||Background/Experience of Juergen Haas, Ph.D. Computer Science, M.Sc. Physics
Tel.: (858) 538-4271
Mobile: (858) 353-3253
Haas founded JSSC and leads the company's technology development. With
a Ph.D. in computer science and Masters degrees in computer science and
physics, Haas has developed extensive experience in software
development and high-tech start-ups, and has multiple invented and
published patents and provisional patents in his name. Haas’
experience with artificial intelligence, computer vision, robotics,
bioinformatics, image processing, simulation, and mobile devices has served him in
management positions with start-up companies Juke Systems, Illumina
(whose IPO raised $100 million) and Gene Logic (whose IPO raised $30
1993 Ph.D. Computer Science, SUNY Buffalo, New York
1988 M.Sc. Computer Science, University of Denver, Colorado
1986 M.Sc. Physics, University of Denver, Colorado
CTO, Juke Systems, Inc., Darien & San Diego, 8/2005-present:
Developed and launched ICE First™, a J2ME mobile phone application for
emergency medical information with wireless connectivity to Internet
databases (see http://icefirst.com). ICE First was purchased by one of the world's largest medical image management companies.
- Developed, implemented
and deployed a comprehensive ringtone, image, and software vending
system for mobile phones. It is implemented as a J2EE-based application
that includes functions and graphical user interfaces for uploading and
managing content and is connected to a payment system through web
services interfaces. This product was purchased by various mobile virtual network operators.
President, JSS Computing, Inc., San Diego, 3/2003-present:
- Developed robotic vision, planning, and control software for intelligent autonomous vehicles.
Developed Java software for text input and optical character
recognition software for camera-enabled mobile phones that can be
purchased and downloaded over the air from the Internet directly to
Consultant, Collegesports Online 6/2004-9/2004:
devices for Collegesports Online which hosts the athletics web sites of
more than 130 division I and II schools.
Developed & implemented Perl scripts for automated processing of
live news feed from the Summer Olympics (Sportsticker) for presentation
on live web site;
- Developed & implemented Perl software for
automated parsing and formatting of XML Sportsxchange news stories for
presentation on live web site.
Senior Scientist, Illumina, Inc., San Diego, CA, 1/2000-3/2003:
Designed and implemented web application server, based on J2EE, Apache
and Java Web Start, for SNP and gene expression probe design; includes
genome selection, tissue selection, multiple splice variant alignment,
RNA view, DNA view, sequence view, choice of assays and probe
- Designed and implemented in Java a
fully automated, flexible, modular, web-based, data analysis pipeline
that facilitates distributed processing; used extensively by scientists
and the array manufacturing team; installed copy at Applied Biosystems,
- Designed and implemented in Java flexible web-based data
analysis and visualization software for SNP genotyping and gene
expression data, that includes genotype clustering procedures and
spread sheet output;
- Designed and implemented in Java and C++
robust image analysis software for Illumina’s bead array images, that
adapts to distortions and provides structure based bead numbering;
- Designed and implemented J2EE-based project tracking database and web-based user interface.
Staff Scientist, Gene Logic, Inc., Gaithersburg, Maryland, 1997-2000:
Led the design, implementation and population of a high-quality
database of DNA sequences to support Gene Logic’s proprietary READS
technology; developed Java programs that use this database for quality
control to help optimize laboratory procedures;
- Played key role in the development and integration of a Java-based system for automating t
he analysis of READS gel images, including automatic data storage in Oracle based database;
Designed and implemented a Java system for analyzing transcription
factor DNA binding sequences generated by Gene Logic’s proprietary MuST
Programmer/Analyst, University of Pennsylvania, Center for Bioinformatics, 1992-1997:
- Designed and implemented a web-accessible database system for gene expression data;
- Developed a system for inferring information about DNA through analogical/case-based reasoning and linguistic techniques;
- Implemented Java graphical user interfaces for the analysis of chromosomal structure;
Academic Honors and Memberships
- Member of the US National Physics Honor Society (Sigma Pi Sigma)
- Associate member of the Scientific Research Society of North America (Sigma Xi)
- Member of the Honor Society for International Scholars (Psi Beta Delta)
- Recipient of Quadrille Ball Scholarship, 1986/87
- Recipient of IRCS Post Doctoral Fellowship, 1994
Languages: Fluent in English and German.
Programming/Software Development Experience:
Languages: Java, Perl, C, C++, SQL, MFC Visual C++, Prolog, Lisp, …
Tools: J2ME, J2EE, Java Enterprise Beans, Java Web Start, Java3D, Web
Services, Rational ClearCase, Rational ClearQuest
IDEs: Eclipse, NetBeans, Visual Café, Visual Studio, JCreator, Emacs, …
Systems: Windows, Linux, UNIX, IRIX, Solaris, DOS
Databases: Oracle, MYSQL, PostgreSQL, JavaDB
Platforms: PC, Mobile Phones, Sun/Sparc, Silicon Graphics
“Method and System for Computationally Identifying Clusters within a
Set of Sequences”, inventor: Juergen Haas, Patent Number: 6109776,
Issue Date: 8/29/2000.
2. "Virtual Gel Profiling System," inventor: Juergen Haas, Patent Number: WO0167370, Publication date: 9/13/2001.
“Automated Information Processing in Randomly Ordered Arrays,”
inventors: Juergen Haas, Bahram Kermani, Todd Dickinson, Mark Chee and
John Stuelpnagel; application filed, 2003, international application
4. “Intelligent Autonomous Vehicle
System”, inventor: Juergen Haas, provisional application filed on
1/18/2005; U.S. PTO file number 60/464175.
5. “Method and System
for Image Based Text Input”, inventor: Juergen Haas, provisional
application filed on 3/22/2004; U.S. PTO file number 60/555342.
“System and method for communicating emergency data”, inventors:
Juergen Haas, Keith Buckley; application filed 11/10/2005, application
Publications and Presentations
1. Juergen Haas has written numerous articles for The New York Times online magazine "About: Focus on Linux".
“Storing Medical Information,” Article by Sarmad Ali on Jukesystem’s
ICE First product for mobile phones (developed by Juergen Haas), THE
WALL STREET JOURNAL, March 21, 2006.
3. “Decoding Randomly
Ordered DNA Arrays,” K. Gunderson, S. Kruglyak, M. Graige, F. Garcia,
B. Kermani, C. Zhao, D. Che, T. Dickinson, E. Wickham, J. Bierle, D.
Doucet, M. Milewski, R. Yang, C. Siegmund, J. Haas, L. Zhou, A.
Oliphant, J. Fan, S. Barnard, and M. Chee, Genome Research, May 2004.
“Flexible Web-Controlled Pipelining of Stand-Alone Windows Data
Analysis Applications,” J. Haas, Proceedings of the German Conference
on Bioinformatics, Braunschweig, Germany, Oct. 7-10, 2001.
“Randomly Assembled Arrays For Highly Parallel Analysis of Nucleic Acid
Sequences,” J. Fan, J. Yeakley, J. Haas, B. Kermani, A. Olifant, C.
Zhao, S. Barnard, J. Izzo, D. Che, K. Gunderson, J. Bierle, L. Mendoza,
M. Wenz, M. Lebl, D. Barker, X. Fu, J. Efcavitch, M. Chee, CSH Genome
Sequencing & Biology Conference, 2001.
Reasoning Driven Gene Annotation,” G. Christian Overton and Juergen
Haas, book chapter in: Computational Methods in Molecular Biology,
Edited by Steven Salzberg, David Searls, and Simon Kasif Published by
Elsevier Science, 1998.
7. “Construction of a High Quality Index
of Human mRNA 3’End Sequences,” Chunhua Yan and Juergen Haas, poster
presentation, Tenth International Genome Sequencing and Analysis
Conference, September 17-20, 1998, Miami Beach, FL.
8. “EpoDB: A
Bioinformatics System for the Analysis of Gene Expression during
Erythropoiesis” presented by Christian J. Stoeckert at the
Bioinformatics and Genome Research Conference, Boston, Massachusetts,
June 15-16, 1998.
9. “EpoDB: A Database of Genes Expressed
during Vertebrate Erythropoiesis,” F. Salas, J. Haas, Brian Brunk, C.
J. Stoeckert and G. C. Overton, Nucleic Acids Research, Vol. 26 no. 1,
10. “Automated Hypothesis Formation of Molecular
Structures and Interactions using Physics-based Modeling and
Simulation,” J. Haas and D.N. Metaxas, Proceedings of the German
Conference on Bioinformatics, Leipzig, Germany, Sept. 30, 1996.
“EpoDB: An Erythropoiesis Gene Expression Database/Knowledge Base,” F.
Salas, J. Haas, C.J. Stoeckert Jr., and G.C. Overton, In:
Bioinformatics- German Conference on Bioinformatics, Leipzig, Germany,
September/October 1996, Springer Lecture Notes in Computer Science, pp.
12. “From Context-Free to Definite-Clause Grammars: A
Type-Theoretic Approach,” J. Haas, B. Jayaraman, Journal of Logic
Programming, Vol 30(1), 1-23, January 1997.
13. “QGB: A
System for Querying Sequence Database Fields and Features,” G.C.
Overton, J.S. Aaronson, J. Haas, and J. Adams, Journal of Computational
Biology, Vol 1 no.1, 3-14, Spring 1994.
14. “Using Analogical
Reasoning for Knowledge Discovery in a Molecular Biology Database,” J.
Haas, J.S. Aaronson, and G.C. Overton, Proceedings of the Second
International Conference on Information and Knowledge Management, ACM
Press, New York, NY, 554-564, 1993.
15. “Knowledge Discovery in
GenBank,” J.S. Aaronson, J. Haas, and G.C. Overton, Proceedings of the
First International Conference on Intelligent Systems for Molecular
Biology, AAAI/MIT Press, 3-11, 1993.
16. “Interactive Synthesis
of Definite-Clause Grammars,” J. Haas and B. Jayaraman, Proceedings of
the Joint International Conference and Symposium on Logic Programming,
Washington, D.C., November 1992.
2004-2007 JSS Computing,