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Artificial intelligence methods available for cancer research

Frontiers of Medicine 2024年第5期18卷 778-797页

作者： Ankita Murmu Balázs Győrffy Institute of Molecular Life Sciences HUN-REN Research Centre for Natural SciencesBudapest 1117Hungary National Laboratory for Drug Research and Development Budapest 1117Hungary Department of Bioinformatics Semmelweis UniversityBudapest 1094Hungary Department of Biophysics University of PecsPecs 7624Hungary

Cancer is a heterogeneous and multifaceted disease with a significant global *** substantial technological advancements for battling cancer,early diagnosis and selection of effective treatment remains a *** the convenience of large-scale datasets including multiple levels of data,new bioinformatic tools are needed to transform this wealth of information into clinically useful decision-support *** this field,artificial intelligence(AI)technologies with their highly diverse applications are rapidly gaining *** learning methods,such as Bayesian networks,support vector machines,decision trees,random forests,gradient boosting,and K-nearest neighbors,including neural network models like deep learning,have proven valuable in predictive,prognostic,and diagnostic *** have recently employed large language models to tackle new dimensions of ***,leveraging the opportunity to utilize AI in clinical settings will require surpassing significant obstacles—a major issue is the lack of use of the available reporting guidelines obstructing the reproducibility of published *** this review,we discuss the applications of AI methods and explore their benefits and *** summarize the available guidelines for AI in healthcare and highlight the potential role and impact of AI models on future directions in cancer research.

关键词： machine learning artificial neural network deep learning natural language processing prediction guideline diagnosis

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PathActMarker:an R package for inferring pathway activity of complex diseases

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Frontiers of Computer Science 2025年第3期19卷 123-124页

作者： Xingyi LI Jun HAO Zhelin ZHAO Junming LI Xingyu LIAO Min LI Xuequn SHANG School of Computer Science Northwestern Polytechnical UniversityXi’an 710072China Research&Development Institute of Northwestern Polytechnical University in Shenzhen Shenzhen 518063China School of Software Northwestern Polytechnical UniversityXi’an 710072China Hunan Provincial Key Lab on Bioinformatics School of Computer Science and EngineeringCentral South UniversityChangsha 410083China

1 Introduction The process of complex diseases is closely linked to the disruption of key biological pathways,it is crucial to identify the dysfunctional pathways and quantify the degree of dysregulation at the indivi... 详细信息

关键词： pathway activity dysregulation complex diseases biological pathways disruption key biological pathwaysit identify dysfunctional pathways

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Alterations in immune cell heterogeneities in the brain of aged zebrafish using single-cell resolution

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Science China(Life Sciences) 2023年第6期66卷 1358-1378页

作者： Jiangyong He Fangying Zhao Bingyue Chen Nianfei Cui Zhifan Li Jie Qin Lingfei Luo Congjian Zhao Li Li Institute of Developmental Biology and Regenerative Medicine Key Laboratory of Freshwater Fish Reproduction and DevelopmentMinistry of EducationSouthwest UniversityChongqing400715China Research Center of Stem cells and Aging Chongqing Institute of Green and Intelligent TechnologyChinese Academy of SciencesChongqing400714China Chongqing Engineering Research Center of Medical Electronics and Information Technology School of BioinformaticsChongqing University of Posts and TelecommunicationsChongqing400065China

Immunocytes,including the microglia,are crucial in the neurodegenerative process in old ***,the understanding regarding microglia heterogeneity and other involved immunocytes remains *** analyzed 26,456 immunocytes from 12-and 26-month-old zebrafish brains at single-cell *** and T lymphocytes were detected in the brain at both time *** types of microglia were annotated,namely,ac+microglia and xr+microglia,which were clustered into subsets 1,2,3,4,5,and subsets 6,7,8,9,*** microglia predominated the adult brains and cooperated with T cells to perform the functions of immune response and neuronal *** validated the specific microglia *** novel transgenic lines,Tg(lgals3bpb:e GFP)and Tg(apoc1:e GFP),were created,which faithfully labeled ac+microglia and served as valuable labeling ***,the microglia population reduced while T cells of six subtypes intriguingly increased to serve as the primary immune cells in aged *** in 12-month-old brains,T cells,together with microglia,exhibited a coordinated signature of inflammation in the 26-month-old *** findings revealed the immunocytes atlas in aged zebrafish *** implied the involvement of microglia and T cells in the progression of neurodegeneration in aging.

关键词： aging scRNA-seq microglia T lymphocyte inflammation zebrafish

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Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors

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中国药理学报（英文版） 2023年第9期44卷 1879-1889页

作者： Szonja Anna Kovács János Tibor Fekete Balázs Gy?rffy Department of Bioinformatics Semmelweis UniversityTüzoltó utca 7-91094 BudapestHungary Doctoral School of Pathological Sciences Semmelweis Universityüll?i út 261085 BudapestHungary National Laboratory for Drug Research and Development Magyar tudósok k?rútja 2 1117BudapestHungary National Laboratory for Drug Research and Development Magyar tudósok k?rútja 2 1117BudapestHungary Research Centre for Natural Sciences Oncology Biomarker Research GroupInstitute of EnzymologyE?tv?s Loránd Research NetworkMagyar Tudósok k?rútja 21117 BudapestHungary Department of Bioinformatics Semmelweis UniversityTüzoltó utca 7-91094 BudapestHungary Department of Pediatrics Semmelweis UniversityTüzoltó utca 7-91094 BudapestHungary

Immune-checkpoint inhibitors show promising effects in the treatment of multiple tumor *** are biological indicators used to select patients for a systemic anticancer treatment,but there are only a few clinically useful biomarkers such as PD-L1 expression and tumor mutational burden,which can be used to predict immunotherapy *** this study,we established a database consisting of both gene expression and clinical data to identify biomarkers of response to anti-PD-1,anti-PD-L1,and anti-CTLA-4 immunotherapies.A GEO screening was executed to identify datasets with simultaneously available clinical response and transcriptomic data regardless of cancer *** screening was restricted to the studies involving administration of anti-PD-1(nivolumab,pembrolizumab),anti-PD-L1(atezolizumab,durvalumab)or anti-CTLA-4(ipilimumab)*** operating characteristic(ROC)analysis and Mann-Whitney test were executed across all genes to identify features related to therapy *** database consisted of 1434 tumor tissue samples from 19 datasets with esophageal,gastric,head and neck,lung,and urothelial cancers,plus *** strongest druggable gene candidates linked to anti-PD-1 resistance were SPIN1(AUC=0.682,P=9.1E-12),SRC(AUC=0.667,P=5.9E-10),SETD7(AUC=0.663,P=1.0E-09),FGFR3(AUC=0.657,P=3.7E-09),YAP1(AUC=0.655,P=6.0E-09),TEAD3(AUC=0.649,P=4.1E-08)and BCL2(AUC=0.634,P=9.7E-08).In the anti-CTLA-4 treatment cohort,BLCAP(AUC=0.735,P=2.1E-06)was the most promising gene *** therapeutically relevant target was found to be predictive in the anti-PD-L1 *** the anti-PD-1 group,we were able to confirm the significant correlation with survival for the mismatch-repair genes MLH1 and MSH6.A web platform for further analysis and validation of new biomarker candidates was set up and available at summary,a database and a web platform were established to investigate biomarkers of immunotherapy response in a large cohort of solid tumor *** re

关键词： immunotherapy immune checkpoint inhibitors gene expression ROC curve druggable genes drug resistance

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A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

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Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global *** investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant *** genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic *** found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor *** genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant *** both its high retention of paleochromosomes and its low mutation rate,*** provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae Polyploidization Multigenome alignment Evolutionary rate Autotetraploidization Karyotype evolution

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The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis

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Horticulture research 2023年第5期10卷 112-125页

作者： Yujiao Zhao Zhengyang Yang Zhongren Zhang Minzhen Yin Shanshan Chu Zhenzhen Tong Yuejian Qin Liangping Zha Qingying Fang Yuan Yuan Luqi Huang Huasheng Peng School of Pharmacy Anhui University of Chinese MedicineHefei 230012China National Resource Center for Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Anhui Province Key Laboratory of Research&Development of Chinese Medicine Hefei 230012China Research Unit of DAO-DI Herbs Chinese Academy of Medical Sciences2019RU57Beijing 100700China Novogene Bioinformatics Institute Beijing 301700China

Fallopia multiflora(Thunb.)Harald,a vine belonging to the Polygonaceae family,is used in traditional *** stilbenes contained in it have significant pharmacological activities in anti-oxidation and *** study describes the assembly of the *** genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data(with a contig N50 of 1.97 megabases),1.44 gigabases of which was assigned to 11 *** genomics confirmed that *** shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after *** genomics,transcriptomics,and metabolomics data to map a network of associated genes and metabolites,we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in *** findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in ***,the reference genome of *** is a useful addition to the genomes of the Polygonaceae family.

关键词： stilbene insight catalysis

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Distinct gut microbiomes in Thai patients with colorectal polyps

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World Journal of Gastroenterology 2024年第27期30卷 3336-3355页

作者： Thoranin Intarajak Ahmad Nuruddin Khoiri Kanthida Kusonmano Weerayuth Kittichotirat Sawannee Sutheeworapong Supapon Cheevadhanarak Wandee Udomchaiprasertkul Chinae Thammarongtham Bioinformatics Unit Chulabhorn Royal AcademyLak Si 10210BangkokThailand Bioinformatics and Systems Biology Program School of Bioresources and Technologyand School of Information TechnologyKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Bioinformatics and Systems Biology ProgramSchool of Bioresources and Technologyand School of Information TechnologyKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Systems Biology and Bioinformatics Unit Pilot Plant Development and Training InstituteKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Molecular Genomic Research Laboratory Chulabhorn Royal AcademyLak Si 10210BangkokThailand National Center for Genetic Engineering and Biotechnology King Mongkut's University of Technology ThonburiBang Khun Thian 10150BangkokThailand School of Bioresources and Technology King Mongkut’s University of Technology ThonburiBank Khun Thian 10150BangkokThailand Fungal Biotechnology Unit Pilot Plant Development and Training InstituteKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand

BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut *** is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal *** To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA *** Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or *** techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway *** Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(***),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA *** gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA *** pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);*** was a major ***-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,wh

关键词： Gut microbiome Colorectal adenoma Hyperplastic polyp Full-length 16s rRNA Microbial correlation networks Predicted functional mechanisms

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Invariant set theory for predicting potential failure of antibiotic cycling

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Infectious Disease Modelling 2025年第3期10卷 897-908页

作者： Anderson, Alejandro Kinahan, Matthew W. Gonzalez, Alejandro H. Udekwu, Klas Hernandez-Vargas, Esteban A. Department of Mathematics and Statistical Science University of Idaho Moscow ID United States Department of Biological Sciences Bioinformatics and Computational Biology University of Idaho Moscow ID United States University of Littoral (UNL) Institute of Technological Development for the Chemical Industry (INTEC) and National Scientific and Technical Research Council (CONICET) Santa Fe Argentina Institute for Modeling Collaboration and Innovation University of Idaho Moscow 83844–1103 ID United States

Collateral sensitivity, where resistance to one drug confers heightened sensitivity to another, offers a promising strategy for combating antimicrobial resistance, yet predicting resultant evolutionary dynamics remains a significant challenge. We propose here a mathematical model that integrates fitness trade-offs and adaptive landscapes to predict the evolution of collateral sensitivity pathways, providing insights into optimizing sequential drug therapies. Our approach embeds collateral information into a network of switched systems, allowing us to abstract the effects of sequential antibiotic exposure on antimicrobial resistance. We analyze the system stability at disease-free equilibrium and employ set-control theory to tailor therapeutic windows. Consequently, we propose a computational algorithm to identify effective sequential therapies to counter antibiotic resistance. By leveraging our theory with data on collateral sensivity interactions, we predict scenarios that may prevent bacterial escape for chronic Pseudomonas aeruginosa infections. © 2025 The Authors

关键词： Antibacterial resistance Collateral sensitivity Control invariant sets Switched systems

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Quantitative Reaction Systems

Quantitative Reaction Systems

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Innovative research in Applied Science, Engineering and Technology (IRASET),Conference on

作者： Victor Mitrana Mihaela Păun Ion Petre Ana-Maria Prelipcean Department of Information Systems Polytechnic University of Madrid Madrid Spain Department of Bioinformatics National Institute of Research and Development for Biological Sciences Bucharest Romania Department of Mathematics and Statistics University of Turku Turku Finland Department of Cellular and Molecular Biology National Institute of Research and Development for Biological Sciences Bucharest Romania

ISBN: (数字)9798331532970

ISBN: (纸本)9798331532987

We propose a new variant of reaction system that intends to take into account a few aspects of a biological reaction that have been considered at most partially in former works. These aspects are: (i) in the former variants, all the substances of the substrate completely vanish after identifying the set of reactants such that the result does not contain any former component of the substrate unless it is produced by the reaction, (ii) in any substrate, each element is either present in an arbitrary large number of copies, or it is not present at al, (iii) the effect of any inhibitor is the same but in biology the effect of inhibitors may be different due to their type. Our model considers multisets of reactants such that it is a more quantitative model than a qualitative one, inhibitors may be of different types such that their role may vary depending on the substrate, the substances that are not involved in the reaction remain in the substrate. We consider a parallel mode of enabling the reactions and prove that this mode may be simulated by sequential enabling. Later on, we define a computational model based on quantitative reaction systems and prove that their computation power equals that of multiset Turing machines.

关键词： Inhibitors Turing machines Biological system modeling Computational modeling Substrates

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Twnbiome: a public database of the healthy Taiwanese gut microbiome

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BMC bioinformatics 2023年第1期24卷 1-13页

作者： Chattopadhyay, Amrita Lee, Chien-Yueh Lee, Ya-Chin Liu, Chiang-Lin Chen, Hsin-Kuang Li, Yung-Hua Lai, Liang-Chuan Tsai, Mong-Hsun Ni, Yen-Hsuan Chiu, Han-Mo Lu, Tzu-Pin Chuang, Eric Y. Bioinformatics and Biostatistics Core Centers of Genomic and Precision Medicine National Taiwan University Taipei Taiwan Department of Biomedical Engineering China Medical University Taichung Taiwan Department of Public Health Institute of Health Data Analytics and Statistics National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Center for Biotechnology National Taiwan University Taipei Taiwan Graduate Institute of Physiology National Taiwan University Taipei Taiwan Institute of Biotechnology National Taiwan University Taipei Taiwan College of Medicine National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan Institute of Health Data Analytics and Statistics National Taiwan University Taipei Taiwan Biomedical Technology and Device Research Laboratories Industrial Technology Research Institute Hsinchu Taiwan Division Research and Development Center for Medical Devices National Taiwan University Taipei Taiwan

With new advances in next generation sequencing (NGS) technology at reduced costs, research on bacterial genomes in the environment has become affordable. Compared to traditional methods, NGS provides high-throughput sequencing reads and the ability to identify many species in the microbiome that were previously unknown. Numerous bioinformatics tools and algorithms have been developed to conduct such analyses. However, in order to obtain biologically meaningful results, the researcher must select the proper tools and combine them to construct an efficient pipeline. This complex procedure may include tens of tools, each of which require correct parameter settings. Furthermore, an NGS data analysis involves multiple series of command-line tools and requires extensive computational resources, which imposes a high barrier for biologists and clinicians to conduct NGS analysis and even interpret their own data. Therefore, we established a public gut microbiome database, which we call Twnbiome, created using healthy subjects from Taiwan, with the goal of enabling microbiota research for the Taiwanese population. Twnbiome provides users with a baseline gut microbiome panel from a healthy Taiwanese cohort, which can be utilized as a reference for conducting case-control studies for a variety of diseases. It is an interactive, informative, and user-friendly database. Twnbiome additionally offers an analysis pipeline, where users can upload their data and download analyzed results. Twnbiome offers an online database which non-bioinformatics users such as clinicians and doctors can not only utilize to access a control set of data, but also analyze raw data with a few easy clicks. All results are customizable with ready-made plots and easily downloadable tables. Database URL: http://***/ . © 2023, The Author(s).

关键词： Database systems

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