GigaByte (Hong Kong, China)最新文献_第3页

Automated management of AWS instances for training. 自动管理用于培训的 AWS 实例。

GigaByte (Hong Kong, China) Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.133

Jorge Buenabad-Chavez, Evelyn Greeves, James P J Chong, Emma Rand

引用次数: 0

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. 黑脸琵鹭（Platalea minor）的染色体级基因组组装和单核苷酸多态性位点。

GigaByte (Hong Kong, China) Pub Date : 2024-07-18 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.130

引用次数: 0

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle. 通过 RAD 测序对牛进行亲缘关系分析和血统重建。

GigaByte (Hong Kong, China) Pub Date : 2024-07-18 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.131

Yiming Xu, Wanqiu Wang, Jiefeng Huang, Minjie Xu, Binhu Wang, Yingsong Wu, Yongzhong Xie, Jianbo Jian

{"title":"Kinship analysis and pedigree reconstruction by RAD sequencing in cattle.","authors":"Yiming Xu, Wanqiu Wang, Jiefeng Huang, Minjie Xu, Binhu Wang, Yingsong Wu, Yongzhong Xie, Jianbo Jian","doi":"10.46471/gigabyte.131","DOIUrl":"10.46471/gigabyte.131","url":null,"abstract":"Kinship and pedigree, used for estimating inbreeding, heritability, selection, and gene flow, are useful for breeding and animal conservation. However, as the size of crossbred populations increases, inaccurate generation and parentage assignment in livestock farms increase. Restriction-site-associated DNA sequencing is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNP panel included 7,305 SNPs capturing the maximum difference between paternal and maternal genome information, allowing us to distinguish F1 from F2 generations with 90% accuracy. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11273509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients. 为高度选择性的严重 COVID-19 患者队列进行低覆盖率全基因组测序。

GigaByte (Hong Kong, China) Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.127

Renato Santos, Víctor Moreno-Torres, Ilduara Pintos, Octavio Corral, Carmen de Mendoza, Vicente Soriano, Manuel Corpas

{"title":"Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients.","authors":"Renato Santos, Víctor Moreno-Torres, Ilduara Pintos, Octavio Corral, Carmen de Mendoza, Vicente Soriano, Manuel Corpas","doi":"10.46471/gigabyte.127","DOIUrl":"10.46471/gigabyte.127","url":null,"abstract":"Despite the advances in genetic marker identification associated with severe COVID-19, the full genetic characterisation of the disease remains elusive. This study explores imputation in low-coverage whole genome sequencing for a severe COVID-19 patient cohort. We generated a dataset of 79 imputed variant call format files using the GLIMPSE1 tool, each containing an average of 9.5 million single nucleotide variants. Validation revealed a high imputation accuracy (squared Pearson correlation ≍0.97) across sequencing platforms, showcasing GLIMPSE1's ability to confidently impute variants with minor allele frequencies as low as 2% in individuals with Spanish ancestry. We carried out a comprehensive analysis of the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms developed to characterise severe COVID-19 symptoms. The methods and findings presented here can be leveraged for future genomic projects to gain vital insights into health challenges like COVID-19.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte127"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible. PhysiCell Studio：一种使基于代理的建模更易于使用的图形工具。

GigaByte (Hong Kong, China) Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.128

Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, Paul Macklin

{"title":"PhysiCell Studio: a graphical tool to make agent-based modeling more accessible.","authors":"Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, Paul Macklin","doi":"10.46471/gigabyte.128","DOIUrl":"10.46471/gigabyte.128","url":null,"abstract":"Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. In the best case, the model will be defined using some format specification - a markup language - that will provide easy model sharing (and a minimal step toward reproducibility). PhysiCell is an open-source, physics-based multicellular simulation framework with an active and growing user community. It uses XML to define a model and, traditionally, users needed to manually edit the XML to modify the model. PhysiCell Studio is a tool to make this task easier. It provides a GUI that allows editing the XML model definition, including the creation and deletion of fundamental objects: cell types and substrates in the microenvironment. It also lets users build their model by defining initial conditions and biological rules, run simulations, and view results interactively. PhysiCell Studio has evolved over multiple workshops and academic courses in recent years, which has led to many improvements. There is both a desktop and cloud version. Its design and development has benefited from an active undergraduate and graduate research program. Like PhysiCell, the Studio is open-source software and contributions from the community are encouraged.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte128"},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis. 用于纳米孔直接 RNA 分析的多细胞、IVT 衍生、未修饰的人类转录组。

GigaByte (Hong Kong, China) Pub Date : 2024-06-17 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.129

Caroline A McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N Klink, Miten Jain, Sara H Rouhanifard

引用次数: 0

Get Free Copy: a multi-repository search platform for biomedical publications. 免费获取副本：生物医学出版物的多库检索平台。

GigaByte (Hong Kong, China) Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.126

Nodir Kosimkhujaev, Kuan-Lin Huang

引用次数: 0

Genome assembly of the rare and endangered Grantham's camellia, Camellia granthamiana. 稀有濒危的格兰瑟姆山茶花（Camellia granthamiana）的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-05-20 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.124

引用次数: 0

Jellyfish in Hong Kong: a citizen science dataset. 香港的水母：公民科学数据集。

GigaByte (Hong Kong, China) Pub Date : 2024-05-20 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.125

John Terenzini, Yannan Fan, Melissa Jean-Yi Liu, Laura J Falkenberg

引用次数: 0

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata). 肥尾盾尾鱼（Sminthopsis crassicaudata）的全新转录组组装和基因组注释。

GigaByte (Hong Kong, China) Pub Date : 2024-05-02 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.118

Neke Ibeh, Charles Y Feigin, Stephen R Frankenberg, Davis J McCarthy, Andrew J Pask, Irene Gallego Romero

{"title":"De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata).","authors":"Neke Ibeh, Charles Y Feigin, Stephen R Frankenberg, Davis J McCarthy, Andrew J Pask, Irene Gallego Romero","doi":"10.46471/gigabyte.118","DOIUrl":"10.46471/gigabyte.118","url":null,"abstract":"Marsupials exhibit distinctive modes of reproduction and early development that set them apart from their eutherian counterparts and render them invaluable for comparative studies. However, marsupial genomic resources still lag far behind those of eutherian mammals. We present a series of novel genomic resources for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that, due to its ease of husbandry and ex-utero development, is emerging as a laboratory model. We constructed a highly representative multi-tissue de novo transcriptome assembly of dunnart RNA-seq reads spanning 12 tissues. The transcriptome includes 2,093,982 assembled transcripts and has a mammalian transcriptome BUSCO completeness score of 93.3%, the highest amongst currently published marsupial transcriptomes. This global transcriptome, along with ab initio predictions, supported annotation of the existing dunnart genome, revealing 21,622 protein-coding genes. Altogether, these resources will enable wider use of the dunnart as a model marsupial and deepen our understanding of mammalian genome evolution.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte118"},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11091235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0