[ { "key": "XDYQLXED", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/XDYQLXED", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/XDYQLXED", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Kechagia et al.", "parsedDate": "2013-01-02", "numChildren": 1 }, "data": { "key": "XDYQLXED", "version": 5522, "itemType": "journalArticle", "title": "Health Benefits of Probiotics: A Review", "creators": [ { "creatorType": "author", "firstName": "Maria", "lastName": "Kechagia" }, { "creatorType": "author", "firstName": "Dimitrios", "lastName": "Basoulis" }, { "creatorType": "author", "firstName": "Stavroula", "lastName": "Konstantopoulou" }, { "creatorType": "author", "firstName": "Dimitra", "lastName": "Dimitriadi" }, { "creatorType": "author", "firstName": "Konstantina", "lastName": "Gyftopoulou" }, { "creatorType": "author", "firstName": "Nikoletta", "lastName": "Skarmoutsou" }, { "creatorType": "author", "firstName": "Eleni Maria", "lastName": "Fakiri" } ], "abstractNote": "Probiotic bacteria have become increasingly popular during the last two decades as a result of the continuously expanding scientific evidence pointing to their beneficial effects on human health. As a result they have been applied as various products with the food industry having been very active in studying and promoting them. Within this market the probiotics have been incorporated in various products, mainly fermented dairy foods. In light of this ongoing trend and despite the strong scientific evidence associating these microorganisms to various health benefits, further research is needed in order to establish them and evaluate their safety as well as their nutritional aspects. The purpose of this paper is to review the current documentation on the concept and the possible beneficial properties of probiotic bacteria in the literature, focusing on those available in food.", "publicationTitle": "ISRN Nutrition", "publisher": "", "place": "", "date": "2013-1-2", "volume": "2013", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "481651", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "ISRN Nutr", "DOI": "10.5402/2013/481651", "citationKey": "", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045285/", "accessDate": "2023-04-25T18:58:26Z", "PMID": "24959545", "PMCID": "PMC4045285", "ISSN": "2314-4068", "archive": "", "archiveLocation": "", "shortTitle": "Health Benefits of Probiotics", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-04-25T18:58:27Z", "dateModified": "2023-04-25T18:58:27Z" } }, { "key": "DN56XJV9", "version": 5511, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/DN56XJV9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/DN56XJV9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/1478/items/XDYQLXED", "type": "application/json" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } } }, "data": { "key": "DN56XJV9", "version": 5511, "parentItem": "XDYQLXED", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2023-04-25T18:58:27Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045285/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2023-04-25T18:58:27Z", "dateModified": "2023-04-25T18:58:27Z" } }, { "key": "JKEBNA2E", "version": 5510, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/JKEBNA2E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/JKEBNA2E", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/1478/items/SPK6AIAT", "type": "application/json" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } } }, "data": { "key": "JKEBNA2E", "version": 5510, "parentItem": "SPK6AIAT", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2023-04-24T04:23:02Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662567/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2023-04-24T04:23:02Z", "dateModified": "2023-04-24T04:23:02Z" } }, { "key": "SPK6AIAT", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/SPK6AIAT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/SPK6AIAT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Kang et al.", "parsedDate": "2019-07-26", "numChildren": 1 }, "data": { "key": "SPK6AIAT", "version": 5522, "itemType": "journalArticle", "title": "MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies", "creators": [ { "creatorType": "author", "firstName": "Dongwan D.", "lastName": "Kang" }, { "creatorType": "author", "firstName": "Feng", "lastName": "Li" }, { "creatorType": "author", "firstName": "Edward", "lastName": "Kirton" }, { "creatorType": "author", "firstName": "Ashleigh", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Rob", "lastName": "Egan" }, { "creatorType": "author", "firstName": "Hong", "lastName": "An" }, { "creatorType": "author", "firstName": "Zhong", "lastName": "Wang" } ], "abstractNote": "We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat.", "publicationTitle": "PeerJ", "publisher": "", "place": "", "date": "2019-7-26", "volume": "7", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e7359", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PeerJ", "DOI": "10.7717/peerj.7359", "citationKey": "", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662567/", "accessDate": "2023-04-24T04:23:01Z", "PMID": "31388474", "PMCID": "PMC6662567", "ISSN": "2167-8359", "archive": "", "archiveLocation": "", "shortTitle": "MetaBAT 2", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-04-24T04:23:01Z", "dateModified": "2023-04-24T04:23:01Z" } }, { "key": "45VZV385", "version": 5509, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/45VZV385", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/45VZV385", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/1478/items/XU7BREZL", "type": "application/json" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } } }, "data": { "key": "45VZV385", "version": 5509, "parentItem": "XU7BREZL", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2023-04-24T04:22:52Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/31388474", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2023-04-24T04:22:52Z", "dateModified": "2023-04-24T04:22:52Z" } }, { "key": "XU7BREZL", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/XU7BREZL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/XU7BREZL", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Kang et al.", "parsedDate": "2019", "numChildren": 1 }, "data": { "key": "XU7BREZL", "version": 5522, "itemType": "journalArticle", "title": "MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies", "creators": [ { "creatorType": "author", "firstName": "Dongwan D.", "lastName": "Kang" }, { "creatorType": "author", "firstName": "Feng", "lastName": "Li" }, { "creatorType": "author", "firstName": "Edward", "lastName": "Kirton" }, { "creatorType": "author", "firstName": "Ashleigh", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Rob", "lastName": "Egan" }, { "creatorType": "author", "firstName": "Hong", "lastName": "An" }, { "creatorType": "author", "firstName": "Zhong", "lastName": "Wang" } ], "abstractNote": "We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat.", "publicationTitle": "PeerJ", "publisher": "", "place": "", "date": "2019", "volume": "7", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e7359", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PeerJ", "DOI": "10.7717/peerj.7359", "citationKey": "", "url": "", "accessDate": "", "PMID": "31388474", "PMCID": "PMC6662567", "ISSN": "2167-8359", "archive": "", "archiveLocation": "", "shortTitle": "MetaBAT 2", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Clustering", "type": 1 }, { "tag": "Metagenome binning", "type": 1 }, { "tag": "Metagenomics", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-04-24T04:22:50Z", "dateModified": "2023-04-24T04:22:50Z" } }, { "key": "VJW5UH6K", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/VJW5UH6K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/VJW5UH6K", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Spasov et al.", "parsedDate": "2020-07", "numChildren": 0 }, "data": { "key": "VJW5UH6K", "version": 5522, "itemType": "journalArticle", "title": "High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant", "creators": [ { "creatorType": "author", "firstName": "Emilie", "lastName": "Spasov" }, { "creatorType": "author", "firstName": "Jackson M.", "lastName": "Tsuji" }, { "creatorType": "author", "firstName": "Laura A.", "lastName": "Hug" }, { "creatorType": "author", "firstName": "Andrew C.", "lastName": "Doxey" }, { "creatorType": "author", "firstName": "Laura A.", "lastName": "Sauder" }, { "creatorType": "author", "firstName": "Wayne J.", "lastName": "Parker" }, { "creatorType": "author", "firstName": "Josh D.", "lastName": "Neufeld" } ], "abstractNote": "Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.", "publicationTitle": "The ISME Journal", "publisher": "Nature Publishing Group", "place": "", "date": "2020-07", "volume": "14", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "1857-1872", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "ISME J", "DOI": "10.1038/s41396-020-0650-2", "citationKey": "", "url": "https://www.nature.com/articles/s41396-020-0650-2", "accessDate": "2023-04-23T21:02:15Z", "PMID": "", "PMCID": "", "ISSN": "1751-7370", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www-nature-com.proxy.cc.uic.edu", "callNumber": "", "rights": "2020 The Author(s)", "extra": "Number: 7", "tags": [ { "tag": "Applied microbiology", "type": 1 }, { "tag": "Microbial ecology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-04-23T21:02:15Z", "dateModified": "2023-04-23T21:02:15Z" } }, { "key": "IMF8P7HB", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/IMF8P7HB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/IMF8P7HB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Spasov et al.", "parsedDate": "2020-07", "numChildren": 0 }, "data": { "key": "IMF8P7HB", "version": 5522, "itemType": "journalArticle", "title": "High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant", "creators": [ { "creatorType": "author", "firstName": "Emilie", "lastName": "Spasov" }, { "creatorType": "author", "firstName": "Jackson M.", "lastName": "Tsuji" }, { "creatorType": "author", "firstName": "Laura A.", "lastName": "Hug" }, { "creatorType": "author", "firstName": "Andrew C.", "lastName": "Doxey" }, { "creatorType": "author", "firstName": "Laura A.", "lastName": "Sauder" }, { "creatorType": "author", "firstName": "Wayne J.", "lastName": "Parker" }, { "creatorType": "author", "firstName": "Josh D.", "lastName": "Neufeld" } ], "abstractNote": "Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.", "publicationTitle": "The ISME Journal", "publisher": "Nature Publishing Group", "place": "", "date": "2020-07", "volume": "14", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "1857-1872", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "ISME J", "DOI": "10.1038/s41396-020-0650-2", "citationKey": "", "url": "https://www.nature.com/articles/s41396-020-0650-2", "accessDate": "2023-04-23T20:58:04Z", "PMID": "", "PMCID": "", "ISSN": "1751-7370", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www-nature-com.proxy.cc.uic.edu", "callNumber": "", "rights": "2020 The Author(s)", "extra": "Number: 7", "tags": [ { "tag": "Applied microbiology", "type": 1 }, { "tag": "Microbial ecology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-04-23T20:58:02Z", "dateModified": "2023-04-23T20:58:02Z" } }, { "key": "HAVIWMAV", "version": 5504, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/HAVIWMAV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/HAVIWMAV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "HAVIWMAV", "version": 5504, "itemType": "webpage", "title": "ChatGPT", "creators": [], "abstractNote": "A conversational AI system that listens, learns, and challenges", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "https://chat.openai.com", "accessDate": "2023-04-20T17:04:47Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-04-20T17:04:48Z", "dateModified": "2023-04-20T17:04:48Z" } }, { "key": "JUV4KBSU", "version": 5453, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/JUV4KBSU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/JUV4KBSU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "JUV4KBSU", "version": 5453, "itemType": "note", "note": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-01-11T21:11:57Z", "dateModified": "2023-01-11T21:11:57Z" } }, { "key": "ENDDCCAJ", "version": 5439, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/ENDDCCAJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/ENDDCCAJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 10394242, "username": "mrasic2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mrasic2", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "ENDDCCAJ", "version": 5439, "itemType": "webpage", "title": "Cookies | bioRxiv", "creators": [], "abstractNote": "", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "https://www.biorxiv.org/help/cookie-policy", "accessDate": "2022-10-24T05:52:20Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-10-24T05:52:20Z", "dateModified": "2022-10-24T05:52:20Z" } }, { "key": "IA62UCAJ", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/IA62UCAJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/IA62UCAJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3659531, "username": "Kocht", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/kocht", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Bot and Lisa", "parsedDate": "2021-07", "numChildren": 0 }, "data": { "key": "IA62UCAJ", "version": 5522, "itemType": "document", "title": "just-a-readme", "creators": [ { "creatorType": "author", "firstName": "Hew", "lastName": "Bot" }, { "creatorType": "author", "firstName": "Mona", "lastName": "Lisa" } ], "abstractNote": "", "type": "", "date": "2021-07", "publisher": "", "place": "", "DOI": "10.5281/zenodo.1234", "citationKey": "", "url": "https://github.com/emmaviolet/just-a-readme", "accessDate": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2021-08-25T07:07:26Z", "dateModified": "2021-08-25T07:07:26Z" } }, { "key": "Z92X55WP", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/Z92X55WP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/Z92X55WP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Passarge et al.", "parsedDate": "1999-12", "numChildren": 0 }, "data": { "key": "Z92X55WP", "version": 5522, "itemType": "journalArticle", "title": "Incorrect use of the term synteny", "creators": [ { "creatorType": "author", "firstName": "E", "lastName": "Passarge" }, { "creatorType": "author", "firstName": "B", "lastName": "Horsthemke" }, { "creatorType": "author", "firstName": "R A", "lastName": "Farber" } ], "abstractNote": "", "publicationTitle": "Nature Genetics", "publisher": "", "place": "", "date": "Dec 1999", "volume": "23", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "387", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Genet", "DOI": "10.1038/70486", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/10581019", "accessDate": "2009-06-08T02:32:49Z", "PMID": "10581019", "PMCID": "", "ISSN": "1061-4036", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0024", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Chromosome Mapping", "type": 1 }, { "tag": "Evolution", "type": 1 }, { "tag": "Genetics", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Terminology as Topic", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:30Z" } }, { "key": "WTVHWNCZ", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/WTVHWNCZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/WTVHWNCZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Miller et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "WTVHWNCZ", "version": 5433, "itemType": "journalArticle", "title": "COMPARATIVE GENOMICS", "creators": [ { "creatorType": "author", "firstName": "Webb", "lastName": "Miller" }, { "creatorType": "author", "firstName": "Kateryna D.", "lastName": "Makova" }, { "creatorType": "author", "firstName": "Anton", "lastName": "Nekrutenko" }, { "creatorType": "author", "firstName": "Ross C.", "lastName": "Hardison" } ], "abstractNote": "", "publicationTitle": "Annual Review of Genomics and Human Genetics", "publisher": "", "place": "", "date": "09/2004", "volume": "5", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "15-56", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Annu. Rev. Genom. Human. Genet.", "DOI": "10.1146/annurev.genom.5.061903.180057", "citationKey": "", "url": "http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.5.061903.180057?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov", "accessDate": "2009-06-08T02:37:45Z", "PMID": "", "PMCID": "", "ISSN": "1527-8204", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "1116", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:29Z" } }, { "key": "W5MHV59Z", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/W5MHV59Z", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/W5MHV59Z", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Hill", "parsedDate": "1988", "numChildren": 0 }, "data": { "key": "W5MHV59Z", "version": 5433, "itemType": "journalArticle", "title": "Why aren't horses faster?", "creators": [ { "creatorType": "author", "firstName": "William G.", "lastName": "Hill" } ], "abstractNote": "", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "4/1988", "volume": "332", "issue": "6166", "section": "", "partNumber": "", "partTitle": "", "pages": "678-678", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "10.1038/332678a0", "citationKey": "", "url": "http://www.nature.com/doifinder/10.1038/332678a0", "accessDate": "2009-06-05T12:54:27Z", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "0019", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:28Z" } }, { "key": "UTBKRAZF", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/UTBKRAZF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/UTBKRAZF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Vilella et al.", "parsedDate": "2009-02", "numChildren": 0 }, "data": { "key": "UTBKRAZF", "version": 5522, "itemType": "journalArticle", "title": "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates", "creators": [ { "creatorType": "author", "firstName": "Albert J", "lastName": "Vilella" }, { "creatorType": "author", "firstName": "Jessica", "lastName": "Severin" }, { "creatorType": "author", "firstName": "Abel", "lastName": "Ureta-Vidal" }, { "creatorType": "author", "firstName": "Li", "lastName": "Heng" }, { "creatorType": "author", "firstName": "Richard", "lastName": "Durbin" }, { "creatorType": "author", "firstName": "Ewan", "lastName": "Birney" } ], "abstractNote": "We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.", "publicationTitle": "Genome Research", "publisher": "", "place": "", "date": "Feb 2009", "volume": "19", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "327-335", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Genome Res", "DOI": "10.1101/gr.073585.107", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19029536", "accessDate": "2009-05-29T08:45:34Z", "PMID": "19029536", "PMCID": "", "ISSN": "1088-9051", "archive": "", "archiveLocation": "", "shortTitle": "EnsemblCompara GeneTrees", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0072", "rights": "", "extra": "", "tags": [ { "tag": "Algorithms", "type": 1 }, { "tag": "Animals", "type": 1 }, { "tag": "Computational Biology", "type": 1 }, { "tag": "Gene Duplication", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Multigene Family", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Sequence Homology", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Synteny", "type": 1 }, { "tag": "Vertebrates", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-05T11:49:14Z", "dateModified": "2011-02-02T20:56:27Z" } }, { "key": "UQ6W2D8R", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/UQ6W2D8R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/UQ6W2D8R", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Aulchenko et al.", "parsedDate": "2007", "numChildren": 0 }, "data": { "key": "UQ6W2D8R", "version": 5433, "itemType": "journalArticle", "title": "GenABEL: an R library for genome-wide association analysis", "creators": [ { "creatorType": "author", "firstName": "Yurii S.", "lastName": "Aulchenko" }, { "creatorType": "author", "firstName": "Stephan", "lastName": "Ripke" }, { "creatorType": "author", "firstName": "Aaron", "lastName": "Isaacs" }, { "creatorType": "author", "firstName": "Cornelia M.", "lastName": "van Duijn" } ], "abstractNote": "Here we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis. We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers. Availability: http://cran.r-project.org Contact: i.aoultchenko@erasmusmc.nl", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "Mai 15, 2007", "volume": "23", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1294-1296", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bioinformatics/btm108", "citationKey": "", "url": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/10/1294", "accessDate": "2009-07-11T10:34:41Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "GenABEL", "language": "", "libraryCatalog": "HighWire", "callNumber": "0109", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-07-11T10:34:55Z", "dateModified": "2011-02-02T20:56:26Z" } }, { "key": "TNJUHBE6", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/TNJUHBE6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/TNJUHBE6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Hardison", "parsedDate": "2003-11", "numChildren": 0 }, "data": { "key": "TNJUHBE6", "version": 5433, "itemType": "journalArticle", "title": "Comparative Genomics", "creators": [ { "creatorType": "author", "firstName": "Ross C", "lastName": "Hardison" } ], "abstractNote": "", "publicationTitle": "PLoS Biology", "publisher": "", "place": "", "date": "2003 November", "volume": "1", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "e58", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS Biol.", "DOI": "10.1371/journal.pbio.0000058", "citationKey": "", "url": "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=261895", "accessDate": "2009-06-08T02:43:31Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "1116", "rights": "", "extra": "PMC261895", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:25Z" } }, { "key": "TMKS9EGT", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/TMKS9EGT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/TMKS9EGT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Hubbard et al.", "parsedDate": "2009-01", "numChildren": 0 }, "data": { "key": "TMKS9EGT", "version": 5522, "itemType": "journalArticle", "title": "Ensembl 2009", "creators": [ { "creatorType": "author", "firstName": "T J P", "lastName": "Hubbard" }, { "creatorType": "author", "firstName": "B L", "lastName": "Aken" }, { "creatorType": "author", "firstName": "S", "lastName": "Ayling" }, { "creatorType": "author", "firstName": "B", "lastName": "Ballester" }, { "creatorType": "author", "firstName": "K", "lastName": "Beal" }, { "creatorType": "author", "firstName": "E", "lastName": "Bragin" }, { "creatorType": "author", "firstName": "S", "lastName": "Brent" }, { "creatorType": "author", "firstName": "Y", "lastName": "Chen" }, { "creatorType": "author", "firstName": "P", "lastName": "Clapham" }, { "creatorType": "author", "firstName": "L", "lastName": "Clarke" }, { "creatorType": "author", "firstName": "G", "lastName": "Coates" }, { "creatorType": "author", "firstName": "S", "lastName": "Fairley" }, { "creatorType": "author", "firstName": "S", "lastName": "Fitzgerald" }, { "creatorType": "author", "firstName": "J", "lastName": "Fernandez-Banet" }, { "creatorType": "author", "firstName": "L", "lastName": "Gordon" }, { "creatorType": "author", "firstName": "S", "lastName": "Gräf" }, { "creatorType": "author", "firstName": "S", "lastName": "Haider" }, { "creatorType": "author", "firstName": "M", "lastName": "Hammond" }, { "creatorType": "author", "firstName": "R", "lastName": "Holland" }, { "creatorType": "author", "firstName": "K", "lastName": "Howe" }, { "creatorType": "author", "firstName": "A", "lastName": "Jenkinson" }, { "creatorType": "author", "firstName": "N", "lastName": "Johnson" }, { "creatorType": "author", "firstName": "A", "lastName": "Kähäri" }, { "creatorType": "author", "firstName": "D", "lastName": "Keefe" }, { "creatorType": "author", "firstName": "S", "lastName": "Keenan" }, { "creatorType": "author", "firstName": "R", "lastName": "Kinsella" }, { "creatorType": "author", "firstName": "F", "lastName": "Kokocinski" }, { "creatorType": "author", "firstName": "E", "lastName": "Kulesha" }, { "creatorType": "author", "firstName": "D", "lastName": "Lawson" }, { "creatorType": "author", "firstName": "I", "lastName": "Longden" }, { "creatorType": "author", "firstName": "K", "lastName": "Megy" }, { "creatorType": "author", "firstName": "P", "lastName": "Meidl" }, { "creatorType": "author", "firstName": "B", "lastName": "Overduin" }, { "creatorType": "author", "firstName": "A", "lastName": "Parker" }, { "creatorType": "author", "firstName": "B", "lastName": "Pritchard" }, { "creatorType": "author", "firstName": "D", "lastName": "Rios" }, { "creatorType": "author", "firstName": "M", "lastName": "Schuster" }, { "creatorType": "author", "firstName": "G", "lastName": "Slater" }, { "creatorType": "author", "firstName": "D", "lastName": "Smedley" }, { "creatorType": "author", "firstName": "W", "lastName": "Spooner" }, { "creatorType": "author", "firstName": "G", "lastName": "Spudich" }, { "creatorType": "author", "firstName": "S", "lastName": "Trevanion" }, { "creatorType": "author", "firstName": "A", "lastName": "Vilella" }, { "creatorType": "author", "firstName": "J", "lastName": "Vogel" }, { "creatorType": "author", "firstName": "S", "lastName": "White" }, { "creatorType": "author", "firstName": "S", "lastName": "Wilder" }, { "creatorType": "author", "firstName": "A", "lastName": "Zadissa" }, { "creatorType": "author", "firstName": "E", "lastName": "Birney" }, { "creatorType": "author", "firstName": "F", "lastName": "Cunningham" }, { "creatorType": "author", "firstName": "V", "lastName": "Curwen" }, { "creatorType": "author", "firstName": "R", "lastName": "Durbin" }, { "creatorType": "author", "firstName": "X M", "lastName": "Fernandez-Suarez" }, { "creatorType": "author", "firstName": "J", "lastName": "Herrero" }, { "creatorType": "author", "firstName": "A", "lastName": "Kasprzyk" }, { "creatorType": "author", "firstName": "G", "lastName": "Proctor" }, { "creatorType": "author", "firstName": "J", "lastName": "Smith" }, { "creatorType": "author", "firstName": "S", "lastName": "Searle" }, { "creatorType": "author", "firstName": "P", "lastName": "Flicek" } ], "abstractNote": "The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "Jan 2009", "volume": "37", "issue": "Database issue", "section": "", "partNumber": "", "partTitle": "", "pages": "D690-697", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res", "DOI": "10.1093/nar/gkn828", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19033362", "accessDate": "2009-05-29T08:42:44Z", "PMID": "19033362", "PMCID": "", "ISSN": "1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0357", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Databases, Genetic", "type": 1 }, { "tag": "Genetic Variation", "type": 1 }, { "tag": "Genomics", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Internet", "type": 1 }, { "tag": "Sequence Alignment", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-05T11:49:14Z", "dateModified": "2011-02-02T20:56:24Z" } }, { "key": "PX39A55C", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/PX39A55C", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/PX39A55C", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Hammann and Westhof", "parsedDate": "2007", "numChildren": 0 }, "data": { "key": "PX39A55C", "version": 5433, "itemType": "journalArticle", "title": "Searching genomes for ribozymes and riboswitches", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Hammann" }, { "creatorType": "author", "firstName": "Eric", "lastName": "Westhof" } ], "abstractNote": "New regulatory RNAs with complex structures have recently been discovered, among them the first catalytic riboswitch, a gene-regulatory RNA sequence with catalytic activity. Here we discuss some of the experimental approaches and theoretical difficulties attached to the identification of new ribozymes in genomes.", "publicationTitle": "Genome Biology", "publisher": "", "place": "", "date": "2007", "volume": "8", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "210", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/gb-2007-8-4-210", "citationKey": "", "url": "http://genomebiology.com/2007/8/4/210", "accessDate": "2008-05-28T13:10:14Z", "PMID": "", "PMCID": "", "ISSN": "1465-6906", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "BioMed Central and More", "callNumber": "0020", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-05T14:50:12Z", "dateModified": "2011-02-02T20:56:23Z" } }, { "key": "NP5Q6J54", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/NP5Q6J54", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/NP5Q6J54", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Valencia and Pazos", "parsedDate": "2002-06-01", "numChildren": 0 }, "data": { "key": "NP5Q6J54", "version": 5433, "itemType": "journalArticle", "title": "Computational methods for the prediction of protein interactions", "creators": [ { "creatorType": "author", "firstName": "Alfonso", "lastName": "Valencia" }, { "creatorType": "author", "firstName": "Florencio", "lastName": "Pazos" } ], "abstractNote": "Establishing protein interaction networks is crucial for understanding cellular operations. Detailed knowledge of the [`]interactome', the full network of protein-protein interactions, in model cellular systems should provide new insights into the structure and properties of these systems. Parallel to the first massive application of experimental techniques to the determination of protein interaction networks and protein complexes, the first computational methods, based on sequence and genomic information, have emerged.", "publicationTitle": "Current Opinion in Structural Biology", "publisher": "", "place": "", "date": "Juni 1, 2002", "volume": "12", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "368-373", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/S0959-440X(02)00333-0", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6VS6-469GK4C-J/2/9c30d085fb9e074bbf1d33355fd723f5", "accessDate": "2009-06-05T13:00:35Z", "PMID": "", "PMCID": "", "ISSN": "0959-440X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "0241", "rights": "", "extra": "", "tags": [ { "tag": "Protein interaction", "type": 1 }, { "tag": "bioinformatics", "type": 1 }, { "tag": "interaction network", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-05T13:01:06Z", "dateModified": "2011-02-02T20:56:22Z" } }, { "key": "NGXS8QW4", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/NGXS8QW4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/NGXS8QW4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Datta et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "NGXS8QW4", "version": 5433, "itemType": "journalArticle", "title": "Berkeley PHOG: PhyloFacts orthology group prediction web server", "creators": [ { "creatorType": "author", "firstName": "Ruchira S.", "lastName": "Datta" }, { "creatorType": "author", "firstName": "Christopher", "lastName": "Meacham" }, { "creatorType": "author", "firstName": "Bushra", "lastName": "Samad" }, { "creatorType": "author", "firstName": "Christoph", "lastName": "Neyer" }, { "creatorType": "author", "firstName": "Kimmen", "lastName": "Sjölander" } ], "abstractNote": "Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm to identify orthologs based on phylogenetic analysis. Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic distances and precision levels through the use of tree-distance thresholds. For instance, OrthoMCL-DB achieved 76% recall and 66% precision on this dataset; at a slightly higher precision (68%) PHOG achieves 10% higher recall (86%). InParanoid achieved 87% recall at 24% precision on this dataset, while a PHOG variant designed for high recall achieves 88% recall at 61% precision, increasing precision by 37% over InParanoid. PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species. Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/.", "publicationTitle": "Nucl. Acids Res.", "publisher": "", "place": "", "date": "Mai 12, 2009", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "gkp373", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/nar/gkp373", "citationKey": "", "url": "http://nar.oxfordjournals.org/cgi/content/abstract/gkp373v1", "accessDate": "2009-06-05T13:11:42Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Berkeley PHOG", "language": "", "libraryCatalog": "HighWire", "callNumber": "0012", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:21Z" } }, { "key": "MT8DB8R8", "version": 5433, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/MT8DB8R8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/MT8DB8R8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5939, "username": "capemaster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/capemaster", "type": "text/html" } } }, "creatorSummary": "Kunin et al.", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "MT8DB8R8", "version": 5433, "itemType": "journalArticle", "title": "A Bioinformatician's Guide to Metagenomics", "creators": [ { "creatorType": "author", "firstName": "Victor", "lastName": "Kunin" }, { "creatorType": "author", "firstName": "Alex", "lastName": "Copeland" }, { "creatorType": "author", "firstName": "Alla", "lastName": "Lapidus" }, { "creatorType": "author", "firstName": "Konstantinos", "lastName": "Mavromatis" }, { "creatorType": "author", "firstName": "Philip", "lastName": "Hugenholtz" } ], "abstractNote": "Summary: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.", "publicationTitle": "Microbiol. Mol. Biol. Rev.", "publisher": "", "place": "", "date": "Dezember 1, 2008", "volume": "72", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "557-578", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1128/MMBR.00009-08", "citationKey": "", "url": "http://mmbr.asm.org/cgi/content/abstract/72/4/557", "accessDate": "2009-06-05T13:12:25Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "HighWire", "callNumber": "0042", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-06-08T02:44:03Z", "dateModified": "2011-02-02T20:56:20Z" } }, { "key": "KGTJQJTT", "version": 5522, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/KGTJQJTT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/KGTJQJTT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Camon et al.", "parsedDate": "2004-01-01", "numChildren": 0 }, "data": { "key": "KGTJQJTT", "version": 5522, "itemType": "journalArticle", "title": "The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology", "creators": [ { "creatorType": "author", "firstName": "Evelyn", "lastName": "Camon" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Magrane" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Barrell" }, { "creatorType": "author", "firstName": "Vivian", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Emily", "lastName": "Dimmer" }, { "creatorType": "author", "firstName": "John", "lastName": "Maslen" }, { "creatorType": "author", "firstName": "David", "lastName": "Binns" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "Harte" }, { "creatorType": "author", "firstName": "Rodrigo", "lastName": "Lopez" }, { "creatorType": "author", "firstName": "Rolf", "lastName": "Apweiler" } ], "abstractNote": "The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of integration of the knowledge represented in UniProt with other databases. This is achieved by converting UniProt annotation into a recognized computational format. GOA provides annotated entries for nearly 60,000 species (GOA-SPTr) and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. By integrating GO annotations from other model organism groups, GOA consolidates specialized knowledge and expertise to ensure the data remain a key reference for up-to-date biological information. Furthermore, the GOA database fully endorses the Human Proteomics Initiative by prioritizing the annotation of proteins likely to benefit human health and disease. In addition to a non-redundant set of annotations to the human proteome (GOA-Human) and monthly releases of its GO annotation for all species (GOA-SPTr), a series of GO mapping files and specific cross-references in other databases are also regularly distributed. GOA can be queried through a simple user-friendly web interface or downloaded in a parsable format via the EBI and GO FTP websites. The GOA data set can be used to enhance the annotation of particular model organism or gene expression data sets, although increasingly it has been used to evaluate GO predictions generated from text mining or protein interaction experiments. In 2004, the GOA team will build on its success and will continue to supplement the functional annotation of UniProt and work towards enhancing the ability of scientists to access all available biological information. Researchers wishing to query or contribute to the GOA project are encouraged to email: goa@ebi.ac.uk.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "Jan 1, 2004", "volume": "32", "issue": "Database issue", "section": "", "partNumber": "", "partTitle": "", "pages": "D262-266", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res", "DOI": "10.1093/nar/gkh021", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/14681408", "accessDate": "2009-05-29T08:39:38Z", "PMID": "14681408", "PMCID": "", "ISSN": "1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "The Gene Ontology Annotation (GOA) Database", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0488", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Computational Biology", "type": 1 }, { "tag": "Databases, Genetic", "type": 1 }, { "tag": "Databases, Protein", "type": 1 }, { "tag": "Genes", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Information Storage and Retrieval", "type": 1 }, { "tag": "Internet", "type": 1 }, { "tag": "Proteome", "type": 1 }, { "tag": "Proteomics", "type": 1 }, { "tag": "Terminology as Topic", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-05T11:49:14Z", "dateModified": "2011-02-02T20:56:19Z" } }, { "key": "IREUWZPU", "version": 5523, "library": { "type": "group", "id": 1478, "name": "Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/1478/items/IREUWZPU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics/items/IREUWZPU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27714, "username": "akloster", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/akloster", "type": "text/html" } } }, "lastModifiedByUser": { "id": 5530973, "username": "alamisoufiane", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/alamisoufiane", "type": "text/html" } } }, "creatorSummary": "Kuzniar et al.", "parsedDate": "2008-11", "numChildren": 0 }, "data": { "key": "IREUWZPU", "version": 5523, "itemType": "journalArticle", "title": "The quest for orthologs: finding the corresponding gene across genomes", "creators": [ { "creatorType": "author", "firstName": "Arnold", "lastName": "Kuzniar" }, { "creatorType": "author", "firstName": "Roeland C H J", "lastName": "van Ham" }, { "creatorType": "author", "firstName": "Sándor", "lastName": "Pongor" }, { "creatorType": "author", "firstName": "Jack A M", "lastName": "Leunissen" } ], "abstractNote": "Orthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene functions, cellular networks and functional genome annotation. Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a phylogenetic approach, which combines both trees and graphs (networks) using reliable species phylogeny and available genomic data from more than two species, and an insight into the processes of molecular evolution. Here, we evaluate the available bioinformatics tools and provide a set of guidelines to aid researchers in choosing the most appropriate tool for any situation.", "publicationTitle": "Trends in Genetics: TIG", "publisher": "", "place": "", "date": "Nov 2008", "volume": "24", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "539-551", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Trends Genet", "DOI": "10.1016/j.tig.2008.08.009", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18819722", "accessDate": "2009-05-29T08:43:39Z", "PMID": "18819722", "PMCID": "", "ISSN": "0168-9525", "archive": "", "archiveLocation": "", "shortTitle": "The quest for orthologs", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0041", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Databases, Genetic", "type": 1 }, { "tag": "Evolution, Molecular", "type": 1 }, { "tag": "Genome", "type": 1 }, { "tag": "Genomics", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Sequence Homology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-06-05T11:49:14Z", "dateModified": "2011-02-02T20:56:18Z" } } ]