Items where Author is "Gilbert, JA"

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Number of items: 43.

Publication - Article

Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Zech Xu, Z, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Jin Song, S, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Rivera, JLA, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, J, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, Q, Campbell, AH, Caporaso, JG, Cardona, C, Carroll, J, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwell, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, Ezenwa, V, Fenner, N, Findlay, HS, Fleming, ID, Fogliano, V, Forsman, A, Freeman, C, Friedman, ES, Galindo, G, Garcia, L, Garcia-Amado, MA, Garshelis, D, Gasser, RB, Gerdts, G, Gibson, MK, Gifford, I, Gill, RT, Giray, T, Gittel, A, Golyshin, P, Gong, D, Grossart, H-P, Guyton, K, Haig, S-J, Hale, V, Hall, RS, Hallam, SJ, Handley, KM, Hasan, NA, Haydon, SR, Hickman, JE, Hidalgo, G, Hofmockel, KS, Hooker, J, Hulth, S, Hultman, J, Hyde, E, Ibáñez-Álamo, JD, Jastrow, JD, Jex, AR, Johnson, LS, Johnston, ER, Joseph, S, Jurburg, SD, Jurelevicius, D, Karlsson, A, Karlsson, R, Kauppinen, S, Kellogg, CTE, Kennedy, SJ, Kerkhof, LJ, King, GM, Kling, GW, Koehler, AV, Krezalek, M, Kueneman, J, Lamendella, R, Landon, EM, Lane-deGraaf, K, LaRoche, J, Larsen, P, Laverock, B, Lax, S, Lentino, M, Levin, II, Liancourt, P, Liang, W, Linz, AM, Lipson, DA, Liu, Y, Lladser, ME, Lozada, M, Spirito, CM, MacCormack, WP, MacRae-Crerar, A, Magris, M, Martín-Platero, AM, Martín-Vivaldi, M, Martínez, LM, Martínez-Bueno, M, Marzinelli, EM, Mason, OU, Mayer, GD, McDevitt-Irwin, JM, McDonald, JE, McGuire, KL, McMahon, KD, McMinds, R, Medina, M, Mendelson, JR, Metcalf, JL, Meyer, F, Michelangeli, F, Miller, K, Mills, DA, Minich, J, Mocali, S, Moitinho-Silva, L, Moore, A, Morgan-Kiss, RM, Munroe, P, Myrold, D, Neufeld, JD, Ni, Y, Nicol, GW, Nielsen, S, Nissimov, JI, Niu, K, Nolan, MJ, Noyce, K, O’Brien, SL, Okamoto, N, Orlando, L, Castellano, YO, Osuolale, O, Oswald, W, Parnell, J, Peralta-Sánchez, JM, Petraitis, P, Pfister, C, Pilon-Smits, E, Piombino, P, Pointing, SB, Pollock, FJ, Potter, C, Prithiviraj, B, Quince, C, Rani, A, Ranjan, R, Rao, S, Rees, AP, Richardson, M, Riebesell, U, Robinson, C, Rockne, KJ, Rodriguezl, SM, Rohwer, F, Roundstone, W, Safran, RJ, Sangwan, N, Sanz, V, Schrenk, M, Schrenzel, MD, Scott, NM, Seger, RL, Seguin-Orlando, A, Seldin, L, Seyler, LM, Shakhsheer, B, Sheets, GM, Shen, C, Shi, Y, Shin, H, Shogan, BD, Shutler, D, Siegel, J, Simmons, S, Sjöling, S, Smith, DP, Soler, JJ, Sperling, M, Steinberg, PD, Stephens, B, Stevens, MA, Taghavi, S, Tai, V, Tait, K, Tan, CL, Tas¸, N, Taylor, DL, Thomas, T, Timling, I, Turner, BL, Urich, T, Ursell, LK, van der Lelie, D, Van Treuren, W, van Zwieten, L, Vargas-Robles, D, Thurber, RV, Vitaglione, P, Walker, DA, Walters, WA, Wang, S, Wang, T, Weaver, T, Webster, NS, Wehrle, B, Weisenhorn, P, Weiss, S, Werner, JJ, West, K, Whitehead, A, Whitehead, SR, Whittingham, LA, Willerslev, E, Williams, AE, Wood, SA, Woodhams, DC, Yang, Y, Zaneveld, J, Zarraonaindia, I, Zhang, Q and Zhao, H 2017 A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551. 457-463. https://doi.org/10.1038/nature24621

Lüchmann, KH, Clark, MS, Bainy, ACD, Gilbert, JA, Craft, JA, Chipman, JK, Thorne, MAS, Mattos, JJ, Siebert, MN and Schroeder, DC 2015 Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana. Aquatic Toxicology, 166. 10-20.

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Kopf, A, Bicak, M, Kottmann, R, Schnetzer, J, Kostadinov, I, Lehmann, K, Fernandez-Guerra, A, Jeanthon, C, Rahav, E, Ullrich, M, Wichels, A, Gerdts, G, Polymenakou, P, Kotoulas, G, Siam, R, Abdallah, RZ, Sonnenschein, EC, Cariou, T, O'Gara, F, Jackson, S, Orlic, S, Steinke, M, Busch, J, Duarte, B, Caçador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, CM, Luna, GM, Quero, GM, Löscher, CR, Kremp, A, DeLorenzo, ME, Øvreås, L, Tolman, J, LaRoche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, CP, Ramos, S, Magalhães, C, Jude-Lemeilleur, F, Aguirre-Macedo, ML, Wang, S, Poulton, N, Jones, S, Collin, R, Fuhrman, JA, Conan, P, Alonso, C, Stambler, N, Goodwin, K, Yakimov, MM, Baltar, F, Bodrossy, L, Van De Kamp, J, Frampton, DMf, Ostrowski, M, Van Ruth, P, Malthouse, P, Claus, S, Deneudt, K, Mortelmans, J, Pitois, SG, Wallom, D, Salter, I, Costa, R, Schroeder, DC, Kandil, MM, Amaral, V, Biancalana, F, Santana, R, Pedrotti, ML, Yoshida, T, Ogata, H, Ingleton, T, Munnik, K, Rodriguez-Ezpeleta, N, Berteaux-Lecellier, V, Wecker, P, Cancio, I, Vaulot, D, Bienhold, C, Ghazal, H, Chaouni, B, Essayeh, S, Ettamimi, S, Zaid, EH, Boukhatem, N, Bouali, A, Chahboune, R, Barrijal, S, Timinouni, M, El Otmani, F, Bennani, M, Mea, M, Todorova, N, Karamfilov, VK, Ten Hoopen, P, Cochrane, G, L'Haridon, S, Bizsel, KC, Vezzi, A, Lauro, FM, Martinez, PG, Jensen, RM, Hinks, J, Gebbels, S, Rosselli, R, De Pascale, F, Schiavon, R, Dos Santos, A, Villar, E, Pesant, S, Cataletto, B, Malfatti, F, Edirisinghe, R, Silveira, JAH, Barbier, M, Turk, V, Tinta, T, Fuller, WJ, Salihoglu, I, Serakinci, N, Ergoren, MC, Bresnan, E, Iriberri, J, Nyhus, PAF, Bente, E, Karlsen, HE, Golyshin, PN, Gasol, JM, Moncheva, S, Dzhembekova, N, Johnson, ZI, Sinigalliano, CD, Gidley, ML, Zingone, A, Danovaro, R, Tsiamis, G, Clark, MS, Costa, AC, El Bour, M, Martins, AM, Collins, RE, Ducluzeau, AL, Martinez, J, Costello, MJ, Amaral-Zettler, LA, Gilbert, JA, Davies, N, Field, D and Glockner, FO 2015 The ocean sampling day consortium.. GigaScience, 4. 27.

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Laverock, B, Tait, K, Gilbert, JA, Osborn, AM and Widdicombe, S 2013 Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. Environmental Microbiology Reports, 6 (1). 113-121. https://doi.org/10.1111/1758-2229.12115

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Laverock, B, Kitidis, V, Tait, K, Gilbert, JA, Osborn, M and Widdicombe, S 2013 Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 368 (1627). 1-13. https://doi.org/10.1098/rstb.2012.0441

Roy, A-S, Gibbons, SM, Schunck, H, Owens, S, Caporaso, JG, Sperling, M, Nissimov, JI, Romac, S, Bittner, L, Muhling, M, Riebesell, U, LaRoche, J and Gilbert, JA 2013 Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences, 10 (1). 555-566. https://doi.org/10.5194/bg-10-555-2013

Sperling, M, Piontek, J, Gerdts, G, Wichels, A, Schunck, H, Roy, A-S, La Roche, J, Gilbert, JA, Nissimov, JI, Bittner, L, Romac, S, Riebesell, U and Engel, A 2013 Effect of elevated CO<sub>2</sub> on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord. Biogeosciences, 10 (1). 181-191. https://doi.org/10.5194/bg-10-181-2013

Willetts, AJ, Joint, IR, Gilbert, JA, Trimble, W and Muhling, M 2012 Isolation and initial characterization of a novel type of Baeyer-Villiger monooxygenase activity from a marine microorganism. Microbial Biotechnology, 5. 549 - 559. https://doi.org/10.1111/j.1751-7915.2012.00337.x

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Gilbert, JA, Steele, JA, Caporaso, JG, Steinbruck, L, Reeder, J, Temperton, B, Huse, S, McHardy, AC, Knight, R, Joint, IR, Somerfield, PJ, Fuhrman, J and Field, D 2012 Defining seasonal marine microbial community dynamics. ISME Journal - Multidisciplinary Journal of Microbial Ecology, 6. 298 - 308. https://doi.org/10.1038/ismej.2011.107

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Gilbert, JA and Dupont, CL 2011 Microbial Metagenomics: Beyond the Genome. Annual Review of Marine Science, 3. 347 - 371. https://doi.org/10.1146/annurev-marine-120709-142811

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Gilbert, JA, Meyer, F, Schriml, L, Joint, IR, Muhling, M and Field, D 2011 Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Standards in Genomic Science, 3. 183 - 193.

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Yilmaz, P, Kottmann, R, Field, D, Knight, R, Cole, JR, Amaral-Zettler, L, Gilbert, JA, Karsch-Mizrachi, I, Johnston, A and Cochrane, G 2011 Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29. 415 - 420. https://doi.org/10.1038/nbt.1823

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Jeffries, TC, Seymour, JR, Gilbert, JA, Dinsdale, EA, Newton, K, Leterme, SSC, Roudnew, B, Smith, RJ, Seuront, L and Mitchell, JG 2011 Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats. PLoS one, 6. 0 - 0. https://doi.org/10.1371/journal.pone.0025173

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Temperton, B, Thomas, S, Tait, K, Parry, HE, Emery, M, Allen, MJ, Quinn, JP, McGrath, JW and Gilbert, JA 2011 Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Standards in Genomic Science, 4. 183 - 190. https://doi.org/10.4056/sigs.1654066

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Laverock, B, Gilbert, JA, Tait, K, Osborn, M and Widdicombe, S 2011 Bioturbation: impact on the marine nitrogen cycle. Biochemical Society Transactions, 39. 315 - 320. https://doi.org/10.1042/BST0390315

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Turk, KA, Rees, AP, Zehr, JP, Pereira, N, Swift, P, Shelley, RU, Lohan, M, Woodward, EMS and Gilbert, JA 2011 Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME Journal - Multidisciplinary Journal of Microbial Ecology. 01-Dec. https://doi.org/10.1038/ismej.2010.205

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Temperton, B, Gilbert, JA, Quinn, JP and McGrath, JW 2011 Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments. PLoS one, 1. 0016499 - 0016499. https://doi.org/10.1371/journal.pone.0016499

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Gilbert, JA, Field, D, Swift, P, Thomas, S, Cummings, DG, Temperton, B, Weynberg, KD, Huse, S, Hughes, M, Joint, IR, Somerfield, PJ and Muhling, M 2010 The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A 'Multi-Omic' Study of Seasonal and Diel Temporal Variation. PLoS one, 5. Jan-17. https://doi.org/10.1371/journal.pone.0015545

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Mitra, S, Gilbert, JA, Field, D and Huson, DH 2010 Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME Journal - Multidisciplinary Journal of Microbial Ecology, 4. 1236 - 1242. https://doi.org/10.1038/ismej.2010.51

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Laverock, B, Widdicombe, S, Tait, K, Smith, C, Osborn, M and Gilbert, JA 2010 Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. ISME Journal - Multidisciplinary Journal of Microbial Ecology, 4. 1531 - 1544. https://doi.org/10.1038/ismej.2010.86

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Field, D, Friedburg, I, Sterk, P, Kottmann, R, Glockner, FO, Hirschman, L, Garrity, G, Cochrane, G, Wooley, J and Gilbert, JA 2010 Meeting Report: Metagenomics Metadata and Meta-analysis (M3) Special Interest Group at ISMB 2009. Standards in Genomic Science, 1. 01-Mar.

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Hirschman, L, Sterk, P, Field, D, Wooley, J, Cochrane, G, Gilbert, JA, Kolker, E, Kyrpides, N, Meyer, F, Mizrachi, I, Nakamura, Y, Sansone, S, Schriml, L, Tatusova, T, White, O and Yilmaz, P 2010 Meeting Report: Metagenomics Metadata and Meta-analysis (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Standards in Genomic Science, 2. 01-Mar.

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Gilbert, JA 2010 Beyond the Infinite - tracking bacterial gene expression. Microbiology Today, 2. 82 - 85.

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Gilbert, JA, Meyer, F, Schriml, L, Joint, IR, Muhling, M and Field, D 2010 Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Standards in Genomic Science, 3. 183 - 193. https://doi.org/10.4056/sigs.1202536

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Heidelberg, KB, Gilbert, JA and Joint, IR 2010 Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microbial Biotechnology, 3. 531 - 543. https://doi.org/10.1111/j.1751-7915.2010.00193.x

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Thomas, S, Burdett, HL, Temperton, B, Wick, R, Snelling, D, McGrath, JW, Quinn, JP, Munn, CB and Gilbert, JA 2010 The diversity of phnA gene homologues in temperature-stressed Cnidarian-associated Bacteria. ISME Journal - Multidisciplinary Journal of Microbial Ecology. 0 - 0.

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Craft, J, Gilbert, JA, Temperton, B, Dempsey, KE, Ashelford, K, Tiwari, B, Hutchinson, TH and Chipman, JK 2010 Pyrosequencing of Mytilus galloprovincialis cDNAs: Tissue-Specific Expression Patterns. PLoS one, 5. 01-May. https://doi.org/10.1371/journal.pone.0008875

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Gilbert, JA, Field, D, Swift, P, Newbold, L, Oliver, A, Smyth, TJ, Somerfield, PJ, Huse, S and Joint, IR 2009 The seasonal structure of microbial communities in the Western English Channel. Environmental Microbiology, 12. 3132 - 3139. https://doi.org/10.1111/j.1462-2920.2009.02017.x

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Temperton, B, Field, D, Oliver, A, Tiwari, B, Muhling, M, Joint, IR and Gilbert, JA 2009 Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME Journal - Multidisciplinary Journal of Microbial Ecology, 3. 792 - 796. https://doi.org/10.1038/ismej.2009.32

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Kulakova, A, Kulakov, L, Villarreal-Chiu, J, Gilbert, JA, McGrath, JW and Quinn, JP 2009 Expression of the phosphonoalanine-degradative gene cluster from Variovorax sp Pal2 is induced by growth on phosphonoalanine and phosphonopyruvate. FEMS Microbiology Letters, 1. 100 - 106. https://doi.org/10.1111/j.1574-6968.2008.01477.x

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Rees, AP, Gilbert, JA and Kelly-Gerreyn, BA 2009 Nitrogen fixation in the western English Channel (NE Atlantic Ocean). Marine Ecology Progress Series, 374. 07-Dec. https://doi.org/10.3354/meps07771

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Gilbert, JA, Thomas, S, Cooley, NA, Kulakova, A, Field, D, Booth, T, McGrath, JW, Quinn, JP and Joint, IR 2009 Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. Environmental Microbiology, 11. 111 - 125. https://doi.org/10.1111/j.1462-2920.2008.01745.x

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Gilbert, JA, Field, D, Huang, Y, Edwards, R, Li, W, Gilna, P and Joint, IR 2008 Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS one, 3. Jan-13. https://doi.org/10.1371/journal.pone.0003042

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Sansone, S, Rocca-Serra, P, Brandizi, M, Brazma, A, Field, D, Fostel, J, Garrow, AG, Gilbert, JA, Goodsaid, F, Hardy, N, Jones, P, Lister, A, Miller, M, Morrison, N, Rayner, T, Skylar, N, Taylor, C, Tong, W, Warner, G and Weimann, S 2008 The first RSBI (ISA-TAB) workshop: Can a Simple Format Work for Complex Studies?. OMICS: A Journal of Integrative Biology, 12. 143 - 149. https://doi.org/10.1089/omi.2008.0019

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Field, D, Garrity, G, Gray, T, Morrison, N, Selengut, J, Sterk, P, Tatusova, T, Thomson, N, Allen, MJ, Angiuolii, SV, Ashburner, M, Axelrod, N, Baldauf, S, Ballard, S, Boore, J, Cochrane, G, Cole, JR, Dawyndt, P, de Vos, P, de Pamphillis, C, Edwards, R, Faruque, N, Feldman, R, Gilbert, JA, Gilna, P, Glockner, FO, Goldstein, P, Guralnick, R, Haft, D, Hancock, D, Hermjakob, H, Hertz-Fowler, C, Hugenholtz, P, Joint, IR, Kagan, L, Kane, M, Kennedy, J, Kowalchuk, G, Kottmann, R, Kolker, E, Kravitz, S, Kyrpides, N, Leebans-Mack, J and Lewis, SC 2008 The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26. 541 - 547. https://doi.org/10.1038/nbt1360

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Gilbert, JA, Muhling, M and Joint, IR 2008 A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome. ISME Journal - Multidisciplinary Journal of Microbial Ecology. Jan-15. https://doi.org/10.1038/ismej.2008.49

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Booth, T, Gilbert, JA, Neufeld, JD, Ball, J, Thurston, M, Chipman, K, Joint, IR and Field, D 2007 Handlebar: a flexible web-based inventory manager for handling barcoded samples. Biotechniques, 42. 300 - 302. https://doi.org/10.2144/000112385

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Publication - Book

Gilbert, JA, Field, D, Huang, Y, Edwards, R and Li, W 2010 Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. UNSPECIFIED, 0 - 0.

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Gilbert, JA 2010 Aquatic metagenome library (archive; expression) generation and analysis. UNSPECIFIED, 4347 - 4352.

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Gilbert, JA, Zhang, K and Neufeld, JD 2010 Multiple displacement amplification. UNSPECIFIED, 4255 - 4263.

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Publication - Book Section

Gilbert, JA and Hughes, M 2011 Gene Expression Profiling: Metatranscriptomics. In: UNSPECIFIED UNSPECIFIED, 195 - 205.

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Gilbert, JA, Laverock, B, Temperton, B, Thomas, S, Muhling, M and Hughes, M 2011 Metagenomics. In: UNSPECIFIED UNSPECIFIED, 173 - 183.

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This list was generated on Fri Jul 19 07:58:54 2024 UTC.