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A Eren

Assistant Professor
meren@uchicago.edu
Websites
Research Summary
With our expertise in computation and microbiology we create and employ advanced 'omics and wet-lab strategies to study the ecology and evolution of naturally occurring microbial life in a wide range of host-associated and marine habitats.
Keywords
Metagenomics, Metatranscriptomics, metapangenomics, phylogenomics, anvi'o, microbial ecology, microbial evolution, human microbiome, microbial symbioses
Biosciences Graduate Program Association
Publications

  1. Roguet A, Newton RJ, Eren AM, McLellan SL. Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure. mSystems. 2022 Jun 28; e0011822. View in: PubMed

  2. Landis EA, Fogarty E, Edwards JC, Popa O, Eren AM, Wolfe BE. Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations. mSystems. 2022 Jun 28; 7(3):e0015722. View in: PubMed

  3. Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol. 2022 04; 7(4):508-523. View in: PubMed

  4. Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, Gloeckner FO, Fernàndez-Guerra A. Unifying the known and unknown microbial coding sequence space. Elife. 2022 Mar 31; 11. View in: PubMed

  5. Paul BG, Eren AM. Eco-evolutionary significance of domesticated retroelements in microbial genomes. Mob DNA. 2022 Feb 23; 13(1):6. View in: PubMed

  6. Trigodet F, Lolans K, Fogarty E, Shaiber A, Morrison HG, Barreiro L, Jabri B, Eren AM. High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes. Mol Ecol Resour. 2022 Jul; 22(5):1786-1802. View in: PubMed

  7. Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Correction to: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J. 2022 Apr; 16(4):1203. View in: PubMed

  8. Zhang W, Foo M, Eren AM, Pan T. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell. 2022 03 03; 82(5):891-906. View in: PubMed

  9. Huang S, Zhang W, Katanski CD, Dersh D, Dai Q, Lolans K, Yewdell J, Eren AM, Pan T. Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling. Genome Biol. 2021 12 06; 22(1):330. View in: PubMed

  10. Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J. 2022 04; 16(4):927-936. View in: PubMed

  11. Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE. STRONG: metagenomics strain resolution on assembly graphs. Genome Biol. 2021 07 26; 22(1):214. View in: PubMed

  12. Miyoshi J, Miyoshi S, Delmont TO, Cham C, Lee STM, Sakatani A, Yang K, Shan Y, Kennedy M, Kiefl E, Yousef M, Crosson S, Sogin M, Antonopoulos DA, Eren AM, Leone V, Chang EB. Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10-/- Mice. Gastroenterology. 2021 09; 161(3):940-952.e15. View in: PubMed

  13. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD. Community-led, integrated, reproducible multi-omics with anvi'o. Nat Microbiol. 2021 01; 6(1):3-6. View in: PubMed

  14. Utter DR, Borisy GG, Eren AM, Cavanaugh CM, Mark Welch JL. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biol. 2020 12 16; 21(1):293. View in: PubMed

  15. Shaiber A, Willis AD, Delmont TO, Roux S, Chen LX, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol. 2020 12 16; 21(1):292. View in: PubMed

  16. Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. Elife. 2020 06 17; 9. View in: PubMed

  17. Dai Z, Sevillano-Rivera MC, Calus ST, Bautista-de Los Santos QM, Eren AM, van der Wielen PWJJ, Ijaz UZ, Pinto AJ. Disinfection exhibits systematic impacts on the drinking water microbiome. Microbiome. 2020 03 20; 8(1):42. View in: PubMed

  18. Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Res. 2020 03; 30(3):315-333. View in: PubMed

  19. Roguet A, Esen ÖC, Eren AM, Newton RJ, McLellan SL. FORENSIC: an Online Platform for Fecal Source Identification. mSystems. 2020 Mar 17; 5(2). View in: PubMed

  20. Yeoman CJ, Brutscher LM, Esen ÖC, Ibaoglu F, Fowler C, Eren AM, Wanner K, Weaver DK. Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus). PeerJ. 2019; 7:e7548. View in: PubMed

  21. Delmont TO, Kiefl E, Kilinc O, Esen OC, Uysal I, Rappé MS, Giovannoni S, Eren AM. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. Elife. 2019 09 03; 8. View in: PubMed

  22. Bunker JJ, Drees C, Watson AR, Plunkett CH, Nagler CR, Schneewind O, Eren AM, Bendelac A. B cell superantigens in the human intestinal microbiota. Sci Transl Med. 2019 08 28; 11(507). View in: PubMed

  23. Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. Author Correction: The Wolbachia mobilome in Culex pipiens includes a putative plasmid. Nat Commun. 2019 Jul 12; 10(1):3153. View in: PubMed

  24. Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. 2019 10; 4(10):1727-1736. View in: PubMed

  25. Shaiber A, Eren AM. Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories. mBio. 2019 06 04; 10(3). View in: PubMed

  26. Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. The Wolbachia mobilome in Culex pipiens includes a putative plasmid. Nat Commun. 2019 03 05; 10(1):1051. View in: PubMed

  27. McKay LJ, Dlakic M, Fields MW, Delmont TO, Eren AM, Jay ZJ, Klingelsmith KB, Rusch DB, Inskeep WP. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat Microbiol. 2019 04; 4(4):614-622. View in: PubMed

  28. Wang X, Li Y, Chen W, Shi H, Eren AM, Morozov A, He C, Luo GZ, Pan T. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 02; 29(2):167-170. View in: PubMed

  29. Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun. 2018 12 17; 9(1):5353. View in: PubMed

  30. Roguet A, Eren AM, Newton RJ, McLellan SL. Fecal source identification using random forest. Microbiome. 2018 10 18; 6(1):185. View in: PubMed

  31. Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018 Aug; 3(8):963. View in: PubMed

  32. Miyoshi J, Leone V, Nobutani K, Musch MW, Martinez-Guryn K, Wang Y, Miyoshi S, Bobe AM, Eren AM, Chang EB. Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome. PeerJ. 2018; 6:e5166. View in: PubMed

  33. Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018 07; 3(7):804-813. View in: PubMed

  34. McIntosh CM, Chen L, Shaiber A, Eren AM, Alegre ML. Gut microbes contribute to variation in solid organ transplant outcomes in mice. Microbiome. 2018 05 25; 6(1):96. View in: PubMed

  35. Meisel M, Hinterleitner R, Pacis A, Chen L, Earley ZM, Mayassi T, Pierre JF, Ernest JD, Galipeau HJ, Thuille N, Bouziat R, Buscarlet M, Ringus DL, Wang Y, Li Y, Dinh V, Kim SM, McDonald BD, Zurenski MA, Musch MW, Furtado GC, Lira SA, Baier G, Chang EB, Eren AM, Weber CR, Busque L, Godley LA, Verdú EF, Barreiro LB, Jabri B. Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host. Nature. 2018 05; 557(7706):580-584. View in: PubMed

  36. Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ. 2018; 6:e4320. View in: PubMed

  37. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 02 06; 36(2):196. View in: PubMed

  38. Courtine D, Alain K, Georges M, Bienvenu N, Morrison HG, Eren AM, Maignien L. Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N. Genome Announc. 2017 Dec 14; 5(50). View in: PubMed

  39. Delmont TO, Eren AM. Simulations predict microbial responses in the environment? This environment disagrees retrospectively. Proc Natl Acad Sci U S A. 2017 10 24; 114(43):E8947-E8949. View in: PubMed

  40. Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun. 2017 10 24; 8(1):1114. View in: PubMed

  41. Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM. DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biol. 2017 09 21; 18(1):181. View in: PubMed

  42. Miyoshi J, Bobe AM, Miyoshi S, Huang Y, Hubert N, Delmont TO, Eren AM, Leone V, Chang EB. Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring. Cell Rep. 2017 07 11; 20(2):491-504. View in: PubMed

  43. Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM. Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics. Microbiome. 2017 05 04; 5(1):50. View in: PubMed

  44. Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D. A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment. Front Microbiol. 2017; 8:264. View in: PubMed

  45. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 Feb 13. View in: PubMed

  46. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 03; 23(3):366-378. View in: PubMed

  47. Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML. Patient-Specific Bacteroides Genome Variants in Pouchitis. mBio. 2016 11 15; 7(6). View in: PubMed

  48. Eren AM, Sogin ML, Maignien L. Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation. Front Microbiol. 2016; 7:1318. View in: PubMed

  49. Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev. 2016 09; 40(5):686-700. View in: PubMed

  50. Zozaya M, Ferris MJ, Siren JD, Lillis R, Myers L, Nsuami MJ, Eren AM, Brown J, Taylor CM, Martin DH. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome. 2016 Apr 19; 4:16. View in: PubMed

  51. Delmont TO, Eren AM. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ. 2016; 4:e1839. View in: PubMed

  52. Delmont TO, Eren AM, Vineis JH, Post AF. Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Front Microbiol. 2015; 6:1090. View in: PubMed

  53. Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K. Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition. Am J Gastroenterol. 2015 Dec; 110(12):1718-29; quiz 1730. View in: PubMed

  54. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ. 2015; 3:e1319. View in: PubMed

  55. Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL. Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups. Appl Environ Microbiol. 2015 Oct; 81(20):7023-33. View in: PubMed

  56. Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol. 2015; 6:358. View in: PubMed

  57. Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, Walter J. The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015 Apr 28; 11(4):527-38. View in: PubMed

  58. Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML. Sewage reflects the microbiomes of human populations. mBio. 2015 Feb 24; 6(2):e02574. View in: PubMed

  59. Mark Welch JL, Utter DR, Rossetti BJ, Mark Welch DB, Eren AM, Borisy GG. Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Front Microbiol. 2014; 5:568. View in: PubMed

  60. Koskey AM, Fisher JC, Eren AM, Ponce-Terashima R, Reis MG, Blanton RE, McLellan SL. Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters. Environ Microbiol Rep. 2014 Dec; 6(6):696-704. View in: PubMed

  61. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2015 Mar 17; 9(4):968-79. View in: PubMed

  62. McLellan SL, Eren AM. Discovering new indicators of fecal pollution. Trends Microbiol. 2014 Dec; 22(12):697-706. View in: PubMed

  63. Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci U S A. 2014 Jul 15; 111(28):E2875-84. View in: PubMed

  64. Eren AM, Sogin ML, Morrison HG, Vineis JH, Fisher JC, Newton RJ, McLellan SL. A single genus in the gut microbiome reflects host preference and specificity. ISME J. 2015 Jan; 9(1):90-100. View in: PubMed

  65. Fischer AH, Mozzherin D, Eren AM, Lans KD, Wilson N, Cosentino C, Smith J. SeaBase: a multispecies transcriptomic resource and platform for gene network inference. Integr Comp Biol. 2014 Jul; 54(2):250-63. View in: PubMed

  66. Apprill A, Robbins J, Eren AM, Pack AA, Reveillaud J, Mattila D, Moore M, Niemeyer M, Moore KM, Mincer TJ. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? PLoS One. 2014; 9(3):e90785. View in: PubMed

  67. Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics. 2014 Feb 05; 15:41. View in: PubMed

  68. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 2013 Mar 04; 1(1):9. View in: PubMed

  69. Maignien L, DeForce EA, Chafee ME, Eren AM, Simmons SL. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. mBio. 2014 Jan 21; 5(1):e00682-13. View in: PubMed

  70. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 2013 Dec 01; 4(12). View in: PubMed

  71. Eren AM, Vineis JH, Morrison HG, Sogin ML. A filtering method to generate high quality short reads using illumina paired-end technology. PLoS One. 2013; 8(6):e66643. View in: PubMed

  72. Eren AM, Morrison HG, Huse SM, Sogin ML. DRISEE overestimates errors in metagenomic sequencing data. Brief Bioinform. 2014 Sep; 15(5):783-7. View in: PubMed

  73. McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML. Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol. 2013 Aug; 15(8):2213-27. View in: PubMed

  74. Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ. Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. PLoS One. 2011; 6(10):e26732. View in: PubMed
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