Curriculum Vitae

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P. Christoph Champ

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. Carlos J. Camacho Laboratory, Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA, March 2006-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. Alex Rich Laboratory, Dept. of Biology, Massachusetts Institute of Technology, USA, Summer 2002/December 2002.
  • Research Assistant: Dr. P. Shing Ho Laboratory, Dept. of Biochemistry & Biophysics, Oregon State University, USA, May 2000–September 2004.
  • English Language Instructor: Berlitz, Ljubljana, Slovenia, December 1996–December 1997.

Publications

  1. Frank Zucker, P. Christoph Champ, and Ethan A. Merritt (2010). "Validation of crystallographic models containing TLS or other descriptions of anisotropy". Acta Cryst., D66:889-900. DOI:10.1107/S0907444910020421
  2. P. Christoph Champ and Carlos J. Camacho (2007). "FastContact: a free energy scoring tool for protein-protein complex structures". Nucleic Acids Research (Web Issue). DOI:10.1093/nar/gkm326 . [HubMed]
  3. P. Christoph Champ, Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). "Genome update: purine strand bias in 280 bacterial chromosomes". Microbiology, 152(3):579-583 DOI:10.1099/mic.0.28637-0 . [HubMed]
  4. Carlos J. Camacho, Ma H, and P. Christoph Champ (2006). "Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions". Proteins, 63(4):868-77 DOI:10.1002/prot.20932 . [HubMed]
  5. 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 DOI:10.1093/nar/gkh988 . [HubMed] (The Online server of ZHunt can be found here)

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 .

Citations

Note: The following is an incomplete list.

  1. 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
  2. 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
  3. 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
  4. 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
  5. Kouzine F, Levens D (2007). "Supercoil-driven DNA structures regulate genetic transactions". Frontiers in Bioscience, 12:4409-4423.
  6. 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
  7. 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
  8. 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 .
  9. 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
  10. Panpan Z, Lijuan W, Wenyuan Q (2006). The junction between B-DNA and Z-DNA. Chemistry, 69(11):822-825.
  11. 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 .
  12. 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 .
  13. 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
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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

Programmer, Server architect, and administrator; November 2005-December 2005.
Programmer, Server architect, and administrator; July 2005–present.
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; November 2004–present.
Server architect and administrator; September 2004–present.
Programmer; May 2000-September 2004 (note: front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.)
An administrator and developer

Technical and Specialized Skills

 see: Technical and Specialized Skills for a detailed listing.
  • Computer operating systems:
Primary OS: Linux (SuSE, RedHat, and Ubuntu); Secondary OS: Windows (9x,2k,XP), Mac OS, and Unix.
  • Computer languages and scripts:
C (+MPI/MPICH), Fortran 77, BASIC, Perl (+CGI), Java, PHP, X/HTML (+CSS), XML, SQL, various shell scripting (awk/gawk, sed, bash, shebang, 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, MrBayes, CHARMm, DOT, GnuPlot (+C API), Grace, RasMol (+scripting), 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, 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).
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 — 56 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 (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 (relating to MSc programme)

  • 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.
  • 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 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

  • 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.

External links

last update: 22-Jul-2006

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