Gilbert JA, Jansson JK, and Knight R. 2014. The Earth Microbiome project: successes and aspirations. BMC Biology*,* 12:69 doi:10.1186/s12915-014-0069-1 Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA: The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Front Microbiol 2014, 5. Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Capek P, Santrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C, Urich T: Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J 2014, 8:841–853. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK: Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 2014. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, et al. (2014) Human and Environmental Impacts on River Sediment Microbial Communities. PLoS ONE 9(5): e97435. doi:10.1371/journal.pone.0097435 Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, et al. (2014) Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome. PLoS ONE 9(6): e99641. doi:10.1371/journal.pone.0099641 Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D: Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine. PLoS ONE 2014, 9:e85611.
Fierer, N., J. Ladau, J.C. Clemente, J. Leff, S.M. Owens, K.S. Pollard, R. Knight, J.A. Gilbert, R.L. McCulley. 2013. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 342: 621-624. Gittel, A. et al. (2013) Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J, doi:10.1038/ismej.2013.219. Jansson J, Prosser J (2013) Microbiology: The life beneath our feet. Nature 494: 40–41. doi:10.1038/494040a. Rubin BER, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, et al. (2013) Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples. PLoS ONE 8(7): e70460. doi:10.1371/journal.pone.0070460
Gewin V: Microbes en masse: The sequencing machine. Nature 2012, 487:156–158. Knight R, Jansson J, Field D, Fierer N, Desai N, et al. (2012) Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology 30: 513–520. doi:10.1038/nbt.2235. Larsen PE, Field D, Gilbert JA (2012) Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods. doi:10.1038/nmeth.1975. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal. doi:10.1038/ismej.2012.8. Gilbert JA, Meyer F. Modeling the Earth’s Microbiome: A real world deliverable for microbial ecology. ASM Microbe Magazine.
Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, et al. (2011) A Holistic Approach to Marine Eco-Systems Biology. PLoS Biol 9(10): e1001177. doi:10.1371/journal.pbio.1001177 Jansson J. 2011. Microbial ecologists are taking a metagenomics approach to analyze complex and diverse soil microbial communities. Microbe Magazine. Gilbert JA, O’Dor R, King N, Vogel T. 2011. The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial Informatics and Experimentation,1:5 Larsen PE, Collart F, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA. 2011. **** Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microbial Informatics and Experimentation 2011, 1:4 (this is one of the modeling techniques being implemented BY the EMP for metagenomic data analysis) Yilmaz et al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29, 415–420 (this is the standard metadata capture schema employed by the EMP) Gilbert JA, ODor R, Vogel T. 2011. Survey studies are still vital to science. Nature. 469, 162. Gilbert JA and Dupont C. 2011. Marine Metagenomics. Annual Review of Marine Science.Volume 3: 347-371.
Gilbert JA, Meyer F, Antonoploulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Kostantindis K, Kostka J, Kyrpides, N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2010. Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Science. 3:3. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glockner FO, Klenk H-P, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. 2010. The Earth Microbiome Project: Meeting report of the 1^st^ EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6^th^ 2010. Standards in Genomic Science. 3:3. Gilbert JA, Meyer F, Knight R, Field D, Kyrpides N, Yilmaz P, Wooley J. 2010. Meeting report: GSC M5 roundtable at the 13^th^ International Society for Microbial Ecology meeting in Seattle, WA, USA, August 22-27^th^ 2010. Standards in Genomic Science. 3:3. Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM. 2010. Metagenomics: A foundling finds its feet. Standards in Genomic Science. Vol 3 (2) Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottman R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O , Wooley J. 2010. Meeting report from the Genomics Standards Consortium (GSC) workshop 10. Standards in Genomic Science*. 3:3*.