matzLABPAPERS
recent and selected older papers
Strader ME, Aglyamova G V, Matz M V. Red fluorescence in coral larvae is associated with a diapause-like state. Mol. Ecol. 2016, 25:559–569. journal link.
Barfield, S., Aglyamova , G.V., Matz, M. V. Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa). Proc. Roy. Soc. B 2016, 283: 20152128. journal link.
Kenkel, C. D., Almanza, A. T. and Matz, M. V. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 2015, 96:3197-3212. journal link.
Strader, M. E., Davies, S. W., and Matz, M. V. Differential responses of coral larvae to the colour of ambient light guide them to suitable settlement microhabitat. Roy. Soc. Opensci. 2015, 2:150358. journal link.
Dixon, G. B., Davies, S. W., Aglyamova, G. V., Meyer, E., Bay, L. K. and Matz, M. V. Genomic determinants of coral heat tolerance across latitudes. Science 2015, 348:1460-1462. journal link.
Wright, R. M., Aglyamova, G. V., Meyer, E. and Matz, M. V. Gene expression associated with white syndromes in a reef-building coral, Acropora hyacinthus. BMC Genomics 2015, 16: 371. journal link.
Davies, S.W., Treml, E.A., Kenkel, C.D, and Matz, M.V. Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean. Mol Ecol 2015, 24: 70-82. journal link.
Dixon, G. B., Bay, L. K., Matz, M. V. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014, 15:1109. journal link.
Green. E.A., Davies, S.W., Matz. M.V., M Medina, M. Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2014, 2:e386. journal link.
Matz, M. V., Wright, R. M., and Scott, J. G. No control genes required: Bayesian analysis of qRT-PCR data. PLoS ONE 2013, 8(8): e71448. journal link.
Willette, D. A., Allendorf, F. W., Barber, P. H., Barshis, D. J., Carpenter, K. E., Crandall, E. D., Cresko, W. A., Fernandez-Silva, I., Matz, M. V, Meyer, E., Santos, M. D., Seeb, L. W., Seeb, J. E. So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute. Bulletin of Marine Science 2013, http://dx.doi.org/10.5343/bms.2013.1008.
Kenkel, C. D., Goodbody-Gringley, G. , Caillaud, D., Davies, S. W., Bartels, E., and Matz, M. V. Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments. Mol Ecol 2013, 22:4335-4348. proofs.pdf
Kenkel, C. D., Meyer, E., and Matz, M. V. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol Ecol 2013, 22:4322-4334. proofs.pdf
Bay LK, Guerecheau A, Andreakis N, Ulstrup KE, Matz MV (2013) Gene expression signatures of energetic acclimatisation in the reef building coral Acropora millepora. PLoS ONE 8(5): e61736. open access
Sierra, R., Matz, M. V., Aglyamova, G., Pillet, L., Decelle, J., Not, F., de Vargas, C., and Pawlowski, J. Deep relationships of Rhizaria revealed by phylogenomics: A farewell to Haeckel’s Radiolaria. Molecular Phylogenetics and Evolution, 2013, 67:53-69 pdf
 
Davies, S. W., Rahman, M., Meyer, E., Green, E. A., Buschizarro, E., Medina, M., and Matz, M. V. Novel polymorphic microsatellite markers for population genetics of the endangered Caribbean star coral, Montastraea faveolata. Marine Biodiversity 2012, pdf
Wang, S., Meyer, E., McKay, J.K., and Matz, M.V. 2b-RAD: a simple and flexible method for whole-genome genotyping. Nature Methods 2012, published online before print: doi:10.1038/nmeth.2023.
Hunt, M. E., Modi, C. K., Aglyamova, G. V., Ravikant, D. V. S., Meyer, E. and Matz, M. V. Multi-domain GFP-like proteins from marine hydrozoans. Photochem Photobiol Sci. 2012, 11:637-644. pdf
 
Kenkel CD, Aglyamova G, Alamaru A, et al. Development of gene expression markers of acute heat-light stress in reef-building corals of the genus Porites. PLoS ONE 2011,  6(10): e26914. doi:10.1371/journal.pone.0026914 open access
Meyer, E., Aglyamova, G. A., and Matz, M. V. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 2011, doi: 10.1111/j.1365-294X.2011.05205.x  pdf
Voolstra, C. A., Sunagawa, S., Matz, M. V, Bayer, T., Aranda, M., Buschiazzo, E., DeSalvo, M. K., Lindquist, E., Szmant, A. M., Coffroth, M. A., and Medina, M. Rapid evolution of coral proteins responsible for interaction with the environment. PLoS ONE 2011, 6(5): e20392.
Aglyamova, G. V., Hunt, M. E., Modi, C. K., and Matz, M.V. Multi-colored homologs of the green fluorescent protein from hydromedusa Obelia sp. Photochem. Photobiol. Sci. 2011, 10: 1303-1309, doi: 10.1039/C1PP05068K .
Kenkel, C. D., Traylor, M. R., Wiedenmann, J., Salih, A., and Matz, M. V. Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress. Proc. R. Soc. B 2011, doi:10.1098/rspb.2010.2344 free full text
Chudakov, D. M., Matz, M. V., Lukyanov, S. A., and Lukyanov, K. A. Fluorescent proteins and their applications in imaging of living cells and tissues. Physiological Reviews 2010, 90:1103-63. pdf
Hunt, M. E., Scherrer, M. P., Ferrari, F. D., and Matz, M. V. Very bright green fluorescent proteins from the pontellid copepod Pontella mimocerami. PLoS ONE 2010, 5(7): e11517. doi:10.1371/journal.pone.0011517. full text
Field, S. F., and Matz, M. V. Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Mol. Biol. Evol. 2010, 27:225-233. pdf
Wang, S., Zhang, L., Meyer, E. and Matz, M.V. Construction of a high-resolution genetic linkage map and comparative genome analysis for a reef-building coral Acropora millepora. Genome Biology 2009 10:R126 fulltext
Meyer, E., Davies, S., Wang, S., Willis, B. L., Abrego, D., Juenger, T. and Matz, M. V. Genetic variation in responses to settlement cue and elevated temperature in a reef-building coral Acropora millepora. Mar Ecol Prog Ser 2009, 392:81-92. fulltext
Meyer, E.,  Aglyamova, G.V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J.K., Willis, B.L., Matz, M.V. Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-Flx. BMC Genomics 2009, 10: 219. fultext  news-entry  protocols  data
Matz, M. V., Frank , T.,  Marshall, N. J., Widder, E. A., and Johnsen, S. Giant deep-sea protist produces bilaterian-like traces. Current Biology 2008, 18: 1849 - 1854. pdf  news-entry
Wang, S., Zhang, L. and Matz, M.V. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). Journal of Heredity 2008, doi: 10.1093/jhered/esn100. pdf  
Alieva, N.O., Konzen, K. A., Field, S. F., Meleshkevitch, E. A., Hunt, M., Beltran-Ramirez,V., Miller, D. J., Wiedenmann, J., Salih, A. and Matz, M. V. Diversity and evolution of coral fluorescent proteins. PLoS ONE 2008, 3(7): e2680.     fulltext    data  news-entry
Cox, G., Matz, M. and Salih, A. Fluorescence lifetime imaging of coral fluorescent proteins. Microscopy Research and Technique 2007, 70: 243-251. PMID: 17279514
Leutenegger, A., D’Angelo, C., Matz, M. V., Denzel, A., Oswald, F., Salih, A., Nienhaus, G. U. and Wiedenmann, J. It’s cheap to be colorful: Anthozoans show a slow turnover of GFP-like proteins. FEBS Journal 2007, 274: 2496-2505.  PMID: 17419724
Oswald, F., Schmitt, F., Leutenegger, A., Ivanchenko, S., D’Angelo, C., Salih, A., Maslakova, S., Bulina, M.; Schirmbeck, R., Nienhaus, G. U., Matz, M. V. and Wiedenmann, J. Contributions of host and symbiont pigments to the coloration of reef corals. FEBS Journal 2007, 274: 1102-1109. PMID: 17244197
Matz, M. V., Marshall, N. J. and Vorobyev, M. Are corals colorful? Photochem. Photobiol., 2006, 82: 345-350. PMID: 16613484
Field, S. F., Bulina, M. Y., Kelmanson, I. V., Bielawski J. P. and Matz, M. V. Adaptive evolution of multi-colored fluorescent proteins in reef-building corals. J. Mol. Evol., 2006, 62:332-339. PMID: 16474984
Nielsen, R. and Matz, M. V. Statistical approaches for DNA barcoding. Syst. Biol. 2006, 55:162-169. PMID: 16507534
Matz, M. V. and Meleshkevith, E. A. Ordered Differential Display. Methods Mol Biol. 2005, 317: 59-74. PMID: 16264221
Matz, M. V. and Nielsen, R. Likelihood ratio test for species membership based on DNA sequence data. Philos. Trans. Roy. Soc. B 2005, 360: 1969-1974.  PMID: 16214754
Chang, B. S. W., Ugalde, J. A. and Matz, M.V. Application of ancestral protein reconstruction in understanding protein function: GFP-like proteins. Meth Enzymol. 2005, 395: 652-670. PMID: 15865989
Lukyanov, K. A., Chudakov, D. M., Fradkov, A. F., Labas, Y. A., Matz, M. V. and Lukyanov, S. A. Discovery and properties of GFP-like proteins from nonbioluminescent Anthozoa. Methods Biochem Anal. 2006; 47:121-138. PMID: 16335712
Matz, M. V., Labas, Y. A. and Ugalde, J. Evolution of function and color in GFP-like proteins. Methods Biochem Anal. 2006; 47:139-161. PMID: 16342417
Ugalde, J. A., Chang, B. S. W. and Matz, M. V. Evolution of coral pigments recreated. Science 2004, 305: 1433. PMID: 15353795
Shagin, D. A., Barsova, E. V., Yanushevich, Y. G., Fradkov, A. F., Lukyanov, K. A., Labas, Y. A., Ugalde, J. A., Meyers, A., Nunez, J. M.,  Widder, E. A., Lukyanov, S. A., Matz, M. V.  GFP-like proteins as ubiquitous Metazoan superfamily: evolution of functional features and structural complexity. Mol Biol Evol.,2004, 21: 841-850. PMID: 14963095
Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res. 2004, 32: e37. PMID: 14973331
Kelmanson, I. K. and Matz, M. V. Molecular basis and evolutionary origins of color diversity in great star coral Montastraea cavernosa (Scleractinia, Faviida). Mol Biol Evol 2003, 20: 1125-1133. PMID: 12777529
Matz, M.V., Alieva, N. A., Chenichik, A and Lukyanov, S.A (2003) Amplification of cDNA ends using PCR-suppression effect and step-out PCR. In: Generation of cDNA libraries: Methods and protocols (Shao-Yao Ying Ed.) Humana press, Totowa, NJ, pp. 41-50.  PMID: 12703732
Matz, M.V. (2003) Amplification of representative cDNA pools from microscopic amounts of animal tissue. In Generation of cDNA libraries: Methods and protocols (Shao-Yao Ying Ed.) Humana press, Totowa, NJ, pp. 103-116. PMID: 12703737
Matz, M.V., Lukyanov, K. A. and Lukyanov, S. A. Family of the Green fluorescent Protein: Journey to the end of the rainbow. BioEssays 2002, 24:953-959. PMID: 12325128
Labas, Y. A., Gurskaya, N. G., Yanushevich, Y. G., Fradkov, A. F., Lukyanov, K. A., Lukyanov, S. A. and Matz, M. V. Diversity and evolution of the green fluorescent protein family. Proc Natl Acad Sci U S A 2002, 99: 4256-61. PMID: 11929996
Gurskaya, N. G., Fradkov, A. F., Terskikh, A., Matz, M. V., Labas, Y. A., Martynov, V. I., Yanushevich, Y. G., Lukyanov, K. A. and Lukyanov, S. A. GFP-like chromoproteins as a source of far-red fluorescent proteins. FEBS Lett 2001, 507: 16-20. PMID: 11682051
Yarbrough, D., Wachter, R., Kallio, K., Matz, M. V., Remington, S. J. Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0 A resolution. Proc. Natl. Acad. Sci. USA 2001, 98: 462-467. PMID: 11209050
Terskikh, A., Fradkov, A., Ermakova, G., Zaraisky, A., Tan, P., Kajava, A. V., Zhao, X., Ding, L., Lukyanov, S., Matz, M., Kim, S., Weissman, I., Siebert, P. “Fluorescent timer”: protein that changes color with time. Science 2000, 290: 1585-1588. PMID: 11090358
Fradkov, A.F., Chen, Y., Ding, L., Barsova, E.V., Matz, M.V. and Lukyanov, S.A. Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence. FEBS Lett 2000, 479: 127-130.  PMID: 10981720
Lukyanov, K.A., Fradkov, A.F., Gurskaya, N.G., Matz, M.V., Labas, Y.A., Savitsky, A.P., Markelov, M.L., Zaraisky, A.G., Zhao, X., Fang, Y., Tan, W., Lukyanov, S.A. Natural animal coloration can be determined by a non-fluorescent GFP homolog. J Biol Chem 2000, 275: 25879-82. PMID: 10852900
Matz, M., Fradkov, A., Labas, Y., Savitsky, A., Zaraisky, A., Markelov, M. and Lukyanov, S. Fluorescent proteins from non-bioluminescent Anthozoa species. Nature Biotechnol. 1999, 17: 969-973. PMID: 10504696
Shagin, D., Lukyanov, K., Vagner, L. Matz, M. Regulation of average length of complex PCR product. Nucleic Acids Res. 1999, 27: e23.  PMID: 10471753
Matz, M., Shagin, D., Bogdanova, E., Britanova, O., Lukyanov, S., Diatchenko, L., Chenchik, A. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 1999, 27: 1558-1560. PMID: 10037822
Matz, M.V., Lukyanov, S.A. Different strategies of differential display: areas of application. Nucleic Acids Res 1998, 26: 5537-5543.  PMID: 9837980
Matz, M., Usman, N., Shagin, D., Bogdanova, E., Lukyanov, S. Ordered differential display: a simple method for systematic comparison of gene expression profiles. Nucleic Acids Res 1997, 25: 2541-2542. PMID: 9171114
 
 
patents
Lukyanov, S. A., Fradkov, A. F., Labas, Y. A., Matz, M. V., Terskikh, A. Novel chromophores/fluorophores and methods for using the same. US patent # 7,166,444 (awarded January 23, 2007, filed December 3, 2001).
Matz, M. V., Kelmanson, I. V., Meleshkevitch, E. A., Salih, A. Fluorescent and colored proteins, and polynucleotides that encode these proteins. US patent # 7,160,698 (awarded January 9, 2007, filed May 20, 2004).
Matz, M. V., Alieva, N.O., Konzen, K. A., Field, S. F., Salih, A. Fluorescent and colored proteins, and polynucleotides that encode these proteins. US patent # 7,230,080, (awarded June 12, 2007, filed February 16, 2005).