Curriculum Vitae

BSc Biochemistry and Biophysics
MSc Bioinformatics (currently working on)

Center for Biological Sequence Analysis
Danmarks Tekniske Universitet
DK-2800 Kgs. Lyngby
Danmark

Professional Experience

• Research Assistant: Dr. Rasmus Nielsen Laboratory, Centre for Bioinformatics, København Universitet, Denmark, December 2005–present.
• Research Assistant: Dr. David W. Ussery Laboratory, Center for Biological Sequence Analysis, Danmarks Tekniske Universitet, Denmark, August 2005–November 2005.
• Research Assistant: Dr. Carlos J. Camacho Laboratory, Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA, October 2004–July 2005.
• Research Assistant: Dr. P. Shing Ho Laboratory, Dept. of Biochemistry & Biophysics, Oregon State University, USA, May 2000–September 2004.
• Research Assistant: Dr. Alex Rich Laboratory, Dept. of Biology, Massachusetts Institute of Technology, USA, Summer 2002/December 2002.
• English Language Instructor: Berlitz, Ljubljana, Slovenia, December 1996–December 1997.

Publications

• P. Christoph Champ, Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510. (The Online server of ZHunt can be found here)
  • Citations:
    • Ha SC, Lowenhaupt K, Rich A, Kim YG, and Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183-1186.
    • Kwon JA, Rich A (2005). Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. Proc Natl Acad Sci USA, 102:12759-12764.

Portfolio

• CBS Fungal Database: DNA structural atlases for complete chromosomes and genomes.

Programmer, Server architect, and administrator; November 2005—December 2005.

• FastContact Server: a free energy scoring tool for protein-protein complex structures.

Programmer, Server architect, and administrator; July 2005–present.

• SmoothDock Server (currently under development):

Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).

• LooseLoops Server (currently under development and construction):

Programmer, Server architect, and administrator; November 2004–present.

• DomainSplit Server:

Server architect and administrator; September 2004–present.

• Able2Know.com:

An administrator and developer

Technical and Specialized Skills

• Computer operating systems:

Windows (9x,2k,XP), Mac OS, Linux (SuSE and RedHat), and Unix.

• Computer languages and scripts:

C (+MPI), Fortran, BASIC, Perl (+CGI), Java, PHP, X/HTML (+CSS), XML, SQL, various shell scripting (awk, gawk, bash, shebang, man, make/gmake, etc.), R, LaTeX, PostScript and PDF generation.

• Web Applications:

WikiMedia, phpBB (+MODs, SEOs, and Fetch All), WordPress, Smarty, phpAdsNew, etc.

• Computer System Administration and Security:

Apache Webserver, Email Server, SSH, FTP, PGP, etc.

• Databases:

MySQL, BLAST (standalone and webserver), MS Access.

• Software (Unix/Linux):

CHARMm, GnuPlot (+C API), Grace, RasMol (+scripting), GIMP (+various image generating techniques), StarOffice, OpenOffice, etc.

• Software (PC/Mac):
  • Adobe Photoshop, Adobe Illustrator, Adobe PageMaker, Adobe Premiere Pro, Microsoft Office(Word, Excel, PowerPoint), Mathematica, Maple, etc.
• Languages Spoken:

English, Spanish (college level), German (college level)

Honors, Awards, Memberships, and Conferences Attended

• 8th Annual Functional Genomics: Quantitative Biology Conference, Runan, Chalmers, Göteborg, Sweden, 29 August 2005.

Attended conference and presented poster ("FastContact: a free energy scoring tool for protein-protein complex structures" - P. Christoph Champ, Hui Ma, and Carlos J. Camacho).

• CAPRI: Critical Assessment of PRediction of Interactions — Round 7

Participant in Round 7 for CAPRI community wide experiment on the comparative evaluation of protein-protein docking for structure prediction (Hosted By EMBL/EBI-MSD Group), May 2005.

• CAPRI: Critical Assessment of PRediction of Interactions — Round 6

Participant in Round 6 for CAPRI community wide experiment on the comparative evaluation of protein-protein docking for structure prediction (Hosted By EMBL/EBI-MSD Group), January 2005.

• 12th Converstation of Biomolecular Structure and Dynamics, Albany, New York, 19-23 June 2001.

Attended conference and presented poster ("Mapping Z-DNA in Human Chromosome 22" - P. Christoph Champ, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho).

• Howard Hughes Medical Institute — Corvallis, Oregon (presented research in 2000 and 2001)

2000 HHMI Summer Undergraduate Research Program at OSU. (Click here for abstract).

2001 HHMI Summer Undergraduate Research Program at OSU, 29-30 August 2001. (Click here for abstract).

• Oregon State University Honor's College (freshman and sophomore years)
• National Dean's List (two consecutive years)
• Phi Theta Kappa Honor Society

Extracurricular and Leadership Activities

• World Travels — 44 Countries to-date
• Volunteer at Biochemistry Workshop for High School Students - Oregon State University, Summer 2000.
• Visual and Audio Production Training - Japan, October 1995—June 1996.
• Volunteer Humanitarian Aid Work - Croatia (Zagreb), Summer 1996.
• Volunteer Humanitarian Aid Work - Hungary (Budapest, Szeged), September 1994—September 1995.
• Volunteer Humanitarian Aid Work - Russia (Moscow), July 1994—September 1994.
• Volunteer Humanitarian Aid Work - Byelorussia (Minsk), June 1994.
• Volunteer Humanitarian Aid Work - Lithuania and Latvia, January 1994.
• Volunteer Humanitarian Aid Work - Poland (Warsaw), December 1993—May 1994.
• Volunteer Humanitarian Aid Work - Hungary (Budapest), September 1993—December 1993.
• Volunteer Humanitarian Aid Work - Ecuador (Guayaquil, Cuenca, Quito), Summer 1993.

Academic Courses Currently Taking (relating to MSc programme)

• DNA Microarray Analysis
  • Professor: Dr. Henrik Bjørn Nielsn
  • Textbook: A Biologist's Guide to Analysis of DNA Microarray Data.
• Perl and Unix for Bioinformatics
  • Professor: Peter Wad Sackett
  • Textbook: Learning Perl, Randal Schwartz and Tom Christiansen, O'Reilly, 3rd Edition.
• Database Systems
  • Professor: Dr. Hans Bruun
  • Textbook: A First Course in Database Systems, Jeffrey D. Ullman, Jennifer Widom Prentice Hall.
• Molecular Evolution
  • Professor: Dr. Anders Gorm Pedersen
  • Textbook: Inferring Phylogenies, Joseph Felsenstein, Sinauer Associates, Inc. (2003).

Academic Courses Taken (relating to MSc programme)

• Java Programming
  • Professor: Dr. Jens Thyge Kristensen
  • Textbook: Object-Oriented Software Development Using Java, Xiaoping Jia, Addison-Wesley, 2nd Edition.
• Molecular Cell Biology
  • Professor: Dr. Uffe Hasbro Mortensen and Dr. Ivan Mijakovic
  • Textbook: Molecular Cell Biology, Scott MP, Matsudaira P, Lodish H, Darnell J, Zipursky L, Kaiser CA, Berk A, and Krieger M. W. H. Freeman, 5th Edition (2003).
• Advanced Bioinformatics
  • Professor: Dr. Søren Brunak
  • Textbook: Guide to Analysis of DNA Microarray Data, Knudsen S, 2nd Edition (2004).
• Comparative Microbial Genomics: A Bioinformatics Approach
  • Professor: Dr. David W. Ussery

Academic Courses Taken (relating to BSc degree)

• General Chemistry I, II, and III (+lab)
  • Professor: Dr. Bridgid Backus
  • Textbook: General Chemistry, Darrell D. Ebbing and Steven D. Gammon, Houghton Mifflin Company, Boston, 6th Edition (1999).
• Organic Chemistry I, II, and III
  • Professor: Dr. David Horne
  • Textbook: Organic Chemistry, Paula Yurkanis Bruice, Prentice Hall, New Jersey, 3rd Edition (2001).
• Experimental Chemistry I and II (+lab)
  • Professor: Dr. Christine Pastorek and Dr. John Loesor
  • Textbook: Principles and Techniques for an Integrated Chemistry Laboratory, David A. Aikens, et. al., Waveland Press, Inc., Prospect Heights (1984).
• Physical Chemistry I, II, and III
  • Professor: Dr. Glenn Evans
  • Textbook: Physical Chemistry, Peter Atkins and Julio de Paula, W.H. Freeman and Company, New York, 7th Edition (2002).
    • Physical Chemistry I: Thermochemistry, Thermodynamics, Equilibrium
    • Physical Chemistry II: Quantum Theory (Schrödinger equation), Atomic Structure, Spectroscopy (rotational and vibrational, electronic transitions, magnetic resonance)
    • Physical Chemistry III: Statistical Thermodynamics, Molecular Interactions, Macromolecules and Aggregates, Kinetics and Molecular Reaction Dynamics)
• Biochemistry I, II, and III (+lab)
  • Professor: Dr. Michael I. Schimerlik, Dr. Tory M. Hagen, Dr. Christopher K. Mathews, and Dr. George D. Pearson.
  • Textbook: Biochemistry, Christopher K. Mathews, K. E. van Holde, and Kevin G. Ahern, Addison Wesley Longman, San Fransisco, 3rd Edition (2000).
    • Biochemistry I: Energetics of Life (Thermodynamics, Chemical Reactions and Equilibrium), Nucleic Acids (Properties, Structure, Function), Protein Structure, Protein Function and Evolution, Protein Dynamics, Carbohydrates
    • Biochemistry I-Laboratory: Biochemical Assays
    • Biochemistry II: Lipids, Membranes, Cellular Transport, Enzymes, Carbohydrate Metabolism, Oxidative Processes, Photosynthesis, Lipid Metabolism, Metabolism of Nitrogenous Compounds, Nucleotide Metabolism, Metabolic Coordination/Control/Signal Transduction
    • Biochemistry II-Laboratory: Molecular Biology
    • Biochemistry III: Information Copying (Replication), Restriction, Repair, Recombination, Rearrangement, Amplification, Transcription, Translation, Expression
    • Biochemistry III-Laboratory: Radioactivity
• General Biology I, II, and III (+lab)
  • Professor: Richard Liebaert
  • Textbook: Biology, Neil A. Campbell, The Benjamin/Cummings Publishing Company, Inc., Redwood City, 5th Edition (1999).
• Molecular and Cellular Biology
  • Professor: Dr. Charles R. Wert
  • Textbook: Essential Cell Biology, Bruce Alberts, et. al., Garland Publishing, Inc. New York (1998).
• Genetics
  • Professor: Dr. Carol Rivin
  • Textbook: Genetics: From Genes to Genomes, Leland H. Hartwell, et. al., McGraw-Hill Companies, Inc. Boston (2000).
• Evolution
  • Professor: Dr. Stephan J. Arnold
  • Textbook: Evolution: An Introduction, Stephen C. Stearns and Rolf F. Hoekstra, Oxford University Press, Oxford (2000).
• Physics with Calculus I, II, and III (+lab)
  • Professor: Dr. Henri Jansen, Dr. Carl A. Kocher, and Dr. Rubin H. Landau
  • Textbook: Physics for Scientists and Engineers, Saunders College Publishing, Philadelphia, 5th Edition (2000).
• Biophysics I, II, and III
  • Professor: Dr. P. Shing Ho, Dr. Victor Hsu, and Dr. P. Andrew Karplus
  • Textbook: Physical Biochemistry, Kensal E. van Holde, W. Curtis Johnson, and P. Shing Ho, Prentice Hall, New Jersey (1998).
    • Biophysics I: Biological Macromolecules (Interactions, Environments, Symmetry, Structure), Molecular Thermodynamics, Statistical Thermodynamics (Structural Transitions in Polypeptides and Proteins, Structural Transitions in Polynucleotides and DNA, Nonregular Structures)
    • Biophysics II: Quantum Mechanics, Spectroscopy (Absorption, Linear and Circular Dichroism, Emisson, NMR)
    • Biophysics III: Macromolecular Structure Determination, X-ray Crystallography, Hydrogen Exchange (Dynamics, Thermodynamics, Structure), Atomic Force Microscopy, Mass Spectroscopy, Protein Folding

• Calculus I: Differential Calculus
• Calculus II: Integral Calculus
• Calculus III: Infinite Series and Sequences
• Calculus IV: Vector Calculus
• Calculus V: Differential Equations
• Mathematical Biology
• Chemical Information
• Introduction to C Programming
• Introduction to Web Authoring

Academic Courses (not relating to degrees)

• Communication: Interpersonal
• Economics: Introduction to Microeconomics
• English: Literature of the Western Civilisation
• Writing: English Composition I
• Writing: English Composition III
• Geography: Geography of Africa and the Middle East
• Geography: Population Geography
• History: History of the United States of America – Colonial Period
• Philosophy: Ethics
• Philosophy: Great Ideas in Philosophy
• Political Science: Introduction to U.S. Government & Politics
• German: Year I, II, and III
• German Conversation: Level I, II, and III
• German Culture
• Health: Emergency First Aid
• Health: Lifetime Wellness
• Physical Activity: Karate
• Physical Activity: Jogging
• Theatre Arts: Improvisation

References

• P. Shing Ho, Professor and Chair of Biochemistry and Biophysics, Oregon State University.
• Kevin Ahern, Senior Instructor of Biochemistry and Biophysics, Oregon State University.
• Alex Rich, Professor of Biology, Massachusetts Institute of Technology.
• Carlos J. Camacho, Associate Professor of Computational Biology, University of Pittsburgh.

last update: 21-Dec-2005

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