Christopher John Mason
9004 SW 7th Ave
Portland, OR 97219 507.202.3755
SUMMARY: Computational biology software developer and manager with over nine years experience who is passionate about creating powerful and usable software that betters the human condition.
EXPERIENCE: Proteome Software Portland, OR
(selected) Staff Scientist May 2008-present
– Designed, architected and led development of rich web service for quality control of tandem mass spectrometry data. Project completed on time using novel Flex, Flash, Action-script, Java, Hibernate, MySQL, JSON, cloud model. Concept to product in three months.
– Rearchitected Java Swing application for increased performance.
– Managed in-house and contract developers; delivered projects on time and budget.
Mayo Clinic Proteomics Research Center (MPRC) Rochester, MN
Senior Analyst Programmer March 2004–April 2008
Analyst Programmer August 2003–March 2004
– Hired and led a team of bioinformatics developers; helped secure >$3M in grants.
– 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, THRASH, 18O etc.
– Led development of 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.)
EDUCATION: BS in Biological Sciences and Computer Science Carnegie Mellon University May 2001
Honors: Merck Computational Biology Summer Scholar, 1999.
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Christopher Mason Resume Page 2 of 2
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: Java, AS3/Javascript, C++ (strong template skills), Perl, Groovy, 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: Flex/Flash, Swing (Java2D, SWT), OpenGL, VTK, 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. 200901