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    Susan Lynch, PhD

    TitleAssociate Professor
    SchoolUCSF School of Medicine
    Address513 Parnassus Ave, Med Sci
    San Francisco CA 94122
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      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.
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      1. Huang YJ, Nariya S, Harris JM, Lynch SV, Choy DF, Arron JR, Boushey H. The airway microbiome in patients with severe asthma: Associations with disease features and severity. J Allergy Clin Immunol. 2015 Oct; 136(4):874-84.
        View in: PubMed
      2. Panzer AR, Lynch SV. Influence and effect of the human microbiome in allergy and asthma. Curr Opin Rheumatol. 2015 Jul; 27(4):373-80.
        View in: PubMed
      3. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. Does pet-keeping modify the association of delivery mode with offspring body size? Matern Child Health J. 2015 Jun; 19(6):1426-33.
        View in: PubMed
      4. Fujimura KE, Lynch SV. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe. 2015 May 13; 17(5):592-602.
        View in: PubMed
      5. Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens. PLoS One. 2015; 10(2):e0117617.
        View in: PubMed
      6. Lynch SV. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Pediatric Patients: Encouragement Wrapped in Caution. J Pediatr Gastroenterol Nutr. 2015 Jan; 60(1):1-3.
        View in: PubMed
      7. Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch SV, Hartigan-O'Connor DJ. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci Transl Med. 2014 Sep 3; 6(252):252ra120.
        View in: PubMed
      8. Merenstein D, El-Nachef N, Lynch SV. Fecal microbial therapy: promises and pitfalls. J Pediatr Gastroenterol Nutr. 2014 Aug; 59(2):157-61.
        View in: PubMed
      9. Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch SV. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Gut Microbes. 2014 Jul 1; 5(4):494-503.
        View in: PubMed
      10. Lynch SV, Wood RA, Boushey H, Bacharier LB, Bloomberg GR, Kattan M, O'Connor GT, Sandel MT, Calatroni A, Matsui E, Johnson CC, Lynn H, Visness CM, Jaffee KF, Gergen PJ, Gold DR, Wright RJ, Fujimura K, Rauch M, Busse WW, Gern JE. Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children. J Allergy Clin Immunol. 2014 Sep; 134(3):593-601.e12.
        View in: PubMed PMC4151305
      11. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014 Aug; 52(8):2813-23.
        View in: PubMed PMC4136157
      12. Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV. The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients. PLoS One. 2014; 9(4):e95726.
        View in: PubMed PMC3994144
      13. Lynch SV. Viruses and microbiome alterations. Ann Am Thorac Soc. 2014 Jan; 11 Suppl 1:S57-60.
        View in: PubMed
      14. Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):805-10.
        View in: PubMed PMC3896155
      15. Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91.
        View in: PubMed PMC4094294
      16. Nagalingam NA, Cope EK, Lynch SV. Probiotic strategies for treatment of respiratory diseases. Trends Microbiol. 2013 Sep; 21(9):485-92.
        View in: PubMed
      17. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013 May 15; 187(10):1067-75.
        View in: PubMed PMC3734620
      18. Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013 May 15; 187(10):1110-7.
        View in: PubMed PMC3734615
      19. Lynch SV, Bruce KD. The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med. 2013 Mar; 3(3):a009738.
        View in: PubMed
      20. Lynch SV, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL. Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Gut Microbes. 2013 Jan-Feb; 4(1):41-7.
        View in: PubMed PMC3555885
      21. Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, Lynch SV. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med. 2012 Sep 12; 4(151):151ra124.
        View in: PubMed
      22. Fujimura KE, Rauch M, Matsui E, Iwai S, Calatroni A, Lynn H, Mitchell H, Johnson CC, Gern JE, Togias A, Boushey HA, Kennedy S, Lynch SV. Development of a standardized approach for environmental microbiota investigations related to asthma development in children. J Microbiol Methods. 2012 Nov; 91(2):231-9.
        View in: PubMed PMC3615718
      23. Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SV, Huang L. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol. 2012 Sep; 50(9):2995-3002.
        View in: PubMed PMC3421777
      24. Scanlan PD, Buckling A, Kong W, Wild Y, Lynch SV, Harrison F. Gut dysbiosis in cystic fibrosis. J Cyst Fibros. 2012 Sep; 11(5):454-5.
        View in: PubMed
      25. Huang YJ, Lynch SV, Wiener-Kronish JP. From microbe to microbiota: considering microbial community composition in infections and airway diseases. Am J Respir Crit Care Med. 2012 Apr 1; 185(7):691-2.
        View in: PubMed
      26. Schwarzer C, Fu Z, Patanwala M, Hum L, Lopez-Guzman M, Illek B, Kong W, Lynch SV, Machen TE. Pseudomonas aeruginosa biofilm-associated homoserine lactone C12 rapidly activates apoptosis in airway epithelia. Cell Microbiol. 2012 May; 14(5):698-709.
        View in: PubMed PMC4112999
      27. Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ. Significance of the microbiome in obstructive lung disease. Thorax. 2012 May; 67(5):456-63.
        View in: PubMed PMC3578398
      28. Ramsey BW, Banks-Schlegel S, Accurso FJ, Boucher RC, Cutting GR, Engelhardt JF, Guggino WB, Karp CL, Knowles MR, Kolls JK, LiPuma JJ, Lynch S, McCray PB, Rubenstein RC, Singh PK, Sorscher E, Welsh M. Future directions in early cystic fibrosis lung disease research: an NHLBI workshop report. Am J Respir Crit Care Med. 2012 Apr 15; 185(8):887-92.
        View in: PubMed PMC3360572
      29. Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch SV. PcrV antibody-antibiotic combination improves survival in Pseudomonas aeruginosa-infected mice. Eur J Clin Microbiol Infect Dis. 2012 Aug; 31(8):1837-45.
        View in: PubMed
      30. Huang YJ, Lynch SV. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med. 2011 Dec; 5(6):809-21.
        View in: PubMed PMC3359942
      31. Rauch M, Lynch SV. The potential for probiotic manipulation of the gastrointestinal microbiome. Curr Opin Biotechnol. 2012 Apr; 23(2):192-201.
        View in: PubMed
      32. Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. J Leukoc Biol. 2012 Feb; 91(2):275-84.
        View in: PubMed PMC3290427
      33. Nagalingam NA, Lynch SV. Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2012 May; 18(5):968-84.
        View in: PubMed
      34. Havstad S, Wegienka G, Zoratti EM, Lynch SV, Boushey HA, Nicholas C, Ownby DR, Johnson CC. Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood. J Allergy Clin Immunol. 2011 Oct; 128(4):880-885.e4.
        View in: PubMed PMC3185205
      35. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91.
        View in: PubMed PMC3417828
      36. Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch SV, Yang K. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from airways of mechanically ventilated patients and cystic fibrosis patients. Int J Antimicrob Agents. 2011 Apr; 37(4):309-15.
        View in: PubMed PMC3176759
      37. Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011 Feb; 127(2):372-381.e1-3.
        View in: PubMed PMC3037020
      38. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SV. Man's best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol. 2010 Aug; 126(2):410-2, 412.e1-3.
        View in: PubMed PMC2956425
      39. Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SV. Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy. Am J Rhinol Allergy. 2010 Jul-Aug; 24(4):263-5.
        View in: PubMed
      40. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010; 5(6):e11044.
        View in: PubMed PMC2890402
      41. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010; 1(3).
        View in: PubMed PMC2925076
      42. Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, Heimbach JT, Hempel S, Lynch SV, Sanders ME, Tancredi DJ. Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants. Gut Microbes. 2010 7; 1(4):243-253.
        View in: PubMed
      43. Singh G, Wu B, Baek MS, Camargo A, Nguyen A, Slusher NA, Srinivasan R, Wiener-Kronish JP, Lynch SV. Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration. Microb Pathog. 2010 Oct; 49(4):196-203.
        View in: PubMed PMC2935322
      44. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther. 2010 Apr; 8(4):435-54.
        View in: PubMed PMC2881665
      45. Lynch SV, Flanagan JL, Sawa T, Fang A, Baek MS, Rubio-Mills A, Ajayi T, Yanagihara K, Hirakata Y, Kohno S, Misset B, Nguyen JC, Wiener-Kronish JP. Polymorphisms in the Pseudomonas aeruginosa type III secretion protein, PcrV - implications for anti-PcrV immunotherapy. Microb Pathog. 2010 Jun; 48(6):197-204.
        View in: PubMed PMC2860055
      46. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJ, Green JL, Maurer BA, Kolter R. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. 2010 May; 12(5):1293-303.
        View in: PubMed
      47. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010 Feb; 14(1):9-59.
        View in: PubMed PMC3116451
      48. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One. 2010; 5(1):e8745.
        View in: PubMed PMC2807455
      49. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009 Oct 30; 139(3):485-98.
        View in: PubMed PMC2796826
      50. Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko T, Lory S, LaBaer J. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun. 2009 Nov; 77(11):4877-86.
        View in: PubMed PMC2772540
      51. El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SV, Wiener-Kronish JP. Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia. J Infect. 2009 Jul; 59(1):49-55.
        View in: PubMed PMC2756421
      52. Lynch SV, Wiener-Kronish JP. Novel strategies to combat bacterial virulence. Curr Opin Crit Care. 2008 Oct; 14(5):593-9.
        View in: PubMed PMC2859961
      53. Zhuo H, Yang K, Lynch SV, Dotson RH, Glidden DV, Singh G, Webb WR, Elicker BM, Garcia O, Brown R, Sawa Y, Misset B, Wiener-Kronish JP. Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection. Crit Care Med. 2008 Sep; 36(9):2495-503.
        View in: PubMed
      54. Ganter MT, Roux J, Su G, Lynch SV, Deutschman CS, Weiss YG, Christiaans SC, Myazawa B, Kipnis E, Wiener-Kronish JP, Howard M, Pittet JF. Role of small GTPases and alphavbeta5 integrin in Pseudomonas aeruginosa-induced increase in lung endothelial permeability. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):108-18.
        View in: PubMed PMC2606944
      55. El Solh AA, Akinnusi ME, Wiener-Kronish JP, Lynch SV, Pineda LA, Szarpa K. Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia. Am J Respir Crit Care Med. 2008 Sep 1; 178(5):513-9.
        View in: PubMed PMC2542430
      56. Song Y, Pittet JF, Huang X, He H, Lynch SV, Violette SM, Weinreb PH, Horan GS, Carmago A, Sawa Y, Bernstein XL, Wiener-Kronish JP. Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa. Infect Immun. 2008 Jun; 76(6):2325-32.
        View in: PubMed PMC2423078
      57. Wong-Beringer A, Wiener-Kronish J, Lynch S, Flanagan J. Comparison of type III secretion system virulence among fluoroquinolone-susceptible and -resistant clinical isolates of Pseudomonas aeruginosa. Clin Microbiol Infect. 2008 Apr; 14(4):330-6.
        View in: PubMed
      58. Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob Agents Chemother. 2007 Oct; 51(10):3650-8.
        View in: PubMed PMC2043260
      59. Yoo J, Tcheurekdjian H, Lynch SV, Cabana M, Boushey HA. Microbial manipulation of immune function for asthma prevention: inferences from clinical trials. Proc Am Thorac Soc. 2007 Jul; 4(3):277-82.
        View in: PubMed PMC2647630
      60. Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol. 2007 Jun; 45(6):1954-62.
        View in: PubMed PMC1933106
      61. Song Y, Wiener-Kronish JP, Flanagan J, Lynch SV. Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia. Crit Care Med. 2007 Feb; 35(2):652-3.
        View in: PubMed
      62. Song Y, Lynch SV, Flanagan J, Zhuo H, Tom W, Dotson RH, Baek MS, Rubio-Mills A, Singh G, Kipnis E, Glidden D, Brown R, Garcia O, Wiener-Kronish JP. Increased plasminogen activator inhibitor-1 concentrations in bronchoalveolar lavage fluids are associated with increased mortality in a cohort of patients with Pseudomonas aeruginosa. Anesthesiology. 2007 Feb; 106(2):252-61.
        View in: PubMed
      63. Augustin DK, Song Y, Baek MS, Sawa Y, Singh G, Taylor B, Rubio-Mills A, Flanagan JL, Wiener-Kronish JP, Lynch SV. Presence or absence of lipopolysaccharide O antigens affects type III secretion by Pseudomonas aeruginosa. J Bacteriol. 2007 Mar; 189(6):2203-9.
        View in: PubMed PMC1899375
      64. Lynch SV, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A. Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system. Appl Environ Microbiol. 2006 Dec; 72(12):7701-10.
        View in: PubMed PMC1694224
      65. Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A. Effect of chromate stress on Escherichia coli K-12. J Bacteriol. 2006 May; 188(9):3371-81.
        View in: PubMed PMC1447458
      66. Barak Y, Thorne SH, Ackerley DF, Lynch SV, Contag CH, Matin A. New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution. Mol Cancer Ther. 2006 Jan; 5(1):97-103.
        View in: PubMed
      67. Gonzalez CF, Ackerley DF, Lynch SV, Matin A. ChrR, a soluble quinone reductase of Pseudomonas putida that defends against H2O2. J Biol Chem. 2005 Jun 17; 280(24):22590-5.
        View in: PubMed
      68. Carmody M, Byrne B, Murphy B, Breen C, Lynch S, Flood E, Finnan S, Caffrey P. Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques. Gene. 2004 Dec 8; 343(1):107-15.
        View in: PubMed
      69. Lynch SV, Brodie EL, Matin A. Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli. J Bacteriol. 2004 Dec; 186(24):8207-12.
        View in: PubMed PMC532419
      70. Irwin JA, Lynch SV, Coughlan S, Baker PJ, Gudmundsson HM, Alfredsson GA, Rice DW, Engel PC. Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis. Extremophiles. 2003 Apr; 7(2):135-43.
        View in: PubMed
      71. Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk M. Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. Chem Biol. 2001 Jul; 8(7):713-23.
        View in: PubMed
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