Christian Zmasek, PhD

Sr. Bioinformatics Engineer
858-200-1897

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

Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).
Virology. 2019-03-01; 529.29-42.
PMID: 30660046
Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH
Influenza Research Database: An integrated bioinformatics resource for influenza virus research.
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
PMID: 27679478
Zmasek CM, Godzik A
Phylogenomic analysis of glycogen branching and debranching enzymatic duo.
BMC evolutionary biology. 2014-08-23; 14.183.
PMID: 25148856
Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A
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
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Journal of biomedical semantics. 2014-02-05; 5.1: 5.
PMID: 24495517
Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE
Divergent evolution of protein conformational dynamics in dihydrofolate reductase.
Nature structural & molecular biology. 2013-11-01; 20.11: 1243-9.
PMID: 24077226
Kuraku S, Zmasek CM, Nishimura O, Katoh K
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
Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
BMC bioinformatics. 2013-05-13; 14.158.
PMID: 23668630
Zmasek CM, Godzik A
Evolution of the animal apoptosis network.
Cold Spring Harbor perspectives in biology. 2013-03-01; 5.3: a008649.
PMID: 23457257
Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.
Journal of biomedical semantics. 2013-02-11; 4.1: 6.
PMID: 23398680
Zmasek CM, Godzik A
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.
PLoS computational biology. 2012-01-01; 8.11: e1002701.
PMID: 23166479
Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, Reedy MC, Zmasek CM, Gucek M, Cole RN, Van Eyk JE, Bodmer R, O'Rourke B, Bernstein SI, Foster DB
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster.
PloS one. 2011-04-25; 6.4: e18497.
PMID: 21541028
Zhang Q, Zmasek CM, Cai X, Godzik A
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
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG
GreenPhylDB v2.0: comparative and functional genomics in plants.
Nucleic acids research. 2011-01-01; 39.Database issue: D1095-102.
PMID: 20864446
Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J
TOPSAN: a dynamic web database for structural genomics.
Nucleic acids research. 2011-01-01; 39.Database issue: D494-6.
PMID: 20961957
Zmasek CM, Godzik A
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
Wachmann K, Pop C, van Raam BJ, Drag M, Mace PD, Snipas SJ, Zmasek C, Schwarzenbacher R, Salvesen GS, Riedl SJ
Activation and specificity of human caspase-10.
Biochemistry. 2010-09-28; 49.38: 8307-15.
PMID: 20795673
Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
Journal of biomedical semantics. 2010-08-21; 1.1: 8.
PMID: 20727200
Zhang Q, Zmasek CM, Godzik A
Domain architecture evolution of pattern-recognition receptors.
Immunogenetics. 2010-05-01; 62.5: 263-72.
PMID: 20195594
Han MV, Zmasek CM
phyloXML: XML for evolutionary biology and comparative genomics.
BMC bioinformatics. 2009-10-27; 10.356.
PMID: 19860910
Jegla TJ, Zmasek CM, Batalov S, Nayak SK
Evolution of the human ion channel set.
Combinatorial chemistry & high throughput screening. 2009-01-01; 12.1: 2-23.
PMID: 19149488
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Genome research. 2008-07-01; 18.7: 1100-11.
PMID: 18562680
Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A
Novel genes dramatically alter regulatory network topology in amphioxus.
Genome biology. 2008-01-01; 9.8: R123.
PMID: 18680598
Zmasek CM, Zhang Q, Ye Y, Godzik A
Surprising complexity of the ancestral apoptosis network.
Genome biology. 2007-01-01; 8.10: R226.
PMID: 17958905
Zmasek CM, Eddy SR
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
BMC bioinformatics. 2002-05-16; 3.14.
PMID: 12028595
Zmasek CM, Eddy SR
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
Hurov JB, Stappenbeck TS, Zmasek CM, White LS, Ranganath SH, Russell JH, Chan AC, Murphy KM, Piwnica-Worms H
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

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.

Virus Pathogen Resource (ViPR)

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Influenza Research Database (IRD)

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Archaeopteryx.js

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Herpesvirus Ortholog Prediction

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