2017

59. Basic surface features of FKBPs facilitate chromatin binding.
Scientific Reports in press. Apr. 2017. View PDF.

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.

58. 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. View PDF.

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.

2016

57. Network-inspired approaches for transcriptomic analyses.
IWBBIO Proceedings 2016:437-440. Aug. 2016. View PDF.

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

56. Unique yeast histone sequences influence octamer and nucleosome stability.
FEBS Letters 590:2629-2638. Aug. 2016. View PDF.

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

55. 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. View PDF.

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

54. Early genotoxic and cytotoxic effects of the toxic dinoflagellate Prorocentrum lima in the mussel Mytilus galloprovincialis.
Toxins 8:159. May. 2016. View PDF.

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

53. The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin.
Epigenetics 11:415-425. Apr. 2016. View PDF.

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

2015

52. Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid.
PeerJ 3:e1429. Nov. 2015. View PDF.

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.

51. Environmental epigenetics: a promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates.
Marine Pollution Bulletin 98:5-13. Sep. 2015. View PDF.

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

50. An unusual role for doublesex in sex determination in the dipteran Sciara.
Genetics 200:1181-1199. Aug. 2015. View PDF.

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

49. 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. View PDF.

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

48. 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. View PDF.

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

47. 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. View PDF.

Gonzalez-Romero R., J.M. Eirin-Lopez, and J. Ausio.
Comment on FIU NEWS

2013

46. 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. View PDF.

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

45. Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds.
Marine Drugs 11:4390-4406. Nov. 2013. View PDF.

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

44. 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. View PDF.

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

43. Clustering of gene expression profiles applied to marine research.
IWANN 2013, Part I, Lecture Notes on Computer Science (LNCS) 7902: 453–462. Jun. 2013. View PDF.

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

42. The evolution of sex-related traits and genes 2012.
International Journal of Evolutionary Biology vol. 2013, Article ID 590769. Mar. 2013. View PDF.

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

41. 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. View PDF.

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.

40. 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. View PDF.

Eirin-Lopez J.M.

2012

39. Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activity.
FASEB Journal 26:4788-4804. Dec. 2012. View PDF.

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

38. A unified phylogeny-based nomenclature for histone variants.
Epigenetics Chromatin. 5:7. May. 2012. View PDF.

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.
Comment on BIOMED CENTRAL
Comment on EPIGENIE

37. 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. View PDF.

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

36. 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. View PDF.

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

2011

35. El papel clave de las histonas.
Investigacion y Ciencia (Scientific American, Spanish edition). Dec. 2011. View PDF.

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

34. The evolution of sex-related traits and genes.
International Journal of Evolutionary Biology vol. 2011, Article ID 807218. Sep. 2011. View PDF.

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

33. Boule and the evolutionary origin of metazoan gametogenesis: a grandpa’s tale.
International Journal of Evolutionary Biology vol. 2011, Article ID 972457. Aug. 2011. View PDF.

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

32. Protamines: structural complexity, evolution and chromatin patterning.
Protein and Peptide Letters 18:755-771. Aug. 2011. View PDF.

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

2010

31. 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. View PDF.

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

30. The gene transformer-2 of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.
BMC Evolutionary Biology 10:140. May. 2010. View PDF.

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

29. 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. View PDF.

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

28. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis.
Nucleic Acids Research 38:1780-1789. Mar. 2010. View PDF.

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.

2009

27. Characterization of H2A.Z-1 and H2A.Z-2 isoforms in vertebrates.
BMC Biology 7:86. Dec. 2009. View PDF.

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.

26. Origin and evolution of chromosomal sperm proteins.
Bioessays 31:1062-1070. Oct. 2009. View PDF.

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

25. Histone genes of the razor clam Solen marginatus unveil new aspects of linker histone evolution in protostomes.
Genome 52:597-607. Jul. 2009. View PDF.

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

24. 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. View PDF.

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

2008

23. 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. View PDF.

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

22. 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. View PDF.

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

21. Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd.
Gene 413:1-7. Apr. 2008. View PDF.

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

20. Insight into ligand diversity and novel biological roles for family 32 carbohydrate binding molecules.
Molecular Biology and Evolution 25:155-167. Jan. 2008. View PDF.

Abbott D.W., Eirin-Lopez J.M., and A. Boraston.
Comment on FUNCTIONAL GLYCOMICS GATEWAY

19. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way.
FASEB Journal 22:316-326. Jan. 2008. View PDF.

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

2007

18. The gene transformer of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.
PLoS ONE 2:e1239. Nov. 2007. View PDF.

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

17. The gene doublesex of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects.
Development, Genes and Evolution 217:725-731. Oct. 2007. View PDF.

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

16. Evolutions and revolutions of nuclear chaperones in chromatin remodeling: the nucleophosmin-nucleoplasmin family.
Biochemistry and Cell Biology 85:527-527. Aug. 2007. View PDF.

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

15. H2A.Z-mediated genome-wide chromatin specialization.
Current Genomics 8:59-66. Mar. 2007. View PDF.

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

14. New insights into the nucleophosmin/nucleoplasmin family of nuclear chaperones.
Bioessays 29:49-59. Jan. 2007. View PDF.

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

2006

13. A unique histone H1-related protamine-like results in an unusual sperm chromatin organization.
FEBS Journal 273:4548-4561. Oct. 2006. View PDF.

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.

12. Histone H1 function and distribution in chromatin: what does molecular evolution tell us about it?.
Biochemistry and Cell Biology 84:658-658. Aug. 2006. View PDF.

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

11. Long-term evolution and functional diversification in the members of the nucleophosmin/nucleoplasmin family of nuclear chaperones.
Genetics 173:1835-1850. Aug. 2006. View PDF.

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

10. The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodeling.
BMC Genomics 7:99. Apr. 2006. View PDF.

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

9. 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. View PDF.

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

8. 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. View PDF.

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

7. Protamines, in the footsteps of linker histone evolution.
Journal of Biological Chemistry 281:1-4. Jan. 2006. View PDF.

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

2005

6. H2AX: tailoring histone H2A for chromatin dependent genomic integrity.
Biochemistry and Cell Biology 83:505-515. Aug. 2005. View PDF.

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

5. 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. View PDF.

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

2004

4. The gene sex-lethal of the Sciaridae family (Order Diptera, Suborder Nematocera) and its phylogeny in dipteran insects.
Genetics 168:907-921. Oct. 2004. View PDF.

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

3. 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. View PDF.

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

2. 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. View PDF.

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

2002

1. 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. View PDF.

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