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
[PubMed]
[PDF]
[Google Scholar]
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
[PubMed]
[PDF]
[Google Scholar]
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
[PubMed]
[PDF]
[Google Scholar]
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
[PubMed]
[PDF]
[TOPSAN]
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
[PubMed]
[PDF]
[GreenPhyl]
[Google Scholar]
Zhang Q, Zmasek CM, and Godzik A (2010)
Domain architecture evolution of pattern-recognition receptors
Immunogenetics, 62, 263-272
[F1000]
[PubMed]
[PDF]
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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
[PubMed]
[PDF]
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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
[PubMed]
[PDF]
[Google Scholar]
Han MV and Zmasek CM (2009)
phyloXML: XML for evolutionary biology and comparative genomics
BMC Bioinformatics, 10:356
[PubMed]
[PDF]
[website]
[Google Scholar]
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
[PubMed]
[PDF]
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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]
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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
[PubMed]
[PDF]
[Google Scholar]
Zmasek CM, Zhang Q, Ye Y, and Godzik A (2007)
Surprising complexity of the ancestral apoptosis network
Genome Biology, 8:R226
[F1000]
[PubMed]
[PDF]
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Lapp H, Bala S, ..., Zmasek CM, ..., and Vision TJ (2007)
The 2006 NESCent phyloinformatics hackathon: A field report
Evolutionary Bioinformatics, 2007:3 287-296
[PDF]
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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
[PubMed]
[PDF]
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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
[PubMed]
[PDF]
[software download]
[Google Scholar]
Zmasek CM and Eddy SR (2002)
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
BMC Bioinformatics, 3:14
[PubMed]
[PDF]
[webserver]
[software download]
[Google Scholar]
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]
[software download]
[Google Scholar]
Zmasek CM and Eddy SR (2001)
ATV: Display and manipulation of annotated phylogenetic trees
Bioinformatics, 17, 383-384
[PubMed]
[PDF]
[software download]
[Google Scholar]
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
[PubMed]
[PDF]
[Google Scholar]
Springer C, Krappmann S, Künzler M, Zmasek C, and Braus GH (1997)
Regulation of the HIS7 gene by the global transcription factor Abf1p
Molecular and General Genetics, 256, 136-146
[PubMed]
[PDF]
[Google Scholar]
Zmasek CM and Godzik A (2010)
Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns
Genome Biology, 11(Suppl 1):P43
[doi:10.1186/gb-2010-11-s1-p43]
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
Zmasek CM (2008)
Emerging data standards for phylogenomics research
Proceedings of TDWG 2008
Zmasek CM (2002)
Functional Analyses of Proteomes by Phylogenetic Methods
Washington University
[PDF]
Last updated 2011.04.30