Publications

Sullivan Lab authors are underlined. For article abstracts, full text, downloadable pdfs, or other information, click on the links at the end of the citations.

Google Scholar Citation Metrics for Dr. Matthew Sullivan

2017

97. Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y., Blanc-Mathieu, R., Lima-Mendez, G., Rocha, F., Tirichine, L., Labadie, K., Kirilovsky, A., Bertrand, A., Engelen, S., Madoui, M.A., Méheust, R., Poulain, J., Romac, S., Richter, D., Yoshikawa, G., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans Coordinators, Jaillon, O., Aury, J.M., Karsenti, E., Sullivan, M.B., Sunagawa, S., Bork, P., Not, F., Hingamp, P., Raes, J., Guidi, L., Ogata, H., de Vargas, C., Iudicone, D., Bowler, C., Wincker, P. 2017. A Global Ocean Atlas of Eukaryotic Genes. Nature Communications.  In press.

96. Pasulka, A., Thamatrakoln, K., Kopf, S., Guan, Y., Poulos, B., Moradian, A., Sweredoski, M., Hess, S., Sullivan, M.B., Bidle, K., Orphan, V.  2017. Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environmental Microbiology. In press.

95. Anderson, C.L., Sullivan, M.B., Fernando, S.C. 2017. Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome. 5: 155.  LINK  PDF

94. Roux, S., Emerson, J.B., Eloe-Fadrosh, E.A., Sullivan, M.B. 2017. Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 5:e3817.  LINK  PDF

93. Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E., Wessner, M., Leconte, L., Mangot, J.F., Poulain, J., Labadie, K., Logares, R., Sunagawa, S., de Berardinis, V., Salanoubat, M., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Pesant, S., Poulton, N., Stepanauskas, R., Bork, P., Bowler, C., Hingamp, P., Sullivan, M.B., Iudicone, D., Massana, R., Aury, J.M., Henrissat, B., Karsenti, E., Jaillon, O., Sieracki, M., de Vargas, C., Wincker, P. 2017. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications.  In press.

92. Roux, S., Chan, L.-K., Egan, R., Malmstrom, R.R., McMahon, K.D., Sullivan, M.B. 2017. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications. 8: 858. LINK  PDF

91. Duhaime, M.B., Solonenko, N., Roux, S., Verberkmoes, N.C., Wichels, A., Sullivan, M.B. 2017. Comparative omics and trait analyses of marine Pseudoalteromonas phages advance the phage OTU concept. Frontiers in Microbiology. 8: 1241.  LINK   PDF

90. Silas, S., Makarova, K., Shmakov, S., Paez-Espino, D., Mohr, G., Liu, Y., Davison, M., Roux, S., Krishnamurthy, S., Fu, B., Hansen, L., Wang, D., Sullivan, M.B., Millard, A., Clokie, M., Bhaya, D., Lambowitz, A., Kyrpides, N., Koonin, E., and Fire, A. 2017. On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyper-diverse, enigmatic spacer repertoires. mBio. 8: 00897-17.  LINK   PDF

89. Alberti, A., Poulain, J., Engelen, S., Labadie, K., Romac, S., Ferrera, I., Albini, G., Aury, J.M., Belser, C., Bertrand, A., Cruaud, C., Da Silva, C., Azema-Dossat, C., Gavory, F., Gas, S., Guy, J., Haquelle, M., Jacoby, E., Jaillon, O., Lemainque, A., Pelletier, E., Samson, G., Wessner, M., Acinas, S., Royo-Llonch, M., Cornejo-Castillo, F., Logares, R., Fernandez-Gomez, B., Bowler, C., Cochrane, G., Amid, C., Hoopen, P.T., de Vargas, C., Grimsley, N., Desgranges, E., Kandels-Lewis, S., Ogata, H., Poulton, N., Sieracki, M., Stepanauskas, R., Sullivan, M.B., Brum, J., Duhaime, M., Poulos B., Hurwitz, B., Pesant, S., Karsenti, E., and Wincker, P. 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data. 4: 170093.  LINK  PDF

88. Vik​, D.R., Roux, S., Brum, J.R., Bolduc, B., Emerson, J.B., Padilla, C.C., Stewart, F.J., Sullivan, M.B. 2017. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 5: 3428.  LINK  PDF

87. Martínez-Hernández, F., Fornas, O., Lluesma Gomez, M., Bolduc, B., de la Cruz Peña, M.J., Martínez Martínez, J., Antón, J., Gasol, J.M., Rosselli, R., Rodríguez-Valera, F., Sullivan, M.B., Acinas, S.G. and Martinez-Garcia, M. 2017. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nature Communications. 8: 15892.  LINK   PDF 

86. Bolduc, B.*, Jang, H.B.*, Doulcier, G., You, Z.Q., Roux, S., Sullivan, M.B., 2017. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ53243. (*=co-first authors)   LINK   PDF

85. Krzysztof, S., Caputi, L., Buttigieg, P.L., D’Alelio, D., Ibarbalz, F.M., Sullivan, M.B., Chaffron, S., Bowler, C., d’Alcala’, M.R., Iudicone, D.. 2017. Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine Genomics. 32: 1-17.   LINK   PDF

84. Murata, K., Zhang, Q.F., Galaz-Montoya, J.G., Fu, C., Coleman, M.C., Osburne, M., Schmid, M., Sullivan, M.B.^, Chisholm, S.W.^, & Chiu, W.^ 2017. Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Scientific Reports. 7: 44176.   LINK   PDF   (^ = co-corresponding authors)

83. Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M.B., Goto, S., Ogata, H. & Yoshida, T. 2017. Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere. 2: 00359-16.   LINK   PDF

82. Howard-Varona, C.*, Hargreaves, K.R.*, Abedon, S.T. & Sullivan, M.B. 2017. Lysogeny in nature – mechanisms, impact and ecology of temperate phages. ISMEJ. 16: 1-10. (*=co-first authors)   LINK   PDF

81. Poulos, B.T., John, S.G., & Sullivan, M.B. 2017. Iron Chloride Flocculation of Bacteriophages from Seawater. Bacteriophages: Methods and Protocols. In press.  (notably two years “in press;” for updated protocol see protocols.io)

80. Kang, D.-W.*, Adams, J.B.*, Gregory, A.C.*, Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E.L., Roux, S., Sadowsky, M.J., Schwarzberg Lipson, K., Sullivan, M.B.^, Caporaso, J.G.^ & Krajmalnik-Brown, R.^ 2017. Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 5: 10. (*=co-first authors,^=co-corresponding authors)   LINK   PDF

79. Simmonds, P., Adams, M.J., Benko, M., Breitbart, M., Brister, J.R., Carstens, E.B., Davison, A.J., Delwart, E., Gorbalenya, A.E., Harrach, B., Hull, R., King, A.M.Q., Koonin, E.V., Krupovic, M., Kuhn, J.H., Lefkowitz, E.J., Nibert, M.L., Orton, R., Roosinck, M.J., Sabanadzovic, S., Sullivan, M.B., Suttle, C.A., Tesh, R.B., van der Vlugt, R.A., Varsani, A., & Zerbini, F.M. 2017. Virus taxonomy in the age of metagenomics. Nature Reviews in Microbiology. 15: 161-168.   LINK   PDF

78. Enault, F., Briet, A., Bouteille, L., Roux, S., & Sullivan, M.B., Petit, M.A. 2017. Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISMEJ. 11: 237-247.   LINK   PREPRINT   PDF

77. Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L.^, & Sullivan, M.B.^ 2017. iVirus: facilitating new insights into viral ecology with software and community datasets imbedded in a cyberinfrastructure. (^=co-corresponding authors). ISMEJ. 11: 7-14.   LINK   PREPRINT   PDF

76. Howard-Varona. C., Roux, S., Dore, H., Solonenko, N., Holmfeldt, K., Markillie, L.M., Orr, G., & Sullivan, M.B. 2017. Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus. ISMEJ. 11: 284-295.   LINK   PDF

2016

75. Sullivan, M.B., Weitz, J.S., & Wilhelm, S. 2016. Crystal Ball: Viral ecology comes of age. Environmental Microbiology Reports. 9: 33-35.   LINK   PDF

74. Paez-Espino, D., Chen, I-M A., Palaniappan, K.,  Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V.M., Nielsen, T., Huntemann, M., Reddy, T.B.K., Pavlopoulos, G.A., Sullivan, M.B., Campbell, B.J., Chen, F., McMahon, K., Hallam, S.J., Denef, V., Cavicchioli, R., Caffrey, S.M., Streit, W.R., Webster, J., Handley, K., Salekdeh, G.H., Tsesmetzis, N., Setubal, J.C., PopeP.B., Liu, W-T., Rivers, A.R., Ivanova, N.N. & Kyrpides, N.C. 2016. IMG/VR: A database of cultured and uncultured DNA Viruses 1 and Retroviruses. Nucleic Acids Research. 45: D457-D465.   LINK   PDF

73. Gregory, A.C., Solonenko, S.A., Ignacio-Espinoza, J.C., LaButti, K., Copeland, A., Sudek, S., Maitland, A., Chittick, L., dos Santos, F., Weitz, J.S., Worden, A.Z., Woyke, T., Sullivan, M.B. 2016. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics. 17: 930.   LINK   PDF

72. Roux, S. Solonenko, N. Dang, V.T. Poulos, B.T. Schwenck, S.M. Goldsmith, D.B. Coleman, M.L. Breitbart, M. Sullivan, M.B. 2016. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 4: e2777.   LINK   PDF

71. Roux, S.Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A.,  Duarte, C.M.M.,  Gasol, J.M.M.,  Vaqué, D., Tara Oceans Coordinators, Bork, P.,  Acinas, S.G., Wincker, P. & Sullivan, M.B. 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 537: 689-693  LINK   PREPRINT   PDF   THE GOV DATASET

70. Holmfeldt, K.^, Solonenko, N., Howard-Varona, C., Moreno, M., Malmstrom, R.R., Blow, M.J. & Sullivan, M.B.^ 2016. Large-scale maps of variable infection efficiencies in aquatic Bacteriodetes phage-host model systems. Environmental Microbiology. 18: 3949-3961. (^=co-corresponding authors).   LINK   PDF

69. Trubl, G, Solonenko, N., Chittick, L., Solonenko, S., Rich, V.I., & Sullivan, M.B. 2016.  Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ. 4:e1999.   LINK   PDF

68. Duhaime, M.B., Wichels, A., & Sullivan, M.B. 2016. Six Pseudoalteromonas strains isolated from surface waters of Kabeltonne, offshore Helgoland, North Sea. Genome Announcements. 4:e01697-15.   LINK   PDF

67. Guidi, L.*, Chaffron, S.*, Bittner, L.*, Eveillard, D.*, Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J.R., Coelho, L.P., Espinoza, J.C., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Tara Oceans Consortium Coordinators, Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J.,, Wincker, P., Acinas, S.G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M.B., Raes, J., Karsenti, E., Bowler, C., & Gorsky, G. 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature. 532: 465-470. (*=co-first authors)   LINK   PDF

  • Highlighted 22 February 2016 in Nature Reviews Microbiology 14: 194.   LINK

66. Brum J.R.*, Ignacio-Espinoza, J.C.*, Kim, E-H.*, Trubl, G., Jones, R., Roux, S., VerBerkmoes, N.C., Rich, V.I.^, & Sullivan, M.B.^ 2016. Illuminating structural proteins in viral “dark matter” with metaproteomics. PNAS. 113: 2436-2441. (*=co-first authors) (^=co-corresponding authors)   LINK   PDF

65. Krupovic, M., Dutilh, B.E., Adriaenssens, E.M., Wittmann, J., Vogensen, F.K., Sullivan M.B., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A.M., Klumpp, J., Gillis, A., Enault, F., Edwards, R.A., Duffy, S., Clokie, M.R., Barylski, J., Ackermann, H.W., & Kuhn, J.H. 2016. Taxonomy of prokaryotic viruses: update from the ICTVbacterial and archaeal viruses subcommittee. Archives of Virology. 161: 1096-9.   LINK

2015

64. Labonté, J.M., Swan, B.K., Poulos, B., Luo, H., Koren, S., Hallam, S.J., Sullivan, M.B., Woyke, T., Wommack, K.E. & Stepanauskas, R. 2015. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton. ISMEJ. 9: 2386-99.   LINK   PDF

63. Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., Dimier, C., Searson, S. & Tara Oceans Consortium Coordinators. 2015. Open science resources for the discovery and analysis of Tara Oceans data. Scientific Data. 2: 150023.   LINK   PDF

62. Dang, V. & Howard-Varona, C., Schwenck, S. & Sullivan, M.B. 2015. Variably lytic infection dynamics of large Bacteroidetes podovirus phi38:1 against two Cellulophaga baltica host strains. Environmental Microbiology. 17: 4659–4671.   LINK   PDF

61. Roux, S., Hallam, S.J., Woyke, T., & Sullivan, M.B. 2015. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife. 4:e08490.   LINK   PDF

60. Brum, J.R., Hurwitz, B., Schofield, O., Ducklow, H., & Sullivan, M.B. 2015. Seasonal time bombs: Dominant temperate viruses affect Southern Ocean microbial dynamics. ISMEJ. 10:437–449.   LINK   PDF

59. Brum, J.R.*, Ignacio-Espinoza, J.C.*, Roux, S.*, Doulcier, G., Acinas, S.G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J.M., Gorsky, G., Gregory, A.C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B.T., Schwenck, S.M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans Coordinators, Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E., & Sullivan, M.B. 2015. Patterns and ecological drivers of ocean viral communities. Science. 348: 1261498. (*=co-first authors)   LINK   PDF

  • TOV_43 dataset: virome predicted proteins, protein clusters, and viral populations
  • Highlighted in Quanta Magazine by Carl Zimmer (21 May 2015)
  • Highlighted on NPR Science Friday with Ira Flatow (21 May 2015)
  • Part of a Tara Oceans Special Issue on Ocean Plankton (references #55-59 here) that was highlighted in the New York Times (21 May 2015), the BBC News (22 May 2015) and Nature Reviews Microbiology (8 June 2015)

58. de Vargas, C.*, Audic, S.*, Henry, N.*, Decelle, J.*, Mahé, F.*, Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Ocean Coordinators, Acinas, S.G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M.E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., & Karsenti, E. 2015. Eukaryotic plankton diversity in the sunlit ocean. Science. 348: 1261605. (*=co-first authors)   LINK   PDF

57. Lima-Mendez, G.*, Faust, K.*, Henry, N.*, Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J.C., Roux, S.,Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A.M., Coppola, L., Cornejo-Castillo, F.M., d’Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S.G., Sunagawa, S., Bork, P., Sullivan, M.B.,Karsenti, E., Bowler, C., de Vargas, C., & Raes, J. 2015. Determinants of community structure in the global plankton interactome. Science. 348: 1262073. (*=co-first authors)   LINK   PDF

56. Villar, E., Farrant, G.K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J.R., Brunet, C., Casotti, R., Chase, A., Dolan, J.R., d’Ortenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C.N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S.M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Acinas, S.G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M.B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., & Iudicone, D. 2015. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science. 348: 1261447.   LINK   PDF

55. Sunagawa, S.*, Coelho, L.P.*, Chaffron, S.*, Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., Cornejo-Castillo, F.M., Costea, P.I., Cruaud, C., d’Ovidio, F., Engelen, S., Ferrera, I., Gasol, J.M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B.T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M.B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S.G., & Bork, P. 2015. Structure and function of the global ocean microbiome. Science. 348. doi:10.1126/science.1261359. (*=co-first authors)  LINK   PDF

54. Roux, S., Enault, F., Hurwitz, B.L., & Sullivan, M.B. 2015. VirSorter: mining viral signal from microbial genomic data. PeerJ. 3:e985.  LINK   PDF

53. Roux, S., Enault, F., Ravet, V., Pereira, O., & Sullivan, M.B. 2015. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Frontiers in Microbiology. 6:199.   LINK   PDF

52. Cunningham, B., Brum, J., Schwenck, S., Sullivan, M.B., & John, S. 2015. An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses. Applied Environmental Microbiology. 81:2995-3000.   LINK   PDF

51. Sullivan, M.B. 2015. Viromes, not gene markers for studying dsDNA viral communities. J Virology. 89:2459-2461.   LINK   PDF

50. Lara, E., Holmfedlt, K., Solonenko, N., Sà, E.L., Ignacio-Espinoza, J.C., Cornejo-Castillo, F.M., Verberkmoes, N.C., Vaqué, D., Sullivan, M.B., & Acinas, S.G. 2015. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the Northwestern Mediterranean Sea. PLoS One. 10:e0114829.   LINK   PDF

49. Brum, J.R., & Sullivan, M.B. 2015. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nature Reviews Microbiology. 13:147–159.   LINK   PDF

48. Hurwitz, B.L., Brum, J.R., & Sullivan, M.B. 2015. Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISMEJ. 9:472–484.   LINK   PDF

2014

47. Dang, V.T. & Sullivan, M.B. 2014. Emerging methods to study bacteriophage infection at the single-cell level. Frontiers in Microbiology. 5:724.   LINK   PDF

46. Sullivan, M.B. 2014. The Phage Metagenomic Revolution. Life in Our Phage World. 2:55-70.   Amazon

45. Roux, S., Hawley, A.K., Beltran, M.T., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S.J., & Sullivan, M.B. 2014. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife.3:e03125.   LINK   PDF

• Highlighted in Nature Reviews in Microbiology
• Highlighted in eLife

44. Hurwitz, B.L., Westveld, A.H., Brum, J.R., & Sullivan, M.B. 2014. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. PNAS. 111:10714–10719.   LINK   PDF

43. Deng, L.*, Ignacio-Espinoza, J.C.*, Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., & Sullivan, M.B. 2014. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 513:242–245. (*=co-first authors)   LINK   PDF

42. Holmfeldt, K.*, Howard-Varona, C.*, Solonenko, N., & Sullivan, M.B. 2014. Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera. Environmental Microbiology. 16:2501–2513. (*=co-first authors)   LINK   PDF

2013

41. Hurwitz, B.L., Hallam, S.J., & Sullivan, M.B. 2013. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biology. 14:R123.   LINK   PDF

40. Solonenko, S.A. & Sullivan, M.B. 2013. Preparation of metagenomic libraries from naturally occurring marine viruses. Methods in Enzymology. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics edition. 531:143–165.   LINK   PDF

39. Ignacio-Espinoza, J.C., Solonenko, S.A., & Sullivan, M.B. 2013. The global virome: Not as big as we thought? Current Opinions in Virology. 3:566–571.   LINK   PDF

38. Holmfeldt, K., Solonenko, N., Shah, M., Corrier, K., Riemann, L., VerBerkmoes, N.C., & Sullivan, M.B. 2013. Twelve previously unknown phage genera are ubiquitous in global oceans. PNAS. 110:12798-12803.   LINK   PDF

37. Solonenko, S.A., Ignacio-Espinoza, J.C., Alberti, A., Cruaud, C., Hallam, S., Konstantinidis, K., Tyson, G., Wincker, P., & Sullivan, M.B. 2013. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics. 14:320.   LINK   PDF

36. Brum, J.R., Schenck, R.O., & Sullivan, M.B. 2013. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISMEJ. 7:1738–1751.   LINK   PDF

35. Ceyssens, P.J., Aertsen, A., Donovan, D.M., Lavigne, R., Sullivan, M.B., Debarbieux, L., & Vaneechoutte, M. 2013. Meeting report of the European Molecular Biology Organization (EMBO) symposium ‘Viruses of Microbes II’, Brussels, July 2012. Res. Microbiol. 164:799–805.   LINK   PDF

34. Zhao, Y.L.*, Temperton, B.*, Thrash, J.C., Schwalbach, M.S., Vergin, K.L., Landry, Z.C., Ellisman, M., Deerinck, T., Sullivan, M.B., & Giovannoni, S.J. 2013. Abundant SAR11 viruses in the ocean. Nature. 494:357-360. (*=co-first authors)   LINK   PDF

33. Allers, E.*, Moraru, C.*, Duhaime, M.B., Beneze, E., Solonenko, N., Barrero-Canosa, J., Amann, R.^, & Sullivan, M.B.^ 2013. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environmental Microbiology. 15:2306–2318. (*=co-first authors) (^=co-corresponding authors)   LINK   PDF

32. Hurwitz, B.L. & Sullivan, M.B. 2013. The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8:e57355.   LINK   PDF

31. Labrie, S.J., Frois-Moniz, K., Osburne, M.S., Kelly, L., Roggensack, S.E., Sullivan, M.B., Gearin, G., Zeng, Q., Fitzgerald, M., Henn, M.R., & Chisholm, S.W. 2013. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environ. Microbiol.15:1356-1376.  LINK  PDF

30. Weitz, J.S., Poisot, T., Meyer, J.R., Flores, C.O., Valverde, S., Sullivan, M.B., & Hochberg, M.E. 2013. Phage-bacteria infection networks. Trends in Microbiology. 21:82-91.   LINK   PDF

2012

29. Duhaime, M.B. & Sullivan, M.B. 2012. Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline.Virology. 434:181-186.   LINK   PDF

28. Deng, L., Gregory, A., Yilmaz, S., Poulos, B.T., Hugenholtz, P., & Sullivan, M.B. 2012. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. mBio. 3:e00373-12.   LINK   PDF

  • Faculty of 1000 Prime recommended this article “of special significance” on 27 Aug 2013

27. Allers, E.*, Wright, J.J.*, Konwar, K.M., Howes, C.G., Beneze, E., Hallam, S.J.^, & Sullivan, M.B.^ 2012. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISMEJ. 7:256-268. (*=co-first authors) (^=co-corresponding authors)   LINK   PDF

26. Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology. 15:1428–1440.   LINK   PDF

25. Duhaime, M.B., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: A rigorous assessment and optimization of the linker amplification method. Environmental Microbiolgy. 14:2526-2537.   LINK   PDF

24. Ignacio-Espinoza, J.C. & Sullivan, M.B. 2012. Phylogenomics of T4 cyanophages: Lateral gene transfer in the ‘core’ and origins of host genes. Environmental Microbiology. 14:2113-2126.   LINK   PDF

23. Holmfeldt, K., Odic, D., Sullivan, M.B., Middelboe, M., & Riemann, L. 2012. Cultivated single-stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA-binding stains. Applied Environmental Microbiology. 78:892-894.   LINK   PDF

2011

22. Marine, R., Polson, S.W., Ravel, J., Hatfull, G., Russell, D., Sullivan, M.B., Syed, F., Dumas, M., & Wommack, K.E. 2011. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied Environmental Microbiology. 77:8071-8079.   LINK   PDF

21. Karsenti, E., Acinas, S.G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M.B, Arendt, D., Benzoni, F., Claverie, J.M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E.G., Sardet, C., Sieracki, M.E., Speich, S., Velayoudon, D., Weissenbach, J., Wincker, P., & the Tara Oceans Consortium. 2011. A holistic approach to marine eco-systems biology. PLoS Biology. 9:e1001177.   LINK   PDF

20. John, S.G., Mendez, C.B., Deng, L., Poulos, B., Kauffman, A.K.M., Kern, S., Brum, J., Polz, M.F., Boyle, E.A., & Sullivan, M.B. 2011. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports. 3:195-202.   LINK   PDF

  • Minor correction concerning buffer recipes:   PDF

2010

19. Sullivan, M.B., Huang, K.H., Ignacio-Espinoza, J.C., Berlin, A.M., Kelly, L., Weigele, P.R., DeFrancesco, A.S., Kern, S.E., Thompson, L.R., Young, S., Yandava, C., Fu, R., Krastins, B., Chase, M., Sarracino, D., Osburne, M.S., Henn, M.R., & Chisholm, S.W. 2010. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology. 12:3035-3056.   LINK   PDF

18. Liu, X.A., Zhang, Q.F., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M.T., Schmid, M.F., Osburne, M.S., Chisholm, S.W., & Chiu, W. 2010. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nature Structural and Molecular Biology. 17:830-836.   LINK   PDF

17. Henn, M.R., Sullivan, M.B., Stange-Thomann, N., Osburne, M.S., Berlin, A.M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q.D., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S.K., Nusbaum, C., Birren, B.W., & Chisholm, S.W. 2010. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS One. 5:e9083.   LINK   PDF

2009

16. Sullivan, M.B., Krastins, B., Hughes, J.L., Kelly, L., Chase, M., Sarracino, D., & Chisholm, S.W. 2009. The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial ‘mobilome’. Environmental Microbiology. 11:2935-2951. LINK   PDF

2008

15. Sullivan, M.B., Coleman, M.L., Quinlivan, V., Rosenkrantz, J.E., DeFrancesco, A.S., Tan, G., Fu, R., Lee, J.A., Waterbury, J.B., Bielawski, J.P., & Chisholm, S.W. 2008. Portal protein diversity and phage ecology. Environmental Microbiology. 10:2810-2823.   LINK   PDF

14. Dammeyer, T., Bagby, S.C., Sullivan, M.B., Chisholm, S.W., & Frankenberg-Dinkel, N. 2008. Efficient phage-mediated pigment biosynthesis in oceanic cyanabacteria. Current Biology. 18:442-448.   LINK   PDF

2007

13. Lindell, D., Jaffe, J.D., Coleman, M.L., Futschik, M.E., Axmann, I.M., Rector, T., Kettler, G., Sullivan, M.B., Steen, R., Hess, W.R., Church, G.M., & Chisholm, S.W. 2007. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 449:83-86.   LINK   PDF

12. Moore, L.R., Coe, A., Zinser, E.R., Saito, M.A., Sullivan, M.B., Lindell, D., Frois-Moniz, K., Waterbury, J., & Chisholm, S.W. 2007. Culturing the marine cyanobacterium Prochlorococcus. Limnology and Oceanographic Methods. 5:353-362.   PDF

11. Breitbart, M., Thompson, L.R., Suttle, C.A., & Sullivan, M.B. 2007. Exploring the vast diversity of marine viruses. Oceanography. 20:135-139.   PDF

2006

10. Sullivan, M.B., Lindell, D., Lee, J.A., Thompson, L.R., Bielawski, J.P., & Chisholm, S.W. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biology. 4:1344-1357.  LINK  PDF

  • Faculty of 1000 “must read” 6 July 2006badgef1000
  • Science (21 Jul 06) & Nat. Rev. Micro. (Sept 06, v.4) Literature Highlightnaturereviews
  • 1 of 4 refs in Goldenfield & Woese, 2007. Nature 445:369

9. Coleman, M.L., Sullivan, M.B., Martiny, A.C., Steglich, C., Barry, K., DeLong, E.F., & Chisholm, S.W. 2006. Genomic islands and the ecology and evolution of Prochlorococcus. Science. 311:1768-1770.   LINK   PDF

8. DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R., Chisholm, S.W., & Karl, D.M. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 311:496-503.  LINK   PDF

  • Faculty of 1000 “Recommended paper” 17 Feb 2006badgef1000

2005

7. Sullivan, M.B., Coleman, M.L., Weigele, P., Rohwer, F., & Chisholm, S.W. 2005. Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biol. 3:790-806.   LINK   PDF

  • Nature Reviews Microbiology, Highlight of the Literature (July 2005, vol. 3, 520)naturereviews

6. Paul, J.H. & Sullivan, M.B. 2005. Marine phage genomics: What have we learned? Current Opinions in Biotechnology. 16:299-307.   LINK   PDF

2004

5. Lindell, D., Sullivan, M.B., Johnson, Z.I., Tolonen, A.C., Rohwer, F., & Chisholm, S.W. 2004. Transfer of photosynthesis genes to and from Prochlorococcus viruses. PNAS. 101:11013-11018.   LINK   PDF

2003

4. Sullivan, M.B., Waterbury, J.B., & Chisholm, S.W. 2003. Cyanophages infecting the oceanic cyanobacterium ProchlorococcusNature. 424:1047-1051.   LINK   PDF

3. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., Arellano, A., Coleman, M., Hauser, L., Hess, W.R., Johnson, Z.I., Land, M., Lindell, D., Post, A.F., Regala, W., Shah, M., Shaw, S.L., Steglich, C., Sullivan, M.B., Ting, C.S., Tolonen, A., Webb, E.A., Zinser, E.R., & Chisholm, S.W. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424:1042-1047.   LINK   PDF

2002

2. Paul, J.H., Sullivan, M.B., Segall, A.M., & Rohwer, F. 2002. Marine phage genomics. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133:463-476.   LINK   PDF

1998

1. Kana, T.M., Sullivan, M.B., Cornwell, J.C., & Groszkowski, K.M. 1998. Denitrification in estuarine sediments determined by membrane inlet mass spectrometry. Limnol. Oceanog. 43:334-339.  PDF