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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 host & microbe. 2024-12-11; 32.12: 2131-2147.e8.
A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice
Case JB, Sanapala S, Dillen C, Rhodes V, Zmasek C, Chicz TM, Switzer CE, Scheaffer SM, Georgiev G, Jacob-Dolan C, Hauser BM, Dos Anjos DCC, Adams LJ, Soudani N, Liang CY, Ying B, McNamara RP, Scheuermann RH, Boon ACM, Fremont DH, Whelan SPJ, Schmidt AG, Sette A, Grifoni A, Frieman MB, Diamond MS
PMID: 39561781
Cell. 2023-10-26; 186.22: 4818-4833.e25.
Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8
Zimmerman O, Zimmerman MI, Raju S, Nelson CA, Errico JM, Madden EA, Holmes AC, Hassan AO, VanBlargan LA, Kim AS, Adams LJ, Basore K, Whitener BM, Palakurty S, Davis-Adams HG, Sun C, Gilliland T, Earnest JT, Ma H, Ebel GD, Zmasek C, Scheuermann RH, Klimstra WB, Fremont DH, Diamond MS
PMID: 37804831
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
Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL
PMID: 36350631
Virology. 2022-05-01; 570.123-133.
Genomic evolution of the Coronaviridae family
Zmasek CM, Lefkowitz EJ, Niewiadomska A, Scheuermann RH
PMID: 35398776
Virology. 2019-03-01; 529.29-42.
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)
Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH
PMID: 30660046
Methods in molecular biology (Clifton, N.J.). 2019-01-01; 1911.47-69.
Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)
Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH
PMID: 30593617
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
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
PMID: 27679478
BMC evolutionary biology. 2014-08-23; 14.183.
Phylogenomic analysis of glycogen branching and debranching enzymatic duo
Zmasek CM, Godzik A
PMID: 25148856
BMC bioinformatics. 2014-04-17; 15.112.
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A
PMID: 24742328
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
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
PMID: 24495517
Nature structural & molecular biology. 2013-11-01; 20.11: 1243-9.
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE
PMID: 24077226
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
Kuraku S, Zmasek CM, Nishimura O, Katoh K
PMID: 23677614
BMC bioinformatics. 2013-05-13; 14.158.
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
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
PMID: 23668630
Cold Spring Harbor perspectives in biology. 2013-03-01; 5.3: a008649.
Evolution of the animal apoptosis network
Zmasek CM, Godzik A
PMID: 23457257
Journal of biomedical semantics. 2013-02-11; 4.1: 6.
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
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
PMID: 23398680
PLoS computational biology. 2012-01-01; 8.11: e1002701.
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes
Zmasek CM, Godzik A
PMID: 23166479
PloS one. 2011-04-25; 6.4: e18497.
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster
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
PMID: 21541028
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
Zhang Q, Zmasek CM, Cai X, Godzik A
PMID: 21110998
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
Zmasek CM, Godzik A
PMID: 21241503
Nucleic acids research. 2011-01-01; 39.Database issue: D494-6.
TOPSAN: a dynamic web database for structural genomics
Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J
PMID: 20961957
Nucleic acids research. 2011-01-01; 39.Database issue: D1095-102.
GreenPhylDB v2.0: comparative and functional genomics in plants
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG
PMID: 20864446
Biochemistry. 2010-09-28; 49.38: 8307-15.
Activation and specificity of human caspase-10
Wachmann K, Pop C, van Raam BJ, Drag M, Mace PD, Snipas SJ, Zmasek C, Schwarzenbacher R, Salvesen GS, Riedl SJ
PMID: 20795673
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*
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
PMID: 20727200
Immunogenetics. 2010-05-01; 62.5: 263-72.
Domain architecture evolution of pattern-recognition receptors
Zhang Q, Zmasek CM, Godzik A
PMID: 20195594
BMC bioinformatics. 2009-10-27; 10.356.
phyloXML: XML for evolutionary biology and comparative genomics
Han MV, Zmasek CM
PMID: 19860910
Combinatorial chemistry & high throughput screening. 2009-01-01; 12.1: 2-23.
Evolution of the human ion channel set
Jegla TJ, Zmasek CM, Batalov S, Nayak SK
PMID: 19149488
Genome research. 2008-07-01; 18.7: 1100-11.
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
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
PMID: 18562680
Genome biology. 2008-01-01; 9.8: R123.
Novel genes dramatically alter regulatory network topology in amphioxus
Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A
PMID: 18680598
Genome biology. 2007-01-01; 8.10: R226.
Surprising complexity of the ancestral apoptosis network
Zmasek CM, Zhang Q, Ye Y, Godzik A
PMID: 17958905
BMC bioinformatics. 2002-05-16; 3.14.
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Zmasek CM, Eddy SR
PMID: 12028595
Bioinformatics (Oxford, England). 2001-09-01; 17.9: 821-8.
A simple algorithm to infer gene duplication and speciation events on a gene tree
Zmasek CM, Eddy SR
PMID: 11590098
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
Hurov JB, Stappenbeck TS, Zmasek CM, White LS, Ranganath SH, Russell JH, Chan AC, Murphy KM, Piwnica-Worms H
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