Shafiq, Muhammad¹ (AUTHOR), Ali, Qurban¹ (AUTHOR), Javed, Muhammad Arshad¹ (AUTHOR), Ali, Ansar^2,3 (AUTHOR) ansarali@utexas.edu

Source: PLoS ONE. 2/14/2025, Vol. 20 Issue 2, p1-15. 15p.

Subject Terms: *GENE expression, *GENE regulatory networks, *CACAO, *GENETIC transcription regulation, *SALICYLIC acid

Transcriptomic and biochemical insights into key gene networks driving bulbil development of Pinellia ternata (Thunb.) Breit.

Authors: Jia, Xiwei^1,2 (AUTHOR), Jiu, Xijia¹ (AUTHOR), Liu, Yuan¹ (AUTHOR), Guo, Chao² (AUTHOR), Liu, Dong¹ (AUTHOR), Zhao, Xin¹ (AUTHOR), Chen, Honggang^1,3 (AUTHOR), Du, Tao^1,3 (AUTHOR) gslzdt@163.com

Source: PLoS ONE. 2/11/2025, Vol. 20 Issue 2, p1-25. 25p.

Subject Terms: *GENE regulatory networks, *TISSUE differentiation, *METABOLITES, *PLANT species, *STARCH, *SUCROSE

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature.

Authors: Musella, Luca¹ (AUTHOR) luca.musella@uk-erlangen.de, Afonso Castro, Alejandro¹ (AUTHOR), Lai, Xin^1,2 (AUTHOR), Widmann, Max^1,3 (AUTHOR), Vera, Julio¹ (AUTHOR) julio.vera-gonzalez@uk-erlangen.de

Source: PLoS Computational Biology. 2/11/2025, Vol. 21 Issue 2, p1-33. 33p.

Subject Terms: *SCIENTIFIC literature, *GENE regulatory networks, *MESH networks, *DATABASES, CANCER case studies

Endoplasmic reticulum stress-related CLIP4 plays a procarcinogenic role in hepatocellular carcinoma: an integrated analysis.

Authors: Wang, Anqi¹ (AUTHOR), Yan, Sitong^1,2 (AUTHOR), Jiang, Weijia¹ (AUTHOR), Chen, Xiang¹ (AUTHOR), Huang, Yuhan¹ (AUTHOR), Zu, Xiangyu¹ (AUTHOR), Du, Xiao¹ (AUTHOR), Fan, Lulu¹ (AUTHOR), Liu, Jiatao³ (AUTHOR), Sun, Guoping¹ (AUTHOR) sungp@ahmu.edu.cn

Source: BMC Cancer. 2/7/2025, Vol. 25 Issue 1, p1-20. 20p.

Subject Terms: *LIFE sciences, *GENE regulatory networks, *ENDOPLASMIC reticulum, *EPITHELIAL-mesenchymal transition, *HEPATOCELLULAR carcinoma

A recombinase-activated ribozyme to knock down endogenous gene expression in zebrafish.

Authors: Juan, Thomas^1,2,3,4 (AUTHOR) thomas.juan@igp.uu.se, Molina, Tonatiuh¹ (AUTHOR), Xie, Lihan¹ (AUTHOR), Papadopoulou, Sofia¹ (AUTHOR), Cardoso, Bárbara¹ (AUTHOR), Jha, Shivam Govind⁴ (AUTHOR), Stainier, Didier Y.R.^1,2,3 (AUTHOR) thomas.juan@igp.uu.se

Source: PLoS Genetics. 2/7/2025, Vol. 21 Issue 2, p1-15. 15p.

Subject Terms: *GENETIC regulation, *GENE regulatory networks, *GENE expression, *PHENOTYPES, *RECOMBINASES

Integrated transcriptomic and metabolomic analyses reveal critical gene regulatory network in response to drought stress in Dendrobium nobile Lindl.

Authors: Lv, Chaoyan¹ (AUTHOR) lvchaoyan1985@126.com, He, Ya¹ (AUTHOR), Jiang, Zaiqian¹ (AUTHOR), Hu, Wenjia¹ (AUTHOR), Zhang, Mei¹ (AUTHOR)

Source: BMC Plant Biology. 2/4/2025, Vol. 25 Issue 1, p1-13. 13p.

Subject Terms: *GENE regulatory networks, *LIFE sciences, *PROLINE metabolism, *STARCH metabolism, *BOTANY, *DROUGHT tolerance

Statistical and machine learning based platform-independent key genes identification for hepatocellular carcinoma.

Authors: Hasan, Md. Al Mehedi¹ (AUTHOR), Maniruzzaman, Md.^2,3 (AUTHOR), Huang, Jie³ (AUTHOR), Shin, Jungpil³ (AUTHOR) jpshin@u-aizu.ac.jp

Source: PLoS ONE. 2/5/2025, Vol. 20 Issue 2, p1-29. 29p.

Subject Terms: *GENE expression, *GENE regulatory networks, *SUPPORT vector machines, *STATISTICAL learning, *LIVER cancer