Christian Zmasek, PhD

Sr. Bioinformatics Engineer



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Christian Zmasek, PhD, joined JCVI in 2016 as Senior Bioinformatics Engineer in Dr. Richard H. Scheuermann’s group. His main responsibilities are the development of novel software tools and algorithms for the Virus Pathogen Resource (ViPR) and Influenza Research Database (IRD), as well as research on the comparative evolutionary genomics and systems biology of viruses.

Dr. Zmasek has a Diploma in Chemistry and Biology from the Swiss Federal Institute of Technology (ETH) in Zürich, Switzerland and a PhD degree in Molecular Genetics from Washington University in St. Louis. He held a principal scientist position at The Genomics Institute of the Novartis Research Foundation and a post-doctoral position at the Sanford Burnham Prebys Medical Discovery Institute where he investigated the comparative evolutionary genomics of eukaryotic regulatory pathways.

Research Priorities

Development of novel software tools and algorithms for the Virus Pathogen Resource (ViPR) and Influenza Research Database (IRD):

  • Development of novel tool for the analysis and visualization of phylogenetic trees (Archaeopteryx.js)

Comparative evolutionary genomics of viruses:

  • Application of phylogenomics for the classification of viral proteins
  • Reconstruction of the minimal proteomes of Herpes-, Pox-, and Coronaviruses

Application of machine learning algorithms to evolutionary systems biology.


Select Publications

Phylogenomic analysis of glycogen branching and debranching enzymatic duo.
BMC evolutionary biology. 2014-08-23; 14.183.
PMID: 25148856
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.
BMC bioinformatics. 2014-04-17; 15.112.
PMID: 24742328
Divergent evolution of protein conformational dynamics in dihydrofolate reductase.
Nature structural & molecular biology. 2013-11-01; 20.11: 1243-9.
PMID: 24077226
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
Nucleic acids research. 2013-07-01; 41.Web Server issue: W22-8.
PMID: 23677614
Evolution of the animal apoptosis network.
Cold Spring Harbor perspectives in biology. 2013-03-01; 5.3: a008649.
PMID: 23457257
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.
PLoS computational biology. 2012-01-01; 8.11: e1002701.
PMID: 23166479
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster.
PloS one. 2011-04-25; 6.4: e18497.
PMID: 21541028
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.
Developmental and comparative immunology. 2011-04-01; 35.4: 461-8.
PMID: 21110998
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.
Genome biology. 2011-01-01; 12.1: R4.
PMID: 21241503
TOPSAN: a dynamic web database for structural genomics.
Nucleic acids research. 2011-01-01; 39.Database issue: D494-6.
PMID: 20961957
GreenPhylDB v2.0: comparative and functional genomics in plants.
Nucleic acids research. 2011-01-01; 39.Database issue: D1095-102.
PMID: 20864446
Activation and specificity of human caspase-10.
Biochemistry. 2010-09-28; 49.38: 8307-15.
PMID: 20795673
Domain architecture evolution of pattern-recognition receptors.
Immunogenetics. 2010-05-01; 62.5: 263-72.
PMID: 20195594
phyloXML: XML for evolutionary biology and comparative genomics.
BMC bioinformatics. 2009-10-27; 10.356.
PMID: 19860910
Evolution of the human ion channel set.
Combinatorial chemistry & high throughput screening. 2009-01-01; 12.1: 2-23.
PMID: 19149488
Novel genes dramatically alter regulatory network topology in amphioxus.
Genome biology. 2008-01-01; 9.8: R123.
PMID: 18680598
Surprising complexity of the ancestral apoptosis network.
Genome biology. 2007-01-01; 8.10: R226.
PMID: 17958905
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
BMC bioinformatics. 2002-05-16; 3.14.
PMID: 12028595
A simple algorithm to infer gene duplication and speciation events on a gene tree.
Bioinformatics (Oxford, England). 2001-09-01; 17.9: 821-8.
PMID: 11590098
Immune system dysfunction and autoimmune disease in mice lacking Emk (Par-1) protein kinase.
Molecular and cellular biology. 2001-05-01; 21.9: 3206-19.
PMID: 11287624