[ { "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": "BVTMJYVK", "version": 2369, "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/BVTMJYVK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/BVTMJYVK", "type": "text/html" } }, "meta": { "creatorSummary": "Davis et al.", "parsedDate": "2022-02", "numChildren": 0 }, "data": { "key": "BVTMJYVK", "version": 2369, "itemType": "journalArticle", "title": "WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Paul", "lastName": "Davis" }, { "creatorType": "author", "firstName": "Magdalena", "lastName": "Zarowiecki" }, { "creatorType": "author", "firstName": "Valerio", "lastName": "Arnaboldi" }, { "creatorType": "author", "firstName": "Andrés", "lastName": "Becerra" }, { "creatorType": "author", "firstName": "Scott", "lastName": "Cain" }, { "creatorType": "author", "firstName": "Juancarlos", "lastName": "Chan" }, { "creatorType": "author", "firstName": "Wen J", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Jaehyoung", "lastName": "Cho" }, { "creatorType": "author", "firstName": "Eduardo", "lastName": "da Veiga Beltrame" }, { "creatorType": "author", "firstName": "Stavros", "lastName": "Diamantakis" }, { "creatorType": "author", "firstName": "Sibyl", "lastName": "Gao" }, { "creatorType": "author", "firstName": "Dionysis", "lastName": "Grigoriadis" }, { "creatorType": "author", "firstName": "Christian A", "lastName": "Grove" }, { "creatorType": "author", "firstName": "Todd W", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Ranjana", "lastName": "Kishore" }, { "creatorType": "author", "firstName": "Tuan", "lastName": "Le" }, { "creatorType": "author", "firstName": "Raymond Y N", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Manuel", "lastName": "Luypaert" }, { "creatorType": "author", "firstName": "Hans-Michael", "lastName": "Müller" }, { "creatorType": "author", "firstName": "Cecilia", "lastName": "Nakamura" }, { "creatorType": "author", "firstName": "Paulo", "lastName": "Nuin" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Paulini" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Quinton-Tulloch" }, { "creatorType": "author", "firstName": "Daniela", "lastName": "Raciti" }, { "creatorType": "author", "firstName": "Faye H", "lastName": "Rodgers" }, { "creatorType": "author", "firstName": "Matthew", "lastName": "Russell" }, { "creatorType": "author", "firstName": "Gary", "lastName": "Schindelman" }, { "creatorType": "author", "firstName": "Archana", "lastName": "Singh" }, { "creatorType": "author", "firstName": "Tim", "lastName": "Stickland" }, { "creatorType": "author", "firstName": "Kimberly", "lastName": "Van Auken" }, { "creatorType": "author", "firstName": "Qinghua", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Gary", "lastName": "Williams" }, { "creatorType": "author", "firstName": "Adam J", "lastName": "Wright" }, { "creatorType": "author", "firstName": "Karen", "lastName": "Yook" }, { "creatorType": "author", "firstName": "Matt", "lastName": "Berriman" }, { "creatorType": "author", "firstName": "Kevin L", "lastName": "Howe" }, { "creatorType": "author", "firstName": "Tim", "lastName": "Schedl" }, { "creatorType": "author", "firstName": "Lincoln", "lastName": "Stein" }, { "creatorType": "author", "firstName": "Paul W", "lastName": "Sternberg" } ], "abstractNote": "WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.", "publicationTitle": "Genetics", "publisher": "", "place": "", "date": "2022-02", "volume": "220", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "iyac003", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/genetics/iyac003", "citationKey": "", "url": "https://doi.org/10.1093/genetics/iyac003", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1943-2631", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "_eprint: https://academic.oup.com/genetics/article-pdf/220/4/iyac003/43256503/iyac003.pdf", "tags": [], "collections": [ "YBEY9V8Y" ], "relations": {}, "dateAdded": "2025-05-13T18:01:03Z", "dateModified": "2025-05-13T18:01:03Z" } }, { "key": "3GKYBX4I", "version": 2367, "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/3GKYBX4I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/3GKYBX4I", "type": "text/html" } }, "meta": { "creatorSummary": "Sefid Dashti and Gamieldien", "parsedDate": "2017", "numChildren": 0 }, "data": { "key": "3GKYBX4I", "version": 2367, "itemType": "journalArticle", "title": "A Practical Guide To Filtering and Prioritizing Genetic Variants", "creators": [ { "creatorType": "author", "firstName": "Mahjoubeh Jalali", "lastName": "Sefid Dashti" }, { "creatorType": "author", "firstName": "Junaid", "lastName": "Gamieldien" } ], "abstractNote": "", "publicationTitle": "BioTechniques", "publisher": "", "place": "", "date": "01/2017", "volume": "62", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "18-30", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BioTechniques", "DOI": "10.2144/000114492", "citationKey": "", "url": "https://www.tandfonline.com/doi/full/10.2144/000114492", "accessDate": "2025-01-14T02:13:08Z", "PMID": "", "PMCID": "", "ISSN": "0736-6205, 1940-9818", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-01-14T02:13:08Z", "dateModified": "2025-01-14T02:13:08Z" } }, { "key": "RAQNPWPL", "version": 2365, "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/RAQNPWPL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/RAQNPWPL", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/P6MEST57", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "RAQNPWPL", "version": 2365, "parentItem": "P6MEST57", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2025-01-14T02:11:45Z", "url": "https://www.nature.com/articles/s41598-022-06547-3.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Nicora et al. - 2022 - A machine learning approach based on ACMGAMP guid.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2025-01-14T02:11:45Z", "dateModified": "2025-01-14T02:11:45Z" } }, { "key": "P6MEST57", "version": 2364, "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/P6MEST57", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/P6MEST57", "type": "text/html" } }, "meta": { "creatorSummary": "Nicora et al.", "parsedDate": "2022-02-15", "numChildren": 1 }, "data": { "key": "P6MEST57", "version": 2364, "itemType": "journalArticle", "title": "A machine learning approach based on ACMG/AMP guidelines for genomic variant classification and prioritization", "creators": [ { "creatorType": "author", "firstName": "Giovanna", "lastName": "Nicora" }, { "creatorType": "author", "firstName": "Susanna", "lastName": "Zucca" }, { "creatorType": "author", "firstName": "Ivan", "lastName": "Limongelli" }, { "creatorType": "author", "firstName": "Riccardo", "lastName": "Bellazzi" }, { "creatorType": "author", "firstName": "Paolo", "lastName": "Magni" } ], "abstractNote": "Abstract\n Genomic variant interpretation is a critical step of the diagnostic procedure, often supported by the application of tools that may predict the damaging impact of each variant or provide a guidelines-based classification. We propose the application of Machine Learning methodologies, in particular Penalized Logistic Regression, to support variant classification and prioritization. Our approach combines ACMG/AMP guidelines for germline variant interpretation as well as variant annotation features and provides a probabilistic score of pathogenicity, thus supporting the prioritization and classification of variants that would be interpreted as uncertain by the ACMG/AMP guidelines. We compared different approaches in terms of variant prioritization and classification on different datasets, showing that our data-driven approach is able to solve more variant of uncertain significance (VUS) cases in comparison with guidelines-based approaches and in silico prediction tools.", "publicationTitle": "Scientific Reports", "publisher": "", "place": "", "date": "2022-02-15", "volume": "12", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "2517", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Sci Rep", "DOI": "10.1038/s41598-022-06547-3", "citationKey": "", "url": "https://www.nature.com/articles/s41598-022-06547-3", "accessDate": "2025-01-14T02:11:41Z", "PMID": "", "PMCID": "", "ISSN": "2045-2322", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-01-14T02:11:41Z", "dateModified": "2025-01-14T02:11:41Z" } }, { "key": "5HA6K24S", "version": 2362, "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/5HA6K24S", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/5HA6K24S", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/CFRAKTWK", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "5HA6K24S", "version": 2362, "parentItem": "CFRAKTWK", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2023-02-06T17:08:57Z", "url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009785&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Melidis et al. - 2022 - GenOtoScope Towards automating ACMG classificatio.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2023-02-06T17:08:57Z", "dateModified": "2023-02-06T17:08:57Z" } }, { "key": "CFRAKTWK", "version": 2362, "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/CFRAKTWK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/CFRAKTWK", "type": "text/html" } }, "meta": { "creatorSummary": "Melidis et al.", "parsedDate": "2022-09-21", "numChildren": 1 }, "data": { "key": "CFRAKTWK", "version": 2362, "itemType": "journalArticle", "title": "GenOtoScope: Towards automating ACMG classification of variants associated with congenital hearing loss", "creators": [ { "creatorType": "author", "firstName": "Damianos P.", "lastName": "Melidis" }, { "creatorType": "author", "firstName": "Christian", "lastName": "Landgraf" }, { "creatorType": "author", "firstName": "Gunnar", "lastName": "Schmidt" }, { "creatorType": "author", "firstName": "Anja", "lastName": "Schöner-Heinisch" }, { "creatorType": "author", "firstName": "Sandra", "lastName": "von Hardenberg" }, { "creatorType": "author", "firstName": "Anke", "lastName": "Lesinski-Schiedat" }, { "creatorType": "author", "firstName": "Wolfgang", "lastName": "Nejdl" }, { "creatorType": "author", "firstName": "Bernd", "lastName": "Auber" }, { "creatorType": "editor", "firstName": "Dina", "lastName": "Schneidman-Duhovny" } ], "abstractNote": "Since next-generation sequencing (NGS) has become widely available, large gene panels containing up to several hundred genes can be sequenced cost-efficiently. However, the interpretation of the often large numbers of sequence variants detected when using NGS is laborious, prone to errors and is often difficult to compare across laboratories. To overcome this challenge, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have introduced standards and guidelines for the interpretation of sequencing variants. Additionally, disease-specific refinements have been developed that include accurate thresholds for many criteria, enabling highly automated processing. This is of particular interest for common but heterogeneous disorders such as hearing impairment. With more than 200 genes associated with hearing disorders, the manual inspection of possible causative variants is particularly difficult and time-consuming.\n \n To this end, we developed the open-source bioinformatics tool\n GenOtoScope\n , which automates the analysis of all ACMG/AMP criteria that can be assessed without further individual patient information or human curator investigation, including the refined loss of function criterion (“PVS1”). Two types of interfaces are provided: (i) a command line application to classify sequence variants in batches for a set of patients and (ii) a user-friendly website to classify single variants.\n \n \n We compared the performance of our tool with two other variant classification tools using two hearing loss data sets, which were manually annotated either by the ClinGen Hearing Loss Gene Curation Expert Panel or the diagnostics unit of our human genetics department.\n GenOtoScope\n achieved the best average accuracy and precision for both data sets. Compared to the second-best tool,\n GenOtoScope\n improved the accuracy metric by 25.75% and 4.57% and precision metric by 52.11% and 12.13% on the two data sets, respectively. The web interface is accessible via:\n http://genotoscope.mh-hannover.de:5000\n and the command line interface via:\n https://github.com/damianosmel/GenOtoScope\n .", "publicationTitle": "PLOS Computational Biology", "publisher": "", "place": "", "date": "2022-9-21", "volume": "18", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "e1009785", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS Comput Biol", "DOI": "10.1371/journal.pcbi.1009785", "citationKey": "", "url": "https://dx.plos.org/10.1371/journal.pcbi.1009785", "accessDate": "2023-02-06T17:08:55Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "GenOtoScope", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-02-06T17:08:55Z", "dateModified": "2023-02-06T17:08:55Z" } }, { "key": "KVF9LSHT", "version": 2360, "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/KVF9LSHT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/KVF9LSHT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/FXJMJCTI", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "KVF9LSHT", "version": 2360, "parentItem": "FXJMJCTI", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2023-02-06T16:59:24Z", "url": "https://academic.oup.com/bioinformatics/article-pdf/36/24/5709/36899411/btaa943.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Benevenuta et al. - 2021 - Calibrating variant-scoring methods for clinical d.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2023-02-06T16:59:24Z", "dateModified": "2023-02-06T16:59:24Z" } }, { "key": "FXJMJCTI", "version": 2359, "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/FXJMJCTI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/FXJMJCTI", "type": "text/html" } }, "meta": { "creatorSummary": "Benevenuta et al.", "parsedDate": "2021-04-05", "numChildren": 1 }, "data": { "key": "FXJMJCTI", "version": 2359, "itemType": "journalArticle", "title": "Calibrating variant-scoring methods for clinical decision making", "creators": [ { "creatorType": "author", "firstName": "Silvia", "lastName": "Benevenuta" }, { "creatorType": "author", "firstName": "Emidio", "lastName": "Capriotti" }, { "creatorType": "author", "firstName": "Piero", "lastName": "Fariselli" }, { "creatorType": "editor", "firstName": "Alfonso", "lastName": "Valencia" } ], "abstractNote": "Abstract\n \n Summary\n Identifying pathogenic variants and annotating them is a major challenge in human genetics, especially for the non-coding ones. Several tools have been developed and used to predict the functional effect of genetic variants. However, the calibration assessment of the predictions has received little attention. Calibration refers to the idea that if a model predicts a group of variants to be pathogenic with a probability P, it is expected that the same fraction P of true positive is found in the observed set. For instance, a well-calibrated classifier should label the variants such that among the ones to which it gave a probability value close to 0.7, approximately 70% actually belong to the pathogenic class. Poorly calibrated algorithms can be misleading and potentially harmful for clinical decision making.\n \n \n Avaliability and implementation\n The dataset used for testing the methods is available through the DOI:10.5281/zenodo.4448197.\n \n \n Supplementary information\n Supplementary data are available at Bioinformatics online.", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "2021-04-05", "volume": "36", "issue": "24", "section": "", "partNumber": "", "partTitle": "", "pages": "5709-5711", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bioinformatics/btaa943", "citationKey": "", "url": "https://academic.oup.com/bioinformatics/article/36/24/5709/6119340", "accessDate": "2023-02-06T16:59:20Z", "PMID": "", "PMCID": "", "ISSN": "1367-4803, 1460-2059", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-02-06T16:59:20Z", "dateModified": "2023-02-06T16:59:20Z" } }, { "key": "6RDX73ZQ", "version": 2357, "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/6RDX73ZQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/6RDX73ZQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/8MJG9D4C", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "6RDX73ZQ", "version": 2357, "parentItem": "8MJG9D4C", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T18:03:28Z", "url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006080&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Samadian et al. - 2018 - Bamgineer Introduction of simulated allele-specif.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T18:03:28Z", "dateModified": "2023-02-06T16:44:26Z" } }, { "key": "4F9XTPNZ", "version": 2357, "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/4F9XTPNZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/4F9XTPNZ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/8MJG9D4C", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "4F9XTPNZ", "version": 2357, "parentItem": "8MJG9D4C", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T18:02:03Z", "url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006080&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Samadian et al. - 2018 - Bamgineer Introduction of simulated allele-specif.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T18:02:03Z", "dateModified": "2023-02-06T16:44:26Z" } }, { "key": "8MJG9D4C", "version": 2357, "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/8MJG9D4C", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/8MJG9D4C", "type": "text/html" } }, "meta": { "creatorSummary": "Samadian et al.", "parsedDate": "2018-03-28", "numChildren": 4 }, "data": { "key": "8MJG9D4C", "version": 2357, "itemType": "journalArticle", "title": "Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets", "creators": [ { "creatorType": "author", "firstName": "Soroush", "lastName": "Samadian" }, { "creatorType": "author", "firstName": "Jeff P.", "lastName": "Bruce" }, { "creatorType": "author", "firstName": "Trevor J.", "lastName": "Pugh" } ], "abstractNote": "Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20–100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.", "publicationTitle": "PLOS Computational Biology", "publisher": "", "place": "", "date": "Mar 28, 2018", "volume": "14", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "e1006080", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1006080", "citationKey": "", "url": "http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006080", "accessDate": "2018-04-16T19:48:22Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "Bamgineer", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Alleles", "type": 1 }, { "tag": "Copy number variation", "type": 1 }, { "tag": "DNA sequence analysis", "type": 1 }, { "tag": "DNA sequencing", "type": 1 }, { "tag": "Genome analysis", "type": 1 }, { "tag": "Haplotypes", "type": 1 }, { "tag": "Molecular genetics", "type": 1 }, { "tag": "Sequence alignment", "type": 1 } ], "collections": [], "relations": { "dc:replaces": [ "http://zotero.org/users/5379/items/D7Y4EF5B", "http://zotero.org/users/5379/items/S74JWX5G" ] }, "dateAdded": "2018-04-16T19:48:22Z", "dateModified": "2023-02-06T16:44:26Z" } }, { "key": "MKT5TRIV", "version": 2357, "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/MKT5TRIV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/MKT5TRIV", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/K7JKXQPM", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "MKT5TRIV", "version": 2357, "parentItem": "K7JKXQPM", "itemType": "attachment", "linkMode": "imported_url", "title": "Submitted Version", "accessDate": "2023-02-06T16:43:32Z", "url": "https://www.biorxiv.org/content/biorxiv/early/2018/06/18/348565.full.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Heldenbrand et al. - 2018 - Performance benchmarking of GATK3.8 and GATK4.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2023-02-06T16:43:32Z", "dateModified": "2023-02-06T16:43:32Z" } }, { "key": "K7JKXQPM", "version": 2357, "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/K7JKXQPM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/K7JKXQPM", "type": "text/html" } }, "meta": { "creatorSummary": "Heldenbrand et al.", "parsedDate": "2018-06-18", "numChildren": 1 }, "data": { "key": "K7JKXQPM", "version": 2357, "itemType": "report", "title": "Performance benchmarking of GATK3.8 and GATK4", "creators": [ { "creatorType": "author", "firstName": "Jacob R.", "lastName": "Heldenbrand" }, { "creatorType": "author", "firstName": "Saurabh", "lastName": "Baheti" }, { "creatorType": "author", "firstName": "Matthew A.", "lastName": "Bockol" }, { "creatorType": "author", "firstName": "Travis M.", "lastName": "Drucker" }, { "creatorType": "author", "firstName": "Steven N.", "lastName": "Hart" }, { "creatorType": "author", "firstName": "Matthew E.", "lastName": "Hudson" }, { "creatorType": "author", "firstName": "Ravishankar K.", "lastName": "Iyer" }, { "creatorType": "author", "firstName": "Michael T.", "lastName": "Kalmbach" }, { "creatorType": "author", "firstName": "Eric W.", "lastName": "Klee" }, { "creatorType": "author", "firstName": "Eric D.", "lastName": "Wieben" }, { "creatorType": "author", "firstName": "Mathieu", "lastName": "Wiepert" }, { "creatorType": "author", "firstName": "Derek E.", "lastName": "Wildman" }, { "creatorType": "author", "firstName": "Liudmila S.", "lastName": "Mainzer" } ], "abstractNote": "Abstract\n Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computational performance improvements have been introduced in GATK3.8 through collaboration with Intel in 2017. The first release of GATK4 in early 2018 revealed significant rewrites in the code base, as the stepping stone toward a Spark implementation. As the software continues to be a moving target for optimal deployment in highly productive environments, we present a detailed analysis of these improvements, to help the community stay abreast with changes in performance. We re-evaluated the options previously identified as advantageous, such as threading, parallel garbage collection, I/O options and data-level parallelization. Based on our results, we consider the performance and cost trade-offs of using GATK3.8 and GATK4 for different types of analyses.", "reportNumber": "", "reportType": "preprint", "institution": "Bioinformatics", "place": "", "date": "2018-06-18", "seriesTitle": "", "seriesNumber": "", "pages": "", "DOI": "", "ISBN": "", "citationKey": "", "url": "http://biorxiv.org/lookup/doi/10.1101/348565", "accessDate": "2023-02-06T16:43:25Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "DOI: 10.1101/348565", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-02-06T16:43:25Z", "dateModified": "2023-02-06T16:43:25Z" } }, { "key": "W3LRI2FB", "version": 2355, "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/W3LRI2FB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/W3LRI2FB", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/HUQQQAFY", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "W3LRI2FB", "version": 2355, "parentItem": "HUQQQAFY", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T18:46:12Z", "url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008984&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Abeysooriya et al. - 2021 - Gene name errors Lessons not learned.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T18:46:12Z", "dateModified": "2022-09-21T18:46:12Z" } }, { "key": "HUQQQAFY", "version": 2355, "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/HUQQQAFY", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/HUQQQAFY", "type": "text/html" } }, "meta": { "creatorSummary": "Abeysooriya et al.", "parsedDate": "2021-07-30", "numChildren": 1 }, "data": { "key": "HUQQQAFY", "version": 2355, "itemType": "journalArticle", "title": "Gene name errors: Lessons not learned", "creators": [ { "creatorType": "author", "firstName": "Mandhri", "lastName": "Abeysooriya" }, { "creatorType": "author", "firstName": "Megan", "lastName": "Soria" }, { "creatorType": "author", "firstName": "Mary Sravya", "lastName": "Kasu" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Ziemann" }, { "creatorType": "editor", "firstName": "Christos A.", "lastName": "Ouzounis" } ], "abstractNote": "Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% (3,436/11,117) of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.", "publicationTitle": "PLOS Computational Biology", "publisher": "", "place": "", "date": "2021-7-30", "volume": "17", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "e1008984", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS Comput Biol", "DOI": "10.1371/journal.pcbi.1008984", "citationKey": "", "url": "https://dx.plos.org/10.1371/journal.pcbi.1008984", "accessDate": "2022-09-21T18:46:09Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "Gene name errors", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-09-21T18:46:09Z", "dateModified": "2022-09-21T18:46:09Z" } }, { "key": "SSPHRAG4", "version": 2353, "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/SSPHRAG4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/SSPHRAG4", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/99TUBYL9", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "SSPHRAG4", "version": 2353, "parentItem": "99TUBYL9", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T18:03:04Z", "url": "https://www.frontiersin.org/articles/10.3389/fonc.2019.00851/pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Petrackova et al. - 2019 - Standardization of Sequencing Coverage Depth in NG.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T18:03:04Z", "dateModified": "2022-09-21T18:03:04Z" } }, { "key": "99TUBYL9", "version": 2353, "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/99TUBYL9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/99TUBYL9", "type": "text/html" } }, "meta": { "creatorSummary": "Petrackova et al.", "parsedDate": "2019-09-04", "numChildren": 1 }, "data": { "key": "99TUBYL9", "version": 2353, "itemType": "journalArticle", "title": "Standardization of Sequencing Coverage Depth in NGS: Recommendation for Detection of Clonal and Subclonal Mutations in Cancer Diagnostics", "creators": [ { "creatorType": "author", "firstName": "Anna", "lastName": "Petrackova" }, { "creatorType": "author", "firstName": "Michal", "lastName": "Vasinek" }, { "creatorType": "author", "firstName": "Lenka", "lastName": "Sedlarikova" }, { "creatorType": "author", "firstName": "Tereza", "lastName": "Dyskova" }, { "creatorType": "author", "firstName": "Petra", "lastName": "Schneiderova" }, { "creatorType": "author", "firstName": "Tomas", "lastName": "Novosad" }, { "creatorType": "author", "firstName": "Tomas", "lastName": "Papajik" }, { "creatorType": "author", "firstName": "Eva", "lastName": "Kriegova" } ], "abstractNote": "", "publicationTitle": "Frontiers in Oncology", "publisher": "", "place": "", "date": "2019-9-4", "volume": "9", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "851", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Front. Oncol.", "DOI": "10.3389/fonc.2019.00851", "citationKey": "", "url": "https://www.frontiersin.org/article/10.3389/fonc.2019.00851/full", "accessDate": "2022-09-21T18:02:58Z", "PMID": "", "PMCID": "", "ISSN": "2234-943X", "archive": "", "archiveLocation": "", "shortTitle": "Standardization of Sequencing Coverage Depth in NGS", "language": "", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-09-21T18:02:58Z", "dateModified": "2022-09-21T18:02:58Z" } }, { "key": "TBEMT98X", "version": 2353, "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/TBEMT98X", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/TBEMT98X", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/YGQYZKHL", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "TBEMT98X", "version": 2353, "parentItem": "YGQYZKHL", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T18:02:49Z", "url": "https://academic.oup.com/gigascience/article-pdf/7/7/giy081/25205161/giy081.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Xia et al. - 2018 - SVEngine an efficient and versatile simulator of .pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T18:02:49Z", "dateModified": "2022-09-21T18:02:49Z" } }, { "key": "YGQYZKHL", "version": 2353, "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/YGQYZKHL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/YGQYZKHL", "type": "text/html" } }, "meta": { "creatorSummary": "Xia et al.", "parsedDate": "2018-07-01", "numChildren": 1 }, "data": { "key": "YGQYZKHL", "version": 2353, "itemType": "journalArticle", "title": "SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution", "creators": [ { "creatorType": "author", "firstName": "Li Charlie", "lastName": "Xia" }, { "creatorType": "author", "firstName": "Dongmei", "lastName": "Ai" }, { "creatorType": "author", "firstName": "Hojoon", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Noemi", "lastName": "Andor" }, { "creatorType": "author", "firstName": "Chao", "lastName": "Li" }, { "creatorType": "author", "firstName": "Nancy R", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Hanlee P", "lastName": "Ji" } ], "abstractNote": "", "publicationTitle": "GigaScience", "publisher": "", "place": "", "date": "2018-07-01", "volume": "7", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/gigascience/giy081", "citationKey": "", "url": "https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giy081/5049476", "accessDate": "2022-09-21T18:02:29Z", "PMID": "", "PMCID": "", "ISSN": "2047-217X", "archive": "", "archiveLocation": "", "shortTitle": "SVEngine", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-09-21T18:02:29Z", "dateModified": "2022-09-21T18:02:29Z" } }, { "key": "3QHH6H4Q", "version": 2349, "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/3QHH6H4Q", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/3QHH6H4Q", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/X49DGGQ4", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "3QHH6H4Q", "version": 2349, "parentItem": "X49DGGQ4", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T17:44:44Z", "url": "https://jmd.amjpathol.org/article/S1525157817302076/pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Kerkhof et al. - 2017 - Clinical Validation of Copy Number Variant Detecti.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T17:44:44Z", "dateModified": "2022-09-21T17:44:44Z" } }, { "key": "X49DGGQ4", "version": 2349, "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/X49DGGQ4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/X49DGGQ4", "type": "text/html" } }, "meta": { "creatorSummary": "Kerkhof et al.", "parsedDate": "2017", "numChildren": 1 }, "data": { "key": "X49DGGQ4", "version": 2349, "itemType": "journalArticle", "title": "Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels", "creators": [ { "creatorType": "author", "firstName": "Jennifer", "lastName": "Kerkhof" }, { "creatorType": "author", "firstName": "Laila C.", "lastName": "Schenkel" }, { "creatorType": "author", "firstName": "Jack", "lastName": "Reilly" }, { "creatorType": "author", "firstName": "Sheri", "lastName": "McRobbie" }, { "creatorType": "author", "firstName": "Erfan", "lastName": "Aref-Eshghi" }, { "creatorType": "author", "firstName": "Alan", "lastName": "Stuart" }, { "creatorType": "author", "firstName": "C. Anthony", "lastName": "Rupar" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Adams" }, { "creatorType": "author", "firstName": "Robert A.", "lastName": "Hegele" }, { "creatorType": "author", "firstName": "Hanxin", "lastName": "Lin" }, { "creatorType": "author", "firstName": "David", "lastName": "Rodenhiser" }, { "creatorType": "author", "firstName": "Joan", "lastName": "Knoll" }, { "creatorType": "author", "firstName": "Peter J.", "lastName": "Ainsworth" }, { "creatorType": "author", "firstName": "Bekim", "lastName": "Sadikovic" } ], "abstractNote": "", "publicationTitle": "The Journal of Molecular Diagnostics", "publisher": "", "place": "", "date": "11/2017", "volume": "19", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "905-920", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "The Journal of Molecular Diagnostics", "DOI": "10.1016/j.jmoldx.2017.07.004", "citationKey": "", "url": "https://linkinghub.elsevier.com/retrieve/pii/S1525157817302076", "accessDate": "2022-09-21T17:44:41Z", "PMID": "", "PMCID": "", "ISSN": "15251578", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-09-21T17:44:41Z", "dateModified": "2022-09-21T17:44:41Z" } }, { "key": "P77UPIGL", "version": 2349, "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/P77UPIGL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/P77UPIGL", "type": "text/html" }, "up": { "href": "https://api.zotero.org/users/5379/items/LHKHWZLL", "type": "application/json" } }, "meta": { "numChildren": false }, "data": { "key": "P77UPIGL", "version": 2349, "parentItem": "LHKHWZLL", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2022-09-21T17:44:22Z", "url": "https://www.jmdjournal.org/article/S1525157817303185/pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Zenagui et al. - 2018 - A Reliable Targeted Next-Generation Sequencing Str.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2022-09-21T17:44:22Z", "dateModified": "2022-09-21T17:44:22Z" } }, { "key": "LHKHWZLL", "version": 2349, "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/LHKHWZLL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/nuin/items/LHKHWZLL", "type": "text/html" } }, "meta": { "creatorSummary": "Zenagui et al.", "parsedDate": "2018", "numChildren": 1 }, "data": { "key": "LHKHWZLL", "version": 2349, "itemType": "journalArticle", "title": "A Reliable Targeted Next-Generation Sequencing Strategy for Diagnosis of Myopathies and Muscular Dystrophies, Especially for the Giant Titin and Nebulin Genes", "creators": [ { "creatorType": "author", "firstName": "Reda", "lastName": "Zenagui" }, { "creatorType": "author", "firstName": "Delphine", "lastName": "Lacourt" }, { "creatorType": "author", "firstName": "Henri", "lastName": "Pegeot" }, { "creatorType": "author", "firstName": "Kevin", "lastName": "Yauy" }, { "creatorType": "author", "firstName": "Raul", "lastName": "Juntas Morales" }, { "creatorType": "author", "firstName": "Corine", "lastName": "Theze" }, { "creatorType": "author", "firstName": "François", "lastName": "Rivier" }, { "creatorType": "author", "firstName": "Claude", "lastName": "Cances" }, { "creatorType": "author", "firstName": "Guilhem", "lastName": "Sole" }, { "creatorType": "author", "firstName": "Dimitri", "lastName": "Renard" }, { "creatorType": "author", "firstName": "Ulrike", "lastName": "Walther-Louvier" }, { "creatorType": "author", "firstName": "Xavier", "lastName": "Ferrer-Monasterio" }, { "creatorType": "author", "firstName": "Caroline", "lastName": "Espil" }, { "creatorType": "author", "firstName": "Marie-Christine", "lastName": "Arné-Bes" }, { "creatorType": "author", "firstName": "Pascal", "lastName": "Cintas" }, { "creatorType": "author", "firstName": "Emmanuelle", "lastName": "Uro-Coste" }, { "creatorType": "author", "firstName": "Marie-Laure", "lastName": "Martin Negrier" }, { "creatorType": "author", "firstName": "Valérie", "lastName": "Rigau" }, { "creatorType": "author", "firstName": "Eric", "lastName": "Bieth" }, { "creatorType": "author", "firstName": "Cyril", "lastName": "Goizet" }, { "creatorType": "author", "firstName": "Mireille", "lastName": "Claustres" }, { "creatorType": "author", "firstName": "Michel", "lastName": "Koenig" }, { "creatorType": "author", "firstName": "Mireille", "lastName": "Cossée" } ], "abstractNote": "", "publicationTitle": "The Journal of Molecular Diagnostics", "publisher": "", "place": "", "date": "07/2018", "volume": "20", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "533-549", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "The Journal of Molecular Diagnostics", "DOI": "10.1016/j.jmoldx.2018.04.001", "citationKey": "", "url": "https://linkinghub.elsevier.com/retrieve/pii/S1525157817303185", "accessDate": "2022-09-21T17:44:18Z", "PMID": "", "PMCID": "", "ISSN": "15251578", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2022-09-21T17:44:18Z", "dateModified": "2022-09-21T17:44:18Z" } } ]