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2013
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31(6):533-8. Abstract
Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW. Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data. PLoS Comput Biol. 2013;9(4):e1003031. Abstract
Willner D, Hugenholtz P. From deep sequencing to viral tagging: Recent advances in viral metagenomics. Bioessays. 2013. Abstract
Willner DL, Hugenholtz P, Yerkovich ST, Tan ME, Daly JN, Lachner N, et al. Re-Establishment of Recipient-Associated Microbiota in the Lung Allograft is Linked to Reduced Risk of Bronchiolitis Obliterans Syndrome. Am J Respir Crit Care Med. 2013. Abstract
He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, et al. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS ONE. 2013;8(4):e61126. Abstract
Harris KJ, Caporaso GJ, Walker JJ, Spear JR, Gold NJ, Robertson CE, et al. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2013;7(1):50-60. Abstract
2012
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488(7409):86-90. Abstract
Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW. Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic acids research. 2012. Abstract
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6(3):610-8. Abstract
Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods. 2012;9(5):425-6.
Deng L, Gregory A, Yilmaz S, Poulos BT, Hugenholtz P, Sullivan MB. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. MBio. 2012;3(6). Abstract
Willner D, Daly JN, Whiley D, Grimwood K, Wainwright CE, Hugenholtz P. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS ONE. 2012;7(4):e34605. Abstract
2011
Klenk H-, Lapidus A, Chertkov O, Copeland A, Glavina Del Rio T, Nolan M, et al. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Raine. Stand Genomic Sci. 2011;5(1):121-34. Abstract
Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, et al. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. The ISME journal. 2011. Abstract
Gladden JM, Allgaier M, Miller CS, Hazen TC, VanderGheynst JS, Hugenholtz P, et al. Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass. Applied and environmental microbiology. 2011. Abstract
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature biotechnology. 2011;29(5):415-20. Abstract
Reddy AP, Allgaier M, Singer SW, Hazen TC, Simmons BA, Hugenholtz P, et al. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and bioengineering. 2011. Abstract
Skennerton CT, Angly FE, Breitbart M, Bragg L, He S, McMahon KD, et al. Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System. PLoS ONE. 2011;6(5):e20095. Abstract
Deangelis KM, Allgaier M, Chavarria Y, Fortney JL, Hugenholtz P, Simmons B, et al. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS ONE. 2011;6(4):e19306. Abstract
Burnum KE, Callister SJ, Nicora CD, Purvine SO, Hugenholtz P, Warnecke F, et al. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J. 2011;5(1):161-4. Abstract
Lykidis A, Chen C-, Tringe SG, McHardy AC, Copeland A, Kyrpides NC, et al. Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J. 2011;5(1):122-30. Abstract
2010
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, et al. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods. 2010;7(10):807-12. Abstract
Yilmaz S, Haroon MF, Rabkin BA, Tyson GW, Hugenholtz P. Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. ISME J. 2010;4(10):1352-6. Abstract
He S, Kunin V, Haynes M, Martin HG, Ivanova N, Rohwer F, et al. Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ Microbiol. 2010;12(5):1205-17. Abstract
Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 2010;4(5):642-7. Abstract