Publications
mendeley profile | google scholar | research gate
Reviews
1. Zmasek CM and Godzik A (2013)
Evolution of the animal apoptosis network
Cold Spring Harbor Perspectives in Biology (Cell Survival and Cell Death), 5(3), a008649
[PubMed] [PDF] [Amazon: http://www.amazon.com/Cell-Survival-Death-Eric-Baehrecke/dp/1936113317] [citations]
Peer reviewed research articles
31. Zmasek CM, Knipe DM, Pellett PE, and Scheuermann RH (2019)
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)
Virology, 529, 29-42
30. Zhang Y, Aevermann BD, Anderson TK, Burke DF, ..., Zmasek CM, Klem EB, and Scheuermann RH (2016)
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
Nucleic Acids Research, D1, D466–D474
29. Zmasek CM and Godzik A (2014)
Phylogenomic analysis of glycogen branching and debranching enzymatic duo
BMC Evolutionary Biology, 14:183
28. Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek C, Axelrod HL, and Godzik, A (2014)
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
BMC Bioinformatics, 15:112
27. Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, ..., Zmasek CM, Kawamoto S, and Takagi T (2014)
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Journal of Biomedical Semantics, 5:5
26. Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, and Wright PE (2013)
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
Nature Structural & Molecular Biology, 20, 1243–1249
[F1000] [PubMed] [PDF] [citations]
25. Kuraku S, Zmasek CM, Nishimura O, and Katoh K (2013)
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
Nucleic Acids Research, 41, W22-W28
[PubMed] [PDF] [aLeaves] [citations]
24. Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, ..., Zmasek CM, Kawamoto S, Okubo K, Asai K, and Takagi T (2013)
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies
Journal of Biomedical Semantics, 4:6
23. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, ..., and Jordan G (2013)
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
BMC Bioinformatics, 14:158
22. Zmasek CM and Godzik A (2012)
This déjà vu feeling – Analysis of multidomain protein evolution in eukaryotic genomes
PLOS Computational Biology, 8(11) e1002701
21. Zmasek CM and Godzik A (2011)
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
Genome Biology, 12:R4
20. Zhang Q, Zmasek CM, Cai X, and Godzik A (2011)
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe–host dialog
Developmental & Comparative Immunology, 35, 461-468
19. 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, and Foster DB (2011)
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster
PLoS ONE, 6(4): e18497
18. Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, and Wooley J (2011)
TOPSAN: a dynamic web database for structural genomics
Nucleic Acids Research, 39, D494-D496
17. Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, and Conte MG (2011)
GreenPhylDB v2.0: comparative and functional genomics in plants
Nucleic Acids Research, 39, D1095-D1102
16. Zhang Q, Zmasek CM, and Godzik A (2010)
Domain architecture evolution of pattern-recognition receptors
Immunogenetics, 62, 263-272
[F1000] [PubMed] [PDF] [citations]
15. Wachmann K, Pop C, van Raam BJ, Drag M, Mace PD, Snipas SJ, Zmasek C, Schwarzenbacher R, Salvesen GS, and Riedl SJ (2010)
Activation and specificity of human caspase-10
Biochemistry, 49, 8307-8315
14. Katayama T, Arakawa K, Nakao M, ..., Zmasek CM, Asai K, and Takagi T (2010)
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Journal of Biomedical Semantics, 1: 8
13. Han MV and Zmasek CM (2009)
phyloXML: XML for evolutionary biology and comparative genomics
BMC Bioinformatics, 10:356
12. Jegla TJ, Zmasek CM, Batalov S, and Nayak SK (2009)
Evolution of the human ion channel set
Combinatorial Chemistry & High Throughput Screening, 12, 2-23
11. Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, and Godzik A (2008)
Novel genes dramatically alter regulatory network topology in amphioxus
Genome Biology, 9:R123
[F1000] [PubMed] [PDF] [citations]
10. Holland LZ, Albalat R, Azumi K, ..., Zmasek CM, ..., and Holland PW (2008)
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome Research, 18, 1100-1111
9. Zmasek CM, Zhang Q, Ye Y, and Godzik A (2007)
Surprising complexity of the ancestral apoptosis network
Genome Biology, 8:R226
[F1000] [PubMed] [PDF] [citations]
8. Lapp H, Bala S, ..., Zmasek CM, ..., and Vision TJ (2007)
The 2006 NESCent phyloinformatics hackathon: A field report
Evolutionary Bioinformatics, 2007:3 287-296
7. Leebens-Mack J, Vision T, ..., and Zmasek C (2006)
Taking the first steps towards a standard for reporting on phylogenies: Minimum information about a phylogenetic analysis
OMICS, 10:231-237
6. Lawrence CJ, Zmasek CM, Kelly Dawe R, and Malmberg RL (2004)
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference
Bioinformatics, 20, 1977-1979
5. Zmasek CM and Eddy SR (2002)
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
BMC Bioinformatics, 3:14
4. Zmasek CM and Eddy SR (2001)
A simple algorithm to infer gene duplication and speciation events on a gene tree
Bioinformatics, 17, 821-828
[F1000] [PubMed] [PDF] [citations]
3. Zmasek CM and Eddy SR (2001)
ATV: Display and manipulation of annotated phylogenetic trees
Bioinformatics, 17, 383-384
2. Hurov JB, Stappenbeck TS, Zmasek CM, White LS, Ranganath SH, Russell JH, Chan AC, Murphy KM, and Piwnica-Worms H (2001)
Immune system dysfunction and autoimmune disease in mice lacking Emk (Par-1) protein kinase
Molecular and Cellular Biology, 21, 3206-3219
1. Springer C, Krappmann S, Künzler M, Zmasek C, and Braus GH (1997)
Regulation of the yeast HIS7 gene by the global transcription factor Abf1p
Molecular and General Genetics, 256(2):136-146
Abstracts and Conference Papers
3. Zmasek CM and Godzik A (2010)
Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns
Genome Biology, 11(Suppl 1):P43
2. Zhang Q, Zmasek CM, Cai X, and Godzik A (2010)
The puzzle of TIR domain-containing proteins in bacteria
The Journal of Immunology, 184, 43.3
1. Zmasek CM (2008)
Emerging data standards for phylogenomics research