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ORCIDFiona S. L. Brinkman
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Journal Articles
- 2023
[j36]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. Nucleic Acids Res. 51(D1): 690-699 (2023)- 2021
- [j35]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. Nucleic Acids Res. 49(Database-Issue): D803-D808 (2021) - 2020
- [j34]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. Bioinform. 36(10): 3043-3048 (2020) - [j33]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. Nucleic Acids Res. 48(Database-Issue): D517-D525 (2020) - 2019
- [j32]Claire Bertelli, Keith E. Tilley, Fiona S. L. Brinkman:
Microbial genomic island discovery, visualization and analysis. Briefings Bioinform. 20(5): 1685-1698 (2019) - 2018
- [j31]Claire Bertelli, Fiona S. L. Brinkman:
Improved genomic island predictions with IslandPath-DIMOB. Bioinform. 34(13): 2161-2167 (2018) - 2017
- [j30]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. Nucleic Acids Res. 45(Database-Issue): D566-D573 (2017) - [j29]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. Nucleic Acids Res. 45(Webserver-Issue): W30-W35 (2017) - 2016
- [j28]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. Nucleic Acids Res. 44(Database-Issue): 646-653 (2016) - [j27]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. Nucleic Acids Res. 44(Database-Issue): 663-668 (2016) - 2015
- [j26]Silvia Frias, Kenneth Bryan, Fiona S. L. Brinkman, David J. Lynn:
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database J. Biol. Databases Curation 2015 (2015) - [j25]Matthew R. Laird, Morgan G. I. Langille, Fiona S. L. Brinkman:
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. Bioinform. 31(20): 3348-3349 (2015) - [j24]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. BMC Bioinform. 16: 362:1-362:19 (2015) - [j23]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. Nucleic Acids Res. 43(Webserver-Issue): W104-W108 (2015) - 2013
- [j22]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. Nucleic Acids Res. 41(Database-Issue): 366-376 (2013) - [j21]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. Nucleic Acids Res. 41(Database-Issue): 1228-1233 (2013) - [j20]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. Nucleic Acids Res. 41(Webserver-Issue): 129-132 (2013) - 2012
- [j19]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. Bioinform. 28(14): 1947-1948 (2012) - 2011
- [j18]Jeong Eun Min, Matthew D. Whiteside, Fiona S. L. Brinkman, Brad McNeney, Jinko Graham:
A statistical approach to high-throughput screening of predicted orthologs. Comput. Stat. Data Anal. 55(1): 935-943 (2011) - [j17]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. Nucleic Acids Res. 39(Database-Issue): 241-244 (2011) - [j16]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. Nucleic Acids Res. 39(Database-Issue): 596-600 (2011) - 2010
- [j15]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. Bioinform. 26(13): 1608-1615 (2010) - [j14]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. BMC Syst. Biol. 4: 117 (2010) - 2009
- [j13]Morgan G. I. Langille, Fiona S. L. Brinkman:
IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinform. 25(5): 664-665 (2009) - [j12]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. Nucleic Acids Res. 37(Database-Issue): 483-488 (2009) - 2008
- [j11]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. Bioinform. 24(23): 2803-2804 (2008) - [j10]Morgan G. I. Langille, William W. L. Hsiao, Fiona S. L. Brinkman:
Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinform. 9 (2008) - 2006
- [j9]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. BMC Bioinform. 7: 270 (2006) - 2005
- [j8]Jennifer L. Gardy, Matthew R. Laird, Fei Chen, 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. Bioinform. 21(5): 617-623 (2005) - [j7]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. Nucleic Acids Res. 33(Database-Issue): 164-168 (2005) - [j6]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. Nucleic Acids Res. 33(Database-Issue): 338-343 (2005) - 2004
- [j5]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. Nucleic Acids Res. 32(Web-Server-Issue): 457-459 (2004) - [j4]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. Nucleic Acids Res. 32(Web-Server-Issue): 471-474 (2004) - 2003
- [j3]William W. L. Hsiao, Ivan Wan, Steven J. M. Jones, Fiona S. L. Brinkman:
IslandPath: aiding detection of genomic islands in prokaryotes. Bioinform. 19(3): 418-420 (2003) - [j2]Jennifer L. Gardy, Cory Spencer, Ke Wang, 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. Nucleic Acids Res. 31(13): 3613-3617 (2003) - 2001
- [j1]Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. M. Jones:
PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinform. 17(4): 385-387 (2001)
Conference and Workshop Papers
- 2017
- [c5]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. ICBO 2017 - [c4]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. JOWO 2017 - 2016
- [c3]Damion M. Dooley, Emma J. Griffiths, Fiona S. L. Brinkman, William W. L. Hsiao:
An OBI Ontology Datum Proof Sheet. ICBO/BioCreative 2016 - [c2]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. ICBO/BioCreative 2016 - 2003
- [c1]Rong She, Fei Chen, Ke Wang, Martin Ester, Jennifer L. Gardy, Fiona S. L. Brinkman:
Frequent-subsequence-based prediction of outer membrane proteins. KDD 2003: 436-445
Coauthor Index
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