IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences最新文献

{"title":"Haplotype-based Parallel PBWT for Biobank Scale Data.","authors":"Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang","doi":"10.1007/978-3-032-02489-3_10","DOIUrl":"10.1007/978-3-032-02489-3_10","url":null,"abstract":"<p><p>Durbin's positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of <math><mi>O</mi> <mo>(</mo> <mi>M</mi> <mi>N</mi> <mo>)</mo></math> for reporting all vs all haplotype matches in a population panel with <math><mi>M</mi></math> haplotypes and <math><mi>N</mi></math> variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To further reduce the run time, in this paper, a parallel version of the PBWT algorithms is introduced for all versus all haplotype matching, which is called HP-PBWT (haplotype-based parallel PBWT). HP-PBWT parallelly executes the PBWT by splitting a haplotype panel into blocks of haplotypes. HP-PBWT algorithms achieve parallelization for PBWT construction, reporting all versus all L-long matches, and reporting all versus all set-maximal matches while maintaining memory efficiency. HP-PBWT has an <math><mi>O</mi> <mfenced> <mrow> <mfenced> <mrow> <mfrac><mrow><mi>M</mi></mrow> <mrow><mi>T</mi></mrow> </mfrac> <mo>+</mo> <mi>T</mi></mrow> </mfenced> <mi>N</mi></mrow> </mfenced> </math> time complexity in PBWT construction, and <math><mi>O</mi> <mfenced> <mrow> <mfenced> <mrow> <mfrac><mrow><mi>M</mi></mrow> <mrow><mi>T</mi></mrow> </mfrac> <mo>+</mo> <mi>T</mi> <mo>+</mo> <msup><mrow><mi>c</mi></mrow> <mrow><mo>*</mo></mrow> </msup> </mrow> </mfenced> <mi>N</mi></mrow> </mfenced> </math> time complexity for reporting all versus all L-long matches and reporting all versus all set-maximal matches, where <math><mi>T</mi></math> is the number of threads and <math> <msup><mrow><mi>c</mi></mrow> <mrow><mo>*</mo></mrow> </msup> </math> is the maximum number of matches (of length L or maximum divergence value for L-long matches and set-maximal matches respectively) per haplotype per site. HP-PBWT achieves 4-fold speed-up in UK Biobank genotyping array data with 30 threads in the IO-included benchmarks. When applying HP-PBWT to a dataset of 8 million randomized haplotypes (random binary strings of equal length) in the IO-excluded benchmarks, it can achieve a 22-fold speed-up with 60 cores on the Amazon EC2 server. With further hardware optimization, HP-PBWT is expected to handle billions of haplotypes efficiently.</p>","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"15599 ","pages":"130-143"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13178698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147966114","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}

{"title":"Computational Advances in Bio and Medical Sciences: 11th International Conference, ICCABS 2021, Virtual Event, December 16–18, 2021, Revised Selected Papers","authors":"","doi":"10.1007/978-3-031-17531-2","DOIUrl":"https://doi.org/10.1007/978-3-031-17531-2","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87422556","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":"Computational Advances in Bio and Medical Sciences: 10th International Conference, ICCABS 2020, Virtual Event, December 10-12, 2020, Revised Selected Papers","authors":"","doi":"10.1007/978-3-030-79290-9","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"147 Pt 10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84052537","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":"Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2","authors":"James J. Cai, Daniel Osório","doi":"10.31219/osf.io/va7ux","DOIUrl":"https://doi.org/10.31219/osf.io/va7ux","url":null,"abstract":"The efficiency of antimalarials, chloroquine (CQ) and hydroxychloroquine (HCQ), in the prevention and treatment of coronavirus disease 2019 (COVID-19) is under intense debate. The mechanisms of action of antimalarials against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been fully elucidated. Here, we applied a network-based comparative analysis, implemented in our machine learning workflow—scTenifoldNet, to scRNA-seq data from COVID-19 patients with different levels of severity. We found that genes of the Malaria pathway expressed in macrophages are significantly differentially regulated between patients with moderate and severe symptoms. Our findings help reveal the mechanisms of action of CQ and HCQ during SARS-CoV-2 infection, providing new evidence to support the use of these antimalarial drugs in the treatment of COVID-19, especially for patients who are mildly affected or in the early stage of the infection.","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"13 1","pages":"88-94"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79418382","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":"MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly Using Minimizers","authors":"F. Andreace, Cinzia Pizzi, M. Comin","doi":"10.1007/978-3-030-79290-9_2","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9_2","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"29 1","pages":"15-25"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83744418","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":"Clustering Based Identification of SARS-CoV-2 Subtypes","authors":"Andrew Melnyk, Fatemeh Mohebbi, S. Knyazev, Bikram Sahoo, Roya Hosseini, P. Skums, A. Zelikovsky, Murray Patterson","doi":"10.1007/978-3-030-79290-9_11","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9_11","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"40 1","pages":"127-141"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91268155","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":"Computational Advances in Bio and Medical Sciences: 9th International Conference, ICCABS 2019, Miami, FL, USA, November 15–17, 2019, Revised Selected Papers","authors":"A. Zelikovsky, I. Măndoiu, T. Murali, G. Narasimhan, S. Rajasekaran, P. Skums","doi":"10.1007/978-3-030-46165-2","DOIUrl":"https://doi.org/10.1007/978-3-030-46165-2","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"350 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79772469","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":"RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences","authors":"Qiaoji Xu, Lingling Jin, Chunfang Zheng, J. Leebens-Mack, D. Sankoff","doi":"10.1007/978-3-030-79290-9_9","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9_9","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"78 1","pages":"97-115"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88236866","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":"DNA Read Feature Importance Using Machine Learning for Read Alignment Categories","authors":"Jacob Porter","doi":"10.1007/978-3-030-79290-9_1","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9_1","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"44 1","pages":"3-14"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77572616","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":"Computational Study of Action Potential Generation in Urethral Smooth Muscle Cell","authors":"C. Mahapatra","doi":"10.1007/978-3-030-79290-9_3","DOIUrl":"https://doi.org/10.1007/978-3-030-79290-9_3","url":null,"abstract":"","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":"1 1","pages":"26-32"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75384836","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}