Category:Academic Research

From Christoph's Personal Wiki

I have been doing academic research (or scientific research) full time since May of 2000. I have done this research at five academic institutions to date.

Research Completed

Below is a list of the academic institutions I have done research at to date (in reverse chronological order):

• 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.

Publications

• 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]
• 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]
• 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]
• 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)

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 .

Curriculum Vitae

• Curriculum Vitae