Works by Brinkman, Fiona S L

Results: 52

From fetus to 8: the CHILD Cohort Study Open Access.

Published in:

American Journal of Epidemiology, 2025, v. 194, n. 7, p. 1984, doi. 10.1093/aje/kwae397

By:

Miliku, Kozeta;
Reyna, Myrtha E;
Medeleanu, Maria;
Dai, Ruixue;
Dubeau, Aimee;
Lefebvre, Diana L;
Wright, Kim;
Dawod, Bassel;
Beck, Marshall;
Brooks, Elissa;
Kobor, Michael;
Duan, Qingling;
Brook, Jeffrey R;
Lou, Wendy;
Brinkman, Fiona S L;
Winsor, Geoffrey L;
Cook, Justin;
Becker, Allan B;
Simons, Elinor;
Mandhane, Piushkumar J

Publication type:

Article

PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3043, doi. 10.1093/bioinformatics/btaa136

By:

Peabody, Michael A;
Lau, Wing Yin Venus;
Hoad, Gemma R;
Jia, Baofeng;
Maguire, Finlay;
Gray, Kristen L;
Beiko, Robert G;
Brinkman, Fiona S L

Publication type:

Article

Improved genomic island predictions with IslandPath-DIMOB.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. 2161, doi. 10.1093/bioinformatics/bty095

By:

Bertelli, Claire;
Brinkman, Fiona S L

Publication type:

Article

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3348, doi. 10.1093/bioinformatics/btv376

By:

Laird, Matthew R.;
Langille, Morgan G. I.;
Brinkman, Fiona S. L.

Publication type:

Article

MicrobeDB: a locally maintainable database of microbial genomic sequences.

Published in:

Bioinformatics, 2012, v. 28, n. 14, p. 1947, doi. 10.1093/bioinformatics/bts273

By:

Langille, Morgan G. I.;
Laird, Matthew R.;
Hsiao, William W. L.;
Chiu, Terry A.;
Eisen, Jonathan A.;
Brinkman, Fiona S. L.

Publication type:

Article

OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D366, doi. 10.1093/nar/gks1241

By:

Whiteside, Matthew D.;
Winsor, Geoffrey L.;
Laird, Matthew R.;
Brinkman, Fiona S. L.

Publication type:

Article

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D1228, doi. 10.1093/nar/gks1147

By:

Breuer, Karin;
Foroushani, Amir K.;
Laird, Matthew R.;
Chen, Carol;
Sribnaia, Anastasia;
Lo, Raymond;
Winsor, Geoffrey L.;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.;
Lynn, David J.

Publication type:

Article

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D596, doi. 10.1093/nar/gkq869

By:

Winsor, Geoffrey L.;
Lam, David K. W.;
Fleming, Leanne;
Lo, Raymond;
Whiteside, Matthew D.;
Yu, Nancy Y.;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.

Publication type:

Article

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D483, doi. 10.1093/nar/gkn861

By:

Winsor, Geoffrey L.;
Van Rossum, Thea;
Lo, Raymond;
Khaira, Bhavjinder;
Whiteside, Matthew D.;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.

Publication type:

Article

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d338

By:

Winsor, Geoffrey L.;
Lo, Raymond;
Sui, Shannan J. Ho;
Ung, Korine S.E.;
Huang, Shaoshan;
Cheng, Dean;
Ching, Wai-Kay Ho;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.

Publication type:

Article

PSORTdb: a protein subcellular localization database for bacteria.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d164

By:

Rey, Sébastien;
Acab, Michael;
Gardy, Jennifer L.;
Laird, Matthew R.;
deFays, Katalin;
Lambert, Christophe;
Brinkman, Fiona S. L.

Publication type:

Article

ArrayPipe: a flexible processing pipeline for microarray data.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w457, doi. 10.1093/nar/gkh446

By:

Hokamp, Karsten;
Roche, Fiona M.;
Acab, Michael;
Rousseau, Marc-Etienne;
Kuo, Byron;
Goode, David;
Aeschliman, Dana;
Bryan, Jenny;
Babiuk, Lorne A.;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.

Publication type:

Article

ProbeLynx: a tool for updating the association of microarray probes to genes.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w471, doi. 10.1093/nar/gkh452

By:

Roche, Fiona M.;
Hokamp, Karsten;
Acab, Michael;
Babiuk, Lorne A.;
Hancock, Robert E. W.;
Brinkman, Fiona S. L.

Publication type:

Article

The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate:pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide.

Published in:

PLoS ONE, 2017, v. 12, n. 12, p. 1, doi. 10.1371/journal.pone.0189066

By:

Panmanee, Warunya;
Charoenlap, Nisanart;
Atichartpongkul, Sopapan;
Mahavihakanont, Aekkapol;
Whiteside, Matthew D.;
Winsor, Geoff;
Brinkman, Fiona S. L.;
Mongkolsuk, Skorn;
Hassett, Daniel J.

Publication type:

Article

High-throughput detection of RNA processing in bacteria.

Published in:

BMC Genomics, 2018, v. 19, p. 1, doi. 10.1186/s12864-018-4538-8

By:

Gill, Erin E.;
Chan, Luisa S.;
Winsor, Geoffrey L.;
Dobson, Neil;
Lo, Raymond;
Ho Sui, Shannan J.;
Dhillon, Bhavjinder K.;
Taylor, Patrick K.;
Shrestha, Raunak;
Spencer, Cory;
Hancock, Robert E. W.;
Unrau, Peter J.;
Brinkman, Fiona S. L.

Publication type:

Article

Evaluation of genomic island predictors using a comparative genomics approach.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-329

By:

Langille, Morgan G. I.;
Hsiao, William W. L.;
Brinkman, Fiona S. L.

Publication type:

Article

Lateral Gene Transfer and Metabolic Adaptation in the Human Parasite Trichomonas vaginalis.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 11, p. 1769, doi. 10.1093/oxfordjournals.molbev.a026275

By:

de Koning, Audrey P.;
Brinkman, Fiona S. L.;
Jones, Steven J. M.;
Keeling, Patrick J.

Publication type:

Article

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

Published in:

Bioinformatics, 2010, v. 26, n. 13, p. 1608, doi. 10.1093/bioinformatics/btq249

By:

Yu, Nancy Y.;
Wagner, James R.;
Laird, Matthew R.;
Melli, Gabor;
Rey, Sébastien;
Lo, Raymond;
Phuong Dao;
Sahinalp, S. Cenk;
Ester, Martin;
Foster, Leonard J.;
Brinkman, Fiona S. L.

Publication type:

Article

IslandViewer: an integrated interface for computational identification and visualization of genomic islands.

Published in:

Bioinformatics, 2009, v. 25, n. 5, p. 664

By:

Morgan G. I. Langille;
Fiona S. L. Brinkman

Publication type:

Article

The Burkholderia Genome Database: facilitating flexible queries and comparative analyses.

Published in:

Bioinformatics, 2008, v. 24, n. 23, p. 2803, doi. 10.1093/bioinformatics/btn524

By:

Geoffrey L. Winsor;
Bhavjinder Khaira;
Thea Van Rossum;
Raymond Lo;
Matthew D. Whiteside;
Fiona S. L. Brinkman

Publication type:

Article

IslandPath: aiding detection of genomic islands in prokaryotes.

Published in:

Bioinformatics, 2003, v. 19, n. 3, p. 418, doi. 10.1093/bioinformatics/btg004

By:

Hsiao, William;
Wan, Ivan;
Jones, Steven J.;
Brinkman, Fiona S. L.

Publication type:

Article

PhyloBLAST: facilitating phylogenetic analysis of BLAST results.

Published in:

Bioinformatics, 2001, v. 17, n. 4, p. 385, doi. 10.1093/bioinformatics/17.4.385

By:

Brinkman, Fiona S. L.;
Wan, Ivan;
Hancock, Robert E. W.;
Rose, Ann M.;
Jones, Steven J.

Publication type:

Article

GlobeCorr: interactive globe-based visualization for correlation datasets.

Published in:

Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbac099

By:

Arab, Mariam;
Woods, Nolan;
Garlock, Emma S;
Winsor, Geoffrey L;
Parks, Jaclyn P;
Jia, Baofeng;
Doiron, Dany;
Takaro, Tim K;
Brook, Jeffrey R;
Brinkman, Fiona S L

Publication type:

Article

From Prescription Drugs to Natural Health Products: Medication Use in Canadian Infants.

Published in:

Children, 2022, v. 9, n. 10, p. 1475, doi. 10.3390/children9101475

By:

Bedard, Pascal;
Winsor, Geoffrey L.;
Garlock, Emma S.;
Azad, Meghan B.;
Becker, Allan B.;
Mandhane, Piush J.;
Moraes, Theo J.;
Sears, Malcolm R.;
Turvey, Stuart E.;
Subbarao, Padmaja;
Brinkman, Fiona S. L.;
Kozyrskyj, Anita L.

Publication type:

Article

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.

Published in:

Frontiers in Microbiology, 2017, p. 1, doi. 10.3389/fmicb.2017.01068

By:

Griffiths, Emma;
Dooley, Damion;
Graham, Morag;
Van Domselaar, Gary;
Brinkman, Fiona S. L.;
Hsiao, William W. L.

Publication type:

Article

Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress.

Published in:

Frontiers in Microbiology, 2017, v. 8, p. 1, doi. 10.3389/fmicb.2017.00369

By:

Hingston, Patricia;
Chen, Jessica;
Dhillon, Bhavjinder K.;
Laing, Chad;
Bertelli, Claire;
Gannon, Victor;
Tasara, Taurai;
Allen, Kevin;
Brinkman, Fiona S. L.;
Hansen, Lisbeth Truelstrup;
Siyun Wang

Publication type:

Article

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Published in:

Nucleic Acids Research, 2016, v. 44, p. D646, doi. 10.1093/nar/gkv1227

By:

Winsor, Geoffrey L.;
Griffiths, Emma J.;
Lo, Raymond;
Dhillon, Bhavjinder K.;
Shay, Julie A.;
Brinkman, Fiona S. L.

Publication type:

Article

PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 1, p. D663, doi. 10.1093/nar/gkv1271

By:

Peabody, Michael A.;
Laird, Matthew R.;
Vlasschaert, Caitlyn;
Lo, Raymond;
Brinkman, Fiona S. L.

Publication type:

Article

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.

Published in:

Nucleic Acids Research, 2015, v. 43, n. W1, p. W104, doi. 10.1093/nar/gkv401

By:

Dhillon, Bhavjinder K.;
Laird, Matthew R.;
Shay, Julie A.;
Winsor, Geoffrey L.;
Lo, Raymond;
Nizam, Fazmin;
Pereira, Sheldon K.;
Waglechner, Nicholas;
McArthur, Andrew G.;
Langille, Morgan G. I.;
Brinkman, Fiona S. L.

Publication type:

Article

IslandViewer update: improved genomic island discovery and visualization.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W129, doi. 10.1093/nar/gkt394

By:

Dhillon, Bhavjinder K.;
Chiu, Terry A.;
Laird, Matthew R.;
Langille, Morgan G. I.;
Brinkman, Fiona S. L.

Publication type:

Article

The proportional lack of archaeal pathogens: Do viruses/phages hold the key?

Published in:

BioEssays, 2011, v. 33, n. 4, p. 248, doi. 10.1002/bies.201000091

By:

Gill, Erin E.;
Brinkman, Fiona S. L.

Publication type:

Article

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/s12859-015-0788-5

By:

Peabody, Michael A.;
Van Rossum, Thea;
Lo, Raymond;
Brinkman, Fiona S. L.

Publication type:

Article

Microbial genomic island discovery, visualization and analysis.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1685, doi. 10.1093/bib/bby042

By:

Bertelli, Claire;
Tilley, Keith E;
Brinkman, Fiona S L

Publication type:

Article

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic.

Published in:

Frontiers in Genetics, 2022, p. 1, doi. 10.3389/fgene.2021.716541

By:

Song, Lingqiao;
Liu, Hanshi;
Brinkman, Fiona S. L;
Gill, Erin;
Griffiths, Emma J.;
Hsiao, William W. L;
Savić-Kallesøe, Sarah;
Moreira, Sandrine;
Van Domselaar, Gary;
Zawati, Ma'n H.;
Joly, Yann

Publication type:

Article

Detecting genomic islands using bioinformatics approaches.

Published in:

Nature Reviews Microbiology, 2010, v. 8, n. 5, p. 373, doi. 10.1038/nrmicro2350

By:

Langille, Morgan G. I.;
Hsiao, William W. L.;
Brinkman, Fiona S. L.

Publication type:

Article

Methods for predicting bacterial protein subcellular localization.

Published in:

2006

By:

Gardy, Jennifer L.;
Brinkman, Fiona S. L.

Publication type:

Correction Notice

Methods for predicting bacterial protein subcellular localization.

Published in:

Nature Reviews Microbiology, 2006, v. 4, n. 10, p. 741, doi. 10.1038/nrmicro1494

By:

Gardy, Jennifer L.;
Brinkman, Fiona S. L.

Publication type:

Article

A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0166-1

By:

Uyaguari-Diaz, Miguel I.;
Chan, Michael;
Chaban, Bonnie L.;
Croxen, Matthew A.;
Finke, Jan F.;
Hill, Janet E.;
Peabody, Michael A.;
Van Rossum, Thea;
Suttle, Curtis A.;
Brinkman, Fiona S. L.;
Isaac-Renton, Judith;
Prystajecky, Natalie A.;
Tang, Patrick

Publication type:

Article

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality.

Published in:

Frontiers in Microbiology, 2015, v. 6, p. 1, doi. 10.3389/fmicb.2015.01405

By:

Van Rossum, Thea;
Peabody, Michael A.;
Uyaguari-Diaz, Miguel I.;
Cronin, Kirby I.;
Chan, Michael;
Slobodan, Jared R.;
Nesbitt, Matthew J.;
Suttle, Curtis A.;
Hsiao, William W. L.;
Tang, Patrick K. C.;
Prystajecky, Natalie A.;
Brinkman, Fiona S. L.

Publication type:

Article

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.

Published in:

2015

By:

Frias, Silvia;
Bryan, Kenneth;
Brinkman, Fiona S. L.;
Lynn, David J.

Publication type:

Product Review

FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.

Published in:

NPJ Science of Food, 2018, v. 2, n. 1, p. N.PAG, doi. 10.1038/s41538-018-0032-6

By:

Dooley, Damion M.;
Griffiths, Emma J.;
Gosal, Gurinder S.;
Buttigieg, Pier L.;
Hoehndorf, Robert;
Lange, Matthew C.;
Schriml, Lynn M.;
Brinkman, Fiona S. L.;
Hsiao, William W. L.

Publication type:

Article

Similarities between bacterial GAD and human GAD65: Implications in gut mediated autoimmune type 1 diabetes.

Published in:

PLoS ONE, 2022, v. 17, n. 2, p. 1, doi. 10.1371/journal.pone.0261103

By:

Bedi, Suhana;
Richardson, Tiffany M.;
Jia, Baofeng;
Saab, Hadeel;
Brinkman, Fiona S. L.;
Westley, Monica

Publication type:

Article

Curating the innate immunity interactome.

Published in:

BMC Systems Biology, 2010, v. 4, p. 117, doi. 10.1186/1752-0509-4-117

By:

Lynn, David J.;
Chan, Calvin;
Naseer, Misbah;
Yau, Melissa;
Lo, Raymond;
Sribnaia, Anastasia;
Ring, Giselle;
Que, Jaimmie;
Wee, Kathleen;
Winsor, Geoffrey L.;
Laird, Matthew R.;
Breuer, Karin;
Foroushani, Amir K.;
Brinkman, Fiona S. L.;
Hancock, Robert E. W.

Publication type:

Article

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Published in:

2011

By:

Aranda, Bruno;
Blankenburg, Hagen;
Kerrien, Samuel;
Brinkman, Fiona S. L.;
Ceol, Arnaud;
Chautard, Emilie;
Dana, Jose M.;
De Las Rivas, Javier;
Dumousseau, Marine;
Galeota, Eugenia;
Gaulton, Anna;
Goll, Johannes;
Hancock, Robert E. W.;
Isserlin, Ruth;
Jimenez, Rafael C.;
Kerssemakers, Jules;
Khadake, Jyoti;
Lynn, David J.;
Michaut, Magali;
O'Kelly, Gavin

Publication type:

Letter to the Editor

The Association of Virulence Factors with Genomic Islands.

Published in:

PLoS ONE, 2009, v. 4, n. 12, p. 1, doi. 10.1371/journal.pone.0008094

By:

Ho Sui, Shannan J.;
Fedynak, Amber;
Hsiao, William W. L.;
Langille, Morgan G. I.;
Brinkman, Fiona S. L.

Publication type:

Article

Identification of 526 Conserved Metazoan Genetic Innovations Exposes a New Role for Cofactor E-like in Neuronal Microtubule Homeostasis.

Published in:

PLoS Genetics, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pgen.1003804

By:

Frédéric, Melissa Y.;
Lundin, Victor F.;
Whiteside, Matthew D.;
Cueva, Juan G.;
Tu, Domena K.;
Kang, S. Y. Catherine;
Singh, Hansmeet;
Baillie, David L.;
Hutter, Harald;
Goodman, Miriam B.;
Brinkman, Fiona S. L.;
Leroux, Michel R.

Publication type:

Article

Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System.

Published in:

PLoS Genetics, 2010, v. 6, n. 3, p. 1, doi. 10.1371/journal.pgen.1000875

By:

Tomljenovic-Berube, Ana M.;
Mulder, David T.;
Whiteside, Matthew D.;
Brinkman, Fiona S. L.;
Coombes, Brian K.

Publication type:

Article

Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands.

Published in:

PLoS Genetics, 2005, v. 1, n. 5, p. 540, doi. 10.1371/journal.pgen.0010062

By:

Hsiao, William W. L.;
Ung, Korine;
Aeschliman, Dana;
Bryan, Jenny;
Finlay, B. Brett;
Brinkman, Fiona S. L.;
Fraser, Claire

Publication type:

Article

Exploring the potential mediating role of systemic antibiotics in the association between early-life lower respiratory tract infections and asthma at age 5 in the CHILD study.

Published in:

Frontiers in Allergy, 2025, p. 1, doi. 10.3389/falgy.2024.1463867

By:

Medeleanu, Maria V.;
Reyna, Myrtha E.;
Dai, Darlene L. Y.;
Winsor, Geoffrey L.;
Brinkman, Fiona S. L.;
Verma, Rahul;
Nugent, Ella;
Riaz, Nashita;
Simons, Elinor;
Mandhane, Piushkumar J.;
Azad, Meghan B.;
Turvey, Stuart E.;
Moraes, Theo J.;
Subbarao, Padmaja

Publication type:

Article

Effective Adjunctive Therapy by an Innate Defense Regulatory Peptide in a Preclinical Model of Severe Malaria.

Published in:

Science Translational Medicine, 2012, v. 4, n. 135, p. 1, doi. 10.1126/scitranslmed.3003515

By:

Achtman, Ariel H.;
Pilat, Sandra;
Law, Charity W.;
Lynn, David J.;
Janot, Laure;
Mayer, Matt L.;
Shuhua Ma;
Kindrachuk, Jason;
Finlay, B. Brett;
Brinkman, Fiona S. L.;
Smyth, Gordon K.;
Hancock, Robert E. W.;
Schofield, Louis

Publication type:

Article