What's New

December 9, 2009: Awards updated (Women's Executive Network, Canada's Top 100 Women award) and publications and personnel updated. Contact info updated to provide new directions, now that there is construction for at least 1 year that will block off the main access to the South Science Building that we normally use. Thanks Iddo for noticing that the date below for the last update was Sept 1, 2010 - I have indeed updated my Tardis now. :)

September 1, 2009: Enjoying updating my page to indicate that I'm a Full Professor now! :) Also updated that I am now Co-Director of the SFU/UBC/BCCA Bioinformatics Graduate Training Program. which was recently awarded renewed funding for a further 5 years. Personnel, and publications also updated. Note that as of today I start a sabbatical for a year at the BC Centre for Disease Control (i.e. still locally around, just not teaching and doing committee work). I aim to learn more about Public Health and how our microbial bioinformatics and genomics methods can further aid infectious disease control efforts.

June 29, 2009: Personnel, new positions and publications updated again. Added links to Brinkman twitter and friendfeed.

May 15, 2009: Personnel, new positions and publications updated.

January 14, 2009: Positions updated. The IslandViewer application goes live, which represents the first web-based applciation that integrates predictions for the most accurate genomic island prediction methods. Genomic islands are clusters of genes in a prokaryotic genome that may have horizontal origins - genomic islands are of increasing interest as their major role in medically relevant pathogen evolution is becoming more recognized.

January 7, 2009: Personnel, research, positions and publications updated. Our recent research was profiled in Cell Host and Microbe (InnateDB) and also in Lancet ID (genomic island research).

September 4, 2008: Personnel and publications updated.

August 8, 2008: Lots to update - its been a while! Personnel, research, positions and publications updated.
- The new Innate DB resource is being released and published. InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.
- The first version of the Burkholderia Genome Database has been made public. This is a sister database to the Pseudomonas Genome Database, with a similar interface and functionality to facilitate analysis of Burkholderia species of interest as important Cystic Fibrosis pathogens.
- The BCID project was initiated and the associated website made public. More funding is being applied for, to further expand components of this seed project.
- Coop, honours and potential graduate students or postdocs are welcome over 2008-2009, as we enter some new areas of research!

September 10, 2007: All phone numbers now completely changed now to the new 778-782- numbers, so please note our new phone numbers (see the Contact Us page). Personnel also updated since yet more positions have been filled. Other than coop and honours projects there are currently no advertized positions currently available.

August 7, 2007: Note that phone numbers across SFU have changed now to new 778-782- numbers, so please note our new phone numbers (see the Contact Us page). Personnel also updated since more positions have been filled.

June 19, 2007: Awards updated after they were publicized (Canadian Society of Microbiologists Fisher Scientific Award and Michael Smith Foundation for Health Research Senior Scholar Award). Thank you everyone for your support! Additional positions have become available.

May 1, 2007: Personnel, research, and funding sources updated. Additional positions have become available.

January 14, 2007: Personnel and news sections updated.

December 2, 2006: Personnel, research, teaching, and publications updated. Also, first pics on this site of the new honorary member of the Brinkman lab (Elise)! Contact info updated to note additional IRMACS lab location. Additional postdoc and staff positions have become available.

June, 2006: Personnel, research and publications updated. Our Ortholuge approach for more precise ortholog identification (which aids comparative genomic analyses) is now public.

May 23, 2006: Updated pages to indicate that I'm now promoted to Associate Professor with tenure (yeay! thanks everyone for your support!). Updated publications too. Note that I anticipate soon going on a second maternity leave from roughly June to October, 2006.

April 25, 2006: Publications, talks & teaching, positions (primarily filled) and personnel updated.

January 14, 2006: Publications, talks & teaching, and personnel updated. A link to better SFU maps was added.

August 25, 2005: The new Genome Canada Pathogenomics Project, entitled The Pathogenomics of Innate Immunity (PI²), has been officially announced. This four year project is anticipated to start in January 2006 and the Brinkman Laboratory will head bioinformatics for this project (including software development for, and higher order analyses of, microarray data and comparative genomics analyses relevant to studies of innate immunity). Additional postdoc and graduate student positions have become available as part of the initiation of this new project.

August 6, 2005: New postdoc and graduate student positions are now becoming available. A beta version of the new Pseudomonas Genome Database, version 2 is now online (this can also be reached through the old Pseudomonas Genome Database site). This expanded database now faciliates inter- and intra-genome comparisons for multiple Pseudomonas species/strains.

May 28, 2005: Publications, teaching and awards, and personnel updated.

March 10, 2005: Publications, talks & teaching, and personnel updated. Under "positions available" it was also clarified that we welcome students to contact us who are interested in honours undergraduate research projects. We can only take on a limited number each year though!

November 16, 2004: Publications, funding sources, and personnel updated. Thanks Jenn for the great "array lab" pic!

Sept 4, 2004: Publications, awards, personnel and links to applications developed have been updated. Note the new version of PSORTb which now predicts protein subcellular localizations for both Gram-negative and Gram-positive bacteria. Also, a new database of bacterial protein localization was developed called PSORTdb, and new microarray analysis software ArrayPipe and ProbeLynx was released that was developed for the Genome Canada Pathogenomics Project. ArrayPipe provides a flexible approach to microarray analysis that is parralellizable, web-based or command-line based, and is freely available under an open source licence (Perl Artistic Licence). ProbeLynx allows you to update annotations for your microarray probes, using sequence data that is also investigated for its potential for cross-hybridization. ProbeLynx is also freely available under an open source licence. Lastly, there are a number of new features in the Pseudomonas Genome Database to check out too!

Feb 7, 2004: Publications updated. Note the PSORTb source code release last week.

Jan 30, 2004: Lab pics and presentations, updated. Note the new PSORT site and PSORTb software which we released last year.

July 28, 2003: A number of updates, as I return from maternity leave. Personnel pic, contact us info (including the location of our new computer lab), publications, etc...

March 5, 2003: A number of updates were made to publications, presentations, research, and personnel. Regarding personnel, note the new special addition to the Brinkman Laboratory!

October 20, 2002: We have released a bioperl module developed as part of our PSORTb project to improve computational prediction of bacterial protein subcellular localization. Bio::Tools::SubLoc and the associated, required Algorithm::SVM module were developed for making SubLoc-based protein subcellular localization predictions. They were developed by Cory Spencer and are also available from any CPAN mirror. For more information about SubLoc, which was developed by S Hua and Z Sun, see their paper in Bioinformatics (2001. 17:721-728). Other modules that are a part of the overall PSORTb application will be released at a later date.

October 17, 2002: Added a link to the new SFU Institute for Health Research and Education, and a new website profiling Bioinformatics at SFU. Updated lab personnel page (with new pics of course...).

October 1, 2002: Publications and positions available have been updated.

September 9, 2002: Our website has moved to our new SFU location at www.pathogenomics.sfu.ca/brinkman. Please update your bookmarks accordingly! Also note a number of updates of the site have been made regarding publications, IslandPath software and the BAEwatch database released fully online, and links to the new Bioinformatics Graduate Program being jointly offered by the BCCA, SFU and UBC.

April 21, 2002: Our laboratory will head Bioinformatics for the new Genome Canada Pathogenomics Project, so a number of positions are now available.

March 27, 2002: A new full-time position is available: We are looking for a senior Bioinformaticist/Database Developer to lead further development of the Pseudomonas Genome Database and the PseudoCAP project. Salary is very competive, so check it out!

March 7, 2002: First course information for two combined bioinformatics courses, MBB 440 (Bioinformatics) and MBB 839-3 (Special Topics in Molecular Biology: Bioinformatics) are now available. These courses will be offered in the Summer 2002, Fall 2002, and every Fall term thereafter. More info is also available. Seminars also updated.

February 16, 2002: Updated lab personnel list, pics, for-the-public facts, and links. Most notably, a link was added to our Pseudomonas aeruginosa outer membrane proteins dataset that will be refered to in an upcoming publication (in press).

January 24, 2002: A mailing list was set up for the PSORT project, to enable researchers to sign up to be notified of updates to the project. If you are interested in being notified about changes in the status of this project, including when publicly available software is released, please subscribe to the psort-update mailing list by emailing maillist@sfu.ca with "subscribe psort-update" in the subject or body of the message.

January 6, 2002: Happy New Year! This site has been updated regarding Dr. Brinkman's appointments, the lab research, and other small updates have been made. Note a new version of the Department of Molecular Biology and Biochemistry website which Dr. Brinkman created. Also note that the bioinformatics.ca site has been revised (headed by B. Francis Ouellette) to list additional bioinformatics information such as bioinformatics programs and courses in Canada (look under "links") and bioinformatics jobs and event announcements.

September 30, 2001: Personnel section now finally contains pics of us! The list of Dr. Brinkman's talks, appointments etc... has also been updated, along with an update in the publications section of the issue of ASM News that highlighted a recent article of ours.

August 29, 2001: Website revised, including the addition of a Personnel section, update of contact information, update of list of invited talks, and addition of more links.

July 19, 2001: All positions for the laboratory for September 2001 are now filled (pending confirmation of one position) however other positions are anticipated to become available. If you are still interested in applying please take note of the positions available page.

June 1, 2001: 1. Publications have been updated. 2. Note the initiation of BIND (Biomolecular Interaction Network Database), by Blueprint, a new not-for-profit organization that is developing centralized, publicly accessible databases to help bring together disparate biomolecular information.

May 1, 2001: The second edition of "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" is now available in hardcover (the former edition is available in paperback).

April 19, 2001: A previous graduate student position has been filled, however new positions are available.

April 11, 2001: The publication for the PhyloBLAST application has been released online.

April 4, 2001: Genome Canada announced $136 million in funding for 22 large scale genomics projects across Canada.

March 21, 2001: Involved in the development of informational resources for the new Canadian Food and Water Safety Network.

March 14, 2001: On March 13th, the B.C. government announced the new $110-million Michael Smith Foundation for Health Research, in honor of the exceptional researcher and person, Dr. Michael Smith.

March 13, 2001: The sample version of the IslandPath web-based application has been updated for the Pathogenomics Project to load faster, and is now beta version 0.95. The full version will be made available upon publication.

March 10, 2001: News section added, with links to what's in the news that's relevant to genomics, bioinformatics and infectious disease.

March 4, 2001: A sample of a beta version of the IslandPath web-based application has been released publicly for the Pathogenomics Project. The full version, which contains a number of improved features (including shorter loading times) will be made available upon publication.

February 26, 2001: BC Bioinformatics, a website listing researchers with an interest in bioinformatics in British Columbia, is now public.

February 23, 2001: The Pathogenomics Project and its website was profiled in the recent issue of Current Opinion in Microbiology (Vol. 4, No. 1, February 2001).

February 12, 2001: This website goes public! Note the positions available.