Fiona S. L. Brinkman

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 14

Top Topics

Owl Dl Ontologies

Subcellular Localization

Top Venues

Nucleic Acids Res.

ICBO/BioCreative

Publications

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) (2023)
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) (2021)
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) (2020)
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) (2020)
Claire Bertelli, Keith E. Tilley, Fiona S. L. Brinkman
Microbial genomic island discovery, visualization and analysis. Briefings Bioinform. 20 (5) (2019)
Claire Bertelli, Fiona S. L. Brinkman
Improved genomic island predictions with IslandPath-DIMOB. Bioinform. 34 (13) (2018)
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)
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)
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) (2017)
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) (2017)
Geoffrey L. Winsor, Emma J. Griffiths, Raymond Lo, Bhavjinder K. Dhillon, Julie A. Shay, Fiona S. L. Brinkman
genomes in the Pseudomonas genome database. Nucleic Acids Res. 44 (Database-Issue) (2016)
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) (2016)
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)
Damion M. Dooley, Emma J. Griffiths, Fiona S. L. Brinkman, William W. L. Hsiao
An OBI Ontology Datum Proof Sheet. ICBO/BioCreative (2016)
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)
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) (2015)
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 (2015)
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) (2015)
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) (2013)
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) (2013)
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) (2013)
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) (2012)
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
genomes. Nucleic Acids Res. 39 (Database-Issue) (2011)
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) (2011)
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) (2011)
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) (2010)
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 (2010)
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) (2009)
Morgan G. I. Langille, Fiona S. L. Brinkman
IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinform. 25 (5) (2009)
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) (2008)
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)
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 (2006)
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) (2005)
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
Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res. 33 (Database-Issue) (2005)
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) (2005)
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) (2004)
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) (2004)
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)
William W. L. Hsiao, Ivan Wan, Steven J. Jones, Fiona S. L. Brinkman
IslandPath: aiding detection of genomic islands in prokaryotes. Bioinform. 19 (3) (2003)
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) (2003)
Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. Jones
PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinform. 17 (4) (2001)