James Wasmuth's Home Page
from the imagination of Jenny MacKendrick
| I am a postdoctoral fellow in John Parkinson's Lab at the Hospital for Sick Children, in Toronto. I shall use this page to post research highlights, when they happen, and perhaps other musings from my work.
Brief CV Here is a slightly embarrassing profile. 2006-present - Postdoctoral Fellow. Program for Molecular Structure and Function. 2003-2005 Ph.D. University of Edinburgh, UK. Title: "Computational analysis of proteomes from parasitic nematodes." 2001-2002 MRes Bioinformatics. University of York, UK 1997-2000 BSc Hons Biochemistry. Imperial College, London, UK October 2005 Awarded Young Bioinformatician of the Year by the UK Bioinformatics Forum. |
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Research Interests
I joined the Parkinson lab in March 2006. I currently have three primary projects:
1. Comparative genomics of parasities.
I have a huge interest in using computational genomics and systems biology to study eukaryotic parasites. The focus is on the phylum Apicomplexa. We have completed a comparison of genome datasets from 15 species of apicomplexans. This work is now available in Genome Research. Building on this work, I have now begun a domain analysis of the parasite proteins. We found a number of protein domains that had unusual phylogenetic distributions; the function of these domains is related to host immune response. We are following up some of these with functional assays to determine the importance of the parasite copy in its survival.
2. Metabolic Networks of apicomplexans
The field of metabolomics is an emerging one. The work I am involved with began with helping develop a sensitive software tool for the sensitive identification of metabolic enzymes, which greatly aids in the reconstruction of an accurate metabolic network [Hung et al. in review]. The metabolic network of P. falciparum is now being examined within a mathematical framework. Specifically, we have used flux balance analysis (FBA) to test various hypotheses taken from the literature [Raja et al. in prep].
3. Exploration of protein domain repertoire in the Eukarya.
The expressed sequence tag (EST) datasets of over 400 species represent a wealth of genomic data. I have predicted and corrected the coding regions of these sequences (using prot4EST). These sequences have been decorated with protein domain annotation from popular databases. Using graph theory methods, I am exploring the extent of protein domain 'movement' and adaptions for different taxa.
My Ph.D. thesis was based on the study of parasitic nematode transcriptomes and I welcome the opportunity to further this work through collaboration with interested parties. Let me know.
Publications
Raja F, Hung S, On T, Wasmuth J & Parkinson J.
Flux balance analysis of Plasmodium falciparum: Insights into a parasite's metabolism.
In review
Hung S, Wasmuth J, Sanford C & Parkinson J.
DETECT - A Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum.
Bioinformatics. 2010 26:1690-1698 - abstract
Crawford J, Lamb E, Wasmuth J, Grujic O, Grigg M & Boulanger M.
Structural and functional characterization of SporoSAG: A SAG2 related surface antigen from Toxoplasma gondii.
Journal of Biological Chemistry. 2010 285(16):12063-70
PMID: 20164173 - abstract
Persaud A, Amsen E, Xiong X, Wasmuth J, Saadon Z, Fladd C, Parkinson J & Rotin D.
Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays
Molecular Systems Biology. 2009 5:333.
PMID: 19953087 - Free Online Access
Wasmuth J, Daub J, Peregrín-Alvarez J-M, Finney C & Parkinson J.
The origins of apicomplexan sequence innovation
Genome Research. 2009 19(7):1202-13.
PMID: 19363216 - abstract
Wasmuth J, Schmid R, Hedley A & Blaxter M.
On the extent and origins of genic novelty in the Phylum Nematoda
PLoS Neglected Tropical Disease. 2008 2(7): e258
PMID: 18596977 - Free Online Access
Cutter A, Wasmuth J & Washington N.
Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing
Genetics. 2008 178:2093-104.
PMID: 18430935 - abstract
Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Krogan N, Boone C, Parkinson J & Rotin D.
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Nat. Mol. Sys. Biol. 2007. 3:116
PMID: 17551511 - Free Online Access
Cutter AD, Wasmuth JD & Blaxter ML.
The evolution of biased codon and amino acid usage in nematode genomes.
Mol Biol Evol. 2006 23:2303
PMID: 16936139 - Free Online Access
Wasmuth JD & Blaxter ML.
prot4EST: translating expressed sequence tags from neglected genomes.
BMC Bioinformatics. 2004 5:187.
PMID: 15571632 - Free Online Access
Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A & Blaxter M.
PartiGene--constructing partial genomes.
Bioinformatics. 2004 20:1398
PMID: 14988115 - Free Online Access
Invited Seminars / Conference Talks
Mar 10 School of Veterinary Medicine, Univ. of Calgary, Canada
Feb 10 Institute of Parasitology, McGill University, Montreal, Canada
Sep 09 School of Biological Sciences, Univ. of Edinburgh
Apr 09 Centre for Ecology and Conservation, Univ. of Exeter, Cornwall Campus (UK)
Apr 09 Program in Molecular Structure and Function, Hosp. for Sick Children, Toronto.
Sep 08 Molecular Parasitology Meeting - MBL, Woods Hole, MA, USA
Nov 07 Program in Genome Biology and Bioinformatics, Toronto
Dec 06 Rocky Mountains Bioinformatics Meeting - Snowmass CO, USA
Mar 06 JSPS-ESF Workshop on Functional Genomics - Kanagawa, Japan
May 05 Seminar for Karolinska Centre for Genomics & Bioinformatics - Stockholm, Sweden
Apr 05 Program for Genetics, Hospital for Sick Children - Toronto, Canada.
Oct 05 Young Bioinformatics Forum, Institute of Physics - London, UK
Dec 04 Department of Biology, University of York - York, UK.
Oct 04 Department of Biochem. & Mol. Biol. Dalhousie University - Halifax, Canada.
(I'll add links to the slide PDFs soon).
Poster abstracts
BioSysBio 2005 - Edinburgh
ESF-JSPS Frontier Conference Functional Genomics - San Feliu de Guixols, Spain.
ISMB 05 - Glasgow, UK.
Computational Genomics Conference 2005 - Reston VA, USA.
Awards
Oct 2008 RTC Trainee Travel Award by Hospital for Sick Children
Dec 2006 RTC Trainee Travel Award by Hospital for Sick Children
Oct 2005 Young Bioinformatician of the Year by the UK Bioinformatics Forum.
2002-2005 Ph.D. Studentship from BBSRC, UK
2002-2005 Industrial CASE award from Astra Zeneca, UK
2001-2002 Masters Studentship from BBSRC, UK
Thank yous
My work is currently funded by a fellowship provided by the Research Institute at Sickkids and a grant from the CIHR.
My Ph.D. work was funded by the BBSRC, UK and a CASE award from Astra Zeneca.
Data Links
NemPep4
NemDom4_pfam23
Gene structures for five genomes
