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Gareth Palidwor

 

me, eating popsicle. by Amelia, age 5

I am a Research Assistant working in Theodore J. Perkins' lab at the Ottawa Hospital Research Institute.

Projects 

I do variety of things here, including:

  • Development of custom data analysis and data visualization software, such as Phyloview, Bluster, ARD and MLTrends.
  • Assorted data aggregation and analysis of Microarray, SAGE, Proteomics, Solexa and other data in support of work by our group and other OHRI and the Stem Cell Network researchers.
  • Maintenance of the StemBase system: extending and maintaining the software and curating data added to the system.
  • Hiring and supervision of high school, college and unversity students.
  • The care and feeding of our compute cluster, various departmental servers, the associated software menagerie and this web server.
  • Setting up and supporting Mascot, a BioWorks Sequest cluster, the Trans Proteomics Pipeline analysis system and the Solexa sequence anaysis pipeline.
  • In supporting and collaborating with students and researchers in the OHRI and the Stem Cell Network, our group provides training in Bioinformatics, microarrays and data analysis:
    • I've participated in the development of an online course on Microarray Analysis, personally developing and delivering two course segments.
    • Collaborated in providing a one day Next Generation Sequencing ChIP-Seq data analysis workshop.

Peer-Reviewed Publications

  • Andrade-Navarro MA, Palidwor GA, Perez-Iratxeta C.  Peer2ref: a peer-reviewer finding web tool that uses author disambiguation., BioData Mining, 2012, [PMID: 22958760]
  • Soleimani VD, Punch VG, Kawabe Y, Jones AE, Palidwor GA, Porter CJ, Cross JW. Carvajal JJ, Kockx CEM, and van IJcken W.F.J.  Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs, Developmental Cell, 2012, [PMID: 22609161]
  • Palidwor GA, Perkins TJ, Xia X.  A General Model of Codon Bias Due to GC Mutational Bias, PLoS ONE, 2010, [PMID: 21048949]
  • Palidwor GA, Andrade-Navarro MA, MLTrends: Graphing MEDLINE term usage over time, J Biomed Discov Collab, 2010, [MLTrends Server] [PDF] [PMID: 20333611]
  • Scimè A, Desrosiers J, Trensz F, Palidwor GA, Caron AZ, Andrade-Navarro MA, Grenier G. Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing. Mech Ageing Dev. 2009 Nov 12. [Epub ahead of print] [PMID: 19913570]
  • Sandie R, Palidwor GA, Huska MR, Porter CJ, Krzyzanowski PM, Muro EM, Perez-Iratxeta C, Andrade-Navarro MA. Recent developments in StemBase: a tool to  study gene expression in human and murine stem cells. BMC Res Notes. 2009 Mar 10;2:39. [PMID: 19284540] [PDF] [StemBase]
  • Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, Arumughan A, Foulle R, Porras P, Sanchez-Pulido L, Wanker EE, Andrade-Navarro MA. Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput Biol. 2009 Mar;5(3):e1000304. Epub 2009 Mar 13. [PMID: 19282972] [PDF] [ARD Server] [Publication Illustration used as Issue Image]
  • Perez-Iratxeta C, Palidwor G, Andrade-Navarro MA. Towards completion of the Earth's proteome. EMBO Rep. 2007 Dec;8(12):1135-41.  [PMID: 18059312][PDF]  [figure from paper adapted for use as cover art for that issue]
  • McCann JA, Muro EM, Palmer C, Palidwor G, Porter CJ, Andrade-Navarro MA, Rudnicki MA. ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation. BMC Genomics. 2007 Sep 14;8:322.  [PMID: 17868463] [PDF]
  • Hailesellasse Sene K, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA. Gene function in early mouse embryonic stem cell differentiation. BMC Genomics. 2007 Mar 29;8:85. [PMID: 17394647] [PDF]
  • Palidwor G, Reynaud EG, Andrade-Navarro MA. Taxonomic colouring of phylogenetic trees of protein sequences. BMC Bioinformatics. 2006 Feb 17;7:79. [PMID: 16503967] [PDF]
  • Xia X, Palidwor G. Genomic adaptation to acidic environment: evidence from Helicobacter pylori. Am Nat. 2005 Dec;166(6):776-84. Epub 2005 Oct 4. [PMID: 16475092] [PDF]
  • Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA, Rudnicki MA, Andrade MA. Study of stem cell function using microarray experiments. FEBS Lett. 2005 Mar 21;579(8):1795-801. [PMID: 15763554] [PDF]

    • Book Chapters

  • Porter, C.J., G.A. Palidwor, R. Sandie, F. Price, P.M. Krzyzanowski, E.M. Muro, S. Hoersch, M. Smith, P.A. Campbell, C. Perez-Iratxeta, M.A. Rudnicki, M.A. Andrade-Navarro. In press. Paired SAGE-microarray expression data sets reveal antisense transcripts differentially expressed in embryonic stem cell differentiation. In Computational Biology of Embryonic Stem Cells. M. Zhang (Ed.). Bentham Scientific Publishers. [In Press]
  • Porter CJ, Palidwor GA, Sandie R, Krzyzanowski PM, Muro EM, Perez-Iratxeta C, Andrade-Navarro MA. StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol Biol. 2007;407:137-48. [PMID: 18453254]

    • Other Publications

    • Andra Waagmeester, Gareth Palidwor, Pawel Szczesny, Istvan Albert, Mary Mangan, Chris Miller, Simon Cockel, Pierre Lindenbaum, Daniel A. M. M. Silvestre, Giovanni Marco Dall’Olio & Chris Evelo. Acknowledging contributions to online expert assistance, Nature Precedings, June 21, 2011
    • Gareth Palidwor. "Book Review: 'Alternative Careers in Science: Leaving the Ivory Tower", Cell Lines, May 2007
    • Gareth Palidwor. "Getting a Job After Your Graduate Degree: Becoming a Patent Agent", Cell Lines, March 2007
    • Gareth Palidwor. "Getting a Job After Your Graduate Degree: Working in  Technology Transfer", Cell Lines, January 2007
    • Gareth Palidwor. "AGM: Trainee Professional Development Day: Jobs in Stem Cell Research: Academia, Industry and Policy", Cell Lines, December 2006
    • Gareth Palidwor. "PHP and ASP.NET: Playing Well with Others", ASP.net 2.0 Training Center, June 2006
    • Gareth Palidwor. "A PHP Developer's Guide to ASP.NET 2.0", ASP.net 2.0 Training Center, March 2006
    • Gareth Palidwor. "HomeBrew: My First Computer". Make Magazine. O'Reilly and Associates. February 2005. 192

    Misc

    • Two units of the online Microarray Analysis Course Tutorial developed by our lab for the Stem Cell Network: "Introduction to Affymetrix Microarrays" and "Microarray Pitfalls".

    Personal

    • In November 2010 I completed an MSc. in Biology at the University of Ottawa with Dr. Xuhua Xia as my supervisor. My thesis concerns the effect of codon bias on gene expression and makes extensive use of StemBase microarray expression data; the paper "A General Model of Codon Bias Due to GC Mutational Bias" published in PLoS ONE is also chapter 4 of my thesis.
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    Contact Information

       Ontario Genomics Innovation Centre
       501 Smyth Road Ottawa, Ontario, K1H 8L6
       (613) 737-8899 x73255 (phone)
       (613) 737-8803 (fax)
      

       (At the Sprott Centre for Stem Cell Research, 5th floor of the General Hospital Eye Institute Building)