Curriculum Vitae

From Christoph's Personal Wiki

P. Christoph Champ

BSc Biochemistry and Biophysics

Education

  • B.S. Biochemistry and Biophysics, Oregon State University; September 2000–June 2004
  • Graduate studies and research: Massachusetts Institute of Technology, University of Pittsburgh, Danmarks Tekniske Universitet, København Universitet, University of Washington; July 2004–March 2010.

Professional Experience

  • System Administrator and Research Assistant: Dr. Ethan A. Merritt Laboratory — Medical Structural Genomics of Pathogenic Protozoa Consortium, Seattle, USA; October 2006-present.
  • System Administrator and Research Assistant: Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA; March 2006-February 2007 (in absentia).
  • Research Assistant: Dr. David W. Ussery Laboratory — Center for Biological Sequence Analysis, Danmarks Tekniske Universitet, Denmark; August 2005–November 2005.
  • Research Assistant and System Administrator: Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA; October 2004–July 2005.
  • Research Assistant: Dr. Alex Rich Laboratory — Department of Biology, Massachusetts Institute of Technology, USA; Summer 2002/December 2002.
  • Research Assistant: Dr. P. Shing Ho Laboratory — Department of Biochemistry & Biophysics, Oregon State University, USA; May 2000–September 2004.
  • English Language Instructor: Berlitz, Ljubljana, Slovenia, December 1996–December 1997.

Publications

Citations:
→ Edwards SF, Siritoc M, Krahec R, Sinden RR (2009). "A Z-DNA sequence reduces slipped-strand structure formation in the myotonic dystrophy type 2 (CCTG).(CAGG) repeat". PNAS, 106(9):3270-327. DOI:10.1073/pnas.0807699106
→ Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". Methods, [Epub ahead of print]. PMID: 18848994. DOI:10.1016/j.ymeth.2008.09.007
→ Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007). "A high-resolution atlas of nucleosome occupancy in yeast". Nature Genetics, 39:1235:1244. DOI:10.1038/ng2117
→ Kulisha VV, Heng L, Dröge P (2007). "Z-DNA-induced super-transport of energy within genomes". Physica A: Statistical Mechanics and its Applications, 384(2):733-738. DOI:10.1016/j.physa.2007.06.023
→ Kouzine F, Levens D (2007). "Supercoil-driven DNA structures regulate genetic transactions". Frontiers in Bioscience, 12:4409-4423.
→ Khuu P, Sandor M, DeYoung J, Ho PS (2007). "Phylogenomic analysis of the emergence of GC-rich transcription elements". PNAS, 104(42):16528-16533. DOI:10.1073/pnas.0707203104
→ Yoshida N, Amanai M, Fukui T, Kajikawa E, Brahmajosyula M, Iwahori A, Nakano Y, Shoji S, Diebold J, Hessel H, Huss R, Perry ACF (2007). "Broad, ectopic expression of the sperm protein PLCZ1 induces parthenogenesis and ovarian tumours in mice". Development, 134:3941-3952. DOI:10.1242/10.1242/dev.007930
→ Lorenzen S, Zhang Y (2007). Identification of near-native structures by clustering protein docking conformations. Proteins: Structure, Function, and Bioinformatics, 68(1):187-194; DOI:10.1002/prot.21442 .
→ Mobley DL, Dumont É, Chodera JD, Dill KA (2007). "Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent". J Phys Chem B, 111(9):2242-2254. DOI:10.1021/jp0667442
→ Panpan Z, Lijuan W, Wenyuan Q (2006). The junction between B-DNA and Z-DNA. Chemistry, 69(11):822-825.
→ Bala Gupta V, Hegde, ML, Jagnnathan Rao KS (2006). Role of Protein Conformational Dynamics and DNA Integrity in Relevance to Neuronal Cell Death in Neurodegeneration. Current Alzheimer Research, 3(4):297-309(13); DOI:10.2174/156720506778249452 .
→ Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG (2006). Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. J Human Genetics, 120(4):519-526; DOI:10.1007/s00439-006-0222-1 .
→ Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M (2006). Effect of Sequence-Directed Nucleosome Disruption on Cell-Type-Specific Repression by α2/Mcm1 in the Yeast Genome. Eukaryotic Cell, 5(11):1925-1933. DOI:10.1128/EC.00105-06
→ Kastenholz MA, Schwartz TU, Hunenberger PH (2006). The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. Biophys J, 91:2976-2990.
→ Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Mol Cell Biol, 26(7):2550-9.
→ Quyen DV, Kim KK, Kim YG (2006). Sequence-dependent kinetic behavior of protein-induced B- to Z-DNA transition. Bulletin of the Korean Chemical Society, 27(7):1071-1074.
→ Ha SC, Lowenhaupt K, Rich A, Kim YG, 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.
Acknowledgments:
→ Camacho CJ, Zhang C (2005). FastContact: rapid estimate of contact and binding free energies. Bioinformatics, 21(10):2534-2536; DOI:10.1093/bioinformatics/bti322 .

Portfolio

Web servers

Server administrator and developer; October 2006–present.
  • Raster3D: a set of tools for generating high quality raster images of proteins or other molecules.
Starting with version 2.7s, I am working to port it to Mac OS X as well as compile binaries using the Intel Fortran Compiler; February 2009–present.
Version 2.0: Programmer, Server architect, and administrator; January 2007–present.
Version 1.0: Programmer, Server architect, and administrator; July 2005–December 2006.
  • SmoothDock Server (currently under development): a fully automated algorithm for finding physical interactions between proteins.
Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).
Programmer, Server architect, and administrator; August 2005–December 2005.
  • LooseLoops Server (currently under development and construction): predicts regions of a protein (PDB format) having highly flexible loops
Programmer, Server architect, and administrator; November 2004–present.
Server architect and administrator; September 2004–present.
  • ZHunt Online Server: predicts the locations of probable Z-DNA forming regions in a given DNA sequence
Primary researcher and programmer; May 2000–September 2004 (note: front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ)
An administrator and developer; January 2005–present.

High-level programming

Probably the most complicated programming project I have worked on was one where we were attempting to predict how two proteins will interact. Since billions of calculations (a minimum of 2.7 x 1010) are needed for each protein/protein complex, I had to write specific (C) code that was optimised to run in parallel on a dedicated cluster of 256 CPUs (using the MPICH compiler). As a side note, I had to translate some original Fortran77 code into C so it could be compiled with MPICC.

We wanted to make our algorithm available to the general scientific community and, so, we decided that a web server would be the best implementation. What we needed was a simple, user-friendly interface to the back-end algorithm. Getting the user input (here the coordinates for each atom in a protein) to be transferred to the cluster required a great deal of pre-processing (data parsing, formatting, and error-checking). Likewise, the results returned by the cluster required post-processing to be eventually sent (via email) to the user.

The entire system had to run autonomously (controlled via crontab scheduling). As the administrator of this setup, I was responsible for keeping the system up at all times. However, since there were thousands of lines of code, if the system should crash it would be difficult to find out where the problem was if I didn't maintain extensive log files. I set these up to be easily parsable and had the system periodically email me the "health" of the system. This server remains up-and-running to this day.

Data mining / data parsing / data manipulation

The algorithm described above is implemented through a combination of Fortran77 and C code. However, the initial data (input) and results (output) are sent through multiple pipes as a series of I/O streams using Perl, awk/gawk, sed, and bash scripts. They are all controlled via makefiles and use extensive regular expressions. (see: SmoothDock for details.)

I would say that working with the command line interface (CLI) and scripting languages are my main skills and strengths. These skills have been developed through over seven years of active data mining through literally hundreds of terabytes of data in a wide array of formats and from multiple sources.

Database experience

A different project I worked on also required extensive data mining. However, here we were more interested in storing our data in easily manageable (MySQL) databases. On this particular project, we were working with the human genome. Each genome has over three billion "letters" (or bits of information). However, after adding annotation we were dealing with tens of gigabytes of data for each genome and for each experiment. After completing a couple of these experiments, we were quickly dealing with nearly 100 gigabytes of data. This required extensive data normalization and carefully constructed databases. (see: ZHunt for details.)

Technical and Specialized Skills

 see: Technical and Specialized Skills for a detailed listing.
  • Computer operating systems:
Primary OS: Linux (SuSE, Mandriva, RedHat, and Ubuntu); Secondary OS: Windows (9x,2k,XP), Mac OS, and Unix.
  • Computer languages and scripts:
C (+MPI/MPICH), Perl (+CGI), Python, PHP, Fortran 77, BASIC, X/HTML (+CSS), XML, SQL, various shell scripting (awk/gawk, sed, bash, man, make/gmake, etc.), regular expressions, R, LaTeX, PostScript and PDF generation.
  • Web Applications:
LAMP, WikiMedia, phpBB (+MODs, SEOs, and Fetch All), WordPress, Smarty, phpAdsNew, etc.
  • Computer System Administration and Security:
Apache HTTP Server (v2+), Email Server, SSH/OpenSSH, FTP, PGP/GPG, etc.
  • Databases:
MySQL, BLAST (standalone and webserver), MS Access.
  • Software (Unix/Linux):
Clustal, CHARMm, CCP4, EMBOSS, TLSMD/Python Macromolecular Library (mmLib), DOT, MrBayes, GnuPlot (+C API), Grace, RasMol (+scripting), PyMOL, GIMP (+various image generating techniques), StarOffice, OpenOffice, vi, etc.
  • Software (PC/Mac):
Adobe Photoshop, Adobe Illustrator, Adobe PageMaker, Adobe Premiere Pro, Microsoft Office (Word, Excel, PowerPoint), Mathematica, Maple, etc.
English, Spanish (college level), German (college level).

Honors, Awards, Memberships, Presentations, and Conferences Attended

  • ACA Meeting, Buffalo, New York.
Poster presented ("Identification of Functional Motifs and Binding Site Properties in Potential Drug Targets from Tropical Parasites." — Arakaki TL, Le Trong I, Larson ET, Champ PC, Neely H, Boni E, Mueller N, Napuli A, Kelley A, Krumm1 BE, Xiao1 L, Shibata S, Zhang Z, Deng W, Zucker F, Fan E, Buckner FS, van Voorhis WCE, Verlinde CLMJ, Hol WGJ, Merritt1 EA. Medical Structural Genomics of Pathogenic Protozoa Consortium.) (Click here for abstract).
  • 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).
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.
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 — 47 Countries to-date
  • First aid training (with certificate): 1995, 1999
  • 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/Belarus (Minsk), June 1994.
  • Volunteer Humanitarian Aid Work — Lithuania (Vilnius) and Latvia (Riga), 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 Taken (graduate level)

  • Biocrystallography
    • Professors: Dr. Wim Hol, Dr. Ethan Merritt, Dr. Jack Johnson, Dr. Ning Zheng, Dr. Ron Stenkamp, and Dr. Wenqing Xu
  • Biological X-ray Structure Analysis
    • Professors: Dr. Ron Stenkamp, Dr. Wenqing Xu, and Dr. Werner Kaminsky
    • Textbook: X-ray Structure Determination, Stout and Jensen
  • Molecular Evolution
    • Professor: Dr. Anders Gorm Pedersen
    • Textbook: Inferring Phylogenies, Joseph Felsenstein, Sinauer Associates, Inc. (2003).
  • DNA Microarray Analysis
    • Professor: Dr. Henrik Bjørn Nielsn
    • Textbook: A Biologist's Guide to Analysis of DNA Microarray Data.
  • 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
  • Java Programming
    • Professor: Dr. Jens Thyge Kristensen
    • Textbook: Object-Oriented Software Development Using Java, Xiaoping Jia, Addison-Wesley, 2nd Edition.

Academic Courses Taken (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

  • Ethan A. Merritt, PhD — Research Associate Professor of Biochemistry and Biological Structure, University of Washington. Member of MSGPP.
  • Carlos J. Camacho, PhD — Associate Professor of Computational Biology, University of Pittsburgh.
  • P. Shing Ho, PhD — Professor and Chair of Biochemistry and Biophysics, Oregon State University.
  • Kevin Ahern, PhD — Senior Instructor of Biochemistry and Biophysics, Oregon State University.
  • Alexander Rich, PhD — William Thompson Sedgwick Professor of Biophysics, Massachusetts Institute of Technology.

External links

last update: 4-Aug-2009

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