Peer-Reviewed Literary Works

Scientific Papers, Books and Book Chapters

Our scientific literary production through the years is detailed below, including bibliographic information (journal Impact Factor and quartile ranking Q), as well as the authorship of postdoc (*), graduate student (**) and undergraduate student (***) trainees.

69. Detection of invasive and cryptic species in marine mussels (Bivalvia, Mytilidae): A chromosomal perspective.

Journal for Nature Conservation 39:58-67. Jul. 2017. (IF = 2.60, Q2)

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Garcia-Souto D., Sumner-Hempel D., Fervenza S., Perez-Garcia C., Torreiro A., Gonzalez-Romero R.***, Eirin-Lopez J.M., Moran P., and J.J. Pasantes

68. Molecular and biochemical methods useful for the epigenetic characterization of chromatin-associated proteins in bivalve molluscs.

Frontiers in Physiology 8:490. Jun. 2017. (IF = 3.92, Q1)

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Rivera-Casas C.**, Gonzalez-Romero R.*, Garduño R., Cheema M.S., Ausio J., and J.M. Eirin-Lopez.

67. Transcriptional and biochemical analysis of antioxidant enzymes in the mussel Mytilus galloprovincialis during experimental exposures to the toxic dinoflagellate Prorocentrum lima.

Marine Environmental Research 129:304-315. Jun. 2017. (IF = 2.45, Q1)

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Prego-Faraldo V.**, Vieira L.R., Eirin-Lopez J.M., Mendez J., and L. Guilhermino.

66. Basic surface features of FKBPs facilitate chromatin binding.

Nature Scientific Reports 7:3795. Jun. 2017. (IF = 4.26, Q1)

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Leung A., Jardim F.P., Savic N., Monneau Y.R., Gonzalez-Romero R.*, Gudavicius G., Eirin-Lopez J.M., Bartke T., Mackereth C.D., Ausio J., and C.J. Nelson.

65. Effects of Florida Red Tides on histone variant expression and DNA methylation in the Eastern oyster Crassostrea virginica.

Aquatic Toxicology 186:196-204. Mar. 2017. (IF = 3.45, Q1)

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Gonzalez-Romero R.*, Suarez-Ulloa V.**, Rodriguez-Casariego J.**, Garcia-Souto D., Diaz G.***, Smith A., Pasantes J.J., Rand G., and J.M. Eirin-Lopez.

64. Network-inspired approaches for transcriptomic analyses.

IWBBIO Proceedings 2016:437-440. Aug. 2016.

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Aguiar-Pulido V., Suarez-Ulloa V.**, Eirin-Lopez J.M., and G. Narasimhan.

63. Unique yeast histone sequences influence octamer and nucleosome stability.

FEBS Letters 590:2629-2638. Aug. 2016. (IF = 3.52, Q1)

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Leung A., Cheema M., Gonzalez-Romero R.*, Eirin-Lopez J.M., Ausio J., and C.J. Nelson.

62. Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues from Mytilus.

Biochemistry and Cell Biology 16:1-11. Jun. 2016. (IF = 2.15, Q2)

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Rivera-Casas C.**, Gonzalez-Romero R.*, Vizoso-Vazquez A., Cheema M.S., Cerdan M.E., Mendez J., Ausio J., and J.M. Eirin-Lopez.

61. Early genotoxic and cytotoxic effects of the toxic dinoflagellate Prorocentrum lima in the mussel Mytilus galloprovincialis.

Toxins 8:159. May. 2016. (IF = 3.03, Q1)

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Prego-Faraldo V.**, Valdiglesias V., Laffon B., Mendez J., and J.M. Eirin-Lopez.

60. The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin.

Epigenetics 11:415-425. Apr. 2016. (IF = 5.11, Q1)

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Rivera-Casas C.**, Gonzalez-Romero R.*, Cheema M.S., Ausio J., and J.M. Eirin-Lopez.

59. Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid.

PeerJ 3:e1429. Nov. 2015. (IF = 2.84, Q1)

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Suarez-Ulloa V.**, Fernandez-Tajes J., Aguiar-Pulido V., Prego-Faraldo V.**, Florez-Barros F., Sexto-Iglesias A., Mendez J., and J.M. Eirin-Lopez.

58. Environmental epigenetics: a promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates.

Marine Pollution Bulletin 98:5-13. Sep. 2015. (IF = 3.01, Q1)

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Suarez-Ulloa V.**, Gonzalez-Romero R.*, and J.M. Eirin-Lopez.

57. An unusual role for doublesex in sex determination in the dipteran Sciara.

Genetics 200:1181-1199. Aug. 2015. (IF = 3.79, Q1)

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Ruiz M.F., Alvarez M., Eirin-Lopez J.M., Sarno F., Krimer L., Barbero J.L. and L. Sanchez.

56. In vitro analysis of early genotoxic and cytotoxic effects of okadaic acid in different cell types of the mussel Mytilus galloprovincialis.

Journal of Toxicology and Environmental Health, Part A 78:814-824. Jul. 2015. (IF = 2.67, Q1)

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Prego-Faraldo M.V.**, Valdiglesias V., Laffon B., Eirin-Lopez J.M., and J. Mendez.

55. Computational Methods in Epigenetics.

pp. 154-175 in "Personalized Epigenetics", edited by T. Tollefsbol, ed. Elsevier.

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Aguiar-Pulido V., Suarez-Ulloa V.**, Eirin-Lopez J.M., Pereira J., and G. Narasimhan.

54. The comparative study of five sex determining proteins across insects unveils high rates of evolution at basal components of the sex determination cascade.

Development Genes and Evolution 225:23-30. Jan. 2015. (IF = 2.51, Q2)

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Eirin-Lopez J.M., and L. Sanchez.

53. Evolution of High Mobility Group Nucleosome-binding (HMGN) proteins and its implications for vertebrate chromatin specialization.

Molecular Biology and Evolution 32:121-131. Jan. 2015. (IF = 4.00, Q1)

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Gonzalez-Romero R.*, J.M. Eirin-Lopez, and J. Ausio.

52. Characterization of histone variants in bivalve molluscs and their relevance in the development of chromatin-based tests for evaluating okadaic acid genotoxicity in the marine environment.

Biochemistry and Cell Biology 91:395-395. Dec. 2013. (IF = 1.52, Q4)

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Gonzalez-Romero R.*, Rivera-Casas C.**, Mendez J., Eirin-Lopez J.M., and J. Ausio.

51. Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds.

Marine Drugs 11:4390-4406. Nov. 2013. (IF = 3.51, Q1)

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Suarez-Ulloa V.**, Fernandez-Tajes J., Manfrin C., Gerdol M., Venier P., and J.M. Eirin-Lopez.

50. Okadaic acid meet and greet: an insight into detection methods, response strategies and genotoxic effects in marine invertebrates.

Marine Drugs 11:2829-2845. Aug. 2013. (IF = 3.51, Q1)

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Prego-Faraldo M.V.**, Valdiglesias V., Mendez J., and J.M. Eirin-Lopez.

49. Clustering of gene expression profiles applied to marine research.

IWANN 2013, Part I, Lecture Notes on Computer Science (LNCS) 7902: 453–462. Jun. 2013.

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Aguiar-Pulido V., Suarez-Ulloa V.**, Rivero D., Eirin-Lopez J.M., and J. Dorado.

48. The evolution of sex-related traits and genes 2012.

International Journal of Evolutionary Biology vol. 2013, Article ID 590769. Mar. 2013.

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Civetta A., Eirin-Lopez J.M., Kulathinal R., and J. Marshall.

47. The CHROMEVALOA database: a resource for the evaluation of okadaic acid contamination in the marine environment based on the chromatin-associated transcriptome of the mussel Mytilus galloprovincialis.

Marine Drugs 11:830-841. Mar. 2013. (IF = 3.51, Q1)

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Suarez-Ulloa V.**, Fernandez-Tajes J., Aguiar-Pulido V., Rivera-Casas C.**, Gonzalez-Romero R.*, Ausio J., Mendez J., Dorado J., and J.M. Eirin-Lopez.

 46. About Evolution: keys to understanding how our genetic material evolves.

University of A Coruña Press, Spain.

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Eirin-Lopez J.M.

45. A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course.

Biochemistry and Molecular Biology Education 41:95-102. Feb. 2013. (IF = 0.59, Q4)

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Eirin-Lopez J.M.

44. The birth-and-death evolution of multigene families revisited.

pp. 170-196 in "Genome Dynamics vol. 7: Repetitive DNA", edited by M.A. Garrido-Ramos. Karger, Switzerland

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Eirin-Lopez J.M., Rebordinos L., Rooney A.P., and J. Rozas.

43. Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activity.

FASEB Journal 26:4788-4804. Dec. 2012. (IF = 5.70, Q1)

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Finn R., Ellard K., Eirin-Lopez J.M., and J. Ausio.

42. Insights into the Study of Chromatin in Molluscs: Structure and Molecular Evolution of Histones in Pectinids.

EAE Press, Spain.

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Rivera-Casas C., Mendez J., and J.M. Eirin-Lopez

41. A unified phylogeny-based nomenclature for histone variants.

Epigenetics and Chromatin. 5:7. May. 2012. (IF = 4.19, Q1)

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Talbert, P. B., K. Ahmad, G. Almouzni, J. Ausio, F. Berger, P.L. Bhalla, W.M. Bonner, W.Z. Cande , B.P. Chadwick, S.W.L. Chan, G.A.M. Cross, L. Cui, S.I. Dimitrov, D. Doenecke, J.M. Eirin-López, M.A. Gorovsky, S.B. Hake , B.A. Hamkalo, S. Holec, S.E. Jacobsen, K. Kamieniarz, S. Khochbin, A.G. Ladurner, D. Landsman, J.A. Latham, B. Loppin, H.S. Malik, W.F. Marzluff, J.R. Pehrson, J. Postberg, M. B Singh, R. Schneider, M.M. Smith, E. Thompson , M.E. Torres-Padilla, D.J. Tremethick, B.M. Turner, J.H. Waterborg , H. Wollmann, R. Yelagandula, B. Zhu, and S. Henikoff.

40. Chromatin specialization in bivalve molluscs: a leap forward for the evaluation of okadaic acid genotoxicity in the marine environment.

Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 155:175-181. Mar. 2012. (IF = 2.71, Q3)

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Gonzalez-Romero R.**, Rivera-Casas C.**, Fernandez-Tajes J., Ausio J., Mendez J., and J.M. Eirin-Lopez.

39. Histone H2A (H2A.X and H2A.Z) variants in molluscs: molecular characterization and potential implications for chromatin dynamics.

PLoS ONE 7(1):e30006. Jan. 2012. (IF = 3.73, Q1)

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Gonzalez-Romero R.**, Rivera-Casas C.**, Frehlick L.J., Mendez J., Ausio J., and J.M. Eirin-Lopez.

38. El papel clave de las histonas (The key role of histones)

Investigacion y Ciencia (Scientific American, Spanish edition). Dec. 2011.

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Gonzalez-Romero R.**, Ausio J., Mendez J., and J.M. Eirin-Lopez.

37. The evolution of sex-related traits and genes.

International Journal of Evolutionary Biology vol. 2011, Article ID 807218. Sep. 2011.

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Civetta A., Eirin-Lopez J.M., Kulathinal R., and J. Marshall.

36. Boule and the evolutionary origin of metazoan gametogenesis: a grandpa’s tale.

International Journal of Evolutionary Biology vol. 2011, Article ID 972457. Aug. 2011.

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Eirin-Lopez J.M. and J. Ausio.

35. Protamines: structural complexity, evolution and chromatin patterning.

Protein and Peptide Letters 18:755-771. Aug. 2011. (IF = 1.94, Q3)

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Kasinsky H., Eirin-Lopez J.M., and J. Ausio.

34. Birth-and-death long-term evolution promotes histone H2B variant diversification in the male germinal line.

Molecular Biology and Evolution 27:1802-1812. Aug. 2010. (IF = 5.51, Q1)

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Gonzalez-Romero R.**, Rivera-Casas C.**, Ausio J., Mendez J., and J.M. Eirin-Lopez.

33. The gene transformer-2 of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.

BMC Evolutionary Biology 10:140. May. 2010. (IF = 3.70, Q2)

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Sarno F., Ruiz M.F., Eirin-Lopez J.M., Perondini A., Selivon D., and L. Sanchez.

32. Evolutionary dynamics of the 5S rDNA gene family in the mussel Mytilus: mixed effects of birth-and-death and concerted evolution.

Journal of Molecular Evolution 70:413-426. May. 2010. (IF = 2.31, Q3)

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Freire R., Arias A., Insua A., Mendez J., and J.M. Eirin-Lopez.

31. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis.

Nucleic Acids Research 38:1780-1789. Mar. 2010. (IF = 7.84, Q1)

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Ishibashi T., Li A., Eirin-Lopez J.M., Zhao M., Missiaen K., Abbott D.W., Meistrich M., Hendzel M.J., Hunt D.F. and J. Ausio.

30. Characterization of H2A.Z-1 and H2A.Z-2 isoforms in vertebrates.

BMC Biology 7:86. Dec. 2009. (IF = 5.64, Q1)

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Dryhurst D., Ishibashi T., Rose K.L., Eirin-Lopez J.M., McDonald D., Silva-Moreno B., Veldhoen N., Helbing C.C., Hendzel M.J., Shabanowitz J., and J. Ausio.

29. Origin and evolution of chromosomal sperm proteins.

Bioessays 31:1062-1070. Oct. 2009. (IF = 5.12, Q1)

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Eirin-Lopez J.M., and J. Ausio.

28. Long-term evolution of histone families: old notions and new insights into their mechanisms of diversification across eukaryotes.

pp. 139-162 in "Evolutionary Biology: Concept, Modeling and Application", edited by P. Pontarotti. Springer, Germany.

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Eirin-Lopez J.M., Gonzalez-Romero R.**, Dryhurst D., Mendez J., and J. Ausio.

27. Histone genes of the razor clam Solen marginatus unveil new aspects of linker histone evolution in protostomes.

Genome 52:597-607. Jul. 2009. (IF = 1.71, Q3)

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Gonzalez-Romero R.**, Ausio J., Mendez J., and J.M. Eirin-Lopez.

26. The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues.

BMC Evolutionary Biology 9:31. Feb. 2009. (IF = 4.29, Q1)

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Eirin-Lopez J.M., Gonzalez-Romero R.**, Dryhurst D., Ishibashi T., and J. Ausio.

25. The sperm proteins from amphioxus mirror its basal position among chordates and redefine the origin of vertebrate protamines.

Molecular Biology and Evolution 25:1705-1713. Aug. 2008. (IF = 7.28, Q1)

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Eirin-Lopez J.M., Frehlick L.J., Chiva M., Saperas N., and J. Ausio.

24. Early evolution of histone genes: prevalence of an ‘orphon’ H1 lineage in protostomes and birth-and-death process in the H2A family.

Journal of Molecular Evolution 66:505-518. May. 2008. (IF = 2.76, Q2)

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Gonzalez-Romero R.**, Ausio J., Mendez J., and J.M. Eirin-Lopez.

23. Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd.

Gene 413:1-7. Apr. 2008. (IF = 2.58, Q3)

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Gonzalez-Romero R.**, Mendez J., Ausio J., and J.M. Eirin-Lopez.

22. Insight into ligand diversity and novel biological roles for family 32 carbohydrate binding molecules.

Molecular Biology and Evolution 25:155-167. Jan. 2008. (IF = 7.28, Q1)

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Abbott D.W., Eirin-Lopez J.M., and A. Boraston.

21. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way.

FASEB Journal 22:316-326. Jan. 2008. (IF = 7.05, Q1)

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Eirin-Lopez J.M., Ishibashi T., and J. Ausio.

20. The gene transformer of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.

PLoS ONE 2:e1239. Nov. 2007. (IF = 4.35, Q1)

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Ruiz M.F., Milano A., Salvemini N., Eirin-Lopez J.M., Perondini A.L., Selivon D., Polito C., Saccone G., and L. Sanchez.

19. The gene doublesex of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.

Development, Genes and Evolution 217:725-731. Oct. 2007. (IF = 2.07, Q3)

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Ruiz M.F., Eirin-Lopez J.M., Stefani R.N., Perondini A.L., Selivon D., and L. Sanchez.

18. Evolution of vertebrate chromosomal sperm proteins: implications for fertility and sperm competition.

pp. 63-79 in "Spermatology", edited by E. R. S. Roldan and M. Gomendio. Nottingham University Press, United Kingdom.

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Eirin-Lopez J.M., and J. Ausio.

17. Evolutions and revolutions of nuclear chaperones in chromatin remodeling: the nucleophosmin-nucleoplasmin family.

Biochemistry and Cell Biology 85:527-527. Aug. 2007. (IF = 2.42, Q3)

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Eirin-Lopez J.M., and J. Ausio.

16. H2A.Z-mediated genome-wide chromatin specialization.

Current Genomics 8:59-66. Mar. 2007. (IF = 0.57, Q4)

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Eirin-Lopez J.M., and J. Ausio.

15. New insights into the nucleophosmin/nucleoplasmin family of nuclear chaperones.

Bioessays 29:49-59. Jan. 2007. (IF = 5.40, Q1)

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Frehlick L.J., Eirin-Lopez J.M., and J. Ausio.

14. A unique histone H1-related protamine-like results in an unusual sperm chromatin organization.

FEBS Journal 273:4548-4561. Oct. 2006. (IF = 3.03, Q2)

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Saperas N., Chiva M., Casas M.T., Campos J.L., Eirin-Lopez J.M., Frehlick L.J., Prieto C., Subirana J.A., and J. Ausio.

13. Histone H1 function and distribution in chromatin: what does molecular evolution tell us about it?

Biochemistry and Cell Biology 84:658-658. Aug. 2006. (IF = 3.48, Q2)

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Eirin-Lopez J.M., and J. Ausio.

12. Long-term evolution and functional diversification in the members of the nucleophosmin/nucleoplasmin family of nuclear chaperones.

Genetics 173:1835-1850. Aug. 2006. (IF = 4.24, Q1)

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Eirin-Lopez J.M., Frehlick L.J., and J. Ausio.

11. The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodeling.

BMC Genomics 7:99. Apr. 2006. (IF = 4.03, Q1)

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Frehlick L.J., Eirin-Lopez J.M., Field E.D., Hunt D.F., and J. Ausio.

10. Common phylogenetic origin of protamine-like (PL) proteins and histone H1: evidence from bivalve PL genes.

Molecular Biology and Evolution 23:1304-1317. Jun. 2006. (IF = 6.73, Q1)

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Eirin-Lopez J.M., Lewis J.D., Howe L.A., and J. Ausio.

9. Presence of protamines in the sperm of two closely related species of Scorpaeniform fish with internal (Sebastes maliger) and external (Sebastolobus sp.) sexual reproduction.

Journal of Experimental Zoology. Part A, Comparative Experimental Biology 305:277-287. Mar. 2006. (IF = 1.35, Q2)

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Frehlick L.J., Eirin-Lopez J.M., Prado A., Su H.W., Kasinsky H.E., and J. Ausio.

8. Protamines, in the footsteps of linker histone evolution.

Journal of Biological Chemistry 281:1-4. Jan. 2006. (IF = 5.81, Q1)

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Eirin-Lopez J.M., Frehlick L.J., and J. Ausio.

7. H2AX: tailoring histone H2A for chromatin dependent genomic integrity.

Biochemistry and Cell Biology 83:505-515. Aug. 2005. (IF = 2.87, Q2)

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Li A., Eirin-Lopez J.M., and J. Ausio.

6. Common evolutionary origin and birth-and-death process in the replication independent histone H1 isoforms from vertebrate and invertebrate genomes.

Journal of Molecular Evolution 61:398-407. Sept. 2005. (IF = 2.70, Q2)

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Eirin-Lopez J.M., Ruiz M.F., Gonzalez-Tizon A.M., Martinez A., Ausio J., Sanchez L., and J. Mendez.

5. The gene sex-lethal of the Sciaridae family (Order Diptera, Suborder Nematocera) and its phylogeny in dipteran insects.

Genetics 168:907-921. Oct. 2004. (IF = 4.14, Q1)

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Serna E., Gorab E., Ruiz M.F., Goday C., Eirin-Lopez J.M., and L. Sanchez.

4. Birth-and-death evolution with strong purifying selection in the histone H1 multigene family and the origin of “orphon” H1 genes.

Molecular Biology and Evolution 21:1992-2003. Oct. 2004. (IF = 6.35, Q1)

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Eirin-Lopez J.M., Gonzalez-Tizon A.M., Martinez A., and J. Mendez.

3. Molecular evolutionary analysis of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with “orphon” features.

Journal of Molecular Evolution 58:131-144. Feb. 2004. (IF = 2.75, Q2)

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Eirin-Lopez J. M., Ruiz M.F., Gonzalez-Tizon A. M., Martinez A., Sanchez L. and J. Mendez.

2. Molecular and evolutionary analysis of mussel histone genes (Mytilus spp.): possible evidence of an “orphon” origin for H1 histone genes.

Journal of Molecular Evolution 55:272-283. Sept. 2002. (IF = 3.04, Q2)

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Eirin-Lopez J.M., Gonzalez-Tizon A.M., Martinez A., and J. Mendez.

1. Molecular, phylogenetic and evolutionary study of histone H1 and H3 genes: molecular markers in marine biology and aquaculture.

pp. 52-62 in "5th Meeting of Young Researchers". Xunta de Galicia, Spain.

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Eirin-Lopez J.M.

Marine epigenomic applications

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Beal A., Rodriguez-Casariego J., Rivera-Casas C., Suarez-Ulloa V., and J.M. Eirin-Lopez

Common and unique patterns in the responses of the Pacific oyster to multiple stressors using transcriptomic data series

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Suarez-Ulloa V., Aguiar-Pulido V., Valdes C., Narasimhan G., and J.M. Eirin-Lopez

Epigenetic variation in the flat tree oyster Isognomon alatus over a 2-year period in a mangrove ecosystem from North Biscayne Bay (North Miami, FL)

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Suarez-Ulloa V., Michel M., and J.M. Eirin-Lopez

Epigenetics of marine organisms

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Eirin-Lopez J.M. and H. Putnam

Epigenetic responses to nutrient stress in the staghorn coral Acropora cervicornis

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Rodriguez-Casariego J., Ladd M., Shantz M., Ausio J., Fourqurean J., Burkepile D., and J.M. Eirin-Lopez