Journal of Bioinformatics and Computational Biology最新文献_第10页

The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny. 系统发育中重建祖先基因组的单倍体染色体补体。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-19 DOI: 10.1142/S0219720021400084

Qiaoji Xu, Xiaomeng Zhang, Yue Zhang, Chunfang Zheng, James H Leebens-Mack, Lingling Jin, David Sankoff

引用次数: 0

Incorporating intergenic regions into reversal and transposition distances with indels. 将基因间区与索引结合到反转和转位距离中。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-13 DOI: 10.1142/S0219720021400114

Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias

{"title":"Incorporating intergenic regions into reversal and transposition distances with indels.","authors":"Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias","doi":"10.1142/S0219720021400114","DOIUrl":"https://doi.org/10.1142/S0219720021400114","url":null,"abstract":"Problems in the genome rearrangement field are often formulated in terms of pairwise genome comparison: given two genomes [Formula: see text] and [Formula: see text], find the minimum number of genome rearrangements that may have occurred during the evolutionary process. This broad definition lacks at least two important considerations: the first being which features are extracted from genomes to create a useful mathematical model, and the second being which types of genome rearrangement events should be represented. Regarding the first consideration, seminal works in the genome rearrangement field solely used gene order to represent genomes as permutations of integer numbers, neglecting many important aspects like gene duplication, intergenic regions, and complex interactions between genes. Regarding the second consideration, some rearrangement events are widely studied such as reversals and transpositions. In this paper, we shed light on the first consideration and created a model that takes into account gene order and the number of nucleotides in intergenic regions. In addition, we consider events of reversals, transpositions, and indels (insertions and deletions) of genomic material. We present a 4-approximation algorithm for reversals and indels, a [Formula: see text]-approximation algorithm for transpositions and indels, and a 6-approximation for reversals, transpositions, and indels.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140011"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39889211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost. DNN-Boost:利用深度神经网络和XGBoost对肿瘤全外显子组测序数据进行体细胞突变鉴定。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-12-13 DOI: 10.1142/S0219720021400175

Firda Aminy Maruf, Rian Pratama, Giltae Song

{"title":"DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost.","authors":"Firda Aminy Maruf, Rian Pratama, Giltae Song","doi":"10.1142/S0219720021400175","DOIUrl":"https://doi.org/10.1142/S0219720021400175","url":null,"abstract":"Detection of somatic mutation in whole-exome sequencing data can help elucidate the mechanism of tumor progression. Most computational approaches require exome sequencing for both tumor and normal samples. However, it is more common to sequence exomes for tumor samples only without the paired normal samples. To include these types of data for extensive studies on the process of tumorigenesis, it is necessary to develop an approach for identifying somatic mutations using tumor exome sequencing data only. In this study, we designed a machine learning approach using Deep Neural Network (DNN) and XGBoost to identify somatic mutations in tumor-only exome sequencing data and we integrated this into a pipeline called DNN-Boost. The XGBoost algorithm is used to extract the features from the results of variant callers and these features are then fed into the DNN model as input. The XGBoost algorithm resolves issues of missing values and overfitting. We evaluated our proposed model and compared its performance with other existing benchmark methods. We noted that the DNN-Boost classification model outperformed the benchmark method in classifying somatic mutations from paired tumor-normal exome data and tumor-only exome data.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140017"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39716735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Comparing the topology of phylogenetic network generators. 比较系统发育网络生成器的拓扑结构。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-12-06 DOI: 10.1142/S0219720021400126

Remie Janssen, Pengyu Liu

引用次数: 11

The potential of family-free rearrangements towards gene orthology inference. 无家族重排对基因同源推断的潜力。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-13 DOI: 10.1142/S021972002140014X

Diego P Rubert, Daniel Doerr, Marília D V Braga

{"title":"The potential of family-free rearrangements towards gene orthology inference.","authors":"Diego P Rubert, Daniel Doerr, Marília D V Braga","doi":"10.1142/S021972002140014X","DOIUrl":"https://doi.org/10.1142/S021972002140014X","url":null,"abstract":"Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance, Algorithms Mol Biol 16:4, 2021] for exactly computing the rearrangement distance of two genomes in a family-free setting. In such a setting, neither prior classification of genes into families, nor further restrictions on the genomes are imposed. Given two genomes, the mentioned ILP computes an optimal matching of the genes taking into account simultaneously local mutations, given by gene similarities, and large-scale genome rearrangements. Here, we explore the potential of using this ILP for inferring groups of orthologs across several species. More precisely, given a set of genomes, our method first computes all pairwise optimal gene matchings, which are then integrated into gene families in the second step. Our approach is implemented into a pipeline incorporating the pre-computation of gene similarities. It can be downloaded from gitlab.ub.uni-bielefeld.de/gi/FFGC. We obtained promising results with experiments on both simulated and real data.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140014"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39889208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Colorful orthology clustering in bounded-degree similarity graphs. 有界度相似图的彩色正交聚类。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-13 DOI: 10.1142/S0219720021400102

Alitzel López Sánchez, Manuel Lafond

{"title":"Colorful orthology clustering in bounded-degree similarity graphs.","authors":"Alitzel López Sánchez, Manuel Lafond","doi":"10.1142/S0219720021400102","DOIUrl":"https://doi.org/10.1142/S0219720021400102","url":null,"abstract":"Clustering genes in similarity graphs is a popular approach for orthology prediction. Most algorithms group genes without considering their species, which results in clusters that contain several paralogous genes. Moreover, clustering is known to be problematic when in-paralogs arise from ancient duplications. Recently, we proposed a two-step process that avoids these problems. First, we infer clusters of only orthologs (i.e. with only genes from distinct species), and second, we infer the missing inter-cluster orthologs. In this paper, we focus on the first step, which leads to a problem we call Colorful Clustering. In general, this is as hard as classical clustering. However, in similarity graphs, the number of species is usually small, as well as the neighborhood size of genes in other species. We therefore study the problem of clustering in which the number of colors is bounded by [Formula: see text], and each gene has at most [Formula: see text] neighbors in another species. We show that the well-known cluster editing formulation remains NP-hard even when [Formula: see text] and [Formula: see text]. We then propose a fixed-parameter algorithm in [Formula: see text] to find the single best cluster in the graph. We implemented this algorithm and included it in the aforementioned two-step approach. Experiments on simulated data show that this approach performs favorably to applying only an unconstrained clustering step.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140010"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39889213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Involving repetitive regions in scaffolding improvement. 涉及重复区域的脚手架改进。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-12-17 DOI: 10.1142/S0219720021400163

Quentin Delorme, Rémy Costa, Yasmine Mansour, Anna-Sophie Fiston-Lavier, Annie Chateau

引用次数: 0

BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium. BOPAL 2.0与梭状芽胞杆菌tRNA和rRNA基因进化研究。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-13 DOI: 10.1142/S0219720021400072

Meghan Chua, Anthony Tan, Olivier Tremblay-Savard

{"title":"BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium.","authors":"Meghan Chua, Anthony Tan, Olivier Tremblay-Savard","doi":"10.1142/S0219720021400072","DOIUrl":"https://doi.org/10.1142/S0219720021400072","url":null,"abstract":"We present BOPAL 2.0, an improved version of the BOPAL algorithm for the evolutionary history inference of tRNA and rRNA genes in bacterial genomes. Our approach can infer complete evolutionary scenarios and ancestral gene orders on a phylogeny and considers a wide range of events such as duplications, deletions, substitutions, inversions and transpositions. It is based on the fact that tRNA and rRNA genes are often organized in operons/clusters in bacteria, and this information is used to help identify orthologous genes for each genome comparison. BOPAL 2.0 introduces new features, such as a triple-wise alignment step, context-aware singleton matching and a second pass of the algorithm. Evaluation on simulated datasets shows that BOPAL 2.0 outperforms the original BOPAL in terms of the accuracy of inferred events and ancestral genomes. We also present a study of the tRNA/rRNA gene evolution in the Clostridium genus, in which the organization of these genes is very divergent. Our results indicate that tRNA and rRNA genes in Clostridium have evolved through numerous duplications, losses, transpositions and substitutions, but very few inversions were inferred.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140007"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39889207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Population-specific adaptation in malaria-endemic regions of asia. 亚洲疟疾流行地区的人口特异性适应。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-10 DOI: 10.1142/S0219720021400060

Elena S Gusareva, Paolo Alberto Lorenzini, Nurul Adilah Binte Ramli, Amit Gourav Ghosh, Hie Lim Kim

{"title":"Population-specific adaptation in malaria-endemic regions of asia.","authors":"Elena S Gusareva, Paolo Alberto Lorenzini, Nurul Adilah Binte Ramli, Amit Gourav Ghosh, Hie Lim Kim","doi":"10.1142/S0219720021400060","DOIUrl":"https://doi.org/10.1142/S0219720021400060","url":null,"abstract":"Evolutionary mechanisms of adaptation to malaria are understudied in Asian endemic regions despite a high prevalence of malaria in the region. In our research, we performed a genome-wide screening for footprints of natural selection against malaria by comparing eight Asian population groups from malaria-endemic regions with two non-endemic population groups from Europe and Mongolia. We identified 285 adaptive genes showing robust selection signals across three statistical methods, iHS, XP-EHH, and PBS. Interestingly, most of the identified genes (82%) were found to be under selection in a single population group, while adaptive genes shared across populations were rare. This is likely due to the independent adaptation history in different endemic populations. The gene ontology (GO) analysis for the 285 adaptive genes highlighted their functional processes linked to neuronal organizations or nervous system development. These genes could be related to cerebral malaria and may reduce the inflammatory response and the severity of malaria symptoms. Remarkably, our novel population genomic approach identified population-specific adaptive genes potentially against malaria infection without the need for patient samples or individual medical records.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140006"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39692975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Evidence for exon shuffling is sensitive to model choice. 外显子洗牌的证据对模型选择很敏感。

IF 1 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2021-12-01 Epub Date: 2021-11-19 DOI: 10.1142/S0219720021400138

Xiaoyue Cui, Maureen Stolzer, Dannie Durand

{"title":"Evidence for exon shuffling is sensitive to model choice.","authors":"Xiaoyue Cui, Maureen Stolzer, Dannie Durand","doi":"10.1142/S0219720021400138","DOIUrl":"https://doi.org/10.1142/S0219720021400138","url":null,"abstract":"The exon shuffling theory posits that intronic recombination creates new domain combinations, facilitating the evolution of novel protein function. This theory predicts that introns will be preferentially situated near domain boundaries. Many studies have sought evidence for exon shuffling by testing the correspondence between introns and domain boundaries against chance intron positioning. Here, we present an empirical investigation of how the choice of null model influences significance. Although genome-wide studies have used a uniform null model, exclusively, more realistic null models have been proposed for single gene studies. We extended these models for genome-wide analyses and applied them to 21 metazoan and fungal genomes. Our results show that compared with the other two models, the uniform model does not recapitulate genuine exon lengths, dramatically underestimates the probability of chance agreement, and overestimates the significance of intron-domain correspondence by as much as 100 orders of magnitude. Model choice had much greater impact on the assessment of exon shuffling in fungal genomes than in metazoa, leading to different evolutionary conclusions in seven of the 16 fungal genomes tested. Genome-wide studies that use this overly permissive null model may exaggerate the importance of exon shuffling as a general mechanism of multidomain evolution.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"19 6","pages":"2140013"},"PeriodicalIF":1.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39645906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0