Updated publications can be found here – https://works.bepress.com/jose-lopez/about/
Peer Reviewed Publications
1. Dipaolo, J.A., Woodworth, C.A., Popescu, N.C., Koval, D.L., Lopez, J.V., Doniger, J. (1990). HSV-2-induced tumorigenicity in HPV16-immortalized human genital keratinocytes. Virology 177:777-779.
2. Lopez, J.V., Yuhki, N., Modi, W., Masuda, R., O’Brien, S.J. (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA in the nuclear genome of the domestic cat. J. Mol. Evol. 39:171-190. ncbi.nlm.nih.gov/pubmed/7932781
3. Hoelzel, A.R., Lopez, J.V., Dover, G.A., O’Brien, S.J. (1994) Rapid evolution of a heteroplasmic repetitive region in the mitochondrial control region of carnivores. J. Mol. Evol. 39:191-199.
4. Lopez, J.V. (1994) Taking a cat map: whole genome analysis by supercomputer. In Computational Biomedical Research (Monograph) NCI-Biological Supercomputing Center, NCI-FCRDC.
5. Lopez, J.V., Cevario, S., O’Brien, S.J. (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33:229-246.
6. Masuda, R., Lopez, J.V., Pecon-Slattery, J., Yuhki, N. O’Brien, S.J. (1996) Estimating the phylogeny of the Felidae with two mitochondrial gene sequences. Molecular Phylogenetics and Evolution 6(3):351.
7. Lopez, J.V., Culver, M., Stephens, J.C., Johnson, W.E., O’Brien, S.J. (1997) Rates of nuclear and cytoplasmic mitochondrial sequence divergence in mammals. Mol Biol and Evol. 14(3):277-286.
8. Lopez, J.V., Stephens, J.C, O’Brien, S.J. (1997) The long and short of nuclear mitochondrial lineages. Trends Ecol. Evol. 12(3):114
9. Lopez, J.V., Knowlton, N. (1997) Discrimination of the sibling species of the Montastraea annularis complex with multiple genetic loci. Proceedings of the 8th International Coral Reef Symposium, Rep. of Panama. 2:1613-1618.
10. Pomponi, S.A., Willoughby, R., Wright, A.E., Pecorella, C., Lopez, J. V., Samples, G. (1998) In vitro production of marine-derived compounds. In New Developments in Marine Biotechnology (Eds. Y.Le Gal and H.O. Halvorson) Plenum Press, New York. Pp. 73 – 76.
11. Lopez, J.V., Kersanach, R., Rehner, S.A., Knowlton, N. (1999) Molecular determination of species boundaries in corals: Genetic analysis of the Montastraea annularis complex using amplified fragment length polymorphisms and a microsatellite marker. Biol. Bull. 196:80-93.
12. Lopez, J.V. McCarthy, P.J., Janda, K.E.,Willoughby, R., Pomponi, S.A. (1999) Molecular techniques reveal wide phyletic diversity of heterotrophic microbes associated with the sponge genus Discodermia (Porifera:Demospongiae). Proceedings of the 5th International Sponge Symposium. Memoirs of the Queensland Museum. 44: 329-341. Brisbane ISSN 0079-8835.
13. Lopez, J.V., Peterson, C.L., Morales, F., Brown, L. 2000. Molecular Studies of Biodiversity in the Field: Andros Island Flora and Fauna in the New Millennium. Bahamas Journal of Science. Bahamas Journal of Science. 8:32-41.
14. Lopez, J.V. Peterson, C.L., Willoughby, R., Wright, A.E., Enright, E., Zoladz, S., Pomponi, S.A. 2002. Characterization of genetic markers for in vitro cell line identification of the marine sponge, Axinella corrugata. Journal of Heredity. 93:27-36.
17. Enright, E., Lopez, J.V., Peterson, C.L., Pomponi, S.A. 2002 Cloning and characterization of two cyclin dependent kinase (CDK) homologues from the marine sponge, Axinella corrugata.2002 Boll. Mus Ist. Univ. Genova 66-67:63.
20. Sfanos, K.A.S., Harmody, D.K., McCarthy, P.J., Dang, P., Pomponi, S.A. and Lopez, J.V. 2005. A Molecular Systematic Survey of Cultured Microbial Associates of Deep Water Marine Invertebrates. System Appl Microbiol. 28 (3):242-264.
21. Gunasekera, A., Sfanos, K.A, McCarthy, P.J., Lopez, J.V. 2005. HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates. Applied Microbiol. Biotechnol. 2005 Jan;66(4):373-376. Epub 2004 Nov 16.
22. Snyder,RV , Guerrero,M., Sinigalliano,C., Winshell, J, Perez,R., Lopez, JV and K. S. Rein. 2005.Localization of polyketide synthase encoding genes to the toxic dinoflagellate Karenia brevis. Phytochemistry 66:1767-1780. (HBOI 1607).
23. Lopez, J.V. 2006. Some preservation techniques for (deep water) coral samples. In Deep-sea Coral Collection Protocols. (Ed. Peter Etnoyer SD Cairns, JA Sanchez, J Reed, S Brooke, A Baco-Taylor, L Watling et al.). NOAA Technical Memorandum NMFS-OPR-28 NOAA Office of Ocean Exploration. US Dept. Commerce, 45 pp.
24. Park, Y.C, Gunasekera, S., McCarthy, P.J., Lopez. J.V., and Wright, A.E. 2006. New Metabolites from the Marine Derived Fungus Chromocleista sp. Isolated from the Deep-Water Sediment Sample Collected in the Gulf of Mexico. J. Natl Products 69:580-584.
25. Cassler, M., Winegar, R. , McCarthy, P.J., Pomponi, S.A., Peterson, C.L, Wright, A.E, Lopez, J.V. 2008. Use of Real-Time PCR to quantitate the unculturable heterotrophic bacterial community in deep sea marine sponges of the family Lithistidae. Microbial Ecology 55:384-394.
26. Ranzer, L.K., Brück, TB., Brück, WM., Lopez, J.V, Kerr , RG 2009 A New Prokaryotic Farnesyldiphosphate Synthase from the octocoral, Eunicea Fusca: Differential Display, Inverse PCR, Cloning And Characterization. Marine Biotech. 11(1):62.
27. Roberto Perez, Li Liu, Jose Lopez, Tianying An and Kathleen S. Rein2008 Okadaic acid producing species of dinoflagellates share common polyketide synthase genes. Marine Drugs. 6:164-179
28. Lopez, J.V. Ledger, A. Santiago-Vazquez, L.Z, Pop, M., Sommer, D.D.,Ranzer, L., Feldman, A. Kerr, R.G. 2011. Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral Electronic Journal of Biotechnology, Vol. 13, no. 5. dx.doi.org/10.2225/vol14-issue1-fulltext-3
29. Lopez, J.V., Ranzer, L.,. Ledger, A., Schoch, B., A. Duckworth, P.J. McCarthy, R.G. Kerr. 2010. Comparison of Bacterial Diversity within the Coral Reef Sponge, Axinella corrugata, and the Encrusting Coral Erythropodium caribaeorum and Adjacent Environmental Samples. Proc 11th ICRS. Pp. 1355-1359.
31. Hoffman, M. Fischer, M. Ottesen, A. McCarthy, P.J., Lopez, J.V., Brown, E. Monday. S. 2010 Population dynamics of Vibrio spp. Associated with Marine sponge microcosms. ISME Journal 4(12):1608-12. Epub 2010 Jul 1.
32. Negandhi, K., Blackwelder, P.L, Ereskovsky, A.V., Lopez, J.V. 2010. Florida Reef Sponges Harbor Coral Disease-Associated Bacteria. Symbiosis 51: 117 – 129.
33. Hoffmann, M, Monday, S.R., McCarthy, P.J., Lopez, J.V., Fischer, M and Brown, E.W. 2013. Genetic and phylogenetic evidence for a single panmictic structure among ecologically disparate groups of marine Vibrio. Cladistics. 46-64.
34. Hoffmann M, Monday SR, Allard MW, Strain EA, Whittaker P, Naum M, McCarthy PJ, Lopez JV, Fischer M, Brown EW. 2012. Vibrio carribeanicus sp. Nov., isolated from marine sponge Scleritoderma cyanea. Int Jour Systematic Evol Microbiology. 62, 1736–1743 .
35. Conway, C.A., Esiobu , N., Lopez, J.V. 2012 Co-cultures of Pseudomonas aeroginosa and Roseobacter denitrificans reveal shifts in gene expression levels compared to solo cultures . The Scientific World Journal. Vol 2012, Article ID 120108; http://www.tswj.com/2012/120108/
36. White, J, Patel, J., Ottesen, A., Arce, C., Blackwelder, P., Lopez, J.V 2012.Pyrosequencing of microbes within Axinella corrugata sponges: Diversity and seasonal variability. PLoS ONE 7(6): e38204. doi:10.1371/journal.pone.0038204; http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038204
37. Hill, M., Hill, A., Lopez, J., Pomponi, S., J.V., Reed, J., Tarver, Redmond, N., Diaz, M.C., Boury-Esnault,
N., Cardenas, P., Reiswig, H., Dohrmann, M., Morrow, C. Rubin, E., Chaves-Fonnegra, A., Patel, J., Formica D, Hajdu E, Lobo-Hajdu G, Klontz S, Morrow CC, Patel J, Picton B, Pohlmann, D., Richie, S., di Stefano, M., Russell , Z., Peterson, K. J., Pisani, D., Thacker, R., Collins, A. 2013 Nuclear housekeeping genes help resolve demosponge relationships and taxonomy. PLoS ONE 8(1): e50437. doi:10.1371/journal.pone.0050437
38. Richards V.P, Grieg, TW, Fair, P.A., McCullough, S.D, Politz, C., Natoli, A., Driscoll, C., David, V., Hoelzel, AR, Bossart, G.D., Lopez, J. V. 2013. Patterns of Population Structure for Inshore Bottlenose Dolphins along the Eastern United States. Journal of Heredity. 104 (6): 765-778. doi: 10.1093/jhered/est070
39. GIGA Community of Scientists (Lopez JV as lead author). 2014. The Global Invertebrate Genome Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrates. Journal of Heredity. 105:1-18. doi: 10.1093/jhered/est084. http://jhered.oxfordjournals.org/content/105/1/1.full;
40. Wilson, CEW, Lopez, J, Smith, RP 2014. The Use of Microfluidic Devices in Synthetic Biology. In Recent Developments in Biotechnology Vol. 4: Systems and Synthetic Biology
41. Cuvelier, M., Vega-Thurber, R., Blackwelder, P., McCarthy, P.J., Lopez, J.V. 2014. Two distinct microbial communities revealed in the sponge Cinachyrella. Frontiers in Microbiology. Vol 5. URL= https://www.frontiersin.org/articles/10.3389/fmicb.2014.00581/full DOI=10.3389/fmicb.2014.00581. ISSN=1664-302X, Vol 5: 00581.
42. Campbell, AM. Fleisher, J Sinigalliano, C, White, J.R., J. Lopez, J.V. 2015. Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of Southeast Florida. Microbiol-Open. 4(3); 390-408. http://dx.doi.org/10.1002/mbo3.245. http://onlinelibrary.wiley.com/doi/10.1002/mbo3.245/abstract
43. Chaves-Fonnegra, Maldonado, M. Blackwelder, P. Lopez, J.V. 2015. Asynchronous and multi-spawning in the excavating Caribbean sponge Cliona delitrix. J. Mar Biology UK. http://dx.doi.org/10.1017/S0025315415000636
44. Chaves-Fonnegra, A., Feldheim, K.A, Secord, J., Lopez, J.V. 2015 Population structure and dispersal of the coral excavating sponge Cliona delitrix Molecular Ecology 24: 1447–1466. doi: 10.1111/mec.13134http://onlinelibrary.wiley.com/doi/10.1111/mec.13134/abstract;jsessionid=33AA0B3E3978DB90BAF7609C538D0869.f03t03
45. Klaus-Peter Koepfli, Benedict Paten, Agostinho Antunes, Kathy Belov, Carlos Bustamante, Todd Castoe, Hiram Clawson, Andrew Crawford, Dan Distel, Richard Durbin, Dent Earl, Matt Fujita, Tony Gamble, Arthur Georges, Neil Gemmell, Jennifer Marshall Graves, Richard E. Green, Glenn Hickey, Erich Jarvis, Warren Johnson, Ian Korf, Robert Kuhn, Denis Larkin, Harris Lewin, Jose V. Lopez, Jian Ma, Tomas Marques Bonet, Webb Miller, Robert Murphy, Pavel Pevzner, Beth Shapiro, Cynthia Steiner,Gaik Tamazian, Bryappa Venkatesh, Jun Wang, Edward Wiley, Huanming Yang, Guojie Zhang, and David Haussler, Oliver Ryder, Stephen J. O’Brien for the G10KCOS. 2015. The Genome 10K Project and the State of Vertebrate Genomics: A Way Forward. Reviews in Animal Genetics. 3:57–111.
46. Aranda, D, Lopez, JV, Solo-Gabriele, HM, Fleisher, JM. 2016. Using Probabilities of Enterococci Exceedance and Logistic Regression to Evaluate Long term. Weekly Beach Monitoring Data. J. of Water and Health. 14 (1) 81-89; http://jwh.iwaponline.com/content/14/1/81.full; doi: 10.2166/wh.2015.030.
47. Thomas, T., Moitinho-Silva, L, Lurgi, M., Easson, CG., Björk, J., Astudillo, C,
Erpenbeck, D., Gilbert, J., Knight, R., Lopez, JV, Taylor, M, Thacker, R. Montoya, JM, Hentschel, U, Webster N. 2016. The Global Sponge Microbiome: Symbiosis Insights Derived From A Basal Metazoan Phylum. Nature Communications 7(No:11870), 1-12.doi:10.1038/ncomms11870. http://www.nature.com/articles/ncomms11870
48. Ying Sun; Yu Huang; Xiaofeng Li; Carole C. Baldwin; Zhuocheng Zhou; Zhixiang Yan; Keith A. Crandall; Yong Zhang; Xiaomeng Zhao; Min Wang; Alex Wong; Chao Fang; Xinhui Zhang; Hai Huang; Jose V. Lopez; Kirk Kilfoyle; Yong Zhang; Guillermo Ortí; Byrappa Venkatesh; Qiong Shi.Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies. GIGA Science. Vol 5, Issue 1, published 2016/5/3. http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0124-7
49. Schuster, A. Jose V. Lopez, Leontine E. Becking, Michelle Kelly, Shirley A. Pomponi, Gert Wörheide, Dirk Erpenbeck, Paco Cárdenas 2017. Evolution of group I introns in Porifera: implications for intron mobility, systematics and molecular taxonomy. BMC Evolutionary Biology. 17:82 DOI 10.1186/s12862-017-0928-9. https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-0928-9.
50. GIGA Community of Scientists (Voolstra, C as lead author). 2017. Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA) Invertebrate Systematics. 31: (1) 1-7. http://www.publish.csiro.au/is/Fulltext/IS16059
51. Hampton-Marcell, JT, Lopez, JV, Jack A. Gilbert. 2017. The Human Microbiome: An Emerging Tool in Forensics. Microb Biotechnol. 2017 Mar;10(2):228-230. doi: 10.1111/1751-7915.12699.http://onlinelibrary.wiley.com/doi/10.1111/1751-7915.12699/full
52. Wilson, CE, Allison J. Lopatkin, Travis J. A. Craddock, William Driscoll, Omar T. Eldakar, Jose V. Lopez, Robert P. Smith. 2017. Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria. Scientfic Reports. 7:440. Doi:10:1038/s41598-017-00588-9. http://www.nature.com/articles/s41598-017-00588-9.
53. Guy, Derek S., Cassandra L. Ruck, Jose V. Lopez & Mahmood S. Shivji (2017) Complete mitogenome sequences of smooth hammerhead sharks, Sphyrna zygaena, from the eastern and western Atlantic, Mitochondrial DNA Part B, 2:2, 806-807, DOI: 10.1080/23802359.2017.1390421.
54. Chaves-Fonnegra, A., Riegl, B, Zea, Z., Lopez, J.V., Giliam, D.S. 2017. Bleaching events regulate shifts from corals to excavating sponges in algae dominated reefs. Global Change Biology. 24(2), 773-785. DOI: 10.1111/gcb.13962.
55. Hendry, T. Lindsay Freed, Dana Fadera, Danté Fenolioc, and Jose Lopez. 2018. Recently evolved host dependence in the luminous symbionts of deep sea anglerfish. mBio 9:e01033- https://doi.org/10.1128/mBio.01033-18.
56. Hughes, GM, Leech, JM, Puechmaille, SJ, Lopez, JV., Emma C. Teeling. 2018. Is there a link between aging and microbiome diversity in exceptional mammalian longevity? PeerJ 6:e4174. https://doi.org/10.7717/peerj.4174 and https://peerj.com/articles/4174/
57. O’Connell, L, Gao, S, Fleischer, J., Lopez, JV. 2018. Fine Grained Compositional Analysis of Port Everglades Inlet Microbiome Using High Throughput DNA Sequencing. PeerJ 6:e4671; DOI 10.7717/peerj.4671. https://peerj.com/articles/4671/
58. Widmer, C. SKutas, J, Easson, C., Flax, M. Lopez, J.V., Sayin, T.C. Culture-independent Characterization of the Microbiome of Healthy Pulp. J. Edontics. 44 (7): 1132-1139.e2 https://doi.org/10.1016/j.joen.2018.03.009
59. Easson, C.G, Lopez, J.V. 2019. Environmental drivers of bacterioplankton community structure in the northern Gulf of Mexico. Frontiers in Microbiology. 9:3175 https://doi.org/10.3389/fmicb.2018.03175
60. Milligan, RJ, A.M. Bernard, K.M. Boswell, H.D. Bracken-Grissom, M.A. D’Elia, S. DeRada, C.G. Easson, D. English, R.I. Eytan, C. Hu, C. Lembke, J.V. Lopez, B. Penta, T. Richards, I.C. Romero, M. Shivji, L. Timm, J.D. Warren, M. Weber, R.J.D. Wells, T.T. Sutton. 2018. The application of novel research technologies by the Deep Pelagic Neton Dynamics of the Gulf of Mexico (DEEPEND) Consortium. Marine Technology. 52 (6), 81-86.
61. Lopez, JV, Kamel, B., Medina, M., Collins, T, Baums, IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annual Review of Animal Biosciences. Annu. Rev. Anim. Biosci. 2019. 7:473-497. https://doi.org/10.1146/annurev-animal-020518-115034
62. Urakawa, H., Skutas, J. Lopez, JV. 2019. Draft Genome of Nitrosomonas sp. Strain APG5, a Betaproteobacterial Ammonia-Oxidizing Bacterium Isolated from Supralittoral Beach Sand. Microbiology Resource Announcements. 8(21), e01573-18.
63. Baker, LJ, Freed, LL, Easson, C.G., Lopez, JV., Fenolio, D, Sutton, TT, Nyholm, SV., Hendry, TA. 2019. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife In Press.
64. Lopez, JV, Peixoto, R. Rosado, AS. 2019. Inevitable Future: Space Colonization Beyond Earth with Microbes First. FEMS-Microbiology Ecology. 95 (10) : fiz127, https://doi.org/10.1093/femsec/fiz127.
65. Freed, L., Easson, C., Baker, LJ., Fenolio, D., Blackwelder, P, Khan, Y., Sutton, TT., Hendry, TT., Lopez, JV. 2019. Characterization of the Microbiome and Bioluminescent Symbionts Across Life Stages of Ceratioid Anglerfishes of the Gulf of Mexico. FEMS-Microbiology Ecology. https://doi.org/10.1093/femsec/fiz146.
66. Smith, Robert P, Cole Easson, Sarah M. Lyle, Ritishka Kapoor, Chase P. Donnelly, Eileen J. Davidson, Esha Parikh, Jose. V. Lopez, Jaime L. Tartar. Gut microbiome diversity is associated with sleep physiology in humans (PONE-D-19-19430). PLosOne. 14(10): e0222394. https://doi.org/10.1371/journal.pone.0222394
67. Easson, C. Thacker, R.W. , Chaves-Fonnegra, A. Lopez JV. 2020. Host population genetics and biogeography structure the microbiome of the sponge Cliona delitrix. Ecology and Evolution. https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.6033; doi.org/10.1002/ece3.6033.
68. Rayko, Mikhail, Komissarov, Aleksey, Grace Lim-Fong, Rhodes, Adelaide C. , Kwan, Jason C., Kliver, Sergey, Chesnokova, Polina , O’Brien, Stephen J., Lopez, Jose V. Draft genome of Bryozoan Bugula neritina – a colonial animal packing powerful symbionts and potential medicines. Scientific Data. In Press.
69. *Hampton, J., Larsen, PT., Anton, T., Cralle, L., Sangwan, N., Lax, S., N Gottell, Solas-Garcia , M, Young, C. Duncan, G., Lopez, JV., Gilbert, J. 2020. Detecting Personal Microbiota Signatures at Artificial Crime Scenes. Forensic Science International. 313 https://doi.org/10.1016/j.forsciint.2020.110351
70. Nascimento, Juliana Ribeiro, Cole G Easson; Diogo A Jurelevicius; Edison D Bidone; Elisamara Sabadini-Santos; Jose V Lopez. Microbial community shift under exposure of dredged sediments from an eutrophic bay. Science of the Total Environment. Environ Monit Assess (2020) 192:539 https://doi.org/10.1007/s10661-020-08507-8.
71. Berger, L, Blackwelder, P.,Frank, T., Sutton, T., Pruzinsky, N., Slayden, N.Lopez, JV. Microscopic and Genetic Characterization of Bacterial Bioluminescent Symbionts of the Gulf of Mexico Pyrosome, Pyrosoma atlanticum . Frontiers in Marine Science. 03 February 2021.https://www.frontiersin.org/articles/10.3389/fmars.2021.606818/full
72. Cook, A.B, Andrea M. Bernard1, Kevin M. Boswell2, Heather Bracken-Grissom2, Marta D’Elia2, Sergio deRada3, Cole G. Easson10, David English4, Ron I. Eytan5, Tamara Frank1, Chuanmin Hu4, Matthew W. Johnston1, Heather Judkins6, Chad Lembke4, Jose V. Lopez1, Rosanna J. Milligan1,Jon Moore7,Bradley Penta3, Nina M. Pruzinsky1, John A. Quinlan8, Travis Richards5, Isabel C. Romero4, Mahmood S. Shivji1, Michael Vecchione9, Max D. Weber5, R. J. David Wells5, and Tracey T. Sutton1 . A Multidisciplinary Approach to Investigate Deep-Pelagic Ecosystem Dynamics in the Gulf of Mexico following Deepwater Horizon. Frontiers in Marine Science . 7, 1122.
73. Urakawa, H., Hancock, TL., Steeler, JH, Dahedl, EK, Urakawa, UE, Ndungu, LK, Krausfeldt, LE, Rosen, BH, Lopez, JV. 2020. Complete genome sequence of Microcystis aeruginosa FD4 isolated from a subtropical river in southwest Florida. Microbiology Resource Announcements 9(38) . https://mra.asm.org/content/9/38/e00813-20
74. Storo (Karns), R. Easson, C., Shivji, M., Lopez. JV. 2021. Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species. Frontiers in Microbiology. 12, 139. https://doi.org/10.3389/fmicb.2021.605285; https://www.frontiersin.org/articles/10.3389/fmicb.2021.605285/full.
76. Desplat, Y., Warner, J., Lopez, JV. 2022. Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada. J Heredity.Volume 113, Issue 2, March 2022, Pages 184–187, https://doi.org/10.1093/jhered/esab075
77. Blaxter, M Blaxter, M., Archibald, J. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Di Palma, F., … & Lewin, H. A. 2022. Why sequence all eukaryotes?. Proceedings of the National Academy of Sciences, 119(4). https://doi.org/10.1073/pnas.2115636118
78. Lewin HA, Stephen Richards Miguel L. Allende4,5, John M. Archibald6, Miklós Bálint7,8, Bridget Baumgartner9, Katherine Belov10, Giorgio Bertorelle11, Mark Blaxter12, Jing Cai13, Nicolette Caperello3, Keith Carlson14, Juan Carlos Castilla-Rubio15, Martha Lucia Cepeda-H.16, Shu-Miaw Chaw17, Lei Chen13, Anna K. Childers18, Jonathan A. Coddington19, Dalia A. Conde20,21, Montserrat Corominas22,23, Keith A. Crandall24,25, Andrew J. Crawford26, Peter Decker27, Cyrille A. D’Haese28, Federica DiPalma29, Miklós Dombos30, Richard Durbin31,32, ThankGod E. Ebenezer33, Scott V. Edwards34,35, Guangyi Fan36, Paul Flicek37,32, Richard A. Gibbs38, Marcus T.P. Gilbert39,40, Melissa M. Goldstein41, Carola Greve7, Jennifer A.M. Graves42,43, Henry T. Greely44, Igor V. Grigoriev45,46, Xing Guo36, Kevin J. Hackett47,48, Neil Hall48,29, Leslie Harris49, David Haussler50,51, Kristofer M. Helgen52, Austin J.W. Hendy49, Carolyn Hogg10, Karin Hohberg27, Sachiko Isobe53, Kjetill Sigurd Jakobsen54, Axel Janke7, Erich D. Jarvis55,51, Rebecca Johnson56, Warren E. Johnson57,58, Steven J.M. Jones59, Elinor K. Karlsson60,61, Paul Kersey62, Jin-Hyuong Kim63, Wen-Ya Ko64, W. John Kress65, Shigehiro Kuraku66,67, Sébastien Lavergne68, Mara K.N. Lawniczak12, James Leebens-Mack69, Ricarda Lehmitz27, Xueyan Li70, Yongxin Li13, Kerstin Lindblad-Toh, Huan Liu36, Xin Liu36, Yang Liu36, Jose Lopez72,73, Tomas Marques-Bonet74,75,76,77, Sophie Mazard, Jonna A.K. Mazet79, Camila J. Mazzoni80,81, Karen Meusemann82, Gene Myers83, Kathy Omura, Rachel J. O’Neill84,85, Sadye Paez55, Hyun Park86, N. Dean Pentcheff49, Irfan A. Rather87, Silvia Restrepo, Sarah Richmond, Gene Robinson, Cristina Roquet91,92, Oliver A. Ryder, Jamal S.M. Sabir8, Sunil K. Sahu, Clément Schneider, Fritz J. Sedlazeck38, H. Bradley Shaffer, Beth Shapiro, Jacob S. Sherkow, Pamela S. Soltis, Edi Sudianto17, Nikolaus U. Szucsich, Leho Tedersoo, Marcela Uliano-Silva, Adam R. Wall, Jenessa Wall, Wen Wang, Kun Wang, Sibo Wang, Tzi-Yuan Wang, Xiaofeng Vincent Wei, Jill L. Wegrzyn, Regina Wetzer, Julia L. Wilson, Chung-Shien Wu, Dongdong Wu, Xun Xu, Huanming Yang, Anne D. Yoder, Guanghui Zhang, Guojie Zhang 2022. The Earth BioGenome Project 2020: Starting the Clock. Proc Natl Acad of Sci USA. 119 (4) e2115635118; 18-Jan-2022 DOI: https://www.pnas.org/doi/full/10.1073/pnas.2115635118
79. Mehlrose, M.R., A.M. Bernard, K.A. Finnegan, L.E. Krausfeldt, J.V. Lopez and M.S. Shivji. 2022. Three complete mitochondrialgenomes of shortfin mako sharks, Isurus oxyrinchus, from the Atlantic and Pacific Oceans. Mitochondrial DNA Part B. Vol 7 (4). https://doi.org/10.1080/23802359.2022.2060768.
80. Krausfeldt, LE., Shmakova E, Lee HW, Smith RP, Fortman EP, Mazzei, V, Loftin, KRosen BH, Urakawa H, Dadlani M, Lopez JV. 2024. Microbial biodiversity, genomics and phage-host interactions of cyanobacteria harmful algal blooms. MSystems. e00709-23. https://doi.org/10.1128/msystems.00709-23.
81. Krausfeldt* L, Lopez*, JV, Bilodeau C., Lee HW, Casali, S. 2023. Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs. PeerJ 11:e14288 https://doi.org/10.7717/peerj.14288 (*dual first authors)
82. Urakawa Hidetoshi, Gabrianna A. Andrews, Jorie Skutas, Willm Martens-Habbena, Martin G Klotz, David A. Stahl and Jose V. Lopez. 2022. Nitrosomonas supralitoralis sp. nov., an ammonia-oxidizing bacterium from beach sand in a supralittoral zone. Archives of microbiology, 204(9), 560.
83. Desplat, Y., Warner, J. F., Blake, E. J., Vijayan, N., Cuvelier, M., Blackwelder, P., & Lopez, J. V. (2023). Morphological and transcriptional effects of crude oil and dispersant exposure on the marine sponge Cinachyrella alloclada. Science of The Total Environment, 878, 162832.https://doi.org/10.1016/j.scitotenv.2023.162832
https://www.sciencedirect.com/science/article/pii/S0048969723014481
84. McMaken C, Burkholder D, Milligan R., Lopez JV. 2023 Potential Impacts of Environmental Bacteria on the Microbiota of Loggerhead (Caretta caretta) and Green (Chelonia mydas) Sea Turtle Eggs and Their Hatching Success. MicrobiologyOpen 12:e1363. https://doi.org/10.1002/mbo3.1363
85. Li, R., Jingchun Li, Jose V. Lopez. 2023. The genome sequence of the giant clam, Tridacna crocea (Lamarck, 1819). Open Wellcome Research. 8:571 (https://doi.org/10.12688/wellcomeopenres.20580.1)
86. Li R, J Li, JV Lopez, G Oatley, IA Clayton-Lucey, E Sinclair, E Aunin, … The genome sequence of the horse’s hoof clam, Hippopus hippopus (Linnaeus, 1758) Wellcome Open Research 9, 131. https://wellcomeopenresearch.org/articles/9-131
87. Li R, J Li, S Lemer, JV Lopez, G Oatley, IA Clayton-Lucey, E Sinclair, … The genome sequence of a heart cockle, Fragum whitleyi Iredale, 1929. Wellcome Open Research 9, 130. https://wellcomeopenresearch.org/articles/9-130.
88. Li R, J Li, S Lemer, JV Lopez, G Oatley, IA Clayton-Lucey, E Sinclair, The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758) Wellcome Open Research 9, 129. https://wellcomeopenresearch.org/articles/9-129.
89. Li, R., Li, J., Lopez, J. V., Oatley, G., Clayton-Lucey, I. A., Sinclair, E., … & Portal, E. A. S. G. D. 2024. The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758). Wellcome Open Research, 9(145), 145. https://wellcomeopenresearch.org/articles/9-145/v1
90. Bennice, C, Krausfeldt, L, Brooks, WR, Lopez JV. 2024. Unique skin microbiome: insights to understanding bacterial symbionts in octopuses. Frontiers Mar Sci. 11 – 2024 https://doi.org/10.3389/fmars.2024.1448199
91. Demehri, S.; Vardar, S.; Godoy, C.; Lopez, J.V.; Samuel, P.; Kawai, T.; Ozga, A.T. 2024. Supragingival Plaque Microbiomes in a Diverse South Florida Population. Microorganisms 2024, 12, 1921 https://doi.org/10.3390/microorganisms12091921.
92. Krausfeldt, LE, Samuel P, Smith RP, Urakawa H, Rosen BH, Colwell RR, Lopez JV. 2024 Transcriptional profiles of Microcystis reveal gene expression shifts that promote bloom persistence in in situ mesocosms. Microbiology Spectrum, e01369-24. https://journals.asm.org/doi/full/10.1128/spectrum.01369-24
93. Dotson K, Pisano K, Gellman ER, Roman P, Lopez JV. Degradation of Polyhydroxyalkanoate (PHA).Drinking Straws at an Ocean Shoreline. 2025 J. of Environmental Chemical Engineering. https://doi.org/10.1016/j.jece.2025.117157 (4): 117157
94. Li, R., Li, J., Lemer, S., Lopez, J. V., Oatley, G., Sinclair, E., … & Portal, E. A. S. G. D. (2024). The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869). Wellcome Open Research, 9, 366. https://doi.org/10.12688/wellcomeopenres.22585.1
95. Leys, S. P., Hentschel, U., Easson, C. G., Stimson, D., Lopez, J. V., Oatley, G., … & Aquatic Symbiosis Genomics Project Leadership. (2025). The chromosomal genome sequence of the fragile freshwatersponge, Eunapius fragilis (Leidy, 1851) and its associated microbial metagenome sequences. Wellcome Open Research, 10, 268. https://wellcomeopenresearch.org/articles/10-268/v1.
Lopez JV, Pomponi S, Hentschel U, Erpenbeck D, Pruzinsky N, Fiore C, Mulheron R, Graeme Oatley, Isabelle Ailish Clayton-Lucey, Elizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Victoria McKenna, Rebecca O’Brien, Haoyu Niu, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2024. The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and it associated microbial metagenome sequences. Wellcome Open Res, 10:336 (https://doi.org/10.12688/wellcomeopenres.24173.1) https://wellcomeopenresearch.org/articles/10-336/v1.
97. Hirose E, Lopez JV, Oatley G et al. 2025. The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences [version 1; peer review: awaiting peer review]. Wellcome Open Res 2025, 10:357 (https://doi.org/10.12688/wellcomeopenres.24563.1).
Steindler, L, Martha Alejandra Durán Canché, Micha Ilan, Rinat Bar-ShalomElizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Victoria McKenna, Rebecca O’Brien, Haoyu Niu, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences. Wellcome Open Res. https://wellcomeopenresearch.org/articles/10-466/v1.
Authored Books
Lopez, JV. 2023 Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea. Academic Press. London Paperback ISBN: 9780128241127. Dec 15, 2023. https://tinyurl.com/mryrh32u
Book Chapters
Lopez, J.V., Mouzon, B., McCarthy, P.J., Kerr, R. 2009 The many faces of gene expression profiling: Transcriptome analyses applied towards elucidating marine organismal interactions and metabolism. Textbook on Molecular Biotechnology. IK International Publishing House Pvt. Ltd Amity University Uttar Pradesh (AUUP), ISBN 978-93-80026-37-4. Pp 287-304.
Lopez, J.V. 2006. Some preservation techniques for (deep water) coral samples. In Deep-sea Coral Collection Protocols. (Ed. Peter Etnoyer SD Cairns, JA Sanchez, J Reed, S Brooke, A Baco-Taylor, L Watling et al.). NOAA Technical Memorandum NMFS-OPR-28 NOAA Office of Ocean Exploration. US Dept. Commerce, 45 pp.
Lopez, JV. After the Taxonomic Identification Phase: Addressing the Functions of Symbiotic Communities within Marine Invertebrates. In Symbionts of Marine Sponges and Corals. Springer-Verlag. 2019. 7:473-497. http://www.annualreviews.org/eprint/bSr3PRCJCfbmPz39sH5Q/full/10.1146/annurev-animal-020518-115034.
Lopez Lab @ NSU 