Category:Academic Research

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I have done academic research (or scientific research) full-time from May 2000 to November 2012 at seven academic institutions/universities worldwide.

Research Completed

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

  • September 2015 – present: Cloud Engineer at Redapt, Seattle, USA.
Skills used: Linux, OpenStack, AWS, Docker, etcd, Kubernetes, Rancher, Greenqloud Qstack, CoreOS, KVM, VMware, fuel, pcs/crm, Midokura, MySQL, Sensu, Terraform, Jenkins, GoCD, Ansible, Vagrant, Redis, Bash, Python, sed, awk, HipChat API, Slack API
  • February 2015 – August 2015: Linux Systems Administrator at Trusted Builders, Seattle, USA.
Migrated computing infrastructure to the Cloud.
Skills used: Linux, Ansible, Vagrant, Rackspace Cloud, Nginx, Python
  • May 2013 – January 2015: Linux Administrator II at Rackspace, San Antonio, USA.
Provided Cloud Support (servers, storage, databases, load balancers, etc.), administered Linux servers, Xen, XenServer, KVM, OpenStack, RESTful API, networking, site reliability, maintenance, LAMP-stacks, etc. Also helped develop tools and internal websites to help automate tasks (tools written in PHP, Python, and Django).
Skills used: Linux, Apache, MySQL, PHP, Python, Rackspace Cloud, Xen/XenServer, KVM
  • December 2012 – March 2013: Web Developer at MadLab, Seattle, USA.
Built a RESTful web framework and API using Amazon Web Services' NoSQL DynamoDB and a custom-built/in-house MVC in PHP.
  • August 2012 – November 2012: Research Assistant / Scientific Programmer at the Dr. Elhanan Borenstein Laboratory — Department of Genome Sciences, University of Washington, Seattle, USA.
Conducted scientific research on the collection and organization of metagenomic datasets and the assembly of an analysis pipeline for metagenomic data; and
Analysis of the gut microbiome of children with cystic fibrosis (CF) and on methods to identify enriched functions.
Note: Everything was done in Linux and most of the programming was done in Python (+Pandas).
  • October 2010 – June 2012: Consultant (programmer, web developer) — Greater Chicago Area, USA.
Built a customer relationship management (CRM) website using Django (+Python, MySQL) with extended web services, command line interface, mobile apps, etc.
Note: Everything was done in Linux and/or Amazon Web Services (AWS), and most of the programming was done in Python.
  • October 2006 – October 2010: System Administrator, Research Assistant, and software developer/maintainer at the Dr. Ethan A. Merritt Laboratory — Medical Structural Genomics of Pathogenic Protozoa Consortium, University of Washington, Seattle, USA.
Developed and maintained the Python Macromolecular Library (pymmlib) package and developed and maintained the TLS Motion Determination (TLSMD) webserver/webservices. Contributed code to the CCP4 suite. Performed detailed analysis of thousands of crystallographic structures (both in-house and from the PDB). Programmed in C, Fortran, Python, Perl, Javascript, Bash, etc., maintained multiple MySQL databases, and worked in a LAMP environment for web services. Research produced a paper published in a peer-reviewed journal (see below). Also was the Linux System Administrator for all computers in our lab, performed backups (tape, DVD, xHDDs, etc.), hardware and software support for all personnel, etc.
Note: Everything was done in Linux (and some Mac OS X) and most of the programming was done in Python.
  • March 2006 – February 2007: System Administrator and Research Assistant at the Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA; (in absentia).
Developed an algorithm with a web services front-end to provide a quick estimate for protein-protein interactions and associated energies. Programmed in C, Fortran77, PHP and done in a LAMP environment. Research produced a paper published in a peer-reviewed journal (see below).
Note: Everything was done in Linux.
  • August 2005 – November 2005: Research Assistant, Teaching Assistant, and programmer at the Dr. David W. Ussery Laboratory — Center for Biological Sequence Analysis, Danmarks Tekniske Universitet, Denmark.
Helped develop and maintain algorithms and web services for a Comparative Genomics department. Programmed in C, Perl, Python, Java, Bash, etc., maintained multiple MySQL databases, and worked in a LAMP environment. Also was a Teaching Assistant for a Comparative Genomics class. Research produced a paper publisher in a peer-reviewed journal (see below).
Note: Everything was done in Linux.
  • October 2004 – July 2005: Research Assistant and System Administrator at the Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA.
Modelled protein-protein and protein-DNA interactions from crystallographic data obtained via the Protein Data Bank. Developed and maintained 4 websites to provide access to the algorithms we developed as web services (all done in a LAMP environment). Programmed in C, Fortran77, Perl, PHP, and maintained multiple MySQL databases. Research produced 2 papers published in peer-reviewed journals (see below).
Note: Everything was done in Linux.
  • Summer 2002 / December 2002: Research Assistant at the Dr. Alex Rich Laboratory — Department of Biology, Massachusetts Institute of Technology, USA.
Did research on the function of Z-DNA in various genomes and developed algorithms in C to search through genomes and compare the results against DNA microarray data. Also wrote Perl scripts and maintained a MySQL database.
Note: Everything was done in Linux.
  • May 2000 – September 2004: Research Assistant and software developer at the Dr. P. Shing Ho Laboratory — Department of Biochemistry & Biophysics, Oregon State University, USA.
Did research on the function of Z-DNA in various genomes (resulted in a paper published in a peer-reviewed journal; see CV). Other duties consisted of being an assistant scientific programmer in C and Perl, as well as maintaining a MySQL database.
Note: Everything was done in Linux.
  • September 1998 – April 2000: Lab Assistant for Kevin Krefft microbiology laboratory, Albany, OR, USA
Prepared all kinds of media (e.g., agar solutions and agar plates) to feed our stock of microbes, as well as rotating the colonies.
  • December 1996 – December 1997: English Language Instructor at Berlitz, Ljubljana, Slovenia.
I taught at all levels (beginner, mid-level, and advanced). Most of my students were government officials, businesspersons, and other professionals.
  • July 1996 – November 1996: Volunteer Humanitarian Aid Worker, Croatia.
I drove a van full of food and medical supplies to refugee camps on a nearly daily basis.
  • September 1995 – June 1996: Audio Technician at Audio & Visual Production Centre, Tateyama, 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.
  • September 1994 – August 1995: Deputy Manager 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.


  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)


  • Camacho CJ, Zhang C (2005). "FastContact: rapid estimate of contact and binding free energies". Bioinformatics, 21(10):2534-2536; DOI:10.1093/bioinformatics/bti322 .


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.

Curriculum Vitae


This category has only the following subcategory.