Difference between revisions of "Work experience"

Revision as of 04:47, 10 April 2010

This article will describe my professional work experience / history. See my Curriculum Vitae for an overview.

Note: This article is currently under construction and is far from complete.

2006-present

I presently work in the Dr. Ethan A. Merritt Laboratory in the Biochemistry department, University of Washington.

Published

• Frank Zucker, P. Christoph Champ, Ethan A. Merritt (2010). Validation of crystallographic models containing TLS or other descriptions of anisotropy. Acta Crystallographica Section D (in review).

Programming / Web servers

• TLS Motion Determination (TLSMD): analyzes a protein crystal structure for evidence of flexibility.

Server administrator and lead developer.

• 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. I am also adding Freetype2 support for adding labels / text to graphics output.

• TLSANL: Part of the CCP4 project

Developer; adding more features, checks, etc. to the code

2005

I worked as a research assistant in the Dr. David W. Ussery Laboratory at the Center for Biological Sequence Analysis, Danmarks Tekniske Universitet, Denmark. My research was in bioinformatics; specifically, Comparative Genomics.

Published

• 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]

Programming / Web servers

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

Programmer, Server architect, and administrator; August 2005–December 2005.

2004-2005

I worked as a research assistant and system administrator in the Dr. Carlos J. Camacho Laboratory at the Center for Computational Biology and Bioinformatics, University of Pittsburgh.

Published

• 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]
• 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]

Programming / Web servers

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

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).

• 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.

• DomainSplit Server: predicts the number of domains in a given protein (PDB format)

Server architect and administrator; September 2004–present.

2002

I worked as a research assistant in the Dr. Alex Rich Laboratory in the Department of Biology, Massachusetts Institute of Technology. My research focused on the role of Z-DNA in gene expression in Saccharomyces cerevisiae (common yeast). The research included using Affymetrix GeneChip's and programming (mainly in C and Perl) novel code for analysis of huge amounts of data (most of it stored in MySQL databases).

2000-2004

I worked as a research assistant in the Dr. P. Shing Ho Laboratory in the Department of Biochemistry & Biophysics, Oregon State University. My research focused on the role of Z-DNA in gene expression in the human genome (mainly chromosome 22).

Published

• 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]

Programming / Web servers

• 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)

1998-1999

I worked as a lab assistant for a microbiology laboratory. Prepared all kinds of media (e.g., agar solutions and agar plates) to feed our stock of microbes, as well as rotating the colonies.

1996-1997

English language for Berlitz in Ljubljana, Slovenia. I taught at all levels (beginner, mid-level, and advanced). Most of my students were government officials, businessmen / businesswomen, and other professionals.

1995-1996

I worked at a Audio & Visual Production Centre in Japan. My main role was to oversee a group of audio technicians, as well as performing automated dialogue replacement (ADR; aka "dubbing") for music videos, documentaries, etc.

1994-1995

I worked at a Pan-European Translation and Publishing House in both Vienna, Austria and Budapest, Hungary. My main role there was as deputy manager of the audio and visual department. We would receive recordings of an original English audio or visual media translated into just about every language in Europe and then make thousands of copies of them (cassette tapes, CDs, DAT, VHS-PAl, VHS-NTSC, etc.) and then ship them all over Europe.