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Items: 26

1.

Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).

Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH.

Virology. 2019 Mar;529:29-42. doi: 10.1016/j.virol.2019.01.005. Epub 2019 Jan 6.

2.

Phylogenomic analysis of glycogen branching and debranching enzymatic duo.

Zmasek CM, Godzik A.

BMC Evol Biol. 2014 Aug 23;14:183. doi: 10.1186/s12862-014-0183-2.

3.

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.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

4.

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.

Nat Struct Mol Biol. 2013 Nov;20(11):1243-9. doi: 10.1038/nsmb.2676. Epub 2013 Sep 29.

5.

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.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. doi: 10.1093/nar/gkt389. Epub 2013 May 15.

6.

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.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

7.

Evolution of the animal apoptosis network.

Zmasek CM, Godzik A.

Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a008649. doi: 10.1101/cshperspect.a008649. Review.

8.

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.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

9.

This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.

Zmasek CM, Godzik A.

PLoS Comput Biol. 2012;8(11):e1002701. doi: 10.1371/journal.pcbi.1002701. Epub 2012 Nov 15.

10.

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.

PLoS One. 2011 Apr 25;6(4):e18497. doi: 10.1371/journal.pone.0018497.

11.
12.

TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.

Zhang Q, Zmasek CM, Cai X, Godzik A.

Dev Comp Immunol. 2011 Apr;35(4):461-8. doi: 10.1016/j.dci.2010.11.013. Epub 2010 Nov 24.

13.

TOPSAN: a dynamic web database for structural genomics.

Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D494-6. doi: 10.1093/nar/gkq902. Epub 2010 Oct 20.

14.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1095-102. doi: 10.1093/nar/gkq811. Epub 2010 Sep 22.

15.

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.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

16.

Domain architecture evolution of pattern-recognition receptors.

Zhang Q, Zmasek CM, Godzik A.

Immunogenetics. 2010 May;62(5):263-72. doi: 10.1007/s00251-010-0428-1. Epub 2010 Mar 2.

17.

phyloXML: XML for evolutionary biology and comparative genomics.

Han MV, Zmasek CM.

BMC Bioinformatics. 2009 Oct 27;10:356. doi: 10.1186/1471-2105-10-356.

18.

Evolution of the human ion channel set.

Jegla TJ, Zmasek CM, Batalov S, Nayak SK.

Comb Chem High Throughput Screen. 2009 Jan;12(1):2-23. Review.

PMID:
19149488
19.

Novel genes dramatically alter regulatory network topology in amphioxus.

Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A.

Genome Biol. 2008;9(8):R123. doi: 10.1186/gb-2008-9-8-r123. Epub 2008 Aug 4.

20.

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.

Genome Res. 2008 Jul;18(7):1100-11. doi: 10.1101/gr.073676.107. Epub 2008 Jun 18. Erratum in: Genome Res. 2008 Aug;18(8):1380.

21.

Surprising complexity of the ancestral apoptosis network.

Zmasek CM, Zhang Q, Ye Y, Godzik A.

Genome Biol. 2007;8(10):R226.

22.

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.

Lawrence CJ, Zmasek CM, Dawe RK, Malmberg RL.

Bioinformatics. 2004 Aug 12;20(12):1977-9. Epub 2004 Mar 25.

PMID:
15044241
23.
24.

A simple algorithm to infer gene duplication and speciation events on a gene tree.

Zmasek CM, Eddy SR.

Bioinformatics. 2001 Sep;17(9):821-8.

PMID:
11590098
25.

ATV: display and manipulation of annotated phylogenetic trees.

Zmasek CM, Eddy SR.

Bioinformatics. 2001 Apr;17(4):383-4.

PMID:
11301314
26.

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.

Mol Cell Biol. 2001 May;21(9):3206-19.

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