Jayson Falkner
Doctor of Philosophy in Bioinformatics from University of Michigan, Ann Arbor. Currently working as Chief Executive Officer (CEO) at Single Organism Software Inc.
| Headline: | Scientist |
| Website: | http://www.singleorganism.com |
| Skills: | Business |
| Location: | Portland, OR |
| Groups: | Startup Now! Oregon |
| Interested in: | Consulting opportunities, Learning about entrepreneurship, Meeting new people, Offering Expertise, Patenting my idea, Professional opportunities |
| Tags: | bioinformatics, cluster, genomics, java, life sciences, linux, mr. m, mrm, proteomics, software, srm, tandem mass spectrometry, targeted proteomics, Web development |
| Schools: | University of Miami, University of Michigan System - Ann Arbor |
WORK EXPERIENCE
| Employer: | Single Organism Software Inc, Portland, OR |
| Position: | Chief Executive Officer (CEO) |
| Time period: | May 2008 - Present |
| Description: | After my PhD studies I cofounded SOSI. The company focuses on software development but also collaborates in most areas of proteomics and life sciences research. Many of the ideas and projects from my PhD work are continued with the company. |
| Employer: | Program in Bioinformatics, University of Michigan, Ann Arbor, MI |
| Position: | Graduate Student Teaching Assistant |
| Time period: | January 2005 - December 2006 |
| Description: | Course: Proteome Informatics (Bioinfo. 551)
Dates: Winter Semester 2005 and 2006 (Faculty Organizers: Dan Burns and Phil Andrews) |
| Employer: | Amberjack Software LLC w/ DevelopMentor, Olympia, WA |
| Position: | Instructor |
| Time period: | January 2005 - December 2006 |
| Description: | Courses: Programming Java and Java Web Development |
| Employer: | Amberjack Software LLC, Olympia, WA |
| Position: | Chief Technology Officer (CTO) |
| Time period: | December 2000 - May 2006 |
| Description: | In early 2000 I cofounded a software development company. The company did software consulting, primarily Java/J2EE and ASP/ASP.NET, training, technical publications, and public speaking. I finished my book “Servlets and JavaServer Pages” in 2003 before starting my Ph.D. research, and remained a partner through 2006 while limiting my involvement to participating in the JSP Expert group (JSR 152, JSR 245) and speaking engagements. |
| Employer: | University of Miami Information Technology, Coral Gables, FL |
| Position: | Class Instructor |
| Time period: | March 2000 - May 2003 |
| Description: | As an undergraduate student I worked as a class instructor. I was responsible for teaching
several courses per week about topics such as HTML, JavaScript, Cascading Style Sheets, Microsoft Office, and Adobe Illustrator. I was also responsible for creating and maintaining material for my courses, keeping track of statistics about the classes, and providing private mentoring in various topics including the classes mentioned, and in Microsoft Windows, Mac OS 9/OS X, Unix, and Linux. |
| Employer: | Information Technology, University of Miami, Coral Gables, FL |
| Position: | Class Instructor |
| Time period: | March 2000 - May 2003 |
| Description: | Courses: HTML, JavaScript, CSS, and DHTML |
EDUCATION
| University: | University of Michigan System - Ann Arbor |
| Time period: | 2004 - 2008 |
| Degree: | Doctor of Philosophy in Bioinformatics |
| University: | University of Miami |
| Time period: | 1999 - 2003 |
| Degree: | Information Technology, BSc |
PUBLICATIONS
| Articles: | Peerreviewed Journal Publications
● Falkner JA and Andrews PC, “Fast tandem mass spectrabased protein identification regardless of the number of spectra or potential modifications examined”, Bioinformatics 2005 21(10): 21772184; doi:10.1093/bioinformatics/bti362 ● Falkner JA, Falkner JW, Andrews PC, "ProteomeCommons.org JAF: reference information and tools for proteomics", Bioinformatics 2006 22(5):632633; doi:10.1093/bioinformatics/btk015 ● Falkner JA, Falkner JW, Andrews PC, "ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats", Bioinformatics, 2006, doi: 10.1093/bioinformatics/btl573 ● Falkner JA, Veine DM, Kachman M, Walker A, Strahler JR, and Andrews PC, "Validated MALDITOF/TOF mass spectra for protein standards", JASMS 2007 ● Falkner JA, Andrews PC, "Publicly dissemination large amounts of proteomics data in a secure and scalable fashion", Invited for submission to Molecular and Cellular Proteomics and submitted, http://tranche.proteomecommons.org ● Falkner JA, Falkner JW, Yocum A, Andrews PC, “A Spectral Clustering Approach to MS/MS Identification of PostTranslational Modifications”, J. Proteome Res., 7 (11), 4614–4622, 2008. 10.1021/pr800226w ● Smith RD, Hu L, Falkner JA, Benson ML, Nerothin JP, Carlson HA., “Exploring proteinligand recognition with Binding MOAD” J Mol Graph Model. 2006 May;24(6):41425. Epub 2005 Sep 15 ● Mathivanan S, Chaerkady R, Falkner JA, Björling E, Gnad F, Molina H, Amanchy R, Mohmood R, Bader JS, Xu T, Cantin GT, Gagné P, Bose R, Martens L, Droit A, Helsens K, Purvine SO, Oyama M, Sheng SJ, Sullivan M, van Eyk J, Sugano S, Cagney G, Ohara O, Muddiman DC, Cole PA, Hofmann O, States DJ, Cotter RJ, Hide W, Fenselau C, Bennett KL, SupertiFurga G, Gevaert K, Smith RD, Körner R, Poirier GG, Yates JR, Aebersold R, Uhlen M, Mann M, Andrews PC and Pandey A, “Sharing of Proteomic Data using a Protein Distributed Annotation System (PDAS)”, Nature Biotechnology (2008) Non PeerReviewed Publications ● Falkner JA, Ulintz PJ, and Andrews PC, "A Code and Data Archival and Dissemination Tool for the Proteomics Community", American Biotechnology Laboratory, Apr, 2006 |
| Books: | Book Chapters
● Early Adopter JavaServer Pages Standard Tag Library (JSTL) – Chapters 1 and 8, Wrox Publishing, 2003, ISBN:1861006241 ● Professional JSP 2nd Edition – Chapters 8 and 12(coauthored w/Kenneth Kochmer), Wrox Publishing, 2002, ISBN:1861004958 ● Beginning JSP Chapters 10 and 16, Wrox Publishing, 2002, ISBN:1861002092 Books ● JSP and Servlets the J2EE Web Tier (coauthored w/Kevin Jones), Addison Wesley, 2003, ISBN10: 0321136497 |
INFORMATION
| Memberships: | ● American Society for Mass Spectrometry (ASMS) Member, 2005present
● Association of Biomolecular Resource Facilities (ABRF) Member, 2006present ● US Human Protein Organization (HUPO) Member: 2006present ● ABRF Proteome Informatics Research Group (iPRG) Member: 2008present |
| Awards: | ● Nominated for Outstanding Dissertation Thesis, University of Michigan, Rackham Graduate School, 2008
● ABRF 2007 Outstanding Scientist and Technologist, Sponsored by Thermo Scientific, 2007 ● ABRF 2007 Poster Contest Winner, Sponsored by Waters ○ “Tranche: Data Dissemination for the Proteomics Community” ● Invited Student Presenter: ISMB Bioinformatics Conference 2005 ● Outstanding Graduating EEN/IT Student, University of Miami, 2003 ● Eliahu I. and Joyce Jury Award, University of Miami, 2002 ○ Recognition of outstanding undergraduate work in EEN/IT |
Jayson's Startups (1)
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Single Organism Software Inc
SOSI provides software, data analysis, and training for mass spectrometry based proteomics, specifically MS/MS and MRM. The niche is a key part of high-throughput monitoring of cancer and other disease states in blood, urine, and other bio-fluids.
Jayson's Contacts (1)
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Harvey Mathews
High school history teacher turned legislative policy wonk turned business association lobbyist turned president of the state's software industry association.