[ { "key": "4KECEUS5", "version": 2371, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/4KECEUS5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/4KECEUS5", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/38HHRHFZ", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "4KECEUS5", "version": 2371, "parentItem": "38HHRHFZ", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2025-10-17T20:05:10Z", "url": "https://academic.oup.com/bioinformatics/article-pdf/24/11/1381/49047105/bioinformatics_24_11_1381.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Wren - 2008 - URL decay in MEDLINE—a 4-year follow-up study.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2025-10-17T20:05:10Z", "dateModified": "2025-10-17T20:05:10Z" } }, { "key": "38HHRHFZ", "version": 2370, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/38HHRHFZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/38HHRHFZ", "type": "text/html" } }, "meta": { "creatorSummary": "Wren", "parsedDate": "2008-06-01", "numChildren": 1 }, "data": { "key": "38HHRHFZ", "version": 2370, "itemType": "journalArticle", "title": "URL decay in MEDLINE—a 4-year follow-up study", "creators": [ { "creatorType": "author", "firstName": "Jonathan D.", "lastName": "Wren" } ], "abstractNote": "Abstract\n Motivation: Internet-based electronic resources, as given by Uniform Resource Locators (URLs), are being increasingly used in scientific publications but are also becoming inaccessible in a time-dependant manner, a phenomenon documented across disciplines. Initial reports brought attention to the problem, spawning methods of effectively preserving URL content while some journals adopted policies regarding URL publication and begun storing supplementary information on journal websites. Thus, a reexamination of URL growth and decay in the literature is merited to see if the problem has grown or been mitigated by any of these changes.\n Results: After the 2003 study, three follow-up studies were conducted in 2004, 2005 and 2007. Unfortunately, no significant change was found in the rate of URL decay among any of the studies. However, only 5% of URLs cited more than twice have decayed versus 20% of URLs cited once or twice. The most common types of lost content were computer programs (43%), followed by scholarly content (38%) and databases (19%). Compared to URLs still available, no lost content type was significantly over- or underrepresented. Searching for 30 of these websites using Google, 11 (37%) were found relocated to different URLs.\n Conclusions: URL decay continues unabated, but URLs published by organizations tend to be more stable. Repeated citation of URLs suggests calculation of an electronic impact factor (eIF) would be an objective, quantitative way to measure the impact of Internet-based resources on scientific research.\n Contact:  Jonathan-Wren@OMRF.org", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "2008-06-01", "volume": "24", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "1381-1385", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bioinformatics/btn127", "citationKey": "", "url": "https://academic.oup.com/bioinformatics/article/24/11/1381/191025", "accessDate": "2025-10-17T20:05:05Z", "PMID": "", "PMCID": "", "ISSN": "1367-4811, 1367-4803", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "7EV6NFV9" ], "relations": {}, "dateAdded": "2025-10-17T20:05:05Z", "dateModified": "2025-10-17T20:05:05Z" } }, { "key": "AYAVFFGB", "version": 2129, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/AYAVFFGB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/AYAVFFGB", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/H7XSAS2T", "type": "application/json" } }, "meta": {}, "data": { "key": "AYAVFFGB", "version": 2129, "parentItem": "H7XSAS2T", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2020-01-14T18:05:05Z", "url": "https://academic.oup.com/bib/article/20/6/1972/5055373", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "5055373.html", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2020-01-14T18:05:05Z", "dateModified": "2020-03-06T22:38:43Z" } }, { "key": "A6IZL76E", "version": 2129, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/A6IZL76E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/A6IZL76E", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/H7XSAS2T", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "A6IZL76E", "version": 2129, "parentItem": "H7XSAS2T", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2020-01-14T18:04:55Z", "url": "https://academic.oup.com/bib/article-pdf/20/6/1972/31789375/bby062.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Wang and Guo - 2019 - A review of metrics measuring dissimilarity for ro.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2020-01-14T18:04:55Z", "dateModified": "2020-03-06T22:38:43Z" } }, { "key": "H7XSAS2T", "version": 2129, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/H7XSAS2T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/H7XSAS2T", "type": "text/html" } }, "meta": { "creatorSummary": "Wang and Guo", "parsedDate": "2018-07-17", "numChildren": 2 }, "data": { "key": "H7XSAS2T", "version": 2129, "itemType": "journalArticle", "title": "A review of metrics measuring dissimilarity for rooted phylogenetic networks", "creators": [ { "creatorType": "author", "firstName": "Juan", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Maozu", "lastName": "Guo" } ], "abstractNote": "", "publicationTitle": "Briefings in Bioinformatics", "publisher": "", "place": "", "date": "2018-07-17", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bib/bby062", "citationKey": "", "url": "https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby062/5055373", "accessDate": "2018-07-22T17:14:31Z", "PMID": "", "PMCID": "", "ISSN": "1467-5463, 1477-4054", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Crossref", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "7EV6NFV9" ], "relations": { "dc:replaces": "http://zotero.org/users/5379/items/KT4G8ZRZ" }, "dateAdded": "2018-07-22T17:14:31Z", "dateModified": "2020-03-06T22:38:43Z" } }, { "key": "BCZJZDB3", "version": 2109, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/BCZJZDB3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/BCZJZDB3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/YEHQSQZW", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "BCZJZDB3", "version": 2109, "parentItem": "YEHQSQZW", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2019-12-27T00:44:33Z", "url": "https://academic.oup.com/bioinformatics/article-pdf/28/21/2747/16909471/bts526.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Plagnol et al. - 2012 - A robust model for read count data in exome sequen.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2019-12-27T00:44:33Z", "dateModified": "2020-01-03T21:36:31Z" } }, { "key": "YEHQSQZW", "version": 2109, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/YEHQSQZW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/YEHQSQZW", "type": "text/html" } }, "meta": { "creatorSummary": "Plagnol et al.", "parsedDate": "2012-11-01", "numChildren": 7 }, "data": { "key": "YEHQSQZW", "version": 2109, "itemType": "journalArticle", "title": "A robust model for read count data in exome sequencing experiments and implications for copy number variant calling", "creators": [ { "creatorType": "author", "firstName": "Vincent", "lastName": "Plagnol" }, { "creatorType": "author", "firstName": "James", "lastName": "Curtis" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Epstein" }, { "creatorType": "author", "firstName": "Kin Y.", "lastName": "Mok" }, { "creatorType": "author", "firstName": "Emma", "lastName": "Stebbings" }, { "creatorType": "author", "firstName": "Sofia", "lastName": "Grigoriadou" }, { "creatorType": "author", "firstName": "Nicholas W.", "lastName": "Wood" }, { "creatorType": "author", "firstName": "Sophie", "lastName": "Hambleton" }, { "creatorType": "author", "firstName": "Siobhan O.", "lastName": "Burns" }, { "creatorType": "author", "firstName": "Adrian J.", "lastName": "Thrasher" }, { "creatorType": "author", "firstName": "Dinakantha", "lastName": "Kumararatne" }, { "creatorType": "author", "firstName": "Rainer", "lastName": "Doffinger" }, { "creatorType": "author", "firstName": "Sergey", "lastName": "Nejentsev" } ], "abstractNote": "MOTIVATION: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.\nRESULTS: Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized reference set in order to maximize the power to detect CNVs. As a result, ExomeDepth is effective across a wider range of exome datasets than the previously existing tools, even for small (e.g. one to two exons) and heterozygous deletions. We used this new approach to analyse exome data from 24 patients with primary immunodeficiencies. Depending on data quality and the exact target region, we find between 170 and 250 exonic CNV calls per sample. Our analysis identified two novel causative deletions in the genes GATA2 and DOCK8.\nAVAILABILITY: The code used in this analysis has been implemented into an R package called ExomeDepth and is available at the Comprehensive R Archive Network (CRAN).", "publicationTitle": "Bioinformatics (Oxford, England)", "publisher": "", "place": "", "date": "Nov 01, 2012", "volume": "28", "issue": "21", "section": "", "partNumber": "", "partTitle": "", "pages": "2747-2754", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Bioinformatics", "DOI": "10.1093/bioinformatics/bts526", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1367-4811", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 22942019\nPMCID: PMC3476336", "tags": [ { "tag": "Algorithms", "type": 1 }, { "tag": "Exome", "type": 1 }, { "tag": "False Negative Reactions", "type": 1 }, { "tag": "GATA2 Transcription Factor", "type": 1 }, { "tag": "Gene Deletion", "type": 1 }, { "tag": "Gene Dosage", "type": 1 }, { "tag": "Genetic Variation", "type": 1 }, { "tag": "Guanine Nucleotide Exchange Factors", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Immunologic Deficiency Syndromes", "type": 1 }, { "tag": "Markov Chains", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Models, Statistical", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Sequence Analysis, Protein", "type": 1 } ], "collections": [ "7EV6NFV9" ], "relations": { "dc:replaces": [ "http://zotero.org/users/5379/items/6ZG9UJPR", "http://zotero.org/users/5379/items/CRRQQD39", "http://zotero.org/users/5379/items/5K6M6FJ7", "http://zotero.org/users/5379/items/T4AJ6AGW", "http://zotero.org/users/5379/items/YLMQ6UIH" ] }, "dateAdded": "2017-12-08T23:02:04Z", "dateModified": "2020-01-03T21:36:31Z" } }, { "key": "266MVJ4Q", "version": 2035, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/266MVJ4Q", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/266MVJ4Q", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/7KVA48G3", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "266MVJ4Q", "version": 2035, "parentItem": "7KVA48G3", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2019-08-02T15:45:30Z", "url": "https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-471", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Nuin et al. - 2006 - The accuracy of several multiple sequence alignmen.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2019-08-02T15:45:30Z", "dateModified": "2019-08-02T18:21:01Z" } }, { "key": "YZK9D9YW", "version": 2035, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/YZK9D9YW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/YZK9D9YW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/7KVA48G3", "type": "application/json" } }, "meta": {}, "data": { "key": "YZK9D9YW", "version": 2035, "parentItem": "7KVA48G3", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2019-08-02T15:45:29Z", "url": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-471", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "1471-2105-7-471.html", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2019-08-02T15:45:29Z", "dateModified": "2019-08-02T18:21:01Z" } }, { "key": "7KVA48G3", "version": 2035, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/7KVA48G3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/7KVA48G3", "type": "text/html" } }, "meta": { "creatorSummary": "Nuin et al.", "parsedDate": "2006", "numChildren": 3 }, "data": { "key": "7KVA48G3", "version": 2035, "itemType": "journalArticle", "title": "The accuracy of several multiple sequence alignment programs for proteins", "creators": [ { "creatorType": "author", "firstName": "Paulo A S", "lastName": "Nuin" }, { "creatorType": "author", "firstName": "Zhouzhi", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Elisabeth R M", "lastName": "Tillier" } ], "abstractNote": "BACKGROUND: There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The \"true\" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs. RESULTS: We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30,000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases. CONCLUSION: Our results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i) and ProbCons were consistently the most accurate, with Mafft being the faster of the two.", "publicationTitle": "BMC Bioinformatics", "publisher": "", "place": "", "date": "2006", "volume": "7", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "471", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Bioinformatics", "DOI": "10.1186/1471-2105-7-471", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17062146", "accessDate": "2009-03-20T17:02:52Z", "PMID": "", "PMCID": "", "ISSN": "1471-2105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 17062146", "tags": [ { "tag": "Amino Acid Sequence", "type": 1 }, { "tag": "Computational biology", "type": 1 }, { "tag": "Computer Simulation", "type": 1 }, { "tag": "Databases, Protein", "type": 1 }, { "tag": "Gene Deletion", "type": 1 }, { "tag": "Mutation", "type": 1 }, { "tag": "Protein Conformation", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Sequence alignment", "type": 1 }, { "tag": "Software", "type": 1 } ], "collections": [ "7EV6NFV9" ], "relations": { "dc:replaces": "http://zotero.org/users/5379/items/DY3L653W" }, "dateAdded": "2009-03-20T17:02:52Z", "dateModified": "2019-08-02T18:21:01Z" } }, { "key": "BQQX5Q9Y", "version": 1742, "library": { "type": "user", "id": 5379, "name": "Paulo Nuin", "links": { "alternate": { "href": "https://www.zotero.org/nuin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/users/5379/items/BQQX5Q9Y", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/BQQX5Q9Y", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/N8TWDPMA", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "BQQX5Q9Y", "version": 1742, "parentItem": "N8TWDPMA", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2019-01-28T18:12:40Z", "url": "https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1000311&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Roux and Robinson-Rechavi - 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