[ { "key": "MRH8TXLV", "version": 4, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/MRH8TXLV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/MRH8TXLV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } }, "creatorSummary": "Jeong", "parsedDate": "2020", "numChildren": 0 }, "data": { "key": "MRH8TXLV", "version": 4, "itemType": "journalArticle", "title": "2019 Novel Coronavirus Disease Outbreak and Molecular Genetic Characteristics of Severe Acute Respiratory Syndrome-Coronavirus-2", "creators": [ { "creatorType": "author", "firstName": "Yong Seok", "lastName": "Jeong" } ], "abstractNote": "The 2019 novel coronavirus disease (COVID-19) outbreaks that emerged in Wuhan city, Hubei province, have led to a formidable number of confirmed cases that resulted in >5,700 deaths globally, including 143 countries in all 6 continents. The World Health Organization declared a Public Health Emergency of International Concern with a very high level of global risk assessment. Severe acute respiratory syndrome (SARS)-coronavirus-2 (SARS-CoV-2), the agent of COVID-19, has >79% nucleotide sequence homology to SARS-CoV; therefore, both belong to the genus betacoronavirus and subgenus sarbecovirus. The S1 domains of the two appeared to share the cellular receptor ACE2, but revealed a much higher S1-ACE2 binding affinity. As seen in many other human coronaviruses, SARS-CoV-2 also shows respiratory infection, but the basic reproductive number (R₀) in transmission and the clinical latency are quite dissimilar from those of SARS- or MERS-CoVs. Many scientists infer that the time point of cross-barrier transfer from bats to mediate animals or to humans should be a rather recent event based on the full-length genome analyses obtained from the very first patients. Copy-choice polymerization, which often leads to a significant genome recombination rate in most coronaviruses, predicts the continued emergence of novel coronaviruses.", "publicationTitle": "J Bacteriol Virol", "publisher": "", "place": "", "date": "2020", "volume": "50", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "1-8", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Bacteriol Virol", "DOI": "10.4167/jbv.2020.50.1.001", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": { "owl:sameAs": "http://zotero.org/groups/2465140/items/GA6HQXV4" }, "dateAdded": "2021-02-24T14:16:41Z", "dateModified": "2021-02-24T14:16:41Z" } }, { "key": "B6PJSXSU", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/B6PJSXSU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/B6PJSXSU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/357882/items/QXMITKWR", "type": "application/json" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } } }, "data": { "key": "B6PJSXSU", "version": 3, "parentItem": "QXMITKWR", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-06-07T13:37:55Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24632729", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "PN3TS96I", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/PN3TS96I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/PN3TS96I", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/357882/items/UQ29IRDW", "type": "application/json" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } } }, "data": { "key": "PN3TS96I", "version": 3, "parentItem": "UQ29IRDW", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2015-06-07T13:44:12Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "TJXH6FI7", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/TJXH6FI7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/TJXH6FI7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } }, "creatorSummary": "Pell et al.", "parsedDate": "2012-08-14", "numChildren": 1 }, "data": { "key": "TJXH6FI7", "version": 3, "itemType": "journalArticle", "title": "Scaling metagenome sequence assembly with probabilistic de Bruijn graphs", "creators": [ { "creatorType": "author", "firstName": "Jason", "lastName": "Pell" }, { "creatorType": "author", "firstName": "Arend", "lastName": "Hintze" }, { "creatorType": "author", "firstName": "Rosangela", "lastName": "Canino-Koning" }, { "creatorType": "author", "firstName": "Adina", "lastName": "Howe" }, { "creatorType": "author", "firstName": "James M.", "lastName": "Tiedje" }, { "creatorType": "author", "firstName": "C. Titus", "lastName": "Brown" } ], "abstractNote": "Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for de novo assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for de novo assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "08/14/2012", "volume": "109", "issue": "33", "section": "", "partNumber": "", "partTitle": "", "pages": "13272-13277", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PNAS", "DOI": "10.1073/pnas.1121464109", "citationKey": "", "url": "http://www.pnas.org/content/109/33/13272", "accessDate": "2015-06-07T13:37:53Z", "PMID": "", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.pnas.org", "callNumber": "", "rights": "", "extra": "PMID: 22847406", "tags": [ { "tag": "compression", "type": 1 }, { "tag": "metagenomics", "type": 1 } ], "collections": [ "GD3TED4D" ], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "F3GGF2HT", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/F3GGF2HT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/F3GGF2HT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/357882/items/B6KHSHN7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } } }, "data": { "key": "F3GGF2HT", "version": 3, "parentItem": "B6KHSHN7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-06-07T13:44:07Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21685107", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "FTMWZNNH", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/FTMWZNNH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/FTMWZNNH", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/357882/items/TJXH6FI7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } } }, "data": { "key": "FTMWZNNH", "version": 3, "parentItem": "TJXH6FI7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-06-07T13:37:53Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22847406", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "B6KHSHN7", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/B6KHSHN7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/B6KHSHN7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } }, "creatorSummary": "Peng et al.", "parsedDate": "2011-07-01", "numChildren": 1 }, "data": { "key": "B6KHSHN7", "version": 3, "itemType": "journalArticle", "title": "Meta-IDBA: a de Novo assembler for metagenomic data", "creators": [ { "creatorType": "author", "firstName": "Yu", "lastName": "Peng" }, { "creatorType": "author", "firstName": "Henry C. M.", "lastName": "Leung" }, { "creatorType": "author", "firstName": "S. M.", "lastName": "Yiu" }, { "creatorType": "author", "firstName": "Francis Y. L.", "lastName": "Chin" } ], "abstractNote": "Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated.\nResults: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy.\nAvailability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba.\nContact: chin@cs.hku.hk", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "07/01/2011", "volume": "27", "issue": "13", "section": "", "partNumber": "", "partTitle": "", "pages": "i94-i101", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Bioinformatics", "DOI": "10.1093/bioinformatics/btr216", "citationKey": "", "url": "http://bioinformatics.oxfordjournals.org/content/27/13/i94", "accessDate": "2015-06-07T13:44:07Z", "PMID": "", "PMCID": "", "ISSN": "1367-4803, 1460-2059", "archive": "", "archiveLocation": "", "shortTitle": "Meta-IDBA", "language": "en", "libraryCatalog": "bioinformatics.oxfordjournals.org", "callNumber": "", "rights": "", "extra": "PMID: 21685107", "tags": [], "collections": [ "GD3TED4D" ], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "QXMITKWR", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/QXMITKWR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/QXMITKWR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } }, "creatorSummary": "Howe et al.", "parsedDate": "2014-04-01", "numChildren": 1 }, "data": { "key": "QXMITKWR", "version": 3, "itemType": "journalArticle", "title": "Tackling soil diversity with the assembly of large, complex metagenomes", "creators": [ { "creatorType": "author", "firstName": "Adina Chuang", "lastName": "Howe" }, { "creatorType": "author", "firstName": "Janet K.", "lastName": "Jansson" }, { "creatorType": "author", "firstName": "Stephanie A.", "lastName": "Malfatti" }, { "creatorType": "author", "firstName": "Susannah G.", "lastName": "Tringe" }, { "creatorType": "author", "firstName": "James M.", "lastName": "Tiedje" }, { "creatorType": "author", "firstName": "C. Titus", "lastName": "Brown" } ], "abstractNote": "The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "04/01/2014", "volume": "111", "issue": "13", "section": "", "partNumber": "", "partTitle": "", "pages": "4904-4909", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PNAS", "DOI": "10.1073/pnas.1402564111", "citationKey": "", "url": "http://www.pnas.org/content/111/13/4904", "accessDate": "2015-06-07T13:37:55Z", "PMID": "", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.pnas.org", "callNumber": "", "rights": "", "extra": "PMID: 24632729", "tags": [], "collections": [ "GD3TED4D" ], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } }, { "key": "UQ29IRDW", "version": 3, "library": { "type": "group", "id": 357882, "name": "Assemblotron", "links": { "alternate": { "href": "https://www.zotero.org/groups/assemblotron", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/357882/items/UQ29IRDW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/assemblotron/items/UQ29IRDW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 327401, "username": "Blahah404", "name": "Richard Smith-Unna", "links": { "alternate": { "href": "https://www.zotero.org/blahah404", "type": "text/html" } } }, "creatorSummary": "Grabherr et al.", "parsedDate": "2011-05-15", "numChildren": 1 }, "data": { "key": "UQ29IRDW", "version": 3, "itemType": "journalArticle", "title": "Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data", "creators": [ { "creatorType": "author", "firstName": "Manfred G.", "lastName": "Grabherr" }, { "creatorType": "author", "firstName": "Brian J.", "lastName": "Haas" }, { "creatorType": "author", "firstName": "Moran", "lastName": "Yassour" }, { "creatorType": "author", "firstName": "Joshua Z.", "lastName": "Levin" }, { "creatorType": "author", "firstName": "Dawn A.", "lastName": "Thompson" }, { "creatorType": "author", "firstName": "Ido", "lastName": "Amit" }, { "creatorType": "author", "firstName": "Xian", "lastName": "Adiconis" }, { "creatorType": "author", "firstName": "Lin", "lastName": "Fan" }, { "creatorType": "author", "firstName": "Raktima", "lastName": "Raychowdhury" }, { "creatorType": "author", "firstName": "Qiandong", "lastName": "Zeng" }, { "creatorType": "author", "firstName": "Zehua", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Evan", "lastName": "Mauceli" }, { "creatorType": "author", "firstName": "Nir", "lastName": "Hacohen" }, { "creatorType": "author", "firstName": "Andreas", "lastName": "Gnirke" }, { "creatorType": "author", "firstName": "Nicholas", "lastName": "Rhind" }, { "creatorType": "author", "firstName": "Federica", "lastName": "di Palma" }, { "creatorType": "author", "firstName": "Bruce W.", "lastName": "Birren" }, { "creatorType": "author", "firstName": "Chad", "lastName": "Nusbaum" }, { "creatorType": "author", "firstName": "Kerstin", "lastName": "Lindblad-Toh" }, { "creatorType": "author", "firstName": "Nir", "lastName": "Friedman" }, { "creatorType": "author", "firstName": "Aviv", "lastName": "Regev" } ], "abstractNote": "Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.", "publicationTitle": "Nature biotechnology", "publisher": "", "place": "", "date": "2011-5-15", "volume": "29", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "644-652", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotechnol", "DOI": "10.1038/nbt.1883", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712/", "accessDate": "2015-06-07T13:44:12Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "Trinity", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 21572440\nPMCID: PMC3571712", "tags": [], "collections": [ "GD3TED4D" ], "relations": {}, "dateAdded": "2015-06-08T16:15:34Z", "dateModified": "2015-06-08T16:15:34Z" } } ]