My Bibliography

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Guimond AJ, Ke S, Tworoger SS, Huang T, Chan AT, Kubzansky LD, Liu YY. Fulfilled mind, healthy gut? Relationships of eudaimonic psychological well-being with the gut microbiome in postmenopausal women. Psychosom Med. 2024 Jan 15;. doi: 10.1097/PSY.0000000000001278. [Epub ahead of print] PubMed PMID: 38345311; NIHMSID:NIHMS1955071.

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Carson WK, Baumert JL, Clarke JL, Izard J. Small bowel stomas are associated with higher risk of circulating food-specific-IgG than patients with organic gastrointestinal conditions and colostomies. BMJ Open Gastroenterol. 2022 Jul;9(1). doi: 10.1136/bmjgast-2022-000906. PubMed PMID: 35790301; PubMed Central PMCID: PMC9258506.

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Nguyen LH, Cao Y, Hur J, Mehta RS, Sikavi DR, Wang Y, Ma W, Wu K, Song M, Giovannucci EL, Rimm EB, Willett WC, Garrett WS, Izard J, Huttenhower C, Chan AT. The Sulfur Microbial Diet Is Associated With Increased Risk of Early-Onset Colorectal Cancer Precursors. Gastroenterology. 2021 Nov;161(5):1423-1432.e4. doi: 10.1053/j.gastro.2021.07.008. Epub 2021 Jul 14. PubMed PMID: 34273347; PubMed Central PMCID: PMC8545755.

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Whisenhunt LA, Xu LH, Yang F, Izard J. Output consistency scale to standardize ostomate output description in clinical practice and studies. Academic Journal of Gastroenterology & Hepatology. 2021 October; 3(1):AJGH.MS.ID.000554.

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Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT. The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Clin Transl Gastroenterol. 2021 Aug 1;12(8):e00338. doi: 10.14309/ctg.0000000000000338. PubMed PMID: 34333506; PubMed Central PMCID: PMC8323793.

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Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT. Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Genome Med. 2021 Jun 17;13(1):102. doi: 10.1186/s13073-021-00921-y. PubMed PMID: 34140026; PubMed Central PMCID: PMC8212460.

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Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc. 2021 Jun;16(6):2724-2731. doi: 10.1038/s41596-021-00519-z. Epub 2021 Apr 21. Review. PubMed PMID: 33883746; PubMed Central PMCID: PMC9240631.

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Izard J, Gerbaba TK, Yumul SR. Three-dimensional printing of human microbiome constituents to understand spatial relationships and shape parameters in bacteriology. The American Biology Teacher. 2021 March; 83(3):188-190. doi: https://doi.org/10.1525/abt.2021.83.3.188.

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Chung M, Zhao N, Meier R, Koestler DC, Wu G, de Castillo E, Paster BJ, Charpentier K, Izard J, Kelsey KT, Michaud DS. Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases. J Oral Microbiol. 2021 Feb 14;13(1):1887680. doi: 10.1080/20002297.2021.1887680. PubMed PMID: 33628398; PubMed Central PMCID: PMC7889162.

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Peter S, Pendergraft A, VanDerPol W, Wilcox CM, Kyanam Kabir Baig KR, Morrow C, Izard J, Mannon PJ. Mucosa-Associated Microbiota in Barrett's Esophagus, Dysplasia, and Esophageal Adenocarcinoma Differ Similarly Compared With Healthy Controls. Clin Transl Gastroenterol. 2020 Aug;11(8):e00199. doi: 10.14309/ctg.0000000000000199. PubMed PMID: 32955191; PubMed Central PMCID: PMC7473866.

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Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. 2020 Apr;158(5):1313-1325. doi: 10.1053/j.gastro.2019.12.029. Epub 2020 Jan 20. PubMed PMID: 31972239; PubMed Central PMCID: PMC7384232.

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Ivey KL, Chan AT, Izard J, Cassidy A, Rogers GB, Rimm EB. Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. mBio. 2019 Sep 24;10(5). doi: 10.1128/mBio.01205-19. PubMed PMID: 31551328; PubMed Central PMCID: PMC6759757.

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Del Castillo E, Meier R, Chung M, Koestler DC, Chen T, Paster BJ, Charpentier KP, Kelsey KT, Izard J, Michaud DS. The Microbiomes of Pancreatic and Duodenum Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects. Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):370-383. doi: 10.1158/1055-9965.EPI-18-0542. Epub 2018 Oct 29. PubMed PMID: 30373903; PubMed Central PMCID: PMC6363867.

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Cao Y, Wu K, Mehta R, Drew DA, Song M, Lochhead P, Nguyen LH, Izard J, Fuchs CS, Garrett WS, Huttenhower C, Ogino S, Giovannucci EL, Chan AT. Long-term use of antibiotics and risk of colorectal adenoma. Gut. 2018 Apr;67(4):672-678. doi: 10.1136/gutjnl-2016-313413. Epub 2017 Apr 4. PubMed PMID: 28377387; PubMed Central PMCID: PMC5628103.

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Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm EB, Izard J, Huttenhower C, Chan AT. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018 Mar;3(3):347-355. doi: 10.1038/s41564-017-0096-0. Epub 2018 Jan 15. PubMed PMID: 29335554; PubMed Central PMCID: PMC6016839.

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Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol. 2018 Mar;3(3):356-366. doi: 10.1038/s41564-017-0084-4. Epub 2018 Jan 15. PubMed PMID: 29335555; PubMed Central PMCID: PMC6557121.

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Thomas S, Izard J, Walsh E, Batich K, Chongsathidkiet P, Clarke G, Sela DA, Muller AJ, Mullin JM, Albert K, Gilligan JP, DiGuilio K, Dilbarova R, Alexander W, Prendergast GC. The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists. Cancer Res. 2017 Apr 15;77(8):1783-1812. doi: 10.1158/0008-5472.CAN-16-2929. Epub 2017 Mar 14. Review. PubMed PMID: 28292977; PubMed Central PMCID: PMC5392374.

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Drew DA, Lochhead P, Abu-Ali G, Chan AT, Huttenhower C, Izard J. Fecal Microbiome in Epidemiologic Studies-Letter. Cancer Epidemiol Biomarkers Prev. 2016 May;25(5):869. doi: 10.1158/1055-9965.EPI-16-0063. Epub 2016 Mar 9. PubMed PMID: 26961995; PubMed Central PMCID: PMC4898650.

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Lačević A, Foschi F, Pojskić L, Pojskić N, Bajrović K, Izard J. Correlation of periodontal pathogens in concurrent endodontic-periodontal diseases. Archives of Oral and Dental Research. 2015 September; 2:4.

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Izard J. Steps in metagenomics: let’s avoid garbage in and garbage out.. In: Izard J, Rivera MC, editors. Metagenomics for Microbiology Boston, MA, USA: Academic Press/Elsevier; 2015. p.1-23.

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del Castillo E, Izard J. Metagenomics for bacteriology. In: Izard J, Rivera MC, editors. Metagenomics for Microbiology. Izard J, Rivera MC, editors. Boston, MA, USA: Academic Press/Elsevier; 2015. Metagenomics for bacteriology; p.115-134 Boston, MA, USA: Academic Press/Elsevier; 2015. p.115-134.

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Rivera MC, Izard J. Promises and prospects of microbiome studies. In: Izard J, Rivera MC, editors. Metagenomics for Microbiology. Boston, MA, USA: Academic Press/Elsevier; 2015. p.145-159.

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Izard J, Rivera MC. Izard J, Rivera MC, editors. Metagenomics for Microbiology. Izard J, Rivera MC, editors. Boston, MA, USA: Academic Press/Elsevier; 2015. Boston, MA, USA: Academic Press/Elsevier; 2015.

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Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022. PubMed PMID: 25303518; PubMed Central PMCID: PMC4221798.

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Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19. PubMed PMID: 24843156; PubMed Central PMCID: PMC4050606.

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Michaud DS, Izard J. Microbiota, oral microbiome, and pancreatic cancer. Cancer J. 2014 May-Jun;20(3):203-6. doi: 10.1097/PPO.0000000000000046. Review. PubMed PMID: 24855008; PubMed Central PMCID: PMC4160879.

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Boylan MR, Khalili H, Huang ES, Michaud DS, Izard J, Joshipura KJ, Chan AT. A prospective study of periodontal disease and risk of gastric and duodenal ulcer in male health professionals. Clin Transl Gastroenterol. 2014 Feb 13;5(2):e49. doi: 10.1038/ctg.2013.14. PubMed PMID: 24522171; PubMed Central PMCID: PMC3940834.

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Zimmerman N, Izard J, Klatt CG, Zhou J, Aronson EL. The unseen world: environmental microbial sequencing and identification methods for ecologists. Frontiers in ecology and the environment. 2014; 12(4):224-231. Frontiers in ecology and the environment. 2014; 12(4):224-231. doi: 10.1890/130055.

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Michaud DS, Izard J, Wilhelm-Benartzi CS, You DH, Grote VA, Tjønneland A, Dahm CC, Overvad K, Jenab M, Fedirko V, Boutron-Ruault MC, Clavel-Chapelon F, Racine A, Kaaks R, Boeing H, Foerster J, Trichopoulou A, Lagiou P, Trichopoulos D, Sacerdote C, Sieri S, Palli D, Tumino R, Panico S, Siersema PD, Peeters PH, Lund E, Barricarte A, Huerta JM, Molina-Montes E, Dorronsoro M, Quirós JR, Duell EJ, Ye W, Sund M, Lindkvist B, Johansen D, Khaw KT, Wareham N, Travis RC, Vineis P, Bueno-de-Mesquita HB, Riboli E. Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large European prospective cohort study. Gut. 2013 Dec;62(12):1764-70. doi: 10.1136/gutjnl-2012-303006. Epub 2012 Sep 18. PubMed PMID: 22990306; PubMed Central PMCID: PMC3815505.

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Michaud DS, Izard J, Rubin Z, Johansson I, Weiderpass E, Tjønneland A, Olsen A, Overvad K, Boutron-Ruault MC, Clavel-Chapelon F, Dossus L, Kaaks R, Katzke VA, Boeing H, Foerster J, Trichopoulou A, Naska A, Ziara G, Vineis P, Grioni S, Palli D, Tumino R, Mattiello A, Peeters PH, Siersema PD, Barricarte A, Huerta JM, Molina-Montes E, Dorronsoro M, Quirós JR, Duell EJ, Ohlsson B, Jeppsson B, Johansson A, Lif P, Khaw KT, Wareham N, Travis RC, Key TJ, Freisling H, Duarte-Salles T, Stepien M, Riboli E, Bueno-de-Mesquita HB. Lifestyle, dietary factors, and antibody levels to oral bacteria in cancer-free participants of a European cohort study. Cancer Causes Control. 2013 Nov;24(11):1901-9. doi: 10.1007/s10552-013-0265-2. Epub 2013 Jul 31. PubMed PMID: 23901020; PubMed Central PMCID: PMC3823529.

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Wolfgang WJ, Passaretti TV, Jose R, Cole J, Coorevits A, Carpenter AN, Jose S, Van Landschoot A, Izard J, Kohlerschmidt DJ, Vandamme P, Dewhirst FE, Fisher MA, Musser KA. Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples. Int J Syst Evol Microbiol. 2013 Apr;63(Pt 4):1323-1328. doi: 10.1099/ijs.0.041731-0. Epub 2012 Jul 13. PubMed PMID: 22798652; PubMed Central PMCID: PMC3709538.

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Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 2012;8(7):e1002606. doi: 10.1371/journal.pcbi.1002606. Epub 2012 Jul 12. PubMed PMID: 22807668; PubMed Central PMCID: PMC3395616.

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Izard J, Sasaki H, Kent R. Pathogenicity of Treponema denticola Wild-Type and Mutant Strain Tested by an Active Mode of Periodontal Infection Using Microinjection. Int J Dent. 2012;2012:549169. doi: 10.1155/2012/549169. Epub 2012 Jul 5. PubMed PMID: 22829826; PubMed Central PMCID: PMC3398590.

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Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012 Jun 14;13(6):R42. doi: 10.1186/gb-2012-13-6-r42. PubMed PMID: 22698087; PubMed Central PMCID: PMC3446314.

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Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8(6):e1002358. doi: 10.1371/journal.pcbi.1002358. Epub 2012 Jun 13. PubMed PMID: 22719234; PubMed Central PMCID: PMC3374609.

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A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. PubMed PMID: 22699610; PubMed Central PMCID: PMC3377744.

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Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. PubMed PMID: 22699609; PubMed Central PMCID: PMC3564958.

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Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23. PubMed PMID: 22455878; PubMed Central PMCID: PMC3439974.

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Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011 Jun 24;12(6):R60. doi: 10.1186/gb-2011-12-6-r60. PubMed PMID: 21702898; PubMed Central PMCID: PMC3218848.

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Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. The human oral microbiome. J Bacteriol. 2010 Oct;192(19):5002-17. doi: 10.1128/JB.00542-10. Epub 2010 Jul 23. PubMed PMID: 20656903; PubMed Central PMCID: PMC2944498.

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Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford). 2010 Jul 6;2010:baq013. doi: 10.1093/database/baq013. PubMed PMID: 20624719; PubMed Central PMCID: PMC2911848.

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Gaibani P, Vocale C, Ambretti S, Cavrini F, Izard J, Miragliotta L, Pellegrino MT, Sambri V. Killing of Treponema denticola by mouse peritoneal macrophages. J Dent Res. 2010 May;89(5):521-6. doi: 10.1177/0022034510363105. Epub 2010 Mar 3. PubMed PMID: 20200417; PubMed Central PMCID: PMC2868591.

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The-Forsyth-Metagenomic-Support-Consortium, Izard J. Building the genomic base-layer of the oral “omic” world. In: Sasano T, Suzuki O, editors. Interface Oral Health Science 2009 Tokyo, Japan: Springer; 2010.

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Izard J, Renken C, Hsieh CE, Desrosiers DC, Dunham-Ems S, La Vake C, Gebhardt LL, Limberger RJ, Cox DL, Marko M, Radolf JD. Cryo-electron tomography elucidates the molecular architecture of Treponema pallidum, the syphilis spirochete. J Bacteriol. 2009 Dec;191(24):7566-80. doi: 10.1128/JB.01031-09. Epub 2009 Oct 9. PubMed PMID: 19820083; PubMed Central PMCID: PMC2786590.

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Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, Sutcliffe IC, Wade WG. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int J Syst Evol Microbiol. 2009 May;59(Pt 5):972-80. doi: 10.1099/ijs.0.000364-0. PubMed PMID: 19406777; PubMed Central PMCID: PMC2868594.

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Izard J, Hsieh CE, Limberger RJ, Mannella CA, Marko M. Native cellular architecture of Treponema denticola revealed by cryo-electron tomography. J Struct Biol. 2008 Jul;163(1):10-7. doi: 10.1016/j.jsb.2008.03.009. Epub 2008 Mar 28. PubMed PMID: 18468917; PubMed Central PMCID: PMC2519799.

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Foschi F, Izard J, Sasaki H, Sambri V, Prati C, Müller R, Stashenko P. Treponema denticola in disseminating endodontic infections. J Dent Res. 2006 Aug;85(8):761-5. doi: 10.1177/154405910608500814. PubMed PMID: 16861296; PubMed Central PMCID: PMC3579618.

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Izard J, Limberger RJ. Structural and genomic features of treponemal architecture. In: Radolf J, Lukehart SA, editors. Treponema molecular and cellular biology USA: Horizon Bioscience; 2006.

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Tanner AC, Izard J. Tannerella forsythia, a periodontal pathogen entering the genomic era. Periodontol 2000. 2006;42:88-113. doi: 10.1111/j.1600-0757.2006.00184.x. Review. PubMed PMID: 16930308.

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Izard J. Cytoskeletal cytoplasmic filament ribbon of Treponema: a member of an intermediate-like filament protein family. J Mol Microbiol Biotechnol. 2006;11(3-5):159-66. doi: 10.1159/000094052. Review. PubMed PMID: 16983193.