Eirin Lopez, Jose
- Associate Professor, Biological Sciences , College of Arts, Sciences & Education

Overview
overview
- Dr. Jose M. Eirin-Lopez is an associate professor in the Department of Biological Sciences at Florida International University (Miami, FL). He is also an affiliated faculty in the Center for Coastal Oceans Research at the Institute of Environment, as well as in the CREST Center for Aquatiic Chemistry and Environment at this institution. Since 2007, he is the principal investigator at the Environmental Epigenetics Lab. His research aims to make fundamental contributions to the study of marine environmental epigenetics using molecular, ecological and toxicological approaches.
research interests
- The central goal of our research program is to study the links between Global Change stressors and the epigenetic mechanisms modulating acclimatory and adaptive physiological responses in organisms across different marine ecosystems. We use a multidisciplinary and highly collaborative approach to study Environmental Epigenetics, integrating knowledge and discovery across different levels from Molecular Biology to Physiology, from Genetics to Ecology and from Epigenetics to Evolution. We are pioneering the development of epigenetic toolkits in non model organisms, paving the way for expanding environmental epigenetic analyses and their application to management and conservation of diverse ecologically and commercially relevant species
Scholarly & Creative Works
selected publications
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Article
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2022Coral-bleaching responses to climate change across biological scalesFull Text via DOI: 10.1111/gcb.16192 Web of Science: 000787738600001
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2021Evolution of a histone variant involved in compartmental regulation of NAD metabolismFull Text via DOI: 10.1038/s41594-021-00692-5 Web of Science: 000728721400013
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2021Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biasesFull Text via DOI: 10.1111/1755-0998.13542 Web of Science: 000718383000001
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2021Symbiont shuffling induces differential DNA methylation responses to thermal stress in the coral Montastraea cavernosaFull Text via DOI: 10.1111/mec.16246 Web of Science: 000714863200001
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2021Epigenetic responses in juvenile Lemon sharks (Negaprion brevirostris) during a coastal dredging episode in Bimini, BahamasFull Text via DOI: 10.1016/j.ecolind.2021.107793 Web of Science: 000658937700003
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2019The Bottlenose Dolphin Epigenetic Aging Tool (BEAT): A Molecular Age Estimation Tool for Small CetaceansFull Text via DOI: 10.3389/fmars.2019.00561 Web of Science: 000488121900001
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2019SEASONAL DNA METHYLATION VARIATION IN THE FLAT TREE OYSTER ISOGNOMON ALATUS FROM A MANGROVE ECOSYSTEM IN NORTH BISCAYNE BAY, FLORIDAFull Text via DOI: 10.2983/035.038.0108 Web of Science: 000464930800008
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2018Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)Full Text via DOI: 10.3390/genes9110517 Web of Science: 000451636700002
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2017Detection of invasive and cryptic species in marine mussels (Bivalvia, Mytilidae): A chromosomal perspectiveFull Text via DOI: 10.1016/j.jnc.2017.07.005 Web of Science: 000410880400003
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2017Molecular and Biochemical Methods Useful for the Epigenetic Characterization of Chromatin-Associated Proteins in Bivalve MolluscsFull Text via DOI: 10.3389/fphys.2017.00490 Web of Science: 000407608200001
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2017Basic surface features of nuclear FKBPs facilitate chromatin bindingFull Text via DOI: 10.1038/s41598-017-04194-7 Web of Science: 000403650300038
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2017Effects of Florida Red Tides on histone variant expression and DNA methylation in the Eastern oyster Crassostrea virginicaFull Text via DOI: 10.1016/j.aquatox.2017.03.006 Web of Science: 000401386100020
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2016Characterization of mussel H2AZ2: a new H2A.Z variant preferentially expressed in germinal tissues from MytilusFull Text via DOI: 10.1139/bcb-2016-0056 Web of Science: 000386056700011
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2016Unique yeast histone sequences influence octamer and nucleosome stabilityFull Text via DOI: 10.1002/1873-3468.12266 Web of Science: 000383600300014
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2016Early Genotoxic and Cytotoxic Effects of the Toxic Dinoflagellate Prorocentrum lima in the Mussel Mytilus galloprovincialisFull Text via DOI: 10.3390/toxins8060159 Web of Science: 000378808700002
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2015Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acidFull Text via DOI: 10.7717/peerj.1429 Web of Science: 000365803400013
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2015An Unusual Role for doublesex in Sex Determination in the Dipteran SciaraFull Text via DOI: 10.1534/genetics.115.177972 Web of Science: 000359917000017
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2015Evolution of High Mobility Group Nucleosome-Binding Proteins and Its Implications for Vertebrate Chromatin SpecializationFull Text via DOI: 10.1093/molbev/msu280 Web of Science: 000350050200011
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2013A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*Full Text via DOI: 10.1002/bmb.20667 Web of Science: 000316694400006
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2012
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2011
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2010Birth-and-Death Long-Term Evolution Promotes Histone H2B Variant Diversification in the Male Germinal Cell LineFull Text via DOI: 10.1093/molbev/msq058 Web of Science: 000280296700008
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2010The gene transformer-2 of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insectsFull Text via DOI: 10.1186/1471-2148-10-140 Web of Science: 000279827800001
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2010Evolutionary Dynamics of the 5S rDNA Gene Family in the Mussel Mytilus: Mixed Effects of Birth-and-Death and Concerted EvolutionFull Text via DOI: 10.1007/s00239-010-9341-3 Web of Science: 000278094800002
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2010H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesisFull Text via DOI: 10.1093/nar/gkp1129 Web of Science: 000276304600011
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2009Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebratesFull Text via DOI: 10.1186/1741-7007-7-86 Web of Science: 000273536900001
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2009Histone genes of the razor clam Solen marginatus unveil new aspects of linker histone evolution in protostomesFull Text via DOI: 10.1139/G09-034 Web of Science: 000268853700002
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2008The sperm proteins from amphioxus mirror its basal position among chordates and redefine the origin of vertebrate protaminesFull Text via DOI: 10.1093/molbev/msn121 Web of Science: 000257789200022
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2008H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent wayFull Text via DOI: 10.1096/fj.07-9255com Web of Science: 000252309900033
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2008Insight into ligand diversity and novel biological roles for family 32 carbohydrate-binding modulesFull Text via DOI: 10.1093/molbev/msm243 Web of Science: 000253375900016
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2007The Gene Transformer of Anastrepha Fruit Flies (Diptera, Tephritidae) and Its Evolution in InsectsFull Text via DOI: 10.1371/journal.pone.0001239 Web of Science: 000207459300020
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2007The gene doublesex of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insectsFull Text via DOI: 10.1007/s00427-007-0178-8 Web of Science: 000249968700006
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2007H2A.Z-mediated genome-wide chromatin specializationFull Text via DOI: 10.2174/138920207780076965 Web of Science: 000244925700006
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2006A unique vertebrate histone H1-related protamine-like protein results in an unusual sperm chromatin organizationFull Text via DOI: 10.1111/j.1742-4658.2006.05461.x Web of Science: 000240558500018
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2006Common phylogenetic origin of protamine-like (PL) proteins and histone H1: Evidence from bivalve PL genesFull Text via DOI: 10.1093/molbev/msk021 Web of Science: 000237696800022
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2006The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodelingFull Text via DOI: 10.1186/1471-2164-7-99 Web of Science: 000238291600001
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2005H2AX: tailoring histone H2A for chromatin-dependent genomic integrityFull Text via DOI: 10.1139/O05-114 Web of Science: 000231466300011
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2004Birth-and-death evolution with strong purifying selection in the histone H1 multigene family and the origin of orphon H1 genesFull Text via DOI: 10.1093/molbev/msh213 Web of Science: 000224013100017
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2004The gene Sex-lethal of the Sciaridae family (order Diptera, suborder Nematocera) and its phylogeny in dipteran insectsFull Text via DOI: 10.1534/genetics.104.031278 Web of Science: 000225063100029
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Book Chapter
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2018Environmental Epigenomics and Its Applications in Marine Organisms. 325-359.Full Text via DOI: 10.1007/13836_2018_28
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2015Computational Methods in Epigenetics. 153-180.Full Text via DOI: 10.1016/B978-0-12-420135-4.00006-1
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2015Chapter 6 Computational Methods in Epigenetics. 153-180.Full Text via DOI: 10.1016/b978-0-12-420135-4.00006-1
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Conference
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2017Characterization of epigenetic marks in marine invertebrates. 181-181.Web of Science: 000399165600012
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2017
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2013Clustering of Gene Expression Profiles Applied to Marine Research. 453-+.Web of Science: 000324897700045
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2009Long-Term Evolution of Histone Families: Old Notions and New Insights into Their Mechanisms of Diversification Across Eukaryotes. 139-+.Full Text via DOI: 10.1007/978-3-642-00952-5_8 Web of Science: 000270816600008
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2007
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2006Histone H1 function and distribution in chromatin: what does molecular evolution tell us about it?. 658-658.Full Text via DOI: 10.1139/006-901 Web of Science: 000240053100024
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Editorial Material
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2022Editorial: Adaptation and Phenotypic Plasticity to Climate ChangeFull Text via DOI: 10.3389/fmars.2022.893117
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Other Scholarly Work
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2021Editorial: Marine Environmental EpigeneticsFull Text via DOI: 10.3389/fmars.2021.685075 Web of Science: 000656143100001
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2011Boule and the Evolutionary Origin of Metazoan Gametogenesis: A Grandpa's Tale.. 972457.Full Text via DOI: 10.4061/2011/972457
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Preprint
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Review
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2021Coral environmental memory: causes, mechanisms, and consequences for future reefs. 1011-1023.Full Text via DOI: 10.1016/j.tree.2021.06.014 Web of Science: 000709722700011
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2020Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining QuestionsFull Text via DOI: 10.3390/cells9051167 Web of Science: 000539340200101
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2019Marine Environmental Epigenetics. 335-+.Full Text via DOI: 10.1146/annurev-marine-010318-095114 Web of Science: 000456386600015
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2015Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates. 5-13.Full Text via DOI: 10.1016/j.marpolbul.2015.06.020 Web of Science: 000362134100014
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2013Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds. 4370-4389.Full Text via DOI: 10.3390/md11114370 Web of Science: 000330521400015
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2013Okadaic Acid Meet and Greet: An Insight into Detection Methods, Response Strategies and Genotoxic Effects in Marine Invertebrates. 2829-2845.Full Text via DOI: 10.3390/md11082829 Web of Science: 000330521300010
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2012Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities. 4788-4804.Full Text via DOI: 10.1096/fj.12-216663 Web of Science: 000311838300003
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2012A unified phylogeny-based nomenclature for histone variantsFull Text via DOI: 10.1186/1756-8935-5-7 Web of Science: 000305622000001
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2012Chromatin specialization in bivalve molluscs: A leap forward for the evaluation of Okadaic Acid genotoxicity in the marine environment. 175-181.Full Text via DOI: 10.1016/j.cbpc.2011.09.003 Web of Science: 000299580200001
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2009Origin and evolution of chromosomal sperm proteins. 1062-1070.Full Text via DOI: 10.1002/bies.200900050 Web of Science: 000270769400007
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2008Quickly evolving histones, nucleosome stability and chromatin folding: All about histone H2A.Bbd. 1-7.Full Text via DOI: 10.1016/j.gene.2008.02.003 Web of Science: 000255625000001
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2007New insights into the nucleophosmin/nucleoplasmin family of nuclear chaperones. 49-59.Full Text via DOI: 10.1002/bies.20512 Web of Science: 000243336700007
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2006Protamines, in the footsteps of linker histone evolution. 1-4.Full Text via DOI: 10.1074/jbc.R500018200 Web of Science: 000234307200001
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Works By Students
chaired theses and dissertations
- Ulloa, Maria Victoria Suarez, Transcriptomic and Epigenetic Responses to Environmental Stress in Marine Bivalves with a Focus on Harmful Algal Blooms 2017
advised honors theses
Research
principal investigator on
- Stress Hardening Interventions for Improved Coral Restoration: Benefits, Costs, and Biomarkers awarded by National Oceanic and Atmospheric Admin 2021 - 2024
- COLLABORATIVE RESEARCH: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages awarded by National Science Foundation 2019 - 2024
- RAPID: COLLABORATIVE RESEARCH: Interaction between genotype and acquired environmental modifications during coral responses to extreme climatic events Irma and Maria awarded by National Science Foundation 2017 - 2020
co-principal investigator on
Contact
full name
- Jose Eirin Lopez
Identifiers
ORCID iD
- https://orcid.org/0000-0002-8041-9770 (confirmed)
visualizations
publication subject areas
- Biochemistry & Molecular Biology
- Biodiversity & Conservation
- Biophysics
- Cell Biology
- Developmental Biology
- Education & Educational Research
- Environmental Sciences & Ecology
- Evolutionary Biology
- Food Science & Technology
- Genetics & Heredity
- Marine & Freshwater Biology
- Pharmacology & Pharmacy
- Physiology
- Public, Environmental & Occupational Health
- Science & Technology - Other Topics
- Toxicology