2023
Vancomycin-induced alterations in the gut microbiota supress gut trypsin activity and preserve intestinal barrier function during experimental autoimmune encephalytis (under review)
Myelin associated biomarkers implicate underproduction for the cognitive deficits in schizophrenia versus inflammatory dysmyelination in psychotic and nonpsychotic affective disorders (under review)
Imran Sulaiman, Benjamin G Wu, Matthew Chung, Bradley Isaacs, Jun-Chieh J Tsay, Meredith Holub, Clea R Barnett, Benjmain Kwok, Matthias C Kugler, Jake G Natalini, Shivani Singh , Yonghua Li, Rosemary Schluger, Joseph Carpenito, Destiny Collazo, Luisanny Perez, Yaa Kyeremateng, Miao Chang, Christina D Campbell, Philip M Hansbro, Beno W Oppenheimer, Kenneth I Berger, Roberta M Goldring, Sergei B Koralov, Michael D Weiden, Rui Xiao, Jeanine D'Armiento, Jose C Clemente, Elodie Ghedin, Leopoldo N Segal. Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate COPD. Am J Respir Crit Care Med 2023.
Lepeng Zhou, Wen Qiu, Jie Wang, Aihua Zhao, Chuhui Zhou, Tao Sun, Ziyu Xiong, Peihua Cao, Wei Shen, Jingfen Chen, Xiaolu Lai, Liu-hong Zhao, Yue Wu, Meng Li, Feng Qiu, Yanhong Yu, Zhenjiang Zech Xu, Hongwei Zhou, Wei Jia, Yan Liao, Ravi Retnakaran, Daniel Krewski, Shi Wu Wen, Jose C. Clemente*, Tianlu Chen*, Ri-hua Xie*, Yan He*. Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: a triple-blind randomized controlled trial. Cell Host & Microbe (in press). *Corresponding authors.
Hung N. Luu, Chi Thi-Du Tran, Renwei Wang, Mai Vu-Tuyet Nguyen, Mo Thi Tran, Thuy Thi-Van Tuong, Quang Hong Tran, Linh Cu Le, Huong Thi-Thu Pham, Hien Huy Vu, Nam Chi Bui, Hien Thi-Thu Ha, Dung Tuan Trinh, Claire E. Thomas, Jennifer Adams-Haduch, Liudmilla Velikokhatnaya, Robert E. Schoen, Guoxiang Xie, Wei Jia, Paolo Boffetta, Jose C. Clemente, Jian-Min Yuan. Associations between Ileal Juice Bile Acids and Colorectal Advanced Adenoma. Nutrients. 2023, 15(13), 2930
Jakleen J Lee, Enrica Piras, Sabrina Tamburini, Kevin Bu, David S Wallach, Brooke Remsen, Adam Cantor, Jennifer Kong, Deborah Goetz, Kevin W Hoffman, Mharisi Bonner, Peter Joe, Bridget R Mueller, Jessica Robinson-Papp, Eyal Lotan, Oded Gonen, Dolores Malaspina, Jose C Clemente. Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: A transdiagnostic, multilevel pilot study. Psychiatry Research. 2023 May 30;326:115279.
Alba Boix-Amorós, Michelle H Badri, Julia Manasson, Rebecca B Blank, Rebecca H Haberman, Andrea L Neimann, Parvathy V Girija, Anthony Jimenez Hernandez, Adriana Heguy, Sergei B Koralov, Richard Bonneau, Jose C Clemente*, Jose U Scher*. Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin. Annals of the Rheumatic Diseases, ard-2022-223389. *Corresponding authors.
Georgina R Nyawo, Charissa C Naidoo, Benjamin Wu, Imran Sulaiman, Jose C Clemente, Yonghua Li, Stephanie Minnies, Byron WP Reeve, Suventha Moodley, Cornelia Rautenbach, Colleen Wright, Shivani Singh, Andrew Whitelaw, Pawel Schubert, Robin Warren, Leopoldo Segal, Grant Theron. More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis. Thorax, 78(3):297-308.
2022
Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis. Paola Bianchimano, Graham J Britton, David S Wallach, Emma M Smith, Laura M Cox, Shirong Liu, Kacper Iwanowski, Howard L Weiner, Jeremiah J Faith, Jose C Clemente, Stephanie K Tankou. Microbiome, 10(1):174.
Boix-Amorós, A.*, Monaco, H.*, Sambataro, E., & Clemente, J. C. (2022). Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes, 14(1), 2107866. https://doi.org/10.1080/19490976.2022.2107866
*These two authors contributed equally
Fendrich SJ, Koralnik LR, Bonner M, Goetz D, Joe P, Lee J, Mueller B, Robinson-Papp J, Gonen O, Clemente, JC, & Malaspina D (2022). Patient-reported exposures and outcomes link the gut-brain axis and inflammatory pathways to specific symptoms of severe mental illness. Psychiatry Research, 312, 114526. https://doi.org/https://doi.org/10.1016/j.psychres.2022.114526
Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, Chen-Liaw A, Mitcham J, Bongers G, Gevers D, Clemente JC, Colombel J-F, Grinspan A, & Faith JJ (2022). Author Correction: Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nature Microbiology, 7(5), 736. https://doi.org/10.1038/s41564-022-01118-8
Centa M, Weinstein EG, Clemente JC, Faith JJ, Fiel MI, Lyallpuri R, Herbin O, & Alexandropoulos K (2022). Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis. Journal of Autoimmunity, 128, 102808. https://doi.org/https://doi.org/10.1016/j.jaut.2022.102808
Boix-Amorós A, Lee AG, & Clemente JC (2022). The Rest Is Noise: Finding Signals in Lung Microbiome Data Analysis. In Y. J. Huang & S. Garantziotis (Eds.), The Microbiome in Respiratory Disease: Principles, Tools and Applications (pp. 35–57). Springer International Publishing. https://doi.org/10.1007/978-3-030-87104-8_3
Bu K, Wallach DS, Wilson Z, Shen N, Segal LN, Bagiella E, & Clemente JC (2022). Identifying correlations driven by influential observations in large datasets. Briefings in Bioinformatics, 23(1), bbab482. https://doi.org/10.1093/bib/bbab482
2021
Seppo AE, Bu K, Jumabaeva M, Thakar J, Choudhury RA, Yonemitsu C, Bode L, Martina CA, Allen M, Tamburini S, Piras E, Wallach DS, Looney RJ, Clemente JC, & Järvinen KM (2021). Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle. Allergy, 76(11), 3489–3503. https://doi.org/https://doi.org/10.1111/all.14877
Seppo AE, Choudhury R, Pizzarello C, Palli R, Fridy S, Rajani PS, Stern J, Martina C, Yonemitsu C, Bode L, Bu K, Tamburini S, Piras E, Wallach DS, Allen M, Looney RJ, Clemente JC, Thakar J, & Järvinen KM (2021). Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition. Frontiers in Immunology, 12. https://www.frontiersin.org/articles/10.3389/fimmu.2021.741513
Joe P, Clemente JC, Piras E, Wallach DS, Robinson-Papp J, Boka E, Remsen B, Bonner M, Kimhy D, Goetz D, Hoffman K, Lee J, Ruby E, Fendrich S, Gonen O, & Malaspina D (2021). An integrative study of the microbiome gut-brain-axis and hippocampal inflammation in psychosis: Persistent effects from mode of birth. Schizophrenia Research. https://doi.org/https://doi.org/10.1016/j.schres.2021.09.019
Boix-Amorós A, Piras E, Bu K, Wallach DS, Stapylton M, Fernández-Sesma A, Malaspina D, & Clemente JC (2021). Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner. MSystems, 6(5), e00674-21. https://doi.org/10.1128/mSystems.00674-21
Puthota J, Alatorre A, Walsh S, Clemente JC, Malaspina D, & Spicer J (2021). Prenatal ambient temperature and risk for schizophrenia. Schizophrenia Research. https://doi.org/https://doi.org/10.1016/j.schres.2021.09.020
Sulaiman I, Chung M, Angel L, Tsay J-CJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Pérez-Pérez S, Shen G, Jour G, Meyn P, Carpenito J, Liu X, Ji J, Callazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Heguy A, Evans L, Uyeki TM, Clemente JC, de Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E & Segal LN (2021). Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. Nature Microbiology, 6(10), 1245–1258. https://doi.org/10.1038/s41564-021-00961-5
Sulaiman I, Wu BG, Li Y, Tsay J-C, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, & Segal LN. (2021). Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. European Respiratory Journal, 58(1), 2003434. https://doi.org/10.1183/13993003.03434-2020
Feng Z, Clemente JC, Wong B, & Schadt EE (2021). Detecting and phasing minor single-nucleotide variants from long-read sequencing data. Nature Communications, 12(1), 3032. https://doi.org/10.1038/s41467-021-23289-4
Wu BG, Sulaiman I, Tsay J-CJ, Perez L, Franca B, Li Y, Wang J, Gonzalez AN, El-Ashmawy M, Carpenito J, Olsen E, Sauthoff M, Yie K, Liu X, Shen N, Clemente JC, Kapoor B, Zangari T, Mezzano V, Loomis C, Weiden MD, Koralov SB, D’Armiento J, Ahuja SK, Wu X-R, Weiser JN, & Segal LN (2020). Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae. American Journal of Respiratory and Critical Care Medicine, 203(9), 1099–1111. https://doi.org/10.1164/rccm.202005-1596OC
Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal, LN, & Theron G (2021). Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine, 67, 103374. https://doi.org/https://doi.org/10.1016/j.ebiom.2021.103374
Luu HN, Neelakantan N, Geng T, Wang R, Goh GB-B, Clemente JC, Jin A, van Dam RM, Jia W, Behari J, Koh W-P, & Yuan J-M (2021). Quality diet indexes and risk of hepatocellular carcinoma: Findings from the Singapore Chinese Health Study. International Journal of Cancer, 148(9), 2102–2114. https://doi.org/https://doi.org/10.1002/ijc.33367
Luu HN, Behari J, Goh, GB-B, Wang R, Jin A, Thomas CE, Clemente JC, Odegaard AO, Koh W-P, & Yuan J-M (2021). Composite Score of Healthy Lifestyle Factors and Risk of Hepatocellular Carcinoma: Findings from a Prospective Cohort Study. Cancer Epidemiology, Biomarkers & Prevention, 30(2), 380–387. https://doi.org/10.1158/1055-9965.EPI-20-1201
Tsay J-CJ, Wu BG, Sulaiman I, Gershner K, Schluger R, Li Y, Yie T-A, Meyn P, Olsen E, Perez L, Franca B, Carpenito J, Iizumi T, El-Ashmawy M, Badri M, Morton JT, Shen N, He L, Michaud G, Rafeq S, Bessich J, Smith R, Sauthoff H, Felner K, Pillai R, Zavitsanou A, Koralov S, Mezzano V, Loomis C, Moreira A, Moore W, Tsirigos A, Heguy A, Rom W, Sterman D, Pass H, Clemente JC, Li H, Bonneau R, Wong K, Papagiannakopoulos T, Segal LN (2021). Lower Airway Dysbiosis Affects Lung Cancer Progression. Cancer Discovery, 11(2), 293–307. https://doi.org/10.1158/2159-8290.CD-20-0263
Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC. “Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease”. Cell Host Microbe. 2021 Jan 13;29(1):83-93.e3.
Dubowski K, Kaali S, Jack D, Prah RKD, Clemente JC, Tawiah T, Mujtaba M, Iddrisu L, Carrión D, Konadu DG, Agyei O, Kornu FM, Osei-Owusu S, Lee AG, Asante KP. “Infant Nasopharyngeal Microbiota Subphenotypes and Early Childhood Lung Function: Evidence from a Rural Ghanaian Pregnancy Cohort”. Int J Environ Res Public Health 2021, 18(14):7276.
2020
Wu BG, Kapoor B, Cummings KJ, Stanton ML, Nett RJ, Kreiss K, Abraham JL, Colby Tv, Franko AD, Green FHY, Sanyal S, Clemente JC, Gao Z, Coffre M, Meyn P, Heguy A, Li, Y, Sulaiman I, Borbet TC, Koralov S, Tallaksen R, Wendland D, Bachelder V, Boylstein R, Park J, Cox-Ganser J, Virji M, Crawford J, Edwards N, Veillette M, Duchaine C, Warren K, Lundeen S, Blaser M, Segal LN (2020). Evidence for Environmental–Human Microbiota Transfer at a Manufacturing Facility with Novel Work-related Respiratory Disease. American Journal of Respiratory and Critical Care Medicine, 202(12), 1678–1688. https://doi.org/10.1164/rccm.202001-0197OC
Martineau E & Clemente JC (2020). Chapter 5 - Impact of delivery mode in early life microbiome and risk of disease. In O. Koren & S. Rautava (Eds.), The Human Microbiome in Early Life (pp. 109–133). Academic Press. https://doi.org/https://doi.org/10.1016/B978-0-12-818097-6.00005-5
Britton GJ, Contijoch EJ, Spindler MP, Aggarwala V, Dogan B, Bongers G, San Mateo L, Baltus A, Das A, Gevers D, Borody TJ, Kaakoush NO, Kamm MA, Mitchell H, Paramsothy S, Clemente JC, Colombel J-F, Simpson KW, Dubinsky MC, Grinspan A, Faith JJ (2020). Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas. Proceedings of the National Academy of Sciences, 117(35), 21536–21545. https://doi.org/10.1073/pnas.1922189117
Clemente JC & Iliev ID (2020). Editorial overview: Microbiota united-bacteria, fungi and host responses come into focus. Current Opinion in Microbiology, 56, vi–viii. https://doi.org/https://doi.org/10.1016/j.mib.2020.11.002
Peter I, Maldonado-Contreras A, Eisele C, Frisard C, Simpson S, Nair N, Rendon A, Hawkins K, Cawley, C, Debebe A, Tarassishin L, White S, Dubinsky M, Stone J, Clemente JC, Sabino J, Torres J, Hu J, Colombel J-F, & Olendzki B (2020). A dietary intervention to improve the microbiome composition of pregnant women with Crohn’s disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design. Contemporary Clinical Trials Communications, 18, 100573. https://doi.org/https://doi.org/10.1016/j.conctc.2020.100573
Leonardi I, Paramsothy S, Doron I, Semon A, Kaakoush NO, Clemente JC, Faith JJ, Borody TJ, Mitchell, HM, Colombel J-F, Kamm MA, & Iliev ID (2020). Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. Cell Host & Microbe, 27(5), 823-829.e3. https://doi.org/https://doi.org/10.1016/j.chom.2020.03.006
Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija Pv, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC Scher JU (2020). Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25–Driven Intestinal Inflammation. Arthritis & Rheumatology, 72(4), 645–657. https://doi.org/https://doi.org/10.1002/art.41169
Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, Tarassishin L, Jharap B, Cote-Daigneault J, Mao Q, Mogno I, Britton GJ, Uzzan M, Chen, C-L, Kornbluth A, George J, Legnani P, Maser E, Loudon H, Ston J, Dubinsky M, Faith JJ, Clemente JC, Saurabh M, Colombel J-F, Peter, I. (2020). Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut, 69(1), 42. https://doi.org/10.1136/gutjnl-2018-317855
2019
Carney SM, Clemente JC, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan, TD, Molyneaux PL, Moore BB, O’Dwyer DN, Segal LN, & Garantziotis S (2019). Methods in Lung Microbiome Research. American Journal of Respiratory Cell and Molecular Biology, 62(3), 283–299. https://doi.org/10.1165/rcmb.2019-0273TR
Shen N, Caixàs A, Ahlers M, Patel K, Gao Z, Dutia R, Blaser MJ, Clemente JC, & Laferrère B (2019). Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity. Surgery for Obesity and Related Diseases, 15(8), 1367–1373. https://doi.org/https://doi.org/10.1016/j.soard.2019.05.038
Hirten RP, Grinspan A, Fu S-C, Luo Y, Suarez-Farinas M, Rowland J, Contijoch EJ, Mogno I, Yang N, Luong T, Labrias PR, Peter I, Cho JH, Sands BE, Colombel J-F, Faith JJ, & Clemente JC (2019). Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflammatory Bowel Diseases, 25(6), 969–979. https://doi.org/10.1093/ibd/izy398
Chen LA, Hourigan SK, Grigoryan Z, Gao Z, Clemente JC, Rideout JR, Chirumamilla S, Rabidazeh S, Saeed S, Elson CO, Oliva-Hemker M, Blaser MJ, & Sears CL (2019). Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. Journal of Pediatric Gastroenterology and Nutrition, 68(4). https://journals.lww.com/jpgn/Fulltext/2019/04000/Decreased_Fecal_Bacterial_Diversity_and_Altered.9.aspx
Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, Paramsothy R, Walsh AJ, van den Bogaerde J, Samuel D, Leong RWL, Connor S, Ng W, Lin E, Borody TJ, Wilkins MR, Colombel, J-F, Mitchell HM, & Kaakoush NO (2019). Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis. Gastroenterology, 156(5), 1440-1454.e2. https://doi.org/https://doi.org/10.1053/j.gastro.2018.12.001
Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, Llewellyn SR, Hira S, Johnson C, Rabinowitz KM, Barkan R, Dotan I, Hirten RP, Fu SC, Luo Y, Yang N, Luong T, Labrias PR, Lira S, Peter I, Grinspan A, Clemente JC, Kosoy R, Kim-Schulze S, Qin X, Castillo A, Hurley A, Atreja A, Rogers J, Fasihuddin F, Saliaj M, Nolan A, Reyes-Mercedes P, Rodriguez C, Aly S, Santa-Cruz K, Peters L, Suárez-Fariñas M, Huang R, Hao K, Zhu J, Zhang B, Losic B, Irizar H, Song WM, Di Narzo A, Wang W, Cohen BL, DiMaio C, Greenwald D, Itzkowitz S, Lucas A, Marion J, Maser E, Ungaro R, Naymagon S, Novak J, Shah B, Ullman T, Rubin P, George J, Legnani P, Telesco SE, Friedman JR, Brodmerkel C, Plevy S, Cho JH, Colombel JF, Schadt EE, Argmann C, Dubinsky M, Kasarskis A, Sands B, Faith JJ (2019). Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife, 8, e40553. https://doi.org/10.7554/eLife.40553
Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel J-F, Dubinsky M, Faith JJ (2019). Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice. Immunity, 50(1), 212-224.e4. https://doi.org/https://doi.org/10.1016/j.immuni.2018.12.015
Katz Sand I, Zhu Y, Ntranos A, Clemente JC, Cekanaviciute E, Brandstadter R, Crabtree-Hartman E, Singh S, Bencosme Y, Debelius J, Knight R, Cree BAC, Baranzini SE, & Casaccia P. (2019). Disease-modifying therapies alter gut microbial composition in MS. Neurology - Neuroimmunology Neuroinflammation, 6(1), e517. https://doi.org/10.1212/NXI.0000000000000517
Wu BG, Sulaiman I, Wang J, Shen N, Clemente JC, Li Y, Laumbach RJ, Lu S-E, Udasin I, Le-Hoang O, Perez A, Alimokhtari S, Black K, Plietz M, Twumasi A, Sanders H, Malecha P, Kapoor B, Scaglione BD, Wang A, Blazoski C, Weiden MD, Rapoport DM, Harrison D, Chitkara N, Vicente E, Marin JM, Sunderram J, Ayappa I, Segal, LN (2019). Severe Obstructive Sleep Apnea Is Associated with Alterations in the Nasal Microbiome and an Increase in Inflammation. American Journal of Respiratory and Critical Care Medicine, 199(1), 99–109. https://doi.org/10.1164/rccm.201801-0119OC
2018
Taroncher-Oldenburg G, Jones S, Blaser M, Bonneau R, Christey P, Clemente JC, Elinav E, Ghedin E, Huttenhower C, Kelly D, Kyle D, Littman D, Maiti A, Maue A, Olle B, Segal LN, van Hylckama Vlieg JET, & Wang J (2018). Translating microbiome futures. Nature Biotechnology, 36(11), 1037–1042. https://doi.org/10.1038/nbt.4287
Tsay JCJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, Li Y, Yie T-A, Lhakhang T, Olsen E, Murthy V, Michaud G, Sulaiman I, Tsirigos A, Heguy A, Pass H, Weiden MD, Rom WN, Sterman DH, Bonneau R, Blaser MJ, & Segal LN (2018). Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer. American Journal of Respiratory and Critical Care Medicine, 198(9), 1188–1198. https://doi.org/10.1164/rccm.201710-2118OC
Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel J-F, Lafaille JJ, Sachidanandam R, Furtado GC, & Lira SA (2018). Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology, 155(4), 1177-1191.e16. https://doi.org/https://doi.org/10.1053/j.gastro.2018.06.034
Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN (2018). Evaluation of the airway microbiome in nontuberculous mycobacteria disease. European Respiratory Journal, 52(4), 1800810. https://doi.org/10.1183/13993003.00810-2018
Daniel M, Embriette H, Debelius JW, Morton JT, Antonio G, Gail, A, Aksenov AA, Bahar B, Brennan C, Chen Y, Goldasich LD, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humprey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AC, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe W, Zhu Q, The American Gut Consortium, & Knight R (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. MSystems, 3(3), e00031-18. https://doi.org/10.1128/mSystems.00031-18
Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel J-F, Grinspan A, Clemente JC, Merad M, & Faith JJ (2018). Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice. Gastroenterology, 154(4), 1037-1046.e2. https://doi.org/https://doi.org/10.1053/j.gastro.2017.11.030
Manasson J, Shen N, Garcia Ferrer HR, Ubeda C, Iraheta I, Heguy A, von Feldt JM, Espinoza LR, Garcia Kutzbach A, Segal LN, Ogdie A, Clemente JC, & Scher JU (2018). Gut Microbiota Perturbations in Reactive Arthritis and Postinfectious Spondyloarthritis. Arthritis & Rheumatology, 70(2), 242–254. https://doi.org/https://doi.org/10.1002/art.40359
Clemente JC, Manasson J, & Scher JU (2018). The role of the gut microbiome in systemic inflammatory disease. BMJ, 360, j5145. https://doi.org/10.1136/bmj.j5145
Fernandez DM, Clemente JC, & Giannarelli C (2018). Physical Activity, Immune System, and the Microbiome in Cardiovascular Disease. Frontiers in Physiology, 9. https://www.frontiersin.org/articles/10.3389/fphys.2018.00763
2017
Haro C, García-Carpintero S, Rangel-Zúñiga OA, Alcalá-Díaz JF, Landa BB, Clemente JC, Pérez-Martínez P, López-Miranda J, Pérez-Jiménez F, & Camargo, A (2017). Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients with Metabolic Dysfunction. Molecular Nutrition & Food Research, 61(12), 1700300. https://doi.org/https://doi.org/10.1002/mnfr.201700300
Thompson L, Sanders JG, McDonald D, Amir A, Ladau J, Locey K, Prill R, Tripathi A, Gibbons S, Ackermann G, Navas-Molina J, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton J, Mirarab S, Zech Xu Z, Jiang L, Haroon M, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich N, Lefler J, Brislawn C, Humphrey G, Owens S, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman J, Clauset A, Stevens R, Shade A, Pollard K, Goodwin K, Jansson J, Gilbert J, Knight R, & The Earth Microbiome Project Consortium (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457–463. https://doi.org/10.1038/nature24621
Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, & Eggesbø M (2017). Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLOS ONE, 12(10), e0184336-. https://doi.org/10.1371/journal.pone.0184336
Walker RW, Clemente JC, Peter I, & Loos RJF (2017). The prenatal gut microbiome: are we colonized with bacteria in utero? Pediatric Obesity, 12(S1), 3–17. https://doi.org/https://doi.org/10.1111/ijpo.12217
Tamburini S & Clemente JC (2017). Neonatal gut microbiota induces lung immunity against pneumonia. Nature Reviews Gastroenterology & Hepatology, 14(5), 263–264. https://doi.org/10.1038/nrgastro.2017.34
Segal LN, Clemente JC, Li, Y, Ruan C, Cao J, Danckers M, Morris A, Tapyrik S, Wu BG, Diaz P, Calligaro G, Dawson R, van Zyl-Smit RN, Dheda K, Rom WN, & Weiden MD (2017). Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients. Cell Host & Microbe, 21(4), 530-537.e4. https://doi.org/https://doi.org/10.1016/j.chom.2017.03.003
Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, & Weiden MD (2017). Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Thorax, 72(1), 13. https://doi.org/10.1136/thoraxjnl-2016-208599
2016
Scher JU, Joshua V, Artacho A, Abdollahi-Roodsaz S, Öckinger J, Kullberg S, Sköld M, Eklund A, Grunewald J, Clemente JC, Ubeda C, Segal LN, & Catrina AI (2016). The lung microbiota in early rheumatoid arthritis and autoimmunity. Microbiome, 4(1), 60. https://doi.org/10.1186/s40168-016-0206-x
Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM., Sampson H., Sicherer S, & Clemente JC (2016). Early-life gut microbiome composition and milk allergy resolution. Journal of Allergy and Clinical Immunology, 138(4), 1122–1130. https://doi.org/https://doi.org/10.1016/j.jaci.2016.03.041
Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, Remark R, Mogno I, Ng R, Gnjatic S, Amir ED, Solovyov A, Greenbaum B, Clemente JC, Faith JJ, Belkaid Y, Grigg ME, & Merad M (2016). Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome. Cell, 167(2), 444-456.e14. https://doi.org/https://doi.org/10.1016/j.cell.2016.08.076
Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, Neut C, Vermeire S, Clemente JC, Colombel J-F, Fujioka H, Poulain D, Sendid B, & Ghannoum MA (2016). Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. MBio, 7(5), e01250-16. https://doi.org/10.1128/mBio.01250-16
Tamburini S & Clemente JC (2016). Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments. Cellular and molecular gastroenterology and hepatology, 2(5), 540–541. https://doi.org/10.1016/j.jcmgh.2016.07.001
Tamburini S, Shen N, Wu HC, & Clemente JC (2016). The microbiome in early life: implications for health outcomes. Nature Medicine, 22(7), 713–722. https://doi.org/10.1038/nm.4142
Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F, & Camargo A (2016). Intestinal Microbiota Is Influenced by Gender and Body Mass Index. PLOS ONE, 11(5), e0154090-. https://doi.org/10.1371/journal.pone.0154090
Gacias M, Gaspari S, Santos P-MG, Tamburini S, Andrade M, Zhang F, Shen N, Tolstikov V, Kiebish M A, Dupree JL, Zachariou V, Clemente JC, & Casaccia P (2016). Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior. ELife, 5, e13442. https://doi.org/10.7554/eLife.13442
Segal LN, Clemente JC, Tsay J-CJ, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, & Weiden MD (2016). Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nature Microbiology, 1(5), 16031. https://doi.org/10.1038/nmicrobiol.2016.31
Clemente JC & Dominguez-Bello MG (2016). Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes. BMJ, 352, i1707. https://doi.org/10.1136/bmj.i1707
Dominguez-Bello MG, de Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, & Clemente JC (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine, 22(3), 250–253. https://doi.org/10.1038/nm.4039
Haro C, Garcia-Carpintero S, Alcala-Diaz JF, Gomez-Delgado F, Delgado-Lista J, Perez-Martinez P, Rangel Zuñiga OA, Quintana-Navarro GM, Landa BB, Clemente JC, Lopez-Miranda J, Camargo A, & Perez-Jimenez F (2016). The gut microbial community in metabolic syndrome patients is modified by diet. The Journal of Nutritional Biochemistry, 27, 27–31. https://doi.org/https://doi.org/10.1016/j.jnutbio.2015.08.011
2015
Macklaim JM, Clemente JC, Knight R, Gloor GB, & Reid G (2015). Changes in vaginal microbiota following antimicrobial and probiotic therapy. Microbial Ecology in Health and Disease, 26(1), 27799. https://doi.org/10.3402/mehd.v26.27799
Shen N & Clemente JC (2015). Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases. Current Allergy and Asthma Reports, 15(7), 39. https://doi.org/10.1007/s11882-015-0538-9
Berg D, Clemente JC, & Colombel J-F (2015). Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome? Expert Review of Gastroenterology & Hepatology, 9(6), 781–795. https://doi.org/10.1586/17474124.2015.1013031
Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG (2015). The microbiome of uncontacted Amerindians. Science Advances, 1(3), e1500183. https://doi.org/10.1126/sciadv.1500183
Obregon-Tito AJ., Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, & Lewis CM (2015). Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications, 6(1), 6505. https://doi.org/10.1038/ncomms7505
2014
Segal LN, Alekseyenko Av, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, & Weiden MD (2014). Erratum to: Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome, 2(1), 21. https://doi.org/10.1186/2049-2618-2-21
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 (2014). Advancing the Microbiome Research Community. Cell, 159(2), 227–230. https://doi.org/https://doi.org/10.1016/j.cell.2014.09.022
Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, The Scientists for Advancement of Microbiome Research, White O. “Advancing the Microbiome Research Community.” Cell 2014, 159(2):227–230
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou H, Knight R & Caporaso JG (2014). Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2:e545 https://doi.org/10.7717/peerj.545
Parfrey, L. W., Walters, W. A., Lauber, C. L., Clemente, J. C., Berg-Lyons, D., Teiling, C., Kodira, C., Mohiuddin, M., Brunelle, J., Driscoll, M., Fierer, N., Gilbert, J. A., & Knight, R. (2014). Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Frontiers in Microbiology, 5. https://www.frontiersin.org/articles/10.3389/fmicb.2014.00298
Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, Furtado GC, Ochando J, Kelley KA, Clemente JC, Merad M, van Bakel H, & Lira SA (2014). Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. Journal of Experimental Medicine, 211(3), 457–472. https://doi.org/10.1084/jem.20131587
Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada J-R, Guarner F, & Azpiroz F (2014). Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut, 63(3), 401. https://doi.org/10.1136/gutjnl-2012-303013
2013
Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, & McCulley RL (2013). Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science, 342(6158), 621–624. https://doi.org/10.1126/science.1243768
Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer, MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI (2013). Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice. Science, 341(6150), 1241214. https://doi.org/10.1126/science.1241214
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, & Huttenhower C (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31(9), 814–821. https://doi.org/10.1038/nbt.2676
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman, AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, & Gordon JI (2013). The Long-Term Stability of the Human Gut Microbiota. Science, 341(6141), 1237439. https://doi.org/10.1126/science.1237439
Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, & Dominguez-Bello MG (2013). Biphasic assembly of the murine intestinal microbiota during early development. The ISME Journal, 7(6), 1112–1115. https://doi.org/10.1038/ismej.2013.15
Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, & Knight R (2013). Cohabiting family members share microbiota with one another and with their dogs. eLife, 2, e00458. https://doi.org/10.7554/eLife.00458
Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, & Fierer N (2013). Global biogeography of highly diverse protistan communities in soil. The ISME Journal, 7(3), 652–659. https://doi.org/10.1038/ismej.2012.147
Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, & Janssen PH (2013). Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLOS ONE, 8(2), e47879-. https://doi.org/10.1371/journal.pone.0047879
Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, & Knight R (2013). Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. The ISME Journal, 7(1), 85–95. https://doi.org/10.1038/ismej.2012.81
2012
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, & Caporaso JG (2012). The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience, 1(1), 2047-217X-1–7. https://doi.org/10.1186/2047-217X-1-7
Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, & Krauter KS (2012). Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Research, 22(11), 2146–2152. http://genome.cshlp.org/content/22/11/2146.abstract
Carvalho FA, Koren O, Goodrich JK, Johansson MEV, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, & Gewirtz AT (2012). Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice. Cell Host & Microbe, 12(2), 139–152. https://doi.org/https://doi.org/10.1016/j.chom.2012.07.004
The Human Microbiome Project Consortium (2012). A framework for human microbiome research. Nature, 486(7402), 215–221. https://doi.org/10.1038/nature11209
The Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214. https://doi.org/10.1038/nature11234
Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, & Knight R (2012). The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. Journal of Allergy and Clinical Immunology, 129(5), 1204–1208. https://doi.org/https://doi.org/10.1016/j.jaci.2012.03.010
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–227. https://doi.org/10.1038/nature11053
Clemente JC, Ursell LK, Parfrey LW, & Knight R (2012). The Impact of the Gut Microbiota on Human Health: An Integrative View. Cell, 148(6), 1258–1270. https://doi.org/https://doi.org/10.1016/j.cell.2012.01.035
Tran, V, Clemente JC, Nguyen Duc T, Li J, Dang X, Tu T, Le K, Lan T, Nguyen A, Saethang T, Kubo M, Yamada Y, & Satou K (2012). IMPACT: A novel clustering algorithm based on attraction. Journal of Computers, 7. https://doi.org/10.4304/jcp.7.3.653-665
Kuczynski, J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, & Knight R (2012). Experimental and analytical tools for studying the human microbiome. Nature Reviews Genetics, 13(1), 47–58. https://doi.org/10.1038/nrg3129
2011
Alonso-Alemany D, Clemente JC, Jansson J, Valiente G (2011). Taxonomic Assignment in Metagenomics with TANGO. EMBnet.journal, 17(2), 16-20. doi:https://doi.org/10.14806/ej.17.2.237
Clemente JC, Jansson J, & Valiente G (2011). Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics, 12(1), 8. https://doi.org/10.1186/1471-2105-12-8
Zaneveld, JRR, Parfrey LW, van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, & Knight R (2011). Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends in Microbiology, 19(10), 472–482. https://doi.org/https://doi.org/10.1016/j.tim.2011.07.006
Edgar RC, Haas BJ, Clemente JC, Quince C, & Knight R (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194–2200. https://doi.org/10.1093/bioinformatics/btr381
Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, & Knight R (2011). Our microbial selves: what ecology can teach us. EMBO Reports, 12(8), 775–784. https://doi.org/https://doi.org/10.1038/embor.2011.137
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, & Gordon JI (2011). Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans. Science, 332(6032), 970–974. https://doi.org/10.1126/science.1198719
Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, & Laederach A (2011). Meeting report of the RNA Ontology Consortium January 8–9, 2011. Standards in Genomic Sciences, 4(2), 252–256. https://doi.org/10.4056/sigs.1724282
2010
Clemente JC, Jansson J, & Valiente G (2010). Accurate taxonomic assignment of short pyrosequencing reads. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 3–9. https://doi.org/10.1142/9789814295291_0002
2009
Clemente JC, Ikeo K, Valiente G, & Gojobori T (2009). Optimized ancestral state reconstruction using Sankoff parsimony. BMC Bioinformatics, 10(1), 51. https://doi.org/10.1186/1471-2105-10-51
2008
Jin L, Kryukov K, Clemente JC, Komiyama T, Suzuki Y, Imanishi T, Ikeo K, & Gojobori T (2008). The evolutionary relationship between gene duplication and alternative splicing. Gene, 427(1), 19–31. https://doi.org/https://doi.org/10.1016/j.gene.2008.09.002
2007
Clemente JC, Satou K, & Valiente G (2007). Phylogenetic reconstruction from non-genomic data. Bioinformatics, 23(2), e110–e115. https://doi.org/10.1093/bioinformatics/btl307
2006
Clemente J, Satou K, & Valiente G (2006). Finding Conserved and Non-Conserved Reactions Using a Metabolic Pathway Alignment Algorithm. Genome Informatics, 17(2), 46–56. https://doi.org/10.11234/gi1990.17.2_46
2005
Clemente J, Satou K, & Valiente G (2005). Reconstruction of Phylogenetic Relationships from Metabolic Pathways Based on the Enzyme Hierarchy and the Gene Ontology. Genome Informatics, 16(2), 45–55. https://doi.org/10.11234/gi1990.16.2_45