The InnovationPub Date : 2025-04-30eCollection Date: 2025-08-04DOI: 10.1016/j.xinn.2025.100937
Hongyu Yu, Nan Sun, Ruohan Ren, Tao Zhou, Mengcen Guan, Leqi Zhao, Stephen S-T Yau
{"title":"The grand biological universe: A comprehensive geometric construction of genome space.","authors":"Hongyu Yu, Nan Sun, Ruohan Ren, Tao Zhou, Mengcen Guan, Leqi Zhao, Stephen S-T Yau","doi":"10.1016/j.xinn.2025.100937","DOIUrl":"10.1016/j.xinn.2025.100937","url":null,"abstract":"<p><p>Analyzing the geometric relationships among genomic sequences from a mathematical perspective and revealing the laws hidden within these relationships is a crucial challenge in bioinformatics. The natural vector method constructs a genome space by extracting statistical moments of <i>k</i>-mers to illuminate the relationships among genomes. This approach highlights a fundamental law in biology known as the convex hull principle, which states that natural vectors corresponding to different types of biological sequences form distinct, non-overlapping convex hulls. Previous studies have validated this important principle across various datasets. However, they often focused on specific kingdoms and did not thoroughly analyze the significance of the dimensions required for the convex hull separation. In this study, we integrate all reliable sequences from different kingdoms to construct the grand biological universe, within which we comprehensively validate the multi-level convex hull principle. We demonstrate that the separation of convex hulls arises from biological properties rather than mathematical characteristics of high-dimensional spaces. Furthermore, we develop suitable metrics within the grand biological universe to facilitate efficient sequence classification. This research advances the convex hull principle through both theoretical development and experimental validation, making significant contributions to the understanding of the geometric structure of genome space.</p>","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"6 8","pages":"100937"},"PeriodicalIF":25.7,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12347096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144856674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The InnovationPub Date : 2025-04-29eCollection Date: 2025-08-04DOI: 10.1016/j.xinn.2025.100917
{"title":"Preserving the freedom of science: A call for respect and collaboration.","authors":"","doi":"10.1016/j.xinn.2025.100917","DOIUrl":"10.1016/j.xinn.2025.100917","url":null,"abstract":"","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"6 8","pages":"100917"},"PeriodicalIF":25.7,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12347126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144856672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The InnovationPub Date : 2025-04-29eCollection Date: 2025-08-04DOI: 10.1016/j.xinn.2025.100938
Sijia Li, Dehua Mao, Jonathan M Chase, Kaishan Song, Zongming Wang, Hong Yang
{"title":"Improve water quality of small water bodies.","authors":"Sijia Li, Dehua Mao, Jonathan M Chase, Kaishan Song, Zongming Wang, Hong Yang","doi":"10.1016/j.xinn.2025.100938","DOIUrl":"10.1016/j.xinn.2025.100938","url":null,"abstract":"","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"6 8","pages":"100938"},"PeriodicalIF":25.7,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12347124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144856670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The InnovationPub Date : 2025-04-29eCollection Date: 2025-08-04DOI: 10.1016/j.xinn.2025.100918
Peipei Song, Qiwei Jiang, Xueji Wu, Lang Bu, Wei Xie, Wenyi Wei, Xiaofang Xing, Jianping Guo
{"title":"Palmitic acid and palmitoylation in cancer: Understanding, insights, and challenges.","authors":"Peipei Song, Qiwei Jiang, Xueji Wu, Lang Bu, Wei Xie, Wenyi Wei, Xiaofang Xing, Jianping Guo","doi":"10.1016/j.xinn.2025.100918","DOIUrl":"10.1016/j.xinn.2025.100918","url":null,"abstract":"<p><p>Nutrients from dietary foods not only provide energy and building blocks, but also play critical roles in modulating diverse pathophysiological functions. They achieve these, in part, by accelerating cell signaling transduction processes via modulating various types of protein post-translational modifications (PTMs). Notably, accumulating evidence has identified palmitic acid (PA), a major component of high-fat diets, as a significant contributor to various human disorders, including diabetes and cancer. Hence, further understanding the roles of PA and its involvement in protein palmitoylation, a key PTM, is crucial for uncovering the mechanisms underlying these diseases and exploring potential clinical applications in cancer therapy. This review comprehensively summarizes recent advances in the understanding of PA homeostasis and palmitoylation in tumorigenesis. Specifically, it highlights the connections between palmitoylation and key processes such as oncogenic signaling pathways, cell death mechanisms, innate immune responses, and the tumor microenvironment. The review also emphasizes potential therapeutic strategies, including targeting PA homeostasis, palmitoylation-associated processes, or specific palmitoylated proteins for cancer treatment. Finally, the challenges in the field, such as the regulation of PA homeostasis and the dynamic detection or targeting of palmitoylation, are discussed, underscoring the need for further research to address these critical issues.</p>","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"6 8","pages":"100918"},"PeriodicalIF":25.7,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12347385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144856671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The InnovationPub Date : 2025-04-22eCollection Date: 2025-07-07DOI: 10.1016/j.xinn.2025.100914
Shanghang Zhang, Bingteng Xie, Xin Zhu, Suwei Dong, Mo Li
{"title":"Lactylation in cancer: Unveiling new layers of complexity.","authors":"Shanghang Zhang, Bingteng Xie, Xin Zhu, Suwei Dong, Mo Li","doi":"10.1016/j.xinn.2025.100914","DOIUrl":"10.1016/j.xinn.2025.100914","url":null,"abstract":"","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"6 7","pages":"100914"},"PeriodicalIF":33.2,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}