________________________________________________________________
Markus Krummenacker
P.O. Box 1073
Los Altos, CA 94023-1073
phone: 510-278-0242
e-mail: kr@n-a-n-o.com
________________________________________________________________
Expertise:
In-depth knowledge of enabling technologies leading to
molecular manufacturing and nanotechnology.
Solid understanding of organic chemistry and biochemistry.
Computer Programming. Development of Object-oriented
Knowledge-bases in Bioinformatics. Molecular design and modelling.
Experienced in a diversity of areas, such as biochemistry
lab work, WWW site construction in HTML, PHP, and JavaScript.
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Experience and Education:
2003 : Bioinformatics Scientist, Artificial Intelligence Center,
SRI International, Menlo Park, California.
Temporarily helped with putting together HumanCyc,
accessible at http://humancyc.org
2001-2003: Systems Architect, Pangene Corp., Fremont.
Responsible for putting into production use and improving a
WWW-based tracking system for gene cloning orders, called
Labster/CloneTrek. This involved server-side script programming
in PHP, SQL and Oracle. Additional IT tasks included maintenance
of Linux servers and networking configuration.
2000- : Co-founder, Executive Vice President & Chief Scientist,
Molecubotics, Inc., a company developing a biotech route
to nanotechnology. Our goal is to build an assembler,
and other molecular robotic systems. As a visiting scientist
at CalTech, prepared DNA lattices and imaged them by AFM.
2000 : Part-time Consulting with Libraria Inc., San Jose.
Work on selection of precursor compounds for
combinatorial library synthesis. Used MDL ISIS and the ACD.
1998-1999: Scientific Applications Developer, DoubleTwist Inc., Oakland.
Continued work on EcoCyc and its PathwayTools extension.
EcoCyc is accessible on the WWW at http://ecocyc.org
1996-1997: Computer Scientist, Artificial Intelligence Center,
SRI International, Menlo Park, California.
Collaboration on EcoCyc, a metabolic Knowledge-base of the
bacterium E.Coli. Implementation of program enhancements
(in CommonLISP). Validation and correction of data in
the KB, especially regarding molecules and reactions.
1994-1995: Director of Research,
Nanothinc, San Francisco.
Key work in overall layout of WWW server and company
strategy. Responsible for NanoSci, the scientific part
of the site. Procurement, editing, and organization of
HTML documents. Recruitment of authors and contributors.
1992-1993: Research Associate,
Institute for Molecular Manufacturing, Palo Alto.
Work on enabling technologies for molecular manufacturing,
such as an analysis of Molecular Building Blocks, and
writing the CavityStuffer Program (in CommonLISP). This is
an experimental program for generating proposals for
polymeric molecules that fill a prescribed volume.
1990-1992: Visiting Researcher,
Dept. of Molecular and Cell Biology,
University of California at Berkeley.
Isolation via PCR, and sequence determination of homologous
genes for the Ferric Uptake Repressor, a regulatory protein
for iron uptake in bacteria.
Summer 1990: Software Consulting for Pneumotech AG,
Faellanden, Switzerland.
Restructuring of a custom CAD program for the layout of
embedded pneumatic circuitry (in BASIC).
1986-1990: Student of Biochemistry at the
Universitaet Zurich, Switzerland.
Reached equivalent of one year of graduate school.
1986: Gymnasium, completed with Greek & Latin (Matura Type A).
Zurich, Switzerland.
My main interest during that time was in electronics and
computer hardware; plus some Assembler programming.
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Publications:
1999 "EcoCyc: Encyclopedia of Escherichia coli Genes and
Metabolism"
Peter D. Karp, Monica Riley, Suzanne M. Paley,
Alida Pellegrini-Toole, and Markus Krummenacker.
Nucl. Acids Res., 1999, 27, no.1, p.55
"Integrated pathway/genome databases and their role in
drug discovery"
Karp, P.D., Krummenacker, M., Paley, S., and Wagg, J.
Trends in Biotechnology, 1999, 17, no.7, p.275-281
http://www.ai.sri.com/pkarp/pubs/99trbiotech.ps
"Rome Conference Offers European Perspectives
On Nanotechnology Research"
Short Review of the First EL.B.A. - Foresight Conference
on Nanotechnology, April 1999.
http://www.foresight.org/Updates/Update37/Update37.1.html#RomeConf
1998 "EcoCyc: Encyclopedia of Escherichia coli Genes and
Metabolism"
Peter D. Karp, Monica Riley, Suzanne M. Paley,
Alida Pellegrini-Toole, and Markus Krummenacker.
Nucl. Acids Res., 1998, 26, no.1, p.50-53
1997 "Prediction of Enzyme Classification from Protein Sequence
without Homology"
Marie desJardins, Peter D. Karp, Markus Krummenacker,
Thomas J. Lee, and Christos A. Ouzounis.
submitted to ISMB-97, published in the proceedings
"EcoCyc: Encyclopedia of Escherichia coli Genes and
Metabolism"
Peter D. Karp, Monica Riley, Suzanne M. Paley,
Alida Pellegrini-Toole, and Markus Krummenacker.
Nucl. Acids Res., 1997, 25, no.1, p.43-50
"DNA-Guided Assembly of Proteins as a Pathway to an Assembler"
Bruce Smith and Markus Krummenacker.
Talk presented by Bruce Smith at
The 1997 Albany Conference: Biomolecular Motors and Nanomachines. The Abstract.
1995 "Prospects in Nanotechnology:
Toward Molecular Manufacturing"
M. Krummenacker and J. Lewis, eds.
J. Wiley & Sons, New York.
Serves as the proceedings of the First General Conference
on Nanotechnology: Development, Applications, and
Opportunities. Nov. 11-14, 1992, Palo Alto, California.
Listed in the Foresight Bookstore
1994 "Steps Towards Molecular Manufacturing"
Chem. Design Autom. News, 1994, 9, no.1, p.1
http://www.n-a-n-o.com/nano/cda-news/cda-news.html
1993 "Packing Molecular Building Blocks"
Talk given at "Computer-Aided Design of Molecular
Systems". Third Foresight Conference on Molecular
Nanotechnology. Oct. 14-16, 1993, Palo Alto, California.
1991 "Proposal of issues to be investigated regarding Molecular
Building-Blocks"
Poster presented at "Toward Molecular Control". Second
Foresight Conference on Molecular Nanotechnology.
Nov. 7-9, 1991, Palo Alto, California.
http://www.n-a-n-o.com/
nano/cda-news/prehistoric/mbb-proposal-poster.html
1987 "Unterstuetzung der Halbleiterhersteller fuer den
Entwicklungsingenieur"
Elektroniker (a Swiss publication), 87-2, p.11
1984 "Die Hardware des SHARP PC-1500"
Micro und Kleincomputer (a Swiss publication), 84-1, p.39
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Personal:
References: available
Citizenship: Switzerland
U.S. Visa Status: Permanent Resident (Green Card)
Social Security Number: available
Fluent in German and English.