{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,3]],"date-time":"2024-04-03T13:51:08Z","timestamp":1712152268214},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Algorithms for sparse data require fast search and subset selection capabilities for the determination of point neighborhoods. A natural data representation for such cases are space partitioning data structures. However, the associated range queries assume noise-free observations and cannot take into account observation-specific uncertainty estimates that are present in e.g. modern mass spectrometry data. In order to accommodate the inhomogeneous noise characteristics of sparse real-world datasets, point queries need to be reformulated in terms of box intersection queries, where box sizes correspond to uncertainty regions for each observation.<\/jats:p>\n               <jats:p>Results: This contribution introduces libfbi, a standard C++, header-only template implementation for fast box intersection in an arbitrary number of dimensions, with arbitrary data types in each dimension. The implementation is applied to a data aggregation task on state-of-the-art liquid chromatography\/mass spectrometry data, where it shows excellent run time properties.<\/jats:p>\n               <jats:p>Availability: The library is available under an MIT license and can be downloaded from http:\/\/software.steenlab.org\/libfbi.<\/jats:p>\n               <jats:p>Contact: \u00a0marc.kirchner@childrens.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr084","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T01:18:15Z","timestamp":1297991895000},"page":"1166-1167","source":"Crossref","is-referenced-by-count":5,"title":["libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data"],"prefix":"10.1093","volume":"27","author":[{"given":"Marc","family":"Kirchner","sequence":"first","affiliation":[{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Buote","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanno","family":"Steen","sequence":"additional","affiliation":[{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judith A. J.","family":"Steen","sequence":"additional","affiliation":[{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"},{"name":"1 Proteomics Center, Children's Hospital Boston, 2Department of Pathology, Children's Hospital Boston, 3Department of Pathology, Harvard Medical School and 4Department of Neurobiology, Harvard Medical School and T. M. Kirby Neurobiology Center, Children's Hospital, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,2,16]]},"reference":[{"key":"2023061311474703900_B1","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"Maxquant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2023061311474703900_B2","doi-asserted-by":"crossref","first-page":"15544","DOI":"10.1073\/pnas.0904100106","article-title":"Protein quantification across hundreds of experimental conditions","volume":"106","author":"Khan","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023061311474703900_B3","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1145\/336154.336192","article-title":"Fast software for box intersections","volume-title":"SCG '00: Proceedings of the sixteenth annual symposium on Computational geometry","author":"Zomorodian","year":"2000"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1166\/50580361\/bioinformatics_27_8_1166.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1166\/50580361\/bioinformatics_27_8_1166.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T11:49:33Z","timestamp":1686656973000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/8\/1166\/227746"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,16]]},"references-count":3,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2011,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr084","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,4,15]]},"published":{"date-parts":[[2011,2,16]]}}}