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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 postdoctoral 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.
Publications
Cell. 2023-10-26; 186.22: 4818-4833.e25.
Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8
Nucleic acids research. 2023-01-06; 51.D1: D678-D689.
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Virology. 2022-05-01; 570.123-133.
Genomic evolution of the Coronaviridae family
Virology. 2019-03-01; 529.29-42.
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
BMC evolutionary biology. 2014-08-23; 14.183.
Phylogenomic analysis of glycogen branching and debranching enzymatic duo
BMC bioinformatics. 2014-04-17; 15.112.
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
Journal of biomedical semantics. 2014-02-05; 5.1: 5.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Nature structural & molecular biology. 2013-11-01; 20.11: 1243-9.
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
Nucleic acids research. 2013-07-01; 41.Web Server issue: W22-8.
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
BMC bioinformatics. 2013-05-13; 14.158.
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Cold Spring Harbor perspectives in biology. 2013-03-01; 5.3: a008649.
Evolution of the animal apoptosis network
Journal of biomedical semantics. 2013-02-11; 4.1: 6.
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
PLoS computational biology. 2012-01-01; 8.11: e1002701.
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes
PloS one. 2011-04-25; 6.4: e18497.
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster
Developmental and comparative immunology. 2011-04-01; 35.4: 461-8.
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog
Genome biology. 2011-01-01; 12.1: R4.
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
Nucleic acids research. 2011-01-01; 39.Database issue: D494-6.
TOPSAN: a dynamic web database for structural genomics
Nucleic acids research. 2011-01-01; 39.Database issue: D1095-102.
GreenPhylDB v2.0: comparative and functional genomics in plants
Biochemistry. 2010-09-28; 49.38: 8307-15.
Activation and specificity of human caspase-10
Journal of biomedical semantics. 2010-08-21; 1.1: 8.
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
Immunogenetics. 2010-05-01; 62.5: 263-72.
Domain architecture evolution of pattern-recognition receptors
BMC bioinformatics. 2009-10-27; 10.356.
phyloXML: XML for evolutionary biology and comparative genomics
Combinatorial chemistry & high throughput screening. 2009-01-01; 12.1: 2-23.
Evolution of the human ion channel set
Genome research. 2008-07-01; 18.7: 1100-11.
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome biology. 2008-01-01; 9.8: R123.
Novel genes dramatically alter regulatory network topology in amphioxus
Genome biology. 2007-01-01; 8.10: R226.
Surprising complexity of the ancestral apoptosis network
BMC bioinformatics. 2002-05-16; 3.14.
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Bioinformatics (Oxford, England). 2001-09-01; 17.9: 821-8.
A simple algorithm to infer gene duplication and speciation events on a gene tree
Molecular and cellular biology. 2001-05-01; 21.9: 3206-19.
Immune system dysfunction and autoimmune disease in mice lacking Emk (Par-1) protein kinase
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