 |
Jack Chen, Associate ProfessorDepartment of Molecular Biology and Biochemistry
Office: SSB8111 |
| Nov 10, 2011 | Christian's manuscript entitled "Genome comparison of human and non-human malaria parasites reveals parasites-specific genes potentially linked to human disease" has been accepted for publication in PLoS Computational Biology. |
| Oct 7, 2011 | Ismael obtained his Ph.D. at the Oct 7 Convocation at SFU. Photos |
| Sep 8, 2011 | Christian Frech gave a talk entitled "Genome comparison of human and non-human malaria parasites reveals species-specific genes potentially linked to human disease" at the VanBug meeting. |
| Sep 1, 2011 | Chen and Baillie labs had BBQ today in Rocky Point Park in Port Moody. Photo |
| Sep 1, 2011 | Chen lab welcomes new members: Timothy Warrington (Ph.D. student, M.Sc. from University of Alberta), Ting Zhang (M.Sc. student, B.S. from Fudan University, Shanghai), Zhaozhao Qin (M.Sc. student, B.S. from Shandong University at Weihai), and Raunak Shrestha (CIHR/MSFHR Bioinformatics Training Program rotation student, from University of Kathmandu, Nepal) |
| Aug 6, 2011 | Jeff Chu's manuscript entitled "Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans" has been accepted for publication in Nucleic Acids Research. Co-authors include Maja Tarailo-Graovac, Di Zhang, Jun Wang, Bora Uyar, Domena Tu, Joanne Trinh, David Baillie and Nansheng Chen. |
| Aug 4, 2011 | Ismael Vergara successfully defended his thesis entitled "Comparative Analysis of Caenorhabditis Genomes". Photos |
| Aug 2, 2011 | Di Zhang, an ISS undergradue student in the Chen lab, has been offerred to UBC Pharmacy. |
| July 15, 2011 | Tammy Wong, a M.Sc. student, has been awarded The Frederick Banting and Charles Best Canada Graduate Scholarship (CGS) - Master's Award |
| June 15, 2011 | Jeff Chu obtains his Ph.D. in the Spring 2011 SFU convocation. Photos |
| June 9, 2011 | Jonathan Lim, and ISS student in the lab, defended his ISS thesis entitled "Expression analysis of an isoform of daf-19 in Caenorhabditis elegans." |
| May 29, 2011 | Jeff's manuscript entitled "genBlastG: using BLAST searches to build homologous gene models" has been accepted for publication in Bioinofrmatics. Co-authors include Rong She, Bora Uyar, Jun Wang, Ke Wang and Nansheng Chen. |
| May 6, 2011 | Maja Tarailo-Graovac has been awarded a DeLill Nasser Award to attend the EMBO Meeting in Vienna from September 10 to 13. |
| May 1, 2011 | Jeffry Proctor, a CIHR/MSFHR Bioinformatics Training Program, is entering the lab as a rotation student for one semester. |
| April 14, 2011 | Maja Tarailo-Graovac has been awarded a CIHR Fanconi Anemia Postoctoral Fellowship. |
| March 1, 2011 | Jeffrey Chu enters Dr. Ann Rose's Lab at the University of British Columbia as a Postdoctoral Fellow. |
| Feb 23, 2011 | Jeffrey Chu successfully defended his Ph.D. thesis entitled "Gene prediction and transcriptional regulation analysis using comparative genomics". |
| December 2, 2010 | Bora Uyar defended successfully his M.Sc. thesis, entitled "Homology and evidence-based genome annotation of Caenorhabditis species". Photos |
| September 27, 2010 | Christian Frech's co-authored review paper entitled "The Vibrio cholerae Type VI Secretion System: Evaluating Its Role in the Human Disease Cholera" has been accepted for publication in Frontiers in Cellular and Infection Microbiology. |
| September 21, 2010 | Christian Frech's paper entitled "Genome-wide Comparative Gene Family Classification" has been accepted for publication in PLoS ONE |
| September 17, 2010 | Ismael Vergara's paper entitled "Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster." has been accepted for publication in BMC Genomics |
| September 17, 2010 | Maja Tarailo-Graovac's paper entitled "Spindle assembly checkpoint genes reveal distinct as well as overlapping expression that implic ates MDF-2/Mad2 in postembryonic seam cell development in Caenorhabditis elegans." has been accepted for publication in BMC Cell Biology |
| September 15, 2010 | Group pictures taken for MBB 10 year annierversary slide show. |
| August 24, 2010 | Ismael Vergara's abstract "Loss-of-function mutations in a natural isolate of Caenorhabditis elegans" has been selected to be platform presentation at the CSHL/Hinxton Genome Informatics meeting, which will be held in Hinxton, England in September. |
| July 16, 2010 | Lucie successfully defended her M.Sc. thesis entitled "Characterization of nematode DAF-19 and human RFX6 transcription factors". |
| June 29, 2010 | Christian Frech (Ph.D. student) has been awarded Graduate Fellowships for one semester for the 2009-2010 academic year. |
| June 7, 2010 | Jeff Chu's co-authored manuscript "Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks" has been accepted for publication in PLoS ONE. |
| April 15, 2010 | Ismael Vergara won the second prize for his talk entitled "Identification and Functional Characterization of Genomic Variations: Lessons from C. elegans." at the 2010 MBB Symposium. |
| Mar 23, 2010 | Jeff Chu's paper entitled "Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans" has been accepted for publication in BMC Evolutioanry Biology |
| Mar 11, 2010 | Tammy Wong and Di Zhang have been awarded with SFU VPR USRA, which will support their work in our lab in the summer semester. Their will continue their current research projects, which may lead to the molecular characterization of the genes they will (hopefully) identify in their bioinformatics studies. |
| Feb 24, 2010 | Jeff Chu and collaborators (Allan Mah and others) published a paper entitled "Characterization of the octamer, a cis-regulatory element that modulates excretory cell gene-expression in Caenorhabditis elegans" in BMC Molecular Biology. |
| Feb 22, 2010 | Iris Eom has won a 2010 NSERC USRA (Undergraduate Student Research Award. With this support, Iris will be working in our laboratory in the Summer Semester. Iris is a joint-major student in the School of Computing Science and the Department of Molecular Biology and Biochemistry. |
| Feb 10, 2010 | Bora Uyar gave a talk entitled "Genome annotation improvement of four Caenorhabditis species: C. briggsae, C. remanei, C. brenneri, and C. japonica" at the VanWorm meeting. |
| Dec 15, 2009 | Jeff Chu's manuscript entitled "Fast and accurate gene prediction by decision tree classification", co-authoered with Rong She (SFU CS), has been accepted for publication in the SIAM International Conference in Data Mining (2010). |
| Dec 1, 2009 | Chris Frech won a Weyerhaeuser Molecular Biology Graudate Scholarship for Spring 2009. |
| Nov 16, 2009 | Penny Ng published an article entitled "GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes"." in BMC Genomics. |
| Sep 3, 2009 | Ismael Vergara published a book chapter entitled "Using OrthoCluster for the detection of synteny blocks among multiple genomes." in Current Protocols in Bioinformatics. |
| Aug 24, 2009 | genBlast web server Version 0.1 has been released. It is a test release. This web server was set up by summer student Jacob Sheehy, with support from Jeffrey Chu and many other members of the lab. |
| Aug 13, 2009 | Ismael Vergara is awarded with a DL Baillie Graduate Scholarship in Molecular & Cellular Biology. |
| July 15, 2009 | Ismael Vergara, Maja Tarailo-Graovac and colleagues published a paper entitled "Polymorphic segmental duplication in in the nematode Caenorhabditis elegans" (Vergara, Mah, Huang, Tarailo-Graovac, Johnsen, Baillie and Chen) in BMC Genomics |
| June 30, 2009 | Lucie Semenec (M.Sc. student), Ismael Vergara (Ph.D. candidate) and Christian Frech (Ph.D. student) have been awarded Graduate Fellowships for one semester for the 2009-2010 academic year. |
| June 27, 2009 | Maja Tarailo-Graovac won an award for her artwork at the 17th International C. elegans meeting in Los Angeles. |
| June 27, 2009 | Ismael Vergara present a poster entitled "Polymorphic segmental duplications in C. elegans" (Vergara, Mah, Huang, Tarailo-Graovac, Johnsen, Baillie and Chen) at the 17th International C. elegans meeting in Los Angeles. This poster was awarded a second prize. Ismael also presented two additional posters: "Characterization of synteny blocks and comparative analysis of operons in Caenorhabditis elegans" (Vergara and Chen) and "Annotation and analysis of repeats in five Caenorhabditis species" (Vergara, Fong, Schwartz and Chen). |
| June 26, 2009 | Maja Tarailo-Graovac presented a talk entitled "Spatiotemporal analysis of promoter functionas implicate spindle assembly checkpoint genes in polyploidization in Caenorhabditis elegans" (Tarailo-Graovac, Wang, Chu, Tu, Baillie and Chen) at the 17th International C. elegans meeting in Los Angeles. Her session is Gene Expression. |
| June 25, 2009 | Jeffrey Chu presented a talk entitiled "OrthoCluster and genBlast" at the "Genomics and Evolution" Workshop at the 17th International C. elegans meeting in Los Angeles. Jeff also presented a poster entitled "Reannotating the C. elegans genome using genBlastG, a new homology-based gene finder" (Chu, She, Wang and Chen) |
| June 23, 2009 | Ismael Vergara, Penny Ng, Christian Frech and collaborators published a paper entitled "OrthoClusterDB: a web server for synteny blocks" (Ng, Vergara, Frech, Chen, Zeng, Pei and Chen) in BMC Bioinformatics. |
| April 29, 2009 | Ismael Vergara presented his research entitled "Large synteny blocks and fast operon divergence revealed by comparative analysis of Caenorhabditis elegans and Caenorhabditis briggsae genomes" at the monthly VanWorm meeting, held at the Trinity Western University in Langly, BC. Other members of the lab, Maja Tarailo-Graovac, Ismael Vergara, Lucie Semenec, Jeff Chu, and Jack Chen als attended. |
| April 17, 2009 | Jeff Chu presented his research entitled "DAF-19 represses gene expression in C. elegans via a divergent X-box motif" at the Annual Vancouver-Seattle Worm Meeting held at the University of Washington in Seattle. Other members of the lab, Maja Tarailo-Graovac, Ismael Vergara, Lucie Semenec, and Jack Chen also attended. |
| April 6, 2009 | Matthew Nesbit successfully defended his M.Sc. thesis entitled "Tag-based amplification of cDNA ends (TACE): a new approach to gene discovery". |
| March, 2009 | Two high school students, who were supported by the Canadian Gene Cure Foundation, spend a week in our lab |
| March, 2009 | Maja Tarailo-Graovac and Jack Chen published a book chapter entitled "Using RepeatMasker to identify repetitive elements in genomic sequences" in Current Protocols in Bioinformatics. |
| March 25, 2009 | Jeff Chu won the third prize for his talk entitled "DAF-19 represses a Pellino-like gene in C. elegans via a divergent X-box motif." at the 2009 MBB Symposium. |
| January, 2009 | Jeff Chu, Jack Chen and collaborators published a paper entitled "genBlastA: enabling BLAST to identify homologous gene sequences" in Genome Research. |
| November, 2008 | Jack Chen wrote an invited article entitled "Bioinformatics in the era of genomics" for Biotechnology Focus. | August, 2008 | Syed Aftab, Lucie Semenec, Jeff Chu, and Jack Chen published a paper entitled "Identification and characterization of novel human tissue-specific RFX transcription factors" in BMC Evolutionary Biology. |
| May, 2008 | Jack Chen represented Simon Fraser University at the BC Canada Pavilion in Beijing. |
| March, 2008 | Ismael Vergara, Matt Nesbitt, Jack Chen and colleagues published a paper entitled "OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics" in EDBT'08. |
| September, 2007 | Jeff Chu, Jack Chen, and collaborators published a paper entitled "Transcriptional Regulation of AQP-8, a Caenorhabditis elegans Aquaporin Exclusively Expressed in the Excretory System, by the POU Homeobox Transcription Factor CEH-6" in Journal of Biological Chemistry. |
| May, 2007 | Jack Chen and collaborators published a review article entitled "Genomics and biology of the nematode Caenorhabditis briggsae" in WormBook. |
| March, 2007 | Jack Chen and collaborators published a paper entitled "Comparative Genomics and Adaptive Selection of the ATP-Binding Cassette (ABC) Transporter Family in Caenorhabditis Species" in Genetics. |
| January, 2007 | Jack Chen and collaborators published a paper entitled "WormBase: new content and better access" in Nucleic Acids Research. |
| December, 2006 | Jeff Chu, Jack Chen, and collaborators published a paper entitled "Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics" in Genome Biology. It is marked as "highly accessed". |
| December, 2006 | Jack Chen and collaborators published a paper entitled "A genomic view of the sea urchin nervous system" in Developmental Biology. |
| November, 2006 | Jack Chen and collaborators published a paper entitled "The genome of the sea urchin Strongylocentrotus purpuratus" in Science. |
| Maja Tarailo-Graovac, Ph.D., Postdoctoral fellow (Since January 2008) B.Sc. Univeristy of British Columbia; Ph.D. Universit of British Columbia. CIHR Postodtoral Fellowship (in partership with Fanconi Canada) |
 |
| Christian Frech, Ph.D. candidate (Since September 2008) B.Sc. University of Linz, Austria. |
|
| Jun Wang, Ph.D. candidate (Since September 2008, first as M.Sc. student) B.Sc. Simon Fraser University. |
 |
| Timothy Warrington, Ph.D. student (Since September 2011) B.Sc. University of Alberta; M.Sc. University of Alberta. |
 |
| Tammy Wong, M.Sc. student (Since January 2010, first as ISS, then SFU-USRA) B.Sc. Simon Fraser University CIHR Master's Award |
 |
| Ting Zhang, M.Sc. student (Since September 2011) B.Sc. Fudan University, China. |
 |
| Zhaozhao Qin, M.Sc. student (Since September 2011) B.Sc. Shandong University at Weihai, China. |
 |
| Shanshan Zou, visiting Ph.D. student (January 2010, from The Second Military Medical School, Shanghai) |
|
| Raunak Shrestha, CIHR/MSFHR Bioinformatics Training Program rotation student (September 2011-) |
|
| Collin Massey, volunteer (Since November 2011, from Simon Fraser University) |
|
| Spencer Myrtle, volunteer, SFU VPR-USRA (May - Aug, 2011) (Since September 2010, from Simon Fraser University) |
|
| Caleb Choo, volunteer (Since September 2010, from Simon Fraser University) |
|
| John Koo, volunteer (Since September 2010, from Simon Fraser University) |
|
| Asal Malekzadeh, volunteer (Since September 2010, from Simon Fraser University) |
|
| Tao Luo, Research technician (Since January 2008) |
| Jonathan Lim, ISS student, VPR USRA student (January 2011 - Aug 2011; currently a graduate student at UBC) |
|
| Caroline Wang, Volunteer student (May 2011 - Aug 2011; currently an undergraduate student at Univerity of Toronto) |
|
| Rachel (Jingyi) Hu, Volunteer student (July 2011 - Aug 2011; Shanghai Jiao-Tong Univeristy Medical School) |
Jeffrey Chu, Ph.D. candidate (May 2006 - Feb 2011, first as M.Sc. student; currently Postdoctoral fellow with Dr. Ann Rose at UBC) |
 |
| Ismael Vergara, Ph.D. candidate (September 2007 - August 2011; currently Scientist at GenomeDX Biosciences Inc.) |
 |
| Bora Uyar, M.Sc. student (CIHR/MSFHR Bioinformatics Training Program
) (June 2009 - December 2010; currently Ph.D. student at EMBL, Heidelberg) |
 |
| Lucasz Wieteska, visiting Ph.D. student (August, 2010; currently Ph.D. student in the University of Alberta) |
|
| Di Zhang, volunteer (January 2010 - Aug 2010, first as ISS, then SFU-USRA student; currently in the Pharmacy Program at UBC) |
 |
| Jeffrey Shinoki, volunteer (Since January 2010, from Simon Fraser University) |
|
| John Wu, volunteer (September 2010 - November 2010, from the University of British Columbia) |
|
| Lucie Semenec, M.Sc. student (September 2007 - July 2010; currently works as Market Research Analyst at iData Research) |
 |
| Ava Yap, summer student (June 2010 - August 2010, from Johns Hopkins University) |
|
| Iris Eom, NSERC-USRA student (May 2010 - Aug 2010) |
|
| Jasmine Lin, summer student (Since June 2010, from Cornell University) |
 |
| Victoria Ng, MBB undergraduate research student (January-April 2010) |
|
| Behnaz Kahrobaee-Khorassani, BISC undergraduate research student (January-April 2010) |
|
| Elahe Kahrobaee-Khorassani, BISC undergraduate research student (January-April 2010) |
|
| Eric Chen, Student volunteer (January-April 2010, currently graduate student at the University of Ottawa) |
|
| Bhav (Bhavjinder) Khaira, M.Sc. rotation student (CIHR/MSFHR Bioinformatics Training Program) (January-April 2010; currently Ph.D. student with Dr. Fiona Brinkman at SFU) |
 |
| Joanne Trinh, Student volunteer (June-December 2009) (Home University: Univerisity of British Columbia; currently undergraduate student at the University of British Columbia) |
|
| Benedikt F. Zimmermann, ISS student (May 2009 - November 2009; currently at the company GenomeDX in Vancouver) |
|
| Jacob Sheehy, Summer student (May 2009 - August 2009) (Home University: Concordia University; currently works in NAKISA) |
|
| Christine Wang, Summer student (May 2009 - August) (Home University: University of Pennsylvania) |
|
| Mei Tang, Research technician (June 2009 - November 2009) |
|
| Matthew Nesbitt, Graduate student (January 2007 - April 2009; currently works in Aurora Biomed as Team Leader - Genomics Development.) |
 |
| Fong Chan, ISS student (January 2009 - May 2009; currently graduate student in the CIHR/MSHFR Bioinformatics Training Program) |
|
| Patrick Tan, Student volunteer (January 2009 - May 2009; currently graduate student in the CIHR/MSHFR Bioinformatics Training Program) |
|
| Ken Fong, ISS student (January 2009 - May 2009) |
|
| Levin (Miao) Pan, International Exchange
Student Home University: Tsinghua University (Beijing, China) (August 2008 - December 2008) |
|
| Penny Ng, CO-OP student, NSERC USRA student (January 2008 - August 2008) |
 |
| Syed Aftab, NSERC USRA student, ISS student, Research technician
(May 2007 - July 2008; currently a medical student at Duke-NUS Graduate Medical School) |
|
| Qingkang Chen, NSERC USRA student Home University: University of Waterloo (June 2008 - August 2008) |
|
| Kamran Vahedi-Tafreshi, SFU Work-Study student (January 2007 - March 2007) |
