Jose C. Clemente, Ph.D. - Publications

Affiliations: 
2003 University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Biochemistry

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD. Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Thorax. PMID 27486204 DOI: 10.1136/thoraxjnl-2016-208599  0.52
2016 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. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. PMID 26828196 DOI: 10.1038/nm.4039  0.52
2015 Shen N, Clemente JC. Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases. Current Allergy and Asthma Reports. 15: 39. PMID 26143390 DOI: 10.1007/s11882-015-0538-9  0.52
2015 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, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications. 6: 6505. PMID 25807110 DOI: 10.1038/ncomms7505  0.52
2014 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. 159: 227-30. PMID 25303518 DOI: 10.1016/j.cell.2014.09.022  0.52
2014 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 HW, Knight R, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. Peerj. 2: e545. PMID 25177538 DOI: 10.7717/peerj.545  0.52
2014 Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Frontiers in Microbiology. 5: 298. PMID 24995004 DOI: 10.3389/fmicb.2014.00298  0.52
2014 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. Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. The Journal of Experimental Medicine. 211: 457-72. PMID 24590763 DOI: 10.1084/jem.20131587  0.52
2014 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 JR, Guarner F, et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 63: 401-8. PMID 23766444 DOI: 10.1136/gutjnl-2012-303013  0.52
2013 Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 1: 19. PMID 24450871 DOI: 10.1186/2049-2618-1-19  0.52
2013 Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science (New York, N.Y.). 342: 621-4. PMID 24179225 DOI: 10.1126/science.1243768  0.52
2013 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, ... ... Clemente JC, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (New York, N.Y.). 341: 1241214. PMID 24009397 DOI: 10.1126/science.1241214  0.52
2013 Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 31: 814-21. PMID 23975157 DOI: 10.1038/nbt.2676  0.52
2013 Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. The long-term stability of the human gut microbiota. Science (New York, N.Y.). 341: 1237439. PMID 23828941 DOI: 10.1126/science.1237439  0.52
2013 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. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2: e00458. PMID 23599893 DOI: 10.7554/eLife.00458  0.52
2013 Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, Dominguez-Bello MG. Biphasic assembly of the murine intestinal microbiota during early development. The Isme Journal. 7: 1112-5. PMID 23535917 DOI: 10.1038/ismej.2013.15  0.52
2013 Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. Plos One. 8: e47879. PMID 23408926 DOI: 10.1371/journal.pone.0047879  0.52
2013 Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N. Global biogeography of highly diverse protistan communities in soil. The Isme Journal. 7: 652-9. PMID 23235291 DOI: 10.1038/ismej.2012.147  0.52
2012 Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Research. 22: 2146-52. PMID 23064750 DOI: 10.1101/gr.140608.112  0.52
2012 Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, et al. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host & Microbe. 12: 139-52. PMID 22863420 DOI: 10.1016/j.chom.2012.07.004  0.52
2012 Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. The Journal of Allergy and Clinical Immunology. 129: 1204-8. PMID 22541361 DOI: 10.1016/j.jaci.2012.03.010  0.52
2012 Clemente JC, Nulton E, Nelen M, Todd MJ, Maguire D, Schalk-Hihi C, Kuo LC, Zhang SP, Flores CM, Kranz JK. Screening and characterization of human monoglyceride lipase active site inhibitors using orthogonal binding and functional assays. Journal of Biomolecular Screening. 17: 629-40. PMID 22496098 DOI: 10.1177/1087057112441012  0.52
2011 Zaneveld JRR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation Trends in Microbiology. 19: 472-482. PMID 21872475 DOI: 10.1016/j.tim.2011.07.006  0.52
2011 Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R. Our microbial selves: what ecology can teach us. Embo Reports. 12: 775-84. PMID 21720391 DOI: 10.1038/embor.2011.137  0.52
2011 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, et al. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences. 4: 252-6. PMID 21677862 DOI: 10.4056/sigs.1724282  0.52
2011 Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans Science. 332: 970-974. PMID 21596990 DOI: 10.1126/science.1198719  0.52
2011 Schalk-Hihi C, Schubert C, Alexander R, Bayoumy S, Clemente JC, Deckman I, DesJarlais RL, Dzordzorme KC, Flores CM, Grasberger B, Kranz JK, Lewandowski F, Liu L, Ma H, Maguire D, et al. Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 Ã… resolution. Protein Science : a Publication of the Protein Society. 20: 670-83. PMID 21308848 DOI: 10.1002/pro.596  0.52
2009 Clemente JC, Ikeo K, Valiente G, Gojobori T. Optimized ancestral state reconstruction using Sankoff parsimony. Bmc Bioinformatics. 10: 51. PMID 19200389 DOI: 10.1186/1471-2105-10-51  0.52
2008 Jin L, Kryukov K, Clemente JC, Komiyama T, Suzuki Y, Imanishi T, Ikeo K, Gojobori T. The evolutionary relationship between gene duplication and alternative splicing. Gene. 427: 19-31. PMID 18835337 DOI: 10.1016/j.gene.2008.09.002  0.52
2008 Clemente JC, Robbins A, Graña P, Paleo MR, Correa JF, Villaverde MC, Sardina FJ, Govindasamy L, Agbandje-McKenna M, McKenna R, Dunn BM, Sussman F. Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation. Journal of Medicinal Chemistry. 51: 852-60. PMID 18215016 DOI: 10.1021/jm701170f  0.52
2007 Moose RE, Clemente JC, Jackson LR, Ngo M, Wooten K, Chang R, Bennett A, Chakraborty S, Yowell CA, Dame JB, Agbandje-McKenna M, Dunn BM. Analysis of binding interactions of pepsin inhibitor-3 to mammalian and malarial aspartic proteases. Biochemistry. 46: 14198-205. PMID 18004881 DOI: 10.1021/bi7014844  0.52
2006 Gutiérrez-de-Terán H, Nervall M, Dunn BM, Clemente JC, Aqvist J. Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor. Febs Letters. 580: 5910-6. PMID 17045991 DOI: 10.1016/j.febslet.2006.09.057  0.52
2006 Lauzon HAM, Garcia-Maruniak A, Paolo PM, Clemente JC, Herniou EA, Lucarotti CJ, Arif BM, Maruniak JE. Genomic comparison of Neodiprion sertifer and Neodiprion lecontei nucleopolyhedroviruses and identification of potential hymenopteran baculovirus-specific open reading frames Journal of General Virology. 87: 1477-1489. PMID 16690912 DOI: 10.1099/vir.0.81727-0  0.52
2006 Clemente JC, Coman RM, Thiaville MM, Janka LK, Jeung JA, Nukoolkarn S, Govindasamy L, Agbandje-McKenna M, McKenna R, Leelamanit W, Goodenow MM, Dunn BM. Analysis of HIV-1 CRF_01 A/E protease inhibitor resistance: structural determinants for maintaining sensitivity and developing resistance to atazanavir. Biochemistry. 45: 5468-77. PMID 16634628 DOI: 10.1021/bi051886s  0.52
2006 Clemente JC, Govindasamy L, Madabushi A, Fisher SZ, Moose RE, Yowell CA, Hidaka K, Kimura T, Hayashi Y, Kiso Y, Agbandje-McKenna M, Dame JB, Dunn BM, McKenna R. Structure of the aspartic protease plasmepsin 4 from the malarial parasite Plasmodium malariae bound to an allophenylnorstatine-based inhibitor. Acta Crystallographica. Section D, Biological Crystallography. 62: 246-52. PMID 16510971 DOI: 10.1107/S0907444905041260  0.52
2006 Ersmark K, Nervall M, Gutiérrez-de-Terán H, Hamelink E, Janka LK, Clemente JC, Dunn BM, Gogoll A, Samuelsson B, Qvist J, Hallberg A. Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV. Bioorganic & Medicinal Chemistry. 14: 2197-208. PMID 16307884 DOI: 10.1016/j.bmc.2005.11.003  0.52
2005 Madabushi A, Chakraborty S, Fisher SZ, Clemente JC, Yowell C, Agbandje-McKenna M, Dame JB, Dunn BM, McKenna R. Crystallization and preliminary X-ray analysis of the aspartic protease plasmepsin 4 from the malarial parasite Plasmodium malariae. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 61: 228-31. PMID 16511002 DOI: 10.1107/S1744309105001405  0.52
2005 Ersmark K, Nervall M, Hamelink E, Janka LK, Clemente JC, Dunn BM, Blackman MJ, Samuelsson B, Aqvist J, Hallberg A. Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations. Journal of Medicinal Chemistry. 48: 6090-106. PMID 16162010 DOI: 10.1021/jm050463l  0.52
2005 Pettit SC, Clemente JC, Jeung JA, Dunn BM, Kaplan AH. Ordered processing of the human immunodeficiency virus type 1 GagPol precursor is influenced by the context of the embedded viral protease. Journal of Virology. 79: 10601-7. PMID 16051852 DOI: 10.1128/JVI.79.16.10601-10607.2005  0.52
2005 Castanheira P, Samyn B, Sergeant K, Clemente JC, Dunn BM, Pires E, Van Beeumen J, Faro C. Activation, proteolytic processing, and peptide specificity of recombinant cardosin A. The Journal of Biological Chemistry. 280: 13047-54. PMID 15677463 DOI: 10.1074/jbc.M412076200  0.52
2004 Clemente JC, Moose RE, Hemrajani R, Whitford LR, Govindasamy L, Reutzel R, McKenna R, Agbandje-McKenna M, Goodenow MM, Dunn BM. Comparing the accumulation of active- and nonactive-site mutations in the HIV-1 protease. Biochemistry. 43: 12141-51. PMID 15379553 DOI: 10.1021/bi049459m  0.52
2003 Clemente JC, Hemrajani R, Blum LE, Goodenow MM, Dunn BM. Secondary mutations M36I and A71V in the human immunodeficiency virus type 1 protease can provide an advantage for the emergence of the primary mutation D30N. Biochemistry. 42: 15029-35. PMID 14690411 DOI: 10.1021/bi035701y  0.52
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