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
VDJ重组是免疫系统中的一个关键过程，在这一过程中，V（可变）基因、D（多样性）基因和J（连接）基因随机组合，产生独特的抗原受体基因。这一过程产生了种类繁多的抗体和 T 细胞受体，对于识别和对抗各种病原体至关重要。通过识别和量化这些 VDJ 重组，我们可以更深入、更精确地了解免疫反应，从而提高我们监测和管理免疫相关疾病的能力。
{"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}
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
{"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}
{"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}
{"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}
{"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}
{"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}
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.
{"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}
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.
{"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}
{"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}
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
{"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}
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