CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

Fiona S. L. Brinkman https://orcid.org/0000-0002-0584-4099 https://www.wikidata.org/entity/Q57237122 https://www.researcherid.com/rid/N-3195-2013

Brian P. Alcock William Huynh Romeo Chalil Keaton W. Smith Amogelang R. Raphenya Mateusz A. Wlodarski Arman Edalatmand Aaron J. Petkau Sohaib A. Syed Kara K. Tsang Sheridan J. C. Baker Mugdha Dave Madeline C. McCarthy Karyn M. Mukiri Jalees A. Nasir Bahar Golbon Hamna Imtiaz Xingjian Jiang Komal Kaur Megan Kwong Zi Cheng Liang Keyu C. Niu Prabakar Shan Jasmine Y. J. Yang Kristen L. Gray Gemma Hoad Baofeng Jia Timsy Bhando Lindsey A. Carfrae Maya A. Farha Shawn French Rodion Gordzevich Kenneth Rachwalski Megan M. Tu Emily Bordeleau Damion M. Dooley Emma J. Griffiths Haley L. Zubyk Eric D. Brown Finlay Maguire Robert G. Beiko William W. L. Hsiao Fiona S. L. Brinkman Gary H. Van Domselaar Andrew G. McArthur CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. 690-699 2023 January 51 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkac920 db/journals/nar/nar51.html#AlcockHCSRWEPSTBDMMNGIJKKLNSYGHJBCF23

Wing Yin Venus Lau Gemma Hoad Vivian Jin Geoffrey L. Winsor Ashmeet Madyan Kristen L. Gray Matthew R. Laird Raymond Lo Fiona S. L. Brinkman PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations. D803-D808 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa1095 https://www.wikidata.org/entity/Q104465159 db/journals/nar/nar49.html#LauHJWMGLLB21

Michael A. Peabody Wing Yin Venus Lau Gemma Hoad Baofeng Jia Finlay Maguire Kristen L. Gray Robert G. Beiko Fiona S. L. Brinkman PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. 3043-3048 2020 36 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btaa136 https://www.wikidata.org/entity/Q89934134 db/journals/bioinformatics/bioinformatics36.html#PeabodyLHJMGBB20

Brian P. Alcock Amogelang R. Raphenya Tammy T. Y. Lau Kara K. Tsang Mégane Bouchard Arman Edalatmand William Huynh Anna-Lisa V. Nguyen Annie A. Cheng Sihan Liu Sally Y. Min Anatoly Miroshnichenko Hiu-Ki Tran Rafik E. Werfalli Jalees A. Nasir Martins Oloni David J. Speicher Alexandra Florescu Bhavya Singh Mateusz Faltyn Anastasia Hernández-Koutoucheva Arjun N. Sharma Emily Bordeleau Andrew C. Pawlowski Haley L. Zubyk Damion M. Dooley Emma J. Griffiths Finlay Maguire Geoffrey L. Winsor Robert G. Beiko Fiona S. L. Brinkman William W. L. Hsiao Gary H. Van Domselaar Andrew G. McArthur CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. D517-D525 2020 48 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkz935 https://www.wikidata.org/entity/Q91006744 db/journals/nar/nar48.html#AlcockRLTBEHNCL20

Claire Bertelli Keith E. Tilley Fiona S. L. Brinkman Microbial genomic island discovery, visualization and analysis. 1685-1698 2019 20 Briefings Bioinform. 5 https://doi.org/10.1093/bib/bby042 https://www.wikidata.org/entity/Q88990080 db/journals/bib/bib20.html#BertelliTB19

Claire Bertelli Fiona S. L. Brinkman Improved genomic island predictions with IslandPath-DIMOB. 2161-2167 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty095 https://www.wikidata.org/entity/Q55493301 db/journals/bioinformatics/bioinformatics34.html#BertelliB18

Baofeng Jia Amogelang R. Raphenya Brian P. Alcock Nicholas Waglechner Peiyao Guo Kara K. Tsang Briony A. Lago Biren M. Dave Sheldon K. Pereira Arjun N. Sharma Sachin Doshi Mélanie Courtot Raymond Lo Laura E. Williams Jonathan G. Frye Tariq Elsayegh Daim Sardar Erin L. Westman Andrew C. Pawlowski Timothy A. Johnson Fiona S. L. Brinkman Gerard D. Wright Andrew G. McArthur CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. D566-D573 2017 45 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkw1004 https://www.wikidata.org/entity/Q28584458 db/journals/nar/nar45.html#JiaRAWGTLDPSDCL17

Claire Bertelli Matthew R. Laird Kelly P. Williams Britney Y. Lau Gemma Hoad Geoffrey L. Winsor Fiona S. L. Brinkman IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. W30-W35 2017 45 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkx343 https://www.wikidata.org/entity/Q41511954 db/journals/nar/nar45.html#BertelliLWLHWB17

Dalia A. Alghamdi Damion M. Dooley Gurinder Gosal Emma J. Griffiths Fiona S. L. Brinkman William W. L. Hsiao FoodOn: A Semantic Ontology Approach for Mapping Foodborne Disease Metadata. 2017 ICBO https://ceur-ws.org/Vol-2137/paper_32.pdf conf/icbo/2017 db/conf/icbo/icbo2017.html#AlghamdiDGGBH17 Damion M. Dooley Emma J. Griffiths Gurinder Gosal Fiona S. L. Brinkman William W. L. Hsiao The Genomic Epidemiology Ontology and GEEM Ontology Reusability Platform. 2017 JOWO https://ceur-ws.org/Vol-2050/ODLS_paper_12.pdf conf/jowo/2017 db/conf/jowo/jowo2017.html#DooleyGGBH17

Geoffrey L. Winsor Emma J. Griffiths Raymond Lo Bhavjinder K. Dhillon Julie A. Shay Fiona S. L. Brinkman Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. 646-653 2016 44 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkv1227 https://www.wikidata.org/entity/Q36434832 db/journals/nar/nar44.html#WinsorGLDSB16

Michael A. Peabody Matthew R. Laird Caitlyn Vlasschaert Raymond Lo Fiona S. L. Brinkman PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. 663-668 2016 44 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkv1271 https://www.wikidata.org/entity/Q36434943 db/journals/nar/nar44.html#PeabodyLVLB16

Damion M. Dooley Emma J. Griffiths Fiona S. L. Brinkman William W. L. Hsiao An OBI Ontology Datum Proof Sheet. 2016 ICBO/BioCreative https://ceur-ws.org/Vol-1747/IP24_ICBO2016.pdf conf/icbo/2016 db/conf/icbo/icbo2016.html#DooleyGBH16 Emma J. Griffiths Damion M. Dooley Pier Luigi Buttigieg Robert Hoehndorf Fiona S. L. Brinkman William W. L. Hsiao FoodON: A Global Farm-to-Fork Food Ontology. 2016 ICBO/BioCreative https://ceur-ws.org/Vol-1747/IP21_ICBO2016.pdf conf/icbo/2016 db/conf/icbo/icbo2016.html#GriffithsDBHBH16

Silvia Frias Kenneth Bryan Fiona S. L. Brinkman David J. Lynn CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. 2015 2015 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bav041 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423409/ https://www.wikidata.org/entity/Q40394437 db/journals/biodb/biodb2015.html#FriasBBL15

Matthew R. Laird Morgan G. I. Langille Fiona S. L. Brinkman GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. 3348-3349 2015 31 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btv376 https://www.wikidata.org/entity/Q30975514 db/journals/bioinformatics/bioinformatics31.html#LairdLB15

Michael A. Peabody Thea Van Rossum Raymond Lo Fiona S. L. Brinkman Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. 362:1-362:19 2015 16 BMC Bioinform. https://doi.org/10.1186/s12859-015-0788-5 https://www.wikidata.org/entity/Q35832785 db/journals/bmcbi/bmcbi16.html#PeabodyRLB15

Bhavjinder K. Dhillon Matthew R. Laird Julie A. Shay Geoffrey L. Winsor Raymond Lo Fazmin Nizam Sheldon K. Pereira Nicholas Waglechner Andrew G. McArthur Morgan G. I. Langille Fiona S. L. Brinkman IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. W104-W108 2015 43 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkv401 https://www.wikidata.org/entity/Q41282214 db/journals/nar/nar43.html#DhillonLSWLNPWM15

Matthew D. Whiteside Geoffrey L. Winsor Matthew R. Laird Fiona S. L. Brinkman OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. 366-376 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1241 https://www.wikidata.org/entity/Q36491365 db/journals/nar/nar41.html#WhitesideWLB13

Karin Breuer Amir K. Foroushani Matthew R. Laird Carol Chen Anastasia Sribnaia Raymond Lo Geoffrey L. Winsor Robert E. W. Hancock Fiona S. L. Brinkman David J. Lynn InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. 1228-1233 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1147 https://www.wikidata.org/entity/Q36491232 db/journals/nar/nar41.html#BreuerFLCSLWHBL13

Bhavjinder K. Dhillon Terry A. Chiu Matthew R. Laird Morgan G. I. Langille Fiona S. L. Brinkman IslandViewer update: improved genomic island discovery and visualization. 129-132 2013 41 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkt394 https://www.wikidata.org/entity/Q36953918 db/journals/nar/nar41.html#DhillonCLLB13

Morgan G. I. Langille Matthew R. Laird William W. L. Hsiao Terry A. Chiu Jonathan A. Eisen Fiona S. L. Brinkman MicrobeDB: a locally maintainable database of microbial genomic sequences. 1947-1948 2012 28 Bioinform. 14 https://doi.org/10.1093/bioinformatics/bts273 https://www.wikidata.org/entity/Q36076310 db/journals/bioinformatics/bioinformatics28.html#LangilleLHCEB12

Jeong Eun Min Matthew D. Whiteside Fiona S. L. Brinkman Brad McNeney Jinko Graham A statistical approach to high-throughput screening of predicted orthologs. 935-943 2011 55 Comput. Stat. Data Anal. 1 https://doi.org/10.1016/j.csda.2010.08.002 db/journals/csda/csda55.html#MinWBMG11

Nancy Y. Yu Matthew R. Laird Cory Spencer Fiona S. L. Brinkman PSORTdb - an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. 241-244 2011 39 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkq1093 https://www.wikidata.org/entity/Q34149332 db/journals/nar/nar39.html#YuLSB11

Geoffrey L. Winsor David K. W. Lam Leanne Fleming Raymond Lo Matthew D. Whiteside Nancy Y. Yu Robert E. W. Hancock Fiona S. L. Brinkman Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. 596-600 2011 39 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkq869 https://www.wikidata.org/entity/Q24609340 db/journals/nar/nar39.html#WinsorLFLWYHB11

Nancy Y. Yu James R. Wagner Matthew R. Laird Gabor Melli Sébastien Rey Raymond Lo Phuong Dao Süleyman Cenk Sahinalp Martin Ester Leonard J. Foster Fiona S. L. Brinkman PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. 1608-1615 2010 26 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btq249 https://www.wikidata.org/entity/Q41126055 db/journals/bioinformatics/bioinformatics26.html#YuWLMRLDSEFB10

David J. Lynn Calvin Chan Misbah Naseer Melissa Yau Raymond Lo Anastasia Sribnaia Giselle Ring Jaimmie Que Kathleen Wee Geoffrey L. Winsor Matthew R. Laird Karin Breuer Amir K. Foroushani Fiona S. L. Brinkman Robert E. W. Hancock Curating the innate immunity interactome. 117 2010 4 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-4-117 https://www.wikidata.org/entity/Q33667546 db/journals/bmcsb/bmcsb4.html#LynnCNYLSRQWWLBFBH10

Morgan G. I. Langille Fiona S. L. Brinkman IslandViewer: an integrated interface for computational identification and visualization of genomic islands. 664-665 2009 25 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btp030 https://www.wikidata.org/entity/Q24648176 db/journals/bioinformatics/bioinformatics25.html#LangilleB09

Geoffrey L. Winsor Thea Van Rossum Raymond Lo Bhavjinder Khaira Matthew D. Whiteside Robert E. W. Hancock Fiona S. L. Brinkman Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. 483-488 2009 37 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkn861 https://www.wikidata.org/entity/Q37202614 db/journals/nar/nar37.html#WinsorRLKWHB09

Geoffrey L. Winsor Bhavjinder Khaira Thea Van Rossum Raymond Lo Matthew D. Whiteside Fiona S. L. Brinkman The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. 2803-2804 2008 24 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btn524 https://www.wikidata.org/entity/Q37090715 db/journals/bioinformatics/bioinformatics24.html#WinsorKRLWB08

Morgan G. I. Langille William W. L. Hsiao Fiona S. L. Brinkman Evaluation of genomic island predictors using a comparative genomics approach. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-329 https://www.wikidata.org/entity/Q33357712 db/journals/bmcbi/bmcbi9.html#LangilleHB08

Debra L. Fulton Yvonne Y. Li Matthew R. Laird Benjamin G. S. Horsman Fiona M. Roche Fiona S. L. Brinkman Improving the specificity of high-throughput ortholog prediction. 270 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-270 https://www.wikidata.org/entity/Q24685511 db/journals/bmcbi/bmcbi7.html#FultonLLHRB06

Jennifer L. Gardy Matthew R. Laird Fei Chen 0002 Sébastien Rey C. J. Walsh Martin Ester Fiona S. L. Brinkman PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. 617-623 2005 21 Bioinform. 5 https://doi.org/10.1093/bioinformatics/bti057 https://www.wikidata.org/entity/Q28289386 db/journals/bioinformatics/bioinformatics21.html#GardyLCRWEB05

Sébastien Rey Michael Acab Jennifer L. Gardy Matthew R. Laird Katalin de Fays Christophe G. Lambert Fiona S. L. Brinkman PSORTdb: a protein subcellular localization database for bacteria. 164-168 2005 33 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gki027 https://www.wikidata.org/entity/Q24558590 db/journals/nar/nar33.html#ReyAGLFLB05

Geoffrey L. Winsor Raymond Lo Shannan J. Ho Sui Korine S. E. Ung Shao-Shan Huang Dean Cheng Wai-Kay Ho Ching Robert E. W. Hancock Fiona S. L. Brinkman Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. 338-343 2005 33 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gki047 https://www.wikidata.org/entity/Q24794244 db/journals/nar/nar33.html#WinsorLSUHCCHB05

Karsten Hokamp Fiona M. Roche Michael Acab Marc-Etienne Rousseau Byron Kuo David L. Goode Dana Aeschliman Jenny Bryan Lorne A. Babiuk Robert E. W. Hancock Fiona S. L. Brinkman ArrayPipe: a flexible processing pipeline for microarray data. 457-459 2004 32 Nucleic Acids Res. Web-Server-Issue db/journals/nar/nar32.html#HokampRARKGABBHB04 https://doi.org/10.1093/nar/gkh446 https://www.wikidata.org/entity/Q30939950

Fiona M. Roche Karsten Hokamp Michael Acab Lorne A. Babiuk Robert E. W. Hancock Fiona S. L. Brinkman ProbeLynx: a tool for updating the association of microarray probes to genes. 471-474 2004 32 Nucleic Acids Res. Web-Server-Issue db/journals/nar/nar32.html#RocheHABHB04 https://doi.org/10.1093/nar/gkh452 https://www.wikidata.org/entity/Q41011061

William W. L. Hsiao Ivan Wan Steven J. M. Jones Fiona S. L. Brinkman IslandPath: aiding detection of genomic islands in prokaryotes. 418-420 2003 19 Bioinform. 3 db/journals/bioinformatics/bioinformatics19.html#HsiaoWJB03 https://doi.org/10.1093/bioinformatics/btg004 https://www.wikidata.org/entity/Q48615472

Jennifer L. Gardy Cory Spencer Ke Wang 0001 Martin Ester Gábor E. Tusnády István Simon Sujun Hua Katalin de Fays Christophe G. Lambert Kenta Nakai Fiona S. L. Brinkman PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. 3613-3617 2003 31 Nucleic Acids Res. 13 db/journals/nar/nar31.html#GardySWETSHFLNB03 https://doi.org/10.1093/nar/gkg602 https://www.wikidata.org/entity/Q24671890

Rong She Fei Chen 0002 Ke Wang 0001 Martin Ester Jennifer L. Gardy Fiona S. L. Brinkman Frequent-subsequence-based prediction of outer membrane proteins. 436-445 2003 conf/kdd/2003 KDD https://doi.org/10.1145/956750.956800 db/conf/kdd/kdd2003.html#SheCWEGB03

Fiona S. L. Brinkman Ivan Wan Robert E. W. Hancock Ann M. Rose Steven J. M. Jones PhyloBLAST: facilitating phylogenetic analysis of BLAST results. 385-387 2001 17 Bioinform. 4 db/journals/bioinformatics/bioinformatics17.html#BrinkmanWHRJ01 https://doi.org/10.1093/bioinformatics/17.4.385 https://www.wikidata.org/entity/Q73746255

Michael Acab Dana Aeschliman Brian P. Alcock Dalia A. Alghamdi Lorne A. Babiuk Sheridan J. C. Baker Robert G. Beiko Claire Bertelli Timsy Bhando Emily Bordeleau Mégane Bouchard Karin Breuer Eric D. Brown Jennifer BryanJenny Bryan Kenneth Bryan Pier Luigi Buttigieg Lindsey A. Carfrae Romeo Chalil Calvin Chan Carol Chen Fei Chen 0002 Annie A. Cheng Dean Cheng Wai-Kay Ho Ching Terry A. Chiu Mélanie Courtot Phuong Dao Biren M. Dave Mugdha Dave Bhavjinder K. Dhillon Gary H. Van Domselaar Damion M. Dooley Sachin Doshi Arman Edalatmand Jonathan A. Eisen Tariq Elsayegh Martin Ester Mateusz Faltyn Maya A. Farha Katalin de Fays Leanne Fleming Alexandra Florescu Amir K. Foroushani Leonard J. Foster Shawn French Silvia Frias Jonathan G. Frye Debra L. Fulton Jennifer L. Gardy Bahar Golbon David L. Goode Rodion Gordzevich Gurinder Gosal Jinko Graham Kristen L. Gray Emma J. Griffiths Peiyao Guo Robert E. W. Hancock Anastasia Hernández-Koutoucheva Gemma Hoad Robert Hoehndorf Karsten Hokamp Benjamin G. S. Horsman William W. L. Hsiao Sujun Hua Shao-Shan Huang William Huynh Hamna Imtiaz Baofeng Jia Xingjian Jiang Vivian Jin Timothy A. Johnson Steven J. M. Jones Komal Kaur Bhavjinder Khaira Byron Kuo Megan Kwong Briony A. Lago Matthew R. Laird David K. W. Lam Christophe G. Lambert Morgan G. I. Langille Britney Y. Lau Tammy T. Y. Lau Wing Yin Venus Lau Yvonne Y. Li Zi Cheng Liang Sihan Liu Raymond Lo David J. Lynn Ashmeet Madyan Finlay Maguire Andrew G. McArthur Madeline C. McCarthy Brad McNeney Gabor Melli Jeong Eun Min Sally Y. Min Anatoly Miroshnichenko Karyn M. Mukiri Kenta Nakai Misbah Naseer Jalees A. Nasir Anna-Lisa V. Nguyen Keyu C. Niu Fazmin Nizam Martins Oloni Andrew C. Pawlowski Michael A. Peabody Sheldon K. Pereira Aaron J. Petkau Jaimmie Que Kenneth Rachwalski Amogelang R. Raphenya Sébastien Rey Giselle Ring Fiona M. Roche Ann M. Rose Thea Van Rossum Marc-Etienne Rousseau Süleyman Cenk Sahinalp Daim Sardar Prabakar Shan Arjun N. Sharma Julie A. Shay Rong She István Simon Bhavya Singh Keaton W. Smith David J. Speicher Cory Spencer Anastasia Sribnaia Shannan J. Ho Sui Sohaib A. Syed Keith E. Tilley Hiu-Ki Tran Kara K. Tsang Megan M. Tu Gábor E. Tusnády Korine S. E. Ung Caitlyn Vlasschaert Nicholas Waglechner James R. Wagner C. J. Walsh Ivan Wan Ke Wang 0001 Kathleen Wee Rafik E. Werfalli Erin L. Westman Matthew D. Whiteside Kelly P. Williams Laura E. Williams Geoffrey L. Winsor Mateusz A. Wlodarski Gerard D. Wright Jasmine Y. J. Yang Melissa Yau Nancy Y. Yu Haley L. Zubyk