Lee S Parsons
PhD
Plymouth, MN
Introduction
I began my graduate studies at SUNY Upstate Medical University in August, 2005. By May of 2006 I declared my intention to do my Ph. D. research under the direction of Dr. Stephan Wilkens in the Department of Biochemistry & Molecular Biology. I had previously completed a Bachelor of Science in Biochemistry through the College of Biological Sciences at the University of Minnesota, Twin Cities. I defended my PhD thesis on January 4, 2013, and completed my final requirements for graduation on January 31, 2013.
My undergraduate experience also included bioinformatics work at CCGB (now CBRI (more recently absorbed into MSI)) under Dr. Ernest Retzel (Dr. Retzel is now at NCGR). Other alumni of the CCGB group include Bob Milius (now at the UMN cancer center), Chris Dwan (now with BioTeam), Tim Kunau (now with Realiable Resources), and Martina Stromvik (now at McGill), amongst others. Much of my work was done as part of the Arborea Project in partnership with John MacKay at Universitie Laval.
Current Work
My thesis work involves the Vacuolar ATPase (V-ATPase). The V-ATPase is a structural and functional relative of the better-known F-ATPase (also known as the ATP Synthase). Our collaborator Dr. Patricia Kane has written numerous review articles on the V-ATPase, including this 2007 review article. Both of these rotary molecular engines have rotating and stationary parts - similar to an electric engine or the Wankel rotary engine.
One component of my work involves Mass Spectrometry to identify proteins based on their mass. For those not familiar with mass spec, I have begun writing a web page Mass Spectrometry For Dummies.
The Wilkens Lab
Dr. Wilkens brought his lab from The University of California - Riverside to SUNY Upstate in 2005. As of February 2010, the lab includes three Ph. D. graduate students (including myself).
My Papers
NCBI Pubmed can be searched in my name using the query of
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Parsons,+Lee[Full+Author+Name]
I have one first-author paper from my graduate work:Parsons LS, Wilkens, S
Probing subunit-subunit interactions in the yeast vacuolar ATPase by peptide arrays. PLoS ONE e46960, Epub 2012 Oct 12
I have also aided in authoring the following papers:Mitrea DM, Parsons LS, Loh SN
Engineering an artifical zymogen by alternate frame protein folding. Proc Natl Acad Sci USA 2010 Jan 26 [Epub ahead of print]
Pavy N, Boyle B, Nelson C, Paule C, Giguere I, Caron S, Parsons LS, Dallaire N, Bedon F, Berube H, Cooke J, Mackay J.
Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses. New Phytologist 2008; 180:4, 766-786
Pavy N, Parsons LS, Paule C, MacKay J, Bousquet J.
Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 2006; 7:174
Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Bufferfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Sequin A, Retzel E, Bousquet J, MacKay J.
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 2005; 6:144
I have also been thanked or acknowledged on the following papers:Kish-Trier E, Wilkens S.
Domain architecture of the stator complex of the A1AO-ATP synthase from Thermoplasma acidophilum. J Biol Chem 2009; 284(18):12031-40.
Oot RA, Wilkens S.
Domain characterization and interaction of the yeast vacuolar ATPase subunit C with the peripheral stator stalk subunits E and G. J Biol Chem 2010; 285(32):24654-64.
Posters
Posters I have presented at conferences
Lee S Parsons and Stephan Wilkens, Structural System Intraactomics by Peptide Arrays: Interrogating the Vacuolar ATPase. Presented at the World Congress of the Human Proteomics Organization (HUPO), 2009; Toronto Ontario Canada.
Undergraduate
As mentioned above, my BS in Biochemistry was completed at The University of Minnesota, Twin Cities. After I decided to major in Biochemistry I worked for a while at The Minnesota Daily before going in to Bioinformatics near the end of my degree. While working in bioinformatics I saw the work that was being done in proteomics and decided which way I wanted to go in my graduate career.
Conferences
Conferences I have attended as a graduate student
12th Annual Human Proteome Organization (HUPO) World Congress September 9-13, 2012 - Boston, MA.I had around 40 pages of notes from this conference. Lee S Parsons' notes on HUPO 2012 Boston are available now.7th Annual US Human Proteome Organization (USHUPO) Conference, in Raleigh, North Carolina. This conference ran from 20 - 23 March, 2011.I presented a poster, and took 30 pages of notes at this conference. You can read my notes and thoughts on US HUPO 2011 on my web site.
8th Annual Human Proteome Organization (HUPO) World Congress September 26-30, 2009 - Toronto, ON, CanadaMy notes and thoughts on the conference are posted at HUPO2009 notes and thoughts from Lee S Parsons. I took over 30 pages of notes in that conference, which I have parsed and digitzed for web consumption.16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008) July 19-23, 2008 - Toronto, ON, Canada
My notes and reflections on the conference are posted at ISMB2008 notes and thoughts from Lee S Parsons. This represents over 20 pages of notes and is not yet completely digitized.8th International Conference of the Canadian Proteomics Initiative (CPI) May 3-5, 2008 - Vancouver, BC, Canada
My notes on CPI2008 are available.7th International Conference of the Canadian Proteomics Initiative (CPI) June 16-18, 2007 - Ottawa, ON, Canada
My notes on CPI2007 are available.
Notable Biochemists and Molecular Biologists
I have noticed that people with advanced degrees in biochemistry and/or molecular biology show up in many interesting places beyond the biological sciences. Here is an incomplete list, in no particular order.
Isaac Asimov held a PhD in biochemistry from Columbia University and a faculty position at Boston University. Of course more people know of him for his science fiction writings.
Lincoln Stein is the author of CGI.pm, which is the code that runs many form submission procedures on the world wide web. Dr. Stein currently works at Cold Spring Harbor Labs.
Milo Aukerman, of the punk band The Descendants holds a Ph. D in biochemsitry from University of Wisconsin - Madison.
Dexter Holland, of the band The Offspring holds a masters in Molecular Biology from The University of Southern California and was a Ph. D candidate.
Bill Kennedy is a respected author on WWW topics (notably for the book HTML & XHTML: The Definitive Guide that he co-authored). He holds a Ph. D in biophysics from Loyola University - Chicago.
My Programming Bits
The digital aspect of my work is often assisted significantly by good programming efforts. I sometimes supplement that with some of my own work, some of which is described and available in Lee's Perl Crapplets. That page has small bits of Perl code that I have written over the years to make simple repetitive tasks a little easier to manage.
Disclaimer
This page was written by Lee Parsons. This page has not been reviewed by The Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, The State University of New York, or anyone else associated with the above, and the statements herein should not be taken to be the opinion of any of those.
All rights reserved, 2008-2009.
Links
Other Pages Hosted Here
Musings
- My laptop, this server, and to a lesser degree, my wife's Mac, all run FreeBSD
- I pondered before How much is a cubic yard of cash?
- I wondered before what the numeric values were for black and white in JPG
- Some time ago I received an interesting spam/phishing email titled LIVE OR DIE
- Some of My AntiSpam Writings are posted here as well. Admittedly, that page has not been updated in a while...