Christian Zmasek

Christian Zmasek, PhD

Lead Bioinformatics Engineer

Bio

Christian Zmasek, PhD, joined JCVI is a lead bioinformatics engineer. 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.

Publications

Publications

Cell reports methods. 2026-05-05; 101430.

Resilience of recombinant antibiotic resistance gene-containing plasmids against common cell culture disposal methods

Gluth A, Zmasek C, Chiu S, Moon TS
PMID: 42092359

Nucleic acids research. 2025-11-18;

BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration

Shukla M, Wattam AR, Aleman A, Bhattacharya R, Bowers N, Brettin T, Capria A, Chia N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Gokdemir O, Hendrickson RC, Kenyon RW, Klahn B, Kuscuoglu M, Lefkowitz EJ, Ma H, Machi D, Macken C, Mann CM, Mao C, Nguyen M, Olsen GJ, Olson RD, Overbeek R, Owens SM, Parrello B, Poretsky R, Pusch GD, Ramanathan A, Sheriff JT, Singh I, Stewart L, VanOeffelen M, Vonstein V, Warren AS, Wilke A, Zmasek CM, Zuniga A, Stevens RL
PMID: 41251138

Cell. 2025-10-02; 188.20: 5653-5665.e12.

Highly conserved Betacoronavirus sequences are broadly recognized by human T cells

Pereira Neto TA, Zmasek C, Avalos L, Sidney J, Trevizani R, Phillips E, Mallal S, Frazier A, Tan GS, Scheuermann RH, Sette A, Grifoni A
PMID: 40774254

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

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

Projects