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Annual Review of Biomedical Data Science最新文献

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Probabilistic Machine Learning for Healthcare. 医疗保健领域的概率机器学习。
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-07-20 Epub Date: 2021-06-01 DOI: 10.1146/annurev-biodatasci-092820-033938
Irene Y Chen, Shalmali Joshi, Marzyeh Ghassemi, Rajesh Ranganath
{"title":"Probabilistic Machine Learning for Healthcare.","authors":"Irene Y Chen,&nbsp;Shalmali Joshi,&nbsp;Marzyeh Ghassemi,&nbsp;Rajesh Ranganath","doi":"10.1146/annurev-biodatasci-092820-033938","DOIUrl":"https://doi.org/10.1146/annurev-biodatasci-092820-033938","url":null,"abstract":"<p><p>Machine learning can be used to make sense of healthcare data. Probabilistic machine learning models help provide a complete picture of observed data in healthcare. In this review, we examine how probabilistic machine learning can advance healthcare. We consider challenges in the predictive model building pipeline where probabilistic models can be beneficial, including calibration and missing data. Beyond predictive models, we also investigate the utility of probabilistic machine learning models in phenotyping, in generative models for clinical use cases, and in reinforcement learning.</p>","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":" ","pages":"393-415"},"PeriodicalIF":6.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39370517","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: 33
The Exposome in the Era of the Quantified Self. 自我量化时代的暴露。
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-07-20 DOI: 10.1146/annurev-biodatasci-012721-122807
Xinyue Zhang, Peng Gao, Michael P Snyder
{"title":"The Exposome in the Era of the Quantified Self.","authors":"Xinyue Zhang,&nbsp;Peng Gao,&nbsp;Michael P Snyder","doi":"10.1146/annurev-biodatasci-012721-122807","DOIUrl":"https://doi.org/10.1146/annurev-biodatasci-012721-122807","url":null,"abstract":"<p><p>Human health is regulated by complex interactions among the genome, the microbiome, and the environment. While extensive research has been conducted on the human genome and microbiome, little is known about the human exposome. The exposome comprises the totality of chemical, biological, and physical exposures that individuals encounter over their lifetimes. Traditional environmental and biological monitoring only targets specific substances, whereas exposomic approaches identify and quantify thousands of substances simultaneously using nontargeted high-throughput and high-resolution analyses. The quantified self (QS) aims at enhancing our understanding of human health and disease through self-tracking. QS measurements are critical in exposome research, as external exposures impact an individual's health, behavior, and biology. This review discusses both the achievements and the shortcomings of current research and methodologies on the QS and the exposome and proposes future research directions.</p>","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":" ","pages":"255-277"},"PeriodicalIF":6.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39371088","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: 10
Mutational Signatures: From Methods to Mechanisms. 突变签名:从方法到机制。
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-07-20 Epub Date: 2021-05-11 DOI: 10.1146/annurev-biodatasci-122320-120920
Yoo-Ah Kim, Mark D M Leiserson, Priya Moorjani, Roded Sharan, Damian Wojtowicz, Teresa M Przytycka
{"title":"Mutational Signatures: From Methods to Mechanisms.","authors":"Yoo-Ah Kim,&nbsp;Mark D M Leiserson,&nbsp;Priya Moorjani,&nbsp;Roded Sharan,&nbsp;Damian Wojtowicz,&nbsp;Teresa M Przytycka","doi":"10.1146/annurev-biodatasci-122320-120920","DOIUrl":"https://doi.org/10.1146/annurev-biodatasci-122320-120920","url":null,"abstract":"<p><p>Mutations are the driving force of evolution, yet they underlie many diseases, in particular, cancer. They are thought to arise from a combination of stochastic errors in DNA processing, naturally occurring DNA damage (e.g., the spontaneous deamination of methylated CpG sites), replication errors, and dysregulation of DNA repair mechanisms. High-throughput sequencing has made it possible to generate large datasets to study mutational processes in health and disease. Since the emergence of the first mutational process studies in 2012, this field is gaining increasing attention and has already accumulated a host of computational approaches and biomedical applications.</p>","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":" ","pages":"189-206"},"PeriodicalIF":6.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39370516","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: 17
Perspectives on Allele-Specific Expression. 等位基因特异性表达研究进展
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-07-20 Epub Date: 2021-04-28 DOI: 10.1146/annurev-biodatasci-021621-122219
Siobhan Cleary, Cathal Seoighe
{"title":"Perspectives on Allele-Specific Expression.","authors":"Siobhan Cleary,&nbsp;Cathal Seoighe","doi":"10.1146/annurev-biodatasci-021621-122219","DOIUrl":"https://doi.org/10.1146/annurev-biodatasci-021621-122219","url":null,"abstract":"<p><p>Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to <i>cis</i>-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.</p>","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":" ","pages":"101-122"},"PeriodicalIF":6.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39370512","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: 12
Illuminating the Virosphere Through Global Metagenomics. 通过全球宏基因组学照亮病毒圈。
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-07-20 DOI: 10.1146/annurev-biodatasci-012221-095114
Lee Call, Stephen Nayfach, Nikos C Kyrpides
{"title":"Illuminating the Virosphere Through Global Metagenomics.","authors":"Lee Call,&nbsp;Stephen Nayfach,&nbsp;Nikos C Kyrpides","doi":"10.1146/annurev-biodatasci-012221-095114","DOIUrl":"https://doi.org/10.1146/annurev-biodatasci-012221-095114","url":null,"abstract":"<p><p>Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.</p>","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":" ","pages":"369-391"},"PeriodicalIF":6.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39370510","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: 13
Research progress of incremental hemodialysis 增量式血液透析的研究进展
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-01-01 DOI: 10.47297/wspbdswsp2752-630505.20210102
Weiwei Hu, Wenjun Zhang, Y. Qi, Jianqin Wang
{"title":"Research progress of incremental hemodialysis","authors":"Weiwei Hu, Wenjun Zhang, Y. Qi, Jianqin Wang","doi":"10.47297/wspbdswsp2752-630505.20210102","DOIUrl":"https://doi.org/10.47297/wspbdswsp2752-630505.20210102","url":null,"abstract":"","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":"5 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86928305","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
A Semantic Ontology Structure－based Approach for Re⁃trieving Similar Medical Images 基于语义本体结构的相似医学图像检索方法
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-01-01 DOI: 10.47297/wspbdswsp2752-630501.20210102
Yiwen Wang
{"title":"A Semantic Ontology Structure－based Approach for Re⁃\u0000trieving Similar Medical Images","authors":"Yiwen Wang","doi":"10.47297/wspbdswsp2752-630501.20210102","DOIUrl":"https://doi.org/10.47297/wspbdswsp2752-630501.20210102","url":null,"abstract":"","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":"1 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78541590","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
Establishment of Visual Fear Conditioning in Long－evansRats 长时间迁徙大鼠视觉恐惧条件反射的建立
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-01-01 DOI: 10.47297/wspbdswsp2752-630502.20210102
Xiaoyuan Li, Yun Liu, Hongyu Si, Peng Wu, Zhenlong Wang
{"title":"Establishment of Visual Fear Conditioning in Long－evans\u0000Rats","authors":"Xiaoyuan Li, Yun Liu, Hongyu Si, Peng Wu, Zhenlong Wang","doi":"10.47297/wspbdswsp2752-630502.20210102","DOIUrl":"https://doi.org/10.47297/wspbdswsp2752-630502.20210102","url":null,"abstract":"","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":"16 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78299773","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
Alpha to beta cell reprogramming to treat Type 1 diabetes 细胞重编程治疗1型糖尿病
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-01-01 DOI: 10.47297/wspbdswsp2752-630504.20210102
V. Li
{"title":"Alpha to beta cell reprogramming to treat Type 1 diabetes","authors":"V. Li","doi":"10.47297/wspbdswsp2752-630504.20210102","DOIUrl":"https://doi.org/10.47297/wspbdswsp2752-630504.20210102","url":null,"abstract":"","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":"9 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77628998","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
Genomic Characteristics of SARS-CoV, MERS-CoV and2019-nCoV SARS-CoV、MERS-CoV和2019- ncov的基因组特征
IF 6
Annual Review of Biomedical Data Science Pub Date : 2021-01-01 DOI: 10.47297/wspbdswsp2752-630503.20210102
Tong Li, Xing Yu, Mengxiang Chen, Y. Lv, W. Zha
{"title":"Genomic Characteristics of SARS-CoV, MERS-CoV and\u00002019-nCoV","authors":"Tong Li, Xing Yu, Mengxiang Chen, Y. Lv, W. Zha","doi":"10.47297/wspbdswsp2752-630503.20210102","DOIUrl":"https://doi.org/10.47297/wspbdswsp2752-630503.20210102","url":null,"abstract":"","PeriodicalId":29775,"journal":{"name":"Annual Review of Biomedical Data Science","volume":"64 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76169404","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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