Christopher John Mason		
625 Third Ave SW		
Rochester, MN 55902		
cmason@cmason.com
507.202.3755


SUMMARY:	Computational biology software developer and manager with over eight years experience who 
is passionate about creating powerful and usable software that betters the human condition.  I 
have forged, lead, and participated on diverse teams combining probabilistic/statistical 
algorithms and humane interfaces to solve large and important problems related to human 
health.  I possess the technical background necessary to both implement sophisticated software 
systems and to communicate with developers, statisticians, biologists and chemists alike.  
However, I also know that technical skill in isolation is not sufficient. I believe that great things 
happen when people of varied backgrounds are challenged to collaborate in solving interesting 
and relevant problems and hope to bring my skills to bear on your organization's challenges.


EDUCATION:	BS in Biological Sciences and Computer Science  Carnegie Mellon University	 May  2001	
            Honors: Merck Computational Biology Summer Scholar, 1999.


EXPERIENCE:	(selected)
Mayo Clinic Proteomics Research Center (MPRC)	Rochester, MN
Senior Analyst Programmer		March 2004-present
Analyst Programmer		August 2003-March 2004
- Significant contributions to securing competitive grant awards of over $3M in direct costs.
- Responsible for hiring and leading a team of bioinformatics software developers.
- Interfaced with users, gathered requirements, developed mockups/plans, wrote code.
- Authored three and co-authored four peer-reviewed articles on analysis of mass spectrometry 
  data with a focus on developing algorithms for biomarker discovery by LC-MS.
- Developed open source, object-oriented library (libmprc) in C++ & R for analyzing terabyte-
  scale high-resolution mass spectrometry datasets. Includes FT-ICR transient processing, 
  peak picking, isotope cluster detection (THRASH, 18O labeling), artifact removal, statistics, 
  etc.  Used in support of research on Pancreatic & Ovarian Cancer, Diabetes, others.
- Managed/developed protein identification workflow system using Java/Servlets, GWT, JMS, 
  Groovy, Hibernate/Oracle that combines statistical algorithms (Peptide/Protein Prophet) 
  with a facile Web 2.0 interface, custom visualizations and DRMAA/Grid Engine.
- Developed 3D OpenGL LC-MS chromatogram visualization tool used for quality control.

Sequel Genetics, Inc.		Pittsburgh, PA
Software Group Leader, Programmer	May 2000 - May 2002
- Led Sequel's informatics efforts and developed strategy.  Managed software developers.
- Designed, built and deployed a complex, client-server software system for analyzing and 
  visualizing mass spectrometry data resulting from Sequel's proprietary genotyping process in 
  18 months with two people.  (~100,000 lines of code in C++, Java, and Perl)
- Designed an easy to use, fast, threaded user interface for viewing spectra and implemented in 
  Java Swing and CORBA.  Sophisticated caching architecture; novel visualization algorithms.
- Implemented templated object persistence/query interface using Objectivity object database.
- Performed competitive review of genotyping products and contributed to a technical 
  development plan; both were used in securing second round financing.

Carnegie Mellon University Department of Biological Sciences	Pittsburgh, PA
Merck Scholar, Research for Credit, Rule Lab	August 1998-December 2000	
- Twice awarded support from the Merck foundation for developing a modular C++ tool for 
  determining protein homology using sparse Nuclear Magnetic Resonance (NMR) data.

(I also spent eight summers as intern in software development at IBM Transarc, Texas Instruments, 
  etc.)


PUBLICATIONS: 
A method for automatically interpreting mass spectra of 18O labeled isotopic clusters.  Mason 
CJ, Therneau TM, Eckel-Passow JE, Johnson KL, Oberg AL, Olson JE, Nair KS, Muddiman 
DC, and Bergen HR III.  Molecular and Cellular Proteomics 2007, 6:305-318.

Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass 
spectrometry. Eckel-Passow JE, Oberg AL, Therneau TM, Mason CJ, Mahoney DW, Johnson 
KL, Olson JE and Bergen HR III.  Bioinformatics 2006 22(22):2739-2745.

Reproducibility of Retention Time using a Splitless nanoLC Coupled to an ESI-FTICR Mass 
Spectrometer.  Mason CJ, Johnson KL, Muddiman DC.  Journal of Biomolecular Techniques 
2005 16:414-422.

Analysis of the Low Molecular Weight Fraction of Serum by LC-DualESI-FT-ICR Mass 
Spectrometry:  Precision of Retention Time, Mass, and Amplitude. Johnson KL, Mason CJ, 
Muddiman DC, Eckel JE. Analytical Chemistry 2004 Sep 1;76(17):5097-103. (co-first author)

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic 
distributions in Fourier transform ion cyclotron resonance mass spectrometry. Hawkridge AM, 
Nepomuceno AI, Lovik SL, Mason CJ, Muddiman DC.  Rapid Commununications in Mass 
Spectrometry 2005;19(7):915-8.

Utility of Accurate Monoisotopic Mass Measurements to Confidently Identify Lambda 
Exonuclease Generated Single-Stranded Amplicons Containing 7-Deaza Analogs by 
Electrospray Ionization FT-ICR Mass Spectrometry. J.L. Frahm, C.J. Mason, and D.C. 
Muddiman, International Journal of Mass Spectrometry 2004, 234, 79-87.

Detection of genetic variants of transthyretin by liquid chromatography-dual electrospray 
ionization fourier-transform ion-cyclotron-resonance mass spectrometry. Nepomuceno AI, 
Mason CJ, Muddiman DC, Bergen HR 3rd, Zeldenrust SR.  Clinical Chemistry 2004 
Sep;50(9):1535-43. 

Detection of cystic fibrosis mutations by peptide mass signature genotyping.  Malehorn DE, 
Telmer CA, McEwen SB, An J, Kinsey AD, Retchless AC, Mason C, Vieta WM, Jarvik JW. 
Clinical Chemistry 2003 Aug;49(8):1318-30.


PRESENTATIONS:	 
Introduction to Mass Spectrometry Based Proteomics.  Christopher J Mason.  Invited 
Presentation. Eastern North American Region/International Biometric Society.  March 2007. 

RAAMS: An algorithm for automatically interpreting mass spectra of 18O labeled isotopic 
clusters.  Mason CJ; Eckel-Passow JE; Johnson KL; Therneau TM; Oberg AL; Muddiman DC; 
Bergen, HR III. Poster.  American Society for Mass Spectrometry, 2006.

Informatics Techniques for Biomarker Discovery in Serum using LC-FT-ICR Mass 
Spectrometry. Mason CJ; Hawkridge AM; Muddiman DC; Johnson KL; Oberg AL.  Oral 
Presentation.  American Society for Mass Spectrometry, 2004.


SKILLS:	Languages:  	C++ (strong template skills), Java, Groovy, Perl, Javascript, C, SQL, R/S
	Techniques:	Threading, MPI/PVM, UML/Modeling, Object Orented Design, Boost
	Database:	SQL (MySQL, Postgres, SQLite, Oracle), JDBC, Hibernate, ODBC, Objectivity
	Platforms:  	UNIX (Linux, SunOS, NetBSD, UNICOS, IRIX), MacOS X, Win32 (cygwin)
	Graphics/UI: 	Swing (Java2D, SWT), OpenGL, VTK, ImageMagick, DHTML/Javascript, GWT 
	Networking: 	CORBA (Mico/Orbacus/ACE, ZeroC ICE), Sockets, TCP/IP Network Admin. 
	Other:	UNIX administration, Photography, Technical Writing, GUI design, 
				Fluent French Language, Project Management, Excellent Communication Skills

Please visit my online extended CV at www.cmason.com/resume/	References available upon request.   
200801