Peter Turnbaugh, PhD

Title(s)Professor, Microbiology and Immunology
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSW, #1529
San Francisco CA 94143
Phone415-502-3237
PronounsHe/Him/His
ORCID ORCID Icon0000-0002-0888-2875 Additional info
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    Collapse Biography 
    Collapse education and training
    Whitman College, Walla Walla, WAB.A.05/2003Biochemistry, Biophysics, and Molecular Biology
    Washington University in Saint Louis, St. Louis, MOPh.D.05/2009Molecular Genetics and Genomics
    University of California, San Francisco, CA09/2020Diversity, Equity, and Inclusion Champion Training
    Collapse awards and honors
    1999National Merit Scholar
    2006  - 2009NSF Graduate Fellowship
    2009David Kipnis Award in Biomedical Sciences
    2010Philip Needleman Pharmacology Prize
    2015Young Investigator Grant for Probiotics Research
    2016Damon Runyon-Rachleff Cancer Innovator
    2016Searle Scholar
    2017CZ Biohub Investigator
    2018ASM Young Investigator Award
    Burroughs Wellcome Fund2018Investigators in the Pathogenesis of Infectious Disease

    Collapse Overview 
    Collapse overview
    I lead an interdisciplinary group of microbiome researchers committed to understanding host-associated microbes, reducing these complex microbial ecologies to molecular mechanism, and applying these lessons to improve the practice of medicine. Our three major topics of interest right now are pharmacology, nutrition, and phage biology. While we love sequencing and gnotobiotic mice, our work is question-driven not limited to a specific approach. Prior studies have ranged from the molecular (e.g., biochemistry, bacterial genetics, structural biology) to the organismal (e.g., gnotobiotic mice, conventional animals, and clinical trials) to the ecological (e.g., synthetic microbial communities and metagenomic sequencing). We embrace high-risk, high-reward projects and thrive on collaboration.

    Collapse Research 
    Collapse research activities and funding
    Establishing the feasibility of editing the human gut microbiome
    NIH R01AT011117Aug 1, 2020 - Jul 31, 2024
    Role: Principal Investigator
    Host-microbiome interactions shape the metabolic effects of ketogenic diets
    NIH R01DK114034Jul 1, 2020 - Mar 31, 2025
    Role: Principal Investigator
    Employing the gut microbiome to accelerate effective initiation of rheumatoid arthritis therapy
    NIH R01AR074500Sep 1, 2019 - Aug 31, 2024
    Role: Co-Principal Investigator
    (PQ10) Harnessing the human gut microbiome to predict chemotherapy outcomes
    NIH R21CA227232Jun 21, 2018 - May 31, 2021
    Role: Principal Investigator
    Predicting and preventing drug metabolism by the human gut microbiome
    NIH R01HL122593Mar 1, 2016 - Jul 31, 2025
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Featured Content 
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Microbiome Single Cell Atlases Generated with a Commercial Instrument. Adv Sci (Weinh). 2025 Jun 03; e2409338. Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. PMID: 40462354.
      View in: PubMed   Mentions:
    2. Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity. mBio. 2025 May 20; e0093025. Hillege LE, Trepka KR, Guthrie BGH, Fu X, Aarnoutse R, Paymar MR, Olson C, Zhang C, Ortega E, Ramirez L, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Smidt ML, Ziemons J, Turnbaugh PJ. PMID: 40391895.
      View in: PubMed   Mentions:    Fields:    
    3. Gut Bacterial Lactic Acid Stimulates Lung Epithelial Mitochondria and Exacerbates Acute Lung Injury. American Journal of Respiratory and Critical Care Medicine. 2025 May 1; 211(Abstracts):a5186-a5186. Upadhyay UV, Kaur KG, Ortega OE, Trepka TK, Rock RR, Ramirez Hernandez RL, Cheshire CW, Alipanah-Lechner AN, Calfee CC, Matthay MM, Blume BS, Jain JI, Turnbaugh TP. .
      View in: Publisher Site   Mentions:
    4. Gut Bacterial Lactic Acid Stimulates Lung Epithelial Mitochondria and Exacerbates Acute Lung Injury. American Journal of Respiratory and Critical Care Medicine. 2025 May 1; 211(Abstracts):a5186-a5186. Upadhyay UV, Kaur KG, Ortega OE, Trepka TK, Rock RR, Ramirez Hernandez RL, Cheshire CW, Alipanah-Lechner AN, Calfee CC, Matthay MM, Blume BS, Jain JI, Turnbaugh TP. .
      View in: Publisher Site   Mentions:
    5. Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity. Sci Transl Med. 2025 Apr 16; 17(794):eadq8870. Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. PMID: 40238917; PMCID: PMC12087798.
      View in: PubMed   Mentions: 1     Fields:    
    6. Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury. bioRxiv. 2025 Mar 25. Upadhyay V, Ortega EF, Ramirez Hernandez LA, Alexander M, Kaur G, Trepka K, Rock RR, Shima RT, Cheshire WC, Alipanah-Lechner N, Calfee CS, Matthay MA, Lee JV, Goga A, Jain IH, Turnbaugh PJ. PMID: 40196632; PMCID: PMC11974820.
      View in: PubMed   Mentions:
    7. Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response. Annu Rev Pharmacol Toxicol. 2025 Jan; 65(1):355-373. Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ. PMID: 39107044; PMCID: PMC11864876.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    8. Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states. bioRxiv. 2024 Dec 03. Babdor J, Patel RK, Davidson B, Noecker C, Rahim M, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy E, Shaheed A, Ekstrand C, Weakley AM, Yu FB, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH. PMID: 39677657; PMCID: PMC11642739.
      View in: PubMed   Mentions:
    9. Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome. bioRxiv. 2024 Nov 08. Rendina M, Turnbaugh PJ, Bradley PH. PMID: 39574613; PMCID: PMC11580864.
      View in: PubMed   Mentions:
    10. A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. Cell Rep. 2024 11 26; 43(11):114891. Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ. PMID: 39500329; PMCID: PMC11660937.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    11. Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme. Cell Host Microbe. 2024 Nov 13; 32(11):1887-1896.e8. Bae M, Le C, Mehta RS, Dong X, Pieper LM, Ramirez L, Alexander M, Kiamehr S, Turnbaugh PJ, Huttenhower C, Chan AT, Balskus EP. PMID: 39471822; PMCID: PMC11585353.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    12. Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients. medRxiv. 2024 Oct 15. Hillege LE, Trepka KR, Ziemons J, Aarnoutse R, Guthrie BGH, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Turnbaugh PJ, Smidt ML. PMID: 39484258; PMCID: PMC11527039.
      View in: PubMed   Mentions:
    13. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. bioRxiv. 2024 Oct 15. Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. PMID: 38895199; PMCID: PMC11185696.
      View in: PubMed   Mentions:
    14. Rationale and protocol for a safety, tolerability and feasibility randomized, parallel arm, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms. PLoS One. 2024; 19(9):e0307951. Stubbs BJ, Alvarez Azañedo G, Peralta S, Diaz SR, Gray W, Alexander L, Silverman-Martin W, Garcia TY, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC. PMID: 39292659; PMCID: PMC11410252.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCTClinical Trials
    15. Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice. Environ Health Perspect. 2024 Aug; 132(8):87005. Tian Y, Rimal B, Bisanz JE, Gui W, Wolfe TM, Koo I, Murray IA, Nettleford SK, Yokoyama S, Dong F, Koshkin S, Prabhu KS, Turnbaugh PJ, Walk ST, Perdew GH, Patterson AD. PMID: 39140734; PMCID: PMC11323762.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    16. Digesting the complex metabolic effects of diet on the host and microbiome. Cell. 2024 Jul 25; 187(15):3857-3876. Carmody RN, Varady K, Turnbaugh PJ. PMID: 39059362; PMCID: PMC11309583.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    17. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab. 2024 Jul; 6(7):1225-1236. Noecker C, Turnbaugh PJ. PMID: 38961185.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    18. Short-Term Caloric Restriction Alters the Microbiome Modulating Resistance to Clostridioides difficile Infection. Current Developments in Nutrition. 2024 Jul 1; 8:103447. Zhao ZJ, Sandforth SA, Tian TS, Turnbaugh TP, Von Schwartzenberg VR, Bisanz BJ. .
      View in: Publisher Site   Mentions:
    19. Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice. JBMR Plus. 2024 Aug; 8(8):ziae082. Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ. PMID: 39011468; PMCID: PMC11247189.
      View in: PubMed   Mentions:
    20. Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors. iScience. 2024 Jun 21; 27(6):110122. Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJN, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ. PMID: 38947502; PMCID: PMC11214321.
      View in: PubMed   Mentions: 6  
    21. Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas. Cell. 2024 Jun 06; 187(12):2952-2968.e13. McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS. PMID: 38795705; PMCID: PMC11179439.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    22. A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. bioRxiv. 2024 May 13. Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ. PMID: 37961209; PMCID: PMC10635093.
      View in: PubMed   Mentions:
    23. Microbiome single cell atlases generated with a commercial instrument. bioRxiv. 2024 Mar 16. Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. PMID: 37609281; PMCID: PMC10441329.
      View in: PubMed   Mentions: 1  
    24. High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota. Cell. 2024 Feb 29; 187(5):1191-1205.e15. Lee JY, Tiffany CR, Mahan SP, Kellom M, Rogers AWL, Nguyen H, Stevens ET, Masson HLP, Yamazaki K, Marco ML, Eloe-Fadrosh EA, Turnbaugh PJ, Bäumler AJ. PMID: 38366592; PMCID: PMC11023689.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    25. Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female mice. bioRxiv. 2024 Jan 03. Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ. PMID: 38260245; PMCID: PMC10802297.
      View in: PubMed   Mentions:
    26. Rationale and protocol for a safety, tolerability and feasibility randomized, parallel group, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms. medRxiv. 2023 Oct 26. Stubbs BJ, Alvarez-Azanedo G, Peralta S, Roa-Diaz S, Gray W, Alexander L, Silverman-Martin W, Garcia T, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC. PMID: 37961234; PMCID: PMC10635199.
      View in: PubMed   Mentions:
    27. Simvastatin induces human gut bacterial cell surface genes. Mol Microbiol. 2024 09; 122(3):372-386. Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ. PMID: 37712143; PMCID: PMC10940213.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    28. Microbiome single cell atlases generated with a commercial instrument. Res Sq. 2023 Sep 14. Abate A, Li X, Xu L, Demaree B, Noecker C, Bisanz J, Weisgerber D, Modavi C, Turnbaugh P. PMID: 37790580; PMCID: PMC10543498.
      View in: PubMed   Mentions:
    29. Associations between the Gut Microbiota, Race, and Ethnicity of Patients with Colorectal Cancer: A Pilot and Feasibility Study. Cancers (Basel). 2023 Sep 13; 15(18). Piawah S, Kyaw TS, Trepka K, Stewart AL, Mora RV, Stanfield D, Levine K, Van Blarigan EL, Venook A, Turnbaugh PJ, Nguyen T, Atreya CE. PMID: 37760515; PMCID: PMC10526839.
      View in: PubMed   Mentions: 3  
    30. The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli. mBio. 2023 Oct 31; 14(5):e0157323. Pieper LM, Spanogiannopoulos P, Volk RF, Miller CJ, Wright AT, Turnbaugh PJ. PMID: 37642463; PMCID: PMC10653809.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    31. Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors. Am J Clin Nutr. 2023 09; 118(3):518-529. Kyaw TS, Upadhyay V, Tolstykh I, Van Loon K, Laffan A, Stanfield D, Gempis D, Kenfield SA, Chan JM, Piawah S, Atreya CE, Ng K, Venook A, Kidder W, Turnbaugh PJ, Van Blarigan EL. PMID: 37474105; PMCID: PMC10550847.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    32. SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations. Elife. 2023 Jun 12; 12. Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS. PMID: 37306300; PMCID: PMC10289814.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    33. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio. 2023 08 31; 14(4):e0088923. Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. PMID: 37294090; PMCID: PMC10470529.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    34. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol. 2023 05; 21(5):e3002125. Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. PMID: 37205710; PMCID: PMC10234575.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    35. Forging the microbiome to help us live long and prosper. PLoS Biol. 2023 04; 21(4):e3002087. Rock RR, Turnbaugh PJ. PMID: 37018375; PMCID: PMC10109465.
      View in: PubMed   Mentions: 2     Fields:    
    36. Early-life exposure to a potent Aryl hydrocarbon receptor ligand results in persistent changes to the microbiota and host glucose homeostasis. . 2023 Apr 1. Tian TY, Rimal RB, Bisanz BJ, Gui GW, Wolfe WT, Koo KI, Murray MI, Nettleford NS, Yokoyama YS, Dong DF, Prabhu PK, Turnbaugh TP, Walk WS, Perdew PG, Patterson PA. .
      View in: Publisher Site   Mentions:
    37. Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nat Commun. 2022 Dec 09; 13(1):7624. Dong X, Guthrie BGH, Alexander M, Noecker C, Ramirez L, Glasser NR, Turnbaugh PJ, Balskus EP. PMID: 36494336; PMCID: PMC9734109.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    38. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv. 2022 Dec 08. Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. PMID: 36523400; PMCID: PMC9753784.
      View in: PubMed   Mentions: 2  
    39. nicX-ing bad habits with your microbial friends. Nat Metab. 2022 11; 4(11):1442-1443. Upadhyay V, Turnbaugh PJ. PMID: 36333489.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    40. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol. 2022 10; 7(10):1605-1620. Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ. PMID: 36138165; PMCID: PMC9530025.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    41. Tiny Gatekeepers: Microbial Control of Host Drug Transporters. Clin Pharmacol Ther. 2022 09; 112(3):443-445. Kyaw TS, Turnbaugh PJ. PMID: 35668713; PMCID: PMC9540778.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    42. Designed secretion deters microbiome depletion. Nat Microbiol. 2022 06; 7(6):745-746. Olson CA, Turnbaugh PJ. PMID: 35606423.
      View in: PubMed   Mentions:    Fields:    
    43. The tiny pharmacists within: How the microbiome impacts the treatment of human disease. The FASEB Journal. 2022 May 13; 36(S1). Turnbaugh TP. .
      View in: Publisher Site   Mentions:
    44. Fluoropyrimidine Bioactivation and Metabolism by the Gut Microbiome. The FASEB Journal. 2022 May 13; 36(S1). Guthrie GB, Turnbaugh TP. .
      View in: Publisher Site   Mentions:
    45. Tu1517: MICROBIAL SIGNALS, MYD88, AND LYMPHOTOXIN DRIVE TNFINDEPENDENT DEATH OF A20 AND ABIN-1 DEFICIENT EPITHELIUM. Gastroenterology. 2022 May 1; 162(7):s-995. Rusu RI, Mennillo ME, Bain BJ, Li LZ, Sun SX, Ly LK, Rosli RY, Naser NM, Wang WZ, Advincula AR, Achacoso AP, Shao SL, Razani RB, Klein KO, Marson MA, Turnbaugh TJ, Turnbaugh TP, Malynn MB, Ma MA, Kattah KM. .
      View in: Publisher Site   Mentions:
    46. Effects of caloric restriction on the gut microbiome are linked with immune senescence. Microbiome. 2022 04 04; 10(1):57. Sbierski-Kind J, Grenkowitz S, Schlickeiser S, Sandforth A, Friedrich M, Kunkel D, Glauben R, Brachs S, Mai K, Thürmer A, Radonic A, Drechsel O, Turnbaugh PJ, Bisanz JE, Volk HD, Spranger J, von Schwartzenberg RJ. PMID: 35379337; PMCID: PMC8978410.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    47. Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. Nature. 2022 03; 603(7903):907-912. Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS. PMID: 35296854; PMCID: PMC9132548.
      View in: PubMed   Mentions: 192     Fields:    Translation:HumansCells
    48. Synthetic glycans control gut microbiome structure and mitigate colitis in mice. Nat Commun. 2022 03 10; 13(1):1244. Tolonen AC, Beauchemin N, Bayne C, Li L, Tan J, Lee J, Meehan BM, Meisner J, Millet Y, LeBlanc G, Kottler R, Rapp E, Murphy C, Turnbaugh PJ, von Maltzahn G, Liu CM, van Hylckama Vlieg JET. PMID: 35273143; PMCID: PMC8913648.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    49. Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage. J Clin Invest. 2022 03 01; 132(5). Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, Achacoso P, Shao L, Razani B, Klein OD, Marson A, Turnbaugh JA, Turnbaugh PJ, Malynn BA, Ma A, Kattah MG. PMID: 35077396; PMCID: PMC8884902.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    50. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. PMID: 34822777; PMCID: PMC8785648.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansAnimalsCells
    51. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. Mirzayi C, Renson A, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. PMID: 34789871; PMCID: PMC9105086.
      View in: PubMed   Mentions: 147     Fields:    
    52. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Rep. 2021 11 02; 37(5):109930. Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, Turnbaugh PJ. PMID: 34731631; PMCID: PMC8591988.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
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    112. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015 Jan 14; 17(1):72-84. Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. PMID: 25532804; PMCID: PMC4297240.
      View in: PubMed   Mentions: 493     Fields:    Translation:Animals
    113. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013. Microbiome. 2014 Dec 1; 2(1):16. Ravel RJ, Blaser BM, Braun BJ, Brown BE, Bushman BF, Chang CE, Davies DJ, Dewey DK, Dinan DT, Dominguez-Bello DM, Erdman ES, Finlay FB, Garrett GW, Huffnagle HG, Huttenhower HC, Jansson JJ, Jeffery JI, Jobin JC, Khoruts KA, Kong KH, Lampe LJ, Ley LR, Littman LD, Mazmanian MS, Mills MD, Neish NA, Petrof PE, Relman RD, Rhodes RR, Turnbaugh TP, Young YV, Knight KR, White WO. .
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    114. Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature. 2014 Oct 30; 514(7524):638-41. Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV. PMID: 25274297; PMCID: PMC4214913.
      View in: PubMed   Mentions: 243     Fields:    Translation:AnimalsCells
    115. Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology. Cell Metab. 2014 Nov 04; 20(5):761-768. Patterson AD, Turnbaugh PJ. PMID: 25156450; PMCID: PMC4252706.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimals
    116. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J Clin Invest. 2014 Oct; 124(10):4173-81. Carmody RN, Turnbaugh PJ. PMID: 25105361; PMCID: PMC4191041.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansAnimalsCells
    117. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology. 2014 May; 146(6):1470-6. Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R. PMID: 24631493; PMCID: PMC4102302.
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    118. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes. 2014 Mar-Apr; 5(2):233-8. Haiser HJ, Seim KL, Balskus EP, Turnbaugh PJ. PMID: 24637603; PMCID: PMC4063850.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCells
    119. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23; 505(7484):559-63. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. PMID: 24336217; PMCID: PMC3957428.
      View in: PubMed   Mentions: 4212     Fields:    Translation:HumansCellsPHPublic HealthCTClinical Trials
    120. High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions. Nucleic Acids Res. 2013 Dec; 41(22):e205. Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N. PMID: 24214960; PMCID: PMC3905898.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    121. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science. 2013 Jul 19; 341(6143):295-8. Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ. PMID: 23869020; PMCID: PMC3736355.
      View in: PubMed   Mentions: 300     Fields:    Translation:HumansAnimalsCells
    122. Cancer: An acidic link. Nature. 2013 Jul 04; 499(7456):37-8. Devkota S, Turnbaugh PJ. PMID: 23803768.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    123. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Microbiol Rev. 2013 Sep; 37(5):830-48. Maurice CF, Turnbaugh PJ. PMID: 23550823; PMCID: PMC3729610.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    124. Translating the human microbiome. Nat Biotechnol. 2013 Apr; 31(4):304-8. Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. PMID: 23563424.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimals
    125. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med. 2013 Mar 27; 5(178):178ra41. Liou AP, Paziuk M, Luevano JM, Machineni S, Turnbaugh PJ, Kaplan LM. PMID: 23536013; PMCID: PMC3652229.
      View in: PubMed   Mentions: 428     Fields:    Translation:Animals
    126. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013 Jan 17; 152(1-2):39-50. Maurice CF, Haiser HJ, Turnbaugh PJ. PMID: 23332745; PMCID: PMC3552296.
      View in: PubMed   Mentions: 369     Fields:    Translation:HumansCells
    127. Quantifying and identifying the active and damaged subsets of indigenous microbial communities. Methods Enzymol. 2013; 531:91-107. Maurice CF, Turnbaugh PJ. PMID: 24060117.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    128. Antibiotic exposure promotes fat gain. Cell Metab. 2012 Oct 03; 16(4):408-10. Liou AP, Turnbaugh PJ. PMID: 23040064; PMCID: PMC3494989.
      View in: PubMed   Mentions: 2     Fields:    
    129. Gut microbes make for fattier fish. Cell Host Microbe. 2012 Sep 13; 12(3):259-61. Carmody RN, Turnbaugh PJ. PMID: 22980321; PMCID: PMC3888188.
      View in: PubMed   Mentions: 4     Fields:    
    130. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care. 2012 Sep; 15(5):448-54. Dutton RJ, Turnbaugh PJ. PMID: 22878238.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsPHPublic Health
    131. Developing a metagenomic view of xenobiotic metabolism. Pharmacol Res. 2013 Mar; 69(1):21-31. Haiser HJ, Turnbaugh PJ. PMID: 22902524; PMCID: PMC3526672.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansAnimals
    132. Microbiology: fat, bile and gut microbes. Nature. 2012 Jul 04; 487(7405):47-8. Turnbaugh PJ. PMID: 22763552.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    133. Is it time for a metagenomic basis of therapeutics? Science. 2012 Jun 08; 336(6086):1253-5. Haiser HJ, Turnbaugh PJ. PMID: 22674325.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansAnimalsCells
    134. 515 Weight-Independent Changes in Gut Microbial Ecology Regulate Adiposity Following Roux-en-Y Gastric Bypass Surgery in Mice. Gastroenterology. 2012 May 1; 142(5):s-108. Liou LA, Luevano LJ, Turnbaugh TP, Kaplan KL. .
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    135. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):594-9. Greenblum S, Turnbaugh PJ, Borenstein E. PMID: 22184244; PMCID: PMC3258644.
      View in: PubMed   Mentions: 339     Fields:    Translation:Humans
    136. Detecting novel associations in large data sets. Science. 2011 Dec 16; 334(6062):1518-24. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC. PMID: 22174245; PMCID: PMC3325791.
      View in: PubMed   Mentions: 483     Fields:    
    137. Wild immunology: converging on the real world. Ann N Y Acad Sci. 2011 Oct; 1236:17-29. Babayan SA, Allen JE, Bradley JE, Geuking MB, Graham AL, Grencis RK, Kaufman J, McCoy KD, Paterson S, Smith KG, Turnbaugh PJ, Viney ME, Maizels RM, Pedersen AB. PMID: 22032399.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    138. Human health and disease in a microbial world. Front Microbiol. 2011; 2:190. Turnbaugh PJ, Stintzi A. PMID: 21954396; PMCID: PMC3174398.
      View in: PubMed   Mentions: 7  
    139. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr. 2011 Jul; 94(1):58-65. Jumpertz R, Le DS, Turnbaugh PJ, Trinidad C, Bogardus C, Gordon JI, Krakoff J. PMID: 21543530; PMCID: PMC3127503.
      View in: PubMed   Mentions: 529     Fields:    Translation:HumansCellsCTClinical Trials
    140. Companion animals symposium: microbes and health. J Anim Sci. 2011 May; 89(5):1496-7. Swanson KS, Suchodolski JS, Turnbaugh PJ. PMID: 21521817.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    141. Taxonomic metagenome sequence assignment with structured output models. Nat Methods. 2011 Mar; 8(3):191-2. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC. PMID: 21358620; PMCID: PMC3131843.
      View in: PubMed   Mentions: 64     Fields:    
    142. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011 Jan 28; 12:38. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. PMID: 21276213; PMCID: PMC3045300.
      View in: PubMed   Mentions: 583     Fields:    
    143. The mind-body-microbial continuum. Dialogues Clin Neurosci. 2011; 13(1):55-62. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. PMID: 21485746; PMCID: PMC3139398.
      View in: PubMed   Mentions: 50     Fields:    
    144. Companion animals symposium: humanized animal models of the microbiome. J Anim Sci. 2011 May; 89(5):1531-7. Gootenberg DB, Turnbaugh PJ. PMID: 20833767.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
    145. A microbe-dependent viral key to Crohn's box. Sci Transl Med. 2010 Aug 04; 2(43):43ps39. Peterson DA, Turnbaugh PJ. PMID: 20686177.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    146. Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 01; 66(Pt 10):1261-4. Turnbaugh PJ, Henrissat B, Gordon JI. PMID: 20944220; PMCID: PMC2954214.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    147. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4516-22. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. PMID: 20534432; PMCID: PMC3063599.
      View in: PubMed   Mentions: 3412     Fields:    Translation:Cells
    148. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May; 7(5):335-6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. PMID: 20383131; PMCID: PMC3156573.
      View in: PubMed   Mentions: 14032     Fields:    
    149. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7503-8. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI. PMID: 20363958; PMCID: PMC2867707.
      View in: PubMed   Mentions: 215     Fields:    Translation:HumansCells
    150. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009 Nov 11; 1(6):6ra14. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. PMID: 20368178; PMCID: PMC2894525.
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    151. The core gut microbiome, energy balance and obesity. J Physiol. 2009 Sep 01; 587(Pt 17):4153-8. Turnbaugh PJ, Gordon JI. PMID: 19491241; PMCID: PMC2754355.
      View in: PubMed   Mentions: 436     Fields:    Translation:HumansAnimals
    152. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A. 2009 Apr 07; 106(14):5859-64. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. PMID: 19321416; PMCID: PMC2660063.
      View in: PubMed   Mentions: 299     Fields:    Translation:HumansAnimalsCells
    153. A core gut microbiome in obese and lean twins. Nature. 2009 Jan 22; 457(7228):480-4. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. PMID: 19043404; PMCID: PMC2677729.
      View in: PubMed   Mentions: 3374     Fields:    
    154. An invitation to the marriage of metagenomics and metabolomics. Cell. 2008 Sep 05; 134(5):708-13. Turnbaugh PJ, Gordon JI. PMID: 18775300.
      View in: PubMed   Mentions: 90     Fields:    Translation:Humans
    155. Evolution of mammals and their gut microbes. Science. 2008 Jun 20; 320(5883):1647-51. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. PMID: 18497261; PMCID: PMC2649005.
      View in: PubMed   Mentions: 1557     Fields:    
    156. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008 Apr 17; 3(4):213-23. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. PMID: 18407065; PMCID: PMC3687783.
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    157. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008 Feb; 12(1):109-14. Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R. PMID: 18280814; PMCID: PMC2348432.
      View in: PubMed   Mentions: 43     Fields:    
    158. The human microbiome project. Nature. 2007 Oct 18; 449(7164):804-10. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. PMID: 17943116; PMCID: PMC3709439.
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    159. Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21; 444(7122):1022-3. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. PMID: 17183309.
      View in: PubMed   Mentions: 3613     Fields:    Translation:CTClinical Trials
    160. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006 Dec 21; 444(7122):1027-31. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. PMID: 17183312.
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    161. Metagenomic analysis of the human distal gut microbiome. Science. 2006 Jun 02; 312(5778):1355-9. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. PMID: 16741115; PMCID: PMC3027896.
      View in: PubMed   Mentions: 1780     Fields:    
    162. Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Res. 2005 Aug; 15(8):1145-52. Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA. PMID: 16077013; PMCID: PMC1182227.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    163. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005 Aug 02; 102(31):11070-5. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. PMID: 16033867; PMCID: PMC1176910.
      View in: PubMed   Mentions: 2496     Fields:    Translation:HumansAnimalsCells
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