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An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matching 加速的 Vidjil 算法：通过间隔种子和 Aho-Corasick 模式匹配，V(D)J 重组的识别速度提高了 30 倍
Peer Community In Mathematical and Computational Biology Pub Date : 2024-07-23 DOI: 10.24072/pci.mcb.100268
Giulio Ermanno Pibiri
{"title":"An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matching","authors":"Giulio Ermanno Pibiri","doi":"10.24072/pci.mcb.100268","DOIUrl":"https://doi.org/10.24072/pci.mcb.100268","url":null,"abstract":"VDJ recombination is a crucial process in the immune system, where a V (variable) gene, a D (diversity) gene, and a J (joining) gene are randomly combined to create unique antigen receptor genes. This process generates a vast diversity of antibodies and T-cell receptors, essential for recognizing and combating a wide array of pathogens. By identifying and quantifying these VDJ recombinations, we can gain a deeper and more precise understanding of the immune response, enhancing our ability to monitor and manage immune-related conditions","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"32 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141814008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Decline in Neanderthal effective population size due to geographic structure and gene flow 地理结构和基因流动导致尼安德特人有效种群数量下降
Peer Community In Mathematical and Computational Biology Pub Date : 2024-07-22 DOI: 10.24072/pci.mcb.100232
Raquel Assis
{"title":"Decline in Neanderthal effective population size due to geographic structure and gene flow","authors":"Raquel Assis","doi":"10.24072/pci.mcb.100232","DOIUrl":"https://doi.org/10.24072/pci.mcb.100232","url":null,"abstract":"Published PSMC estimates of Neanderthal effective population size (e) show an approximately five-fold decline over the past 20,000 years [1]. This observation may be attributed to a true decline in Neanderthal e, statistical error that is notorious with PSMC estimation","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"83 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141817204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Collecting, assembling and sharing data in crop sciences 收集、汇总和共享作物科学数据
Peer Community In Mathematical and Computational Biology Pub Date : 2024-02-26 DOI: 10.24072/pci.mcb.100197
Eric Tannier
{"title":"Collecting, assembling and sharing data in crop sciences","authors":"Eric Tannier","doi":"10.24072/pci.mcb.100197","DOIUrl":"https://doi.org/10.24072/pci.mcb.100197","url":null,"abstract":"","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"45 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140431268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Estimates of Effective Population Size in Subdivided Populations 细分群体中有效群体规模的估计
Peer Community In Mathematical and Computational Biology Pub Date : 2023-05-02 DOI: 10.24072/pci.mcb.100150
A. Rogers
{"title":"Estimates of Effective Population Size in Subdivided Populations","authors":"A. Rogers","doi":"10.24072/pci.mcb.100150","DOIUrl":"https://doi.org/10.24072/pci.mcb.100150","url":null,"abstract":"","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126699487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Phylogenetic reconstruction from copy number aberration in large scale, low-depth genome-wide single-cell data. 大规模、低深度全基因组单细胞数据中拷贝数畸变的系统发育重建。
Peer Community In Mathematical and Computational Biology Pub Date : 2023-04-18 DOI: 10.24072/pci.mcb.100112
A. Lambert
{"title":"Phylogenetic reconstruction from copy number aberration in large scale, low-depth genome-wide single-cell data.","authors":"A. Lambert","doi":"10.24072/pci.mcb.100112","DOIUrl":"https://doi.org/10.24072/pci.mcb.100112","url":null,"abstract":"","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125689682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reprogramming of locally-monotone Boolean networks with BoNesis 基于BoNesis的局部单调布尔网络重编程
Peer Community In Mathematical and Computational Biology Pub Date : 2023-03-14 DOI: 10.24072/pci.mcb.100183
Sergiu Ivanov
{"title":"Reprogramming of locally-monotone Boolean networks with BoNesis","authors":"Sergiu Ivanov","doi":"10.24072/pci.mcb.100183","DOIUrl":"https://doi.org/10.24072/pci.mcb.100183","url":null,"abstract":"","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123355463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detecting variation in ploidy within and between genomes 检测基因组内部和基因组之间的倍性变异
Peer Community In Mathematical and Computational Biology Pub Date : 2022-09-19 DOI: 10.24072/pci.mcb.100010
A. Rogers
{"title":"Detecting variation in ploidy within and between genomes","authors":"A. Rogers","doi":"10.24072/pci.mcb.100010","DOIUrl":"https://doi.org/10.24072/pci.mcb.100010","url":null,"abstract":"samples, thus missing this biological event as far as I understand it. Still, this is interpreted as a success of the method. The authors might like to clarify their specific goals with this analysis, and what kind of biological pattern or structure they are targetting. If the idea is to identify polyploid segments having accumulated a certain amount of sequence variation, as seems implicit in the empirical analysis section, then this should probably be stated more explicitly and discussed.","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131828369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Allowing gene transfers doesn't make life easier for inferring orthology and paralogy 允许基因转移并不会让我们更容易推断正畸学和谬误学
Peer Community In Mathematical and Computational Biology Pub Date : 2022-02-21 DOI: 10.24072/pci.mcb.100009
Barbara Holland
{"title":"Allowing gene transfers doesn't make life easier for inferring orthology and paralogy","authors":"Barbara Holland","doi":"10.24072/pci.mcb.100009","DOIUrl":"https://doi.org/10.24072/pci.mcb.100009","url":null,"abstract":"Determining if genes are orthologous (i.e. homologous genes whose most common ancestor represents a speciation) or paralogous (homologous genes whose most common ancestor represents a duplication) is a foundational problem in bioinformatics. For instance, the input to almost all phylogenetic methods is a sequence alignment of genes assumed to be orthologous. Understanding if genes are paralogs or orthologs can also be important for assigning function, for example genes that have diverged following duplication may be more likely to have neofunctionalised or subfunctionalised compared to genes that have diverged following speciation, which may be more likely to have continued in a similar role.","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128234993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Importance of age structure on modeling COVID-19 epidemiological dynamics 年龄结构对COVID-19流行病学动态建模的重要性
Peer Community In Mathematical and Computational Biology Pub Date : 2022-02-04 DOI: 10.24072/pci.mcb.100008
Chen Liao
{"title":"Importance of age structure on modeling COVID-19 epidemiological dynamics","authors":"Chen Liao","doi":"10.24072/pci.mcb.100008","DOIUrl":"https://doi.org/10.24072/pci.mcb.100008","url":null,"abstract":"","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"102 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126261442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modelling within-host evolutionary dynamics of antimicrobial resistance 模拟宿主内抗菌素耐药性的进化动力学
Peer Community In Mathematical and Computational Biology Pub Date : 2021-12-13 DOI: 10.24072/pci.mcb.100007
K. Tsaneva
{"title":"Modelling within-host evolutionary dynamics of antimicrobial resistance","authors":"K. Tsaneva","doi":"10.24072/pci.mcb.100007","DOIUrl":"https://doi.org/10.24072/pci.mcb.100007","url":null,"abstract":"Overview: This paper deals with the construction and analysis of a mathematical model to understand the efficacy of chemotherapy on bacterial growth and evolution. The authors focus on non-binary levels of resistance (i.e. resistance that is continuously changing above and below the minimum inhibitory concentration (MIC)). They use their integro-differential equation mdodel to provide quantitative descriptions of bacterial growth and population size and the evolution of its level of resistance. topic with potential extensions outside of bacterial growth in cancer","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124861375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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