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.

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.

15. Snyder, R.V, Gibbs, P. D. L. , Palacios, A., Abiy, L, Dickey, R., Lopez, J.V, Rein, K.S 2003. Polyketide Synthase Genes from Marine Dinoflagellates.  Marine Biotechnology. 5:1-12.

16. Takabayashi, M., Carter, D.A., Lopez, J.V., Guldberg, O.H. 2003 Genetic Variation of the scleractinian coral, Stylophora pistillata, from Western Pacific reefs.  Coral Reefs 22: 17-22.  

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.

18. Lopez, J.V. 2003 Naturally mosaic secondary metabolite operons: Variability and putative  horizontal transfer of discrete  catalytic domains in  the epothilone polyketide synthase locus.  Mol Genet Genomics 270:420-431.

19. Sandell, K.A., Peterson, C.L., Harmody, D.K., McCarthy, P.J., Pomponi, S.A., Lopez, J.V. 2004 Molecular systematic survey of sponge – derived marine microbes. 6th International Sponge Conference Proceedings. Boll. Mus Ist. Univ. Genova. 68:579-585.

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.

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.

30. Rubin E.T., Lopez, J.V., Gilliam, D.S., Dodge, R.E., Kosmynin, V.N., Moulding, A.L. 2010. Scleractinian coral recruitment patterns to reefs physically damaged by ship groundings. Proc 11th ICRS.  Pp. 326-330.

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;

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;

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.;

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=  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.

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.

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.13134;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;; 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.

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.

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.

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.

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.

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.

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-

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. and

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.

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

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

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.

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,

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.

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.

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.;

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

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

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.