Susan Lynch, PhD

Title(s)Professor, Medicine
SchoolSchool of Medicine
Address550 16th Street, #357D
San Francisco CA 94158
Phone415-476-6784
ORCID ORCID Icon0000-0001-5695-7336 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University College Dublin, IrelandPhD2000Mircobiology
    University College Dublin, IrelandBS1995Microbiology/Biostatistics
    University of California, San Francisco2020Diversity, Equity, and Inclusion Champion Training
    Collapse Awards and Honors
    University of Wisconsin2022  - 2022Odell Lecture
    American Society of Microbiology2017  - 2019Distinguished Lecturer
    Foreign Policy Magazine2016  - 2016Global Thinker
    American Association for Allergy Asthma and Immunology2015  - 2015Rebecca Buckley Lectureship
    International Innovations2014  - 2014Women in Healthcare
    2013  - 2013Irish Health and Science award
    Stanford University2003  - 2005Dean's Fellow

    Collapse Overview 
    Collapse Overview
    Our translational human microbiome research program focuses on gastrointestinal and airway microbiome interactions with host immunity that promote or prevent development/maintenance of chronic inflammatory disease. Taking a "populations to molecules" approach we leverage the microbiome to determine the origins of childhood allergy and asthma and the early life molecular and cellular drivers of immune dysfunction that lead to childhood disease development. We also leverage human population studies and clinical trials to gain insights into the role of the gut microbiome in inflammatory bowel disease. Our studies allow us to develop rationally designed microbial therapeutics, leading to the founding of Siolta Therapeutics which is currently testing a lead product developed in our lab for the prevention of childhood allergy and asthma.
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    Collapse Research Activities and Funding
    Perinatal Precursors of Early Microbiome Development.
    NIH R01HD102604Sep 1, 2020 - Jul 31, 2024
    Role: Co-Principal Investigator
    Binational Early Asthma & Microbiome Study (BEAMS)
    NIH P01AI148104Jul 10, 2020 - Jun 30, 2025
    Role: Co-Principal Investigator
    Integrated Analysis of Microbial and Genomic data in Obstructive Lung Disease (I AM GOLD) Study
    NIH R01HL143998Sep 15, 2019 - Jul 31, 2023
    Role: Co-Principal Investigator
    Interactions between Environmental Microbiome, Maternal Immunity, Neonatal Epigenome and Respiratory Microbiome Development as Determinants of Asthma In Childhood
    NIH R21AI133765Aug 15, 2017 - Jul 31, 2020
    Role: Co-Principal Investigator
    Inner City Asthma Consortium (ICAC): Immunologic Approaches to Reduce Asthma (University of Wisconsin System)
    NIH/NIAID AI114271Sep 1, 2016 - Aug 31, 2023
    Role: UCSF PI
    Children’s Respiratory Research and the Environment Workgroup (CREW).
    NIH/NIAID PO515267Sep 1, 2016 - Aug 31, 2023
    Role: UCSF PI
    Delivery mode, environment and the gut microbiome: influence on childhood body size
    NIH/NICHD R01 DH082147Sep 1, 2015 - Aug 31, 2020
    Role: Co-I
    Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART Initiation and Alcohol Use
    NIH/NIDA R01DA040532Aug 1, 2015 - May 31, 2020
    Role: Co-I
    Fecal microbial transplantation to reduce HIV-associated inflammation.
    NIH/NIDDK R21DK104664Jul 1, 2015 - Jun 30, 2017
    Role: Co-I
    Fungal microbiome of the house environment and its relationship to human microbiome composition
    Sloan Foundation Jun 1, 2013 - May 31, 2016
    Pets and the Infant Microbiome: Effect on Immune Maturation & Atopic Asthma
    NIH P01AI089473Jul 6, 2012 - Jun 30, 2017
    Role: Co-Investigator
    Gut and Airway Microbiome in Allergy and Asthma: Relationships to Immune and Clinical Phenotype. Effects of Inhaled Corticosteroid Treatment
    NIAID Jul 1, 2012 - Jun 30, 2015
    Role: Co-Investigator
    Role of the human microbiome in inflammatory bowel disease amongst migrant South Asian populations.
    Broad Foundation IBD-0327R-2May 1, 2012 - Apr 30, 2015
    Cigarette Smoke Exposure and Acute Lung Injury After Severe Blunt Trauma
    NIH R01HL110969Dec 15, 2011 - Nov 30, 2017
    Role: Co-Investigator
    Sinusitis in Children and the Nasopharyngeal Microbiome
    NIH R01AI097172Dec 1, 2011 - Nov 30, 2016
    Role: Co-Investigator
    Relationships between gut microbiota and immunity in the liver.
    UCSF Liver Center Pilot and Feasibility award May 1, 2011 - Apr 30, 2012
    Role: Co-Investigator
    Lung Microbiome in Cohorts of HIV-Infected Persons (Lung MicroCHIP) Study.
    NIH/NHLBI 1U01HL098964Oct 1, 2009 - Oct 1, 2015
    Probiotic Outcomes of Enteric Microflora (POEM) Study
    NIH/NCCAM R21AT004732Oct 1, 2009 - Sep 30, 2011
    Role: Co-Investigator
    Effect of Probiotics on CF Bacterial Communities.
    CFF Sep 1, 2009 - Aug 31, 2013
    Role: Co-Investigator
    Heterogeneity among human CD4 T lymphocytes.
    NIH/NIAID AI-026322-18A2Jul 1, 2009 - Jun 30, 2011
    Role: Co-Investigator
    The human microbiome in pediatric abdominal pain and Intestinal Inflammation.
    NIH/NIDDK 1UH2DK083990-01Apr 1, 2009 - Mar 31, 2013
    Role: Co-Investigator
    NKT cells recognize and respond to microbes at mucosal surfaces
    NIH/NIAID AI083523-01Mar 1, 2009 - Feb 28, 2011
    Role: Co-Investigator
    S100 protein potentiation of Pseudomonas aeruginosa in cystic fibrosis
    Resource Allocation Project Award, University of California San Francisco Oct 1, 2008 - Sep 30, 2010
    Probiotic Improvement of Genitourinary and Gastrointestinal Health in Girls with Spina Bifida.
    Spina Bifida Association Sep 1, 2008 - Aug 30, 2009
    Description: Young Investigator Award
    Microarray Analysis of Chronic Rhinosinusitis
    American Rhinological Society Jul 1, 2008 - Jun 30, 2009
    Role of PAI-1 in lung injury induced by P. aeruginosa
    UCSF REAC Award Mar 1, 2008 - Feb 28, 2009
    Resequencing microarray for rapid detection &antimicrobial resistance profiling
    NIH U01AI075410Aug 1, 2007 - Jul 31, 2013
    Role: Principal Investigator
    Analysis of bacterial community dynamics in adult patients with exacerbations of Chronic Obstructive Pulmonary Disease
    American Lung Association Jul 1, 2007 - Jun 30, 2009
    Anti-PcrV against P. aeruginosa in CF
    Cystic Fibrosis Foundation Sep 1, 2006 - Aug 31, 2008
    Role: Co-Investigator
    Quantitative Search for Microbes in Bronchial Biopsies from Asthmatic and Healthy Subjects
    NIH/NHLBI HL074207Aug 1, 2006 - Jul 31, 2009
    16S Ancillary Study MIA Supplement
    NIH/NHLBI U10 HL074207Aug 1, 2006 - Jul 31, 2007
    Role: Co-Investigator
    Effect of quorum sensing inhibiting furanones on clinically relevant isolates of pseudomonas aeruginosa
    UCSF Academic Committee on Research Feb 8, 2006 - Mar 1, 2007
    Use of anti-PcrV IgG against P. aeruginosa in Cystic Fibrosis
    CFRDP Jan 9, 2006 - Jan 8, 2007
    Role: Co-Investigator
    The role of infection in asthma pathogenesis
    Sandler Asthma Basic Research Center Jan 1, 2006 - Dec 31, 2007
    Role: Co-Investigator
    Expression and pathogenicity of Pseudomonas aeruginosa The goal of this study is to examine virulence systems and evolution of resistance of P. aeruginosa clinical isolates.
    NIH/NHLBI HL69809Dec 11, 2003 - Nov 30, 2008
    Role: Co-Investigator
    Gene Expression and Pathogenicity of P.aeruginosa
    NIH R01HL069809Dec 11, 2003 - Nov 30, 2008
    Role: Principal Investigator
    Project 2: Mechanisms of Bacterial Induced Lung Injury
    NIH/NHLBI P50 HL074005Dec 1, 2003 - Jun 30, 2008
    Role: Co-Investigator
    Dean's Fellowship
    Stanford University School of Medicine Aug 1, 2002 - Aug 1, 2003
    Postdoctoral Fellowship
    Enterprise Ireland Aug 1, 2001 - Aug 1, 2002
    Research Award
    Enterprise Ireland Basic Aug 1, 1995 - Aug 1, 1998

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    Collapse 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. Early-life Nasal Microbiota Dynamics Relate to Longitudinal Respiratory Phenotypes in Urban Children. J Allergy Clin Immunol. 2024 Feb 27. McCauley KE, Durack J, Lynch KV, Fadrosh DW, Fujimura KE, Vundla F, Özçam M, LeBeau P, Caltroni A, Burns P, Tran HT, Bacharier LB, Kattan M, O'Connor GT, Wood RA, Togias A, Boushey HA, Jackson DJ, Gern JE, Lynch SV, National Institute of Allergy and Infectious Diseases-sponsored Childhood Asthma in Urban Settings C. PMID: 38423369.
      View in: PubMed   Mentions:    Fields:    
    2. Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy. J Bone Miner Res. 2024 Jan 04. Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL. PMID: 38477719.
      View in: PubMed   Mentions:    Fields:    
    3. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med. 2024 01 16; 5(1):101350. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. PMID: 38134931; PMCID: PMC10829755.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    4. Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk. Gut Microbes. 2024 Jan-Dec; 16(1):2290661. Yong GJM, Porsche CE, Sitarik AR, Fujimura KE, McCauley K, Nguyen DT, Levin AM, Woodcroft KJ, Ownby DR, Rundle AG, Johnson CC, Cassidy-Bushrow A, Lynch SV. PMID: 38117587; PMCID: PMC10761186.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset. Ann Clin Transl Neurol. 2024 01; 11(1):169-184. Schoeps VA, Zhou X, Horton MK, Zhu F, McCauley KE, Nasr Z, Virupakshaiah A, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Banwell BL, Bar-Or A, Marrie RA, van Domselaar G, O'Mahony J, Mirza AI, Bernstein CN, Yeh EA, Casper TC, Lynch SV, Tremlett H, Baranzini S, Waubant E, US Network of Pediatric MS Centers. PMID: 37955284; PMCID: PMC10791026.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    6. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med. 2023 Nov; 29(11):2793-2804. Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A. PMID: 37957375.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    7. Contributions of the early-life microbiome to childhood atopy and asthma development. Semin Immunol. 2023 09; 69:101795. Steininger H, Moltzau-Anderson J, Lynch SV. PMID: 37379671.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    8. Progression of C-reactive protein from birth through preadolescence varies by mode of delivery. Front Pediatr. 2023; 11:1155852. Sitarik AR, Johnson CC, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Cassidy-Bushrow AE. PMID: 37388285; PMCID: PMC10304017.
      View in: PubMed   Mentions:
    9. 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: 3     Fields:    Translation:AnimalsCells
    10. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv. 2023 Apr 11. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. PMID: 36945505; PMCID: PMC10029035.
      View in: PubMed   Mentions:
    11. VMAP: Vaginal Microbiome Atlas During Pregnancy. medRxiv. 2023 Apr 05. Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. PMID: 36993193; PMCID: PMC10055588.
      View in: PubMed   Mentions:
    12. The Associations of Maternal Health Characteristics, Newborn Metabolite Concentrations, and Child Body Mass Index among US Children in the ECHO Program. Metabolites. 2023 Apr 01; 13(4). Snyder BM, Gebretsadik T, Rohrig NB, Wu P, Dupont WD, Dabelea DM, Fry RC, Lynch SV, McEvoy CT, Paneth NS, Ryckman KK, Gern JE, Hartert TV. PMID: 37110168; PMCID: PMC10144800.
      View in: PubMed   Mentions: 1  
    13. The impact of prenatal dog keeping on infant gut microbiota development. Clin Exp Allergy. 2023 08; 53(8):833-845. Panzer AR, Sitarik AR, Fadrosh D, Havstad SL, Jones K, Davidson B, Finazzo S, Wegienka GR, Woodcroft K, Lukacs NW, Levin AM, Ownby DR, Johnson CC, Lynch SV, Zoratti EM. PMID: 36916778.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    14. Interactions between host epigenetics and microbiota: Who does what to whom, when, and why? J Allergy Clin Immunol. 2023 06; 151(6):1465-1467. Vercelli D, Lynch SV. PMID: 36720286.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    15. Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients. Microorganisms. 2022 Dec 21; 11(1). Harringer EOS, Durack J, Piceno Y, Andersen V, Lynch SV. PMID: 36677307; PMCID: PMC9867242.
      View in: PubMed   Mentions:
    16. Complete Genome Sequence of Lactobacillus johnsonii MR1, Isolated from a BALB/c Mouse Cecum. Microbiol Resour Announc. 2022 Dec 13; e0107822. Ravi K, Rauch M, Lynch SV, Lukacs NW, Huffnagle GB. PMID: 36511660.
      View in: PubMed   Mentions:
    17. 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  
    18. Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. Cell Rep Med. 2022 08 16; 3(8):100713. McCauley KE, Rackaityte E, LaMere B, Fadrosh DW, Fujimura KE, Panzer AR, Lin DL, Lynch KV, Halkias J, Mendoza VF, Burt TD, Bendixsen C, Barnes K, Kim H, Jones K, Ownby DR, Johnson CC, Seroogy CM, Gern JE, Boushey HA, Lynch SV, ECHO Children’s Respiratory and Environmental Workgroup. PMID: 35932762; PMCID: PMC9418802.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    19. Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome. Invest Ophthalmol Vis Sci. 2022 08 02; 63(9):32. Chang CJ, Somohano K, Zemsky C, Uhlemann AC, Liebmann J, Cioffi GA, Al-Aswad LA, Lynch SV, Winn BJ. PMID: 36036910; PMCID: PMC9434984.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    20. Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis. BMC Pulm Med. 2022 Jul 28; 22(1):287. Ray KJ, Santee C, McCauley K, Panzer AR, Lynch SV. PMID: 35902830; PMCID: PMC9330662.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    21. Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development. Allergy. 2022 12; 77(12):3617-3628. DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. PMID: 35841380; PMCID: PMC9712226.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    22. Microbiome-Immune Interactions in Allergy and Asthma. J Allergy Clin Immunol Pract. 2022 09; 10(9):2244-2251. Huang YJ, Porsche C, Kozik AJ, Lynch SV. PMID: 35724951; PMCID: PMC10566566.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansPHPublic Health
    23. Intestinal inflammation alters the antigen-specific immune response to a skin commensal. Cell Rep. 2022 05 31; 39(9):110891. Merana GR, Dwyer LR, Dhariwala MO, Weckel A, Gonzalez JR, Okoro JN, Cohen JN, Tamaki CM, Han J, Tasoff P, Palacios-Calderon Y, Ha CWY, Lynch SV, Segre JA, Kong HH, Kattah MG, Ma A, Scharschmidt TC. PMID: 35649365; PMCID: PMC9248974.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    24. Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents. Pediatr Res. 2023 Jun; 93(7):2051-2060. Cassidy-Bushrow AE, Sitarik AR, Johnson CC, Johnson-Hooper TM, Kassem Z, Levin AM, Lynch SV, Ownby DR, Phillips JM, Yong GJM, Wegienka G, Straughen JK. PMID: 35440767; PMCID: PMC9582043.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    25. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Sci Rep. 2022 04 01; 12(1):5517. Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. PMID: 35365713; PMCID: PMC8976058.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    26. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. Lancet Microbe. 2022 05; 3(5):e357-e365. Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR. PMID: 35544096.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    27. Prebiotic to Improve Calcium Absorption in Postmenopausal Women After Gastric Bypass: A Randomized Controlled Trial. J Clin Endocrinol Metab. 2022 03 24; 107(4):1053-1064. Wu KC, Cao S, Weaver CM, King NJ, Patel S, Kingman H, Sellmeyer DE, McCauley K, Li D, Lynch SV, Kim TY, Black DM, Shafer MM, Özçam M, Lin DL, Rogers SJ, Stewart L, Carter JT, Posselt AM, Schafer AL. PMID: 34888663; PMCID: PMC8947782.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    28. Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations. J Allergy Clin Immunol. 2022 07; 150(1):204-213. McCauley KE, Flynn K, Calatroni A, DiMassa V, LaMere B, Fadrosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Liu AH, Johnson CC, Kim H, Kattan M, O'Connor GT, Bacharier LB, Teach SJ, Gergen PJ, Wheatley LM, Togias A, LeBeau P, Presnell S, Boushey HA, Busse WW, Gern JE, Jackson DJ, Altman MC, Lynch SV, National Institute of Allergy and Infectious Diseases–sponsored Inner-City Asthma Consortium. PMID: 35149044.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    29. Associations of physical activity with gut microbiota in pre-adolescent children. Phys Act Nutr. 2021 Dec; 25(4):24-37. Santarossa S, Sitarik AR, Johnson CC, Li J, Lynch SV, Ownby DR, Ramirez A, Yong GL, Cassidy-Bushrow AE. PMID: 35152621; PMCID: PMC8843867.
      View in: PubMed   Mentions: 3  
    30. Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis. PLoS One. 2021; 16(12):e0261179. McCauley KE, DeMuri G, Lynch K, Fadrosh DW, Santee C, Nagalingam NN, Wald ER, Lynch SV. PMID: 34962959; PMCID: PMC8714118.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    31. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. medRxiv. 2021 Nov 30. Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Detweiler A, Jones NG, Wu B, Darmanis S, Lynch SV, DeRisi JL, COMET Consortium, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. PMID: 33791731; PMCID: PMC8010763.
      View in: PubMed   Mentions: 1  
    32. 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: 58     Fields:    Translation:HumansAnimalsCells
    33. Maternal gut microbiome regulates immunity to RSV infection in offspring. J Exp Med. 2021 11 01; 218(11). Fonseca W, Malinczak CA, Fujimura K, Li D, McCauley K, Li J, Best SKK, Zhu D, Rasky AJ, Johnson CC, Bermick J, Zoratti EM, Ownby D, Lynch SV, Lukacs NW, Ptaschinski C. PMID: 34613328; PMCID: PMC8500238.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    34. The oral microbiome: Role of key organisms and complex networks in oral health and disease. Periodontol 2000. 2021 10; 87(1):107-131. Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL. PMID: 34463991; PMCID: PMC8457218.
      View in: PubMed   Mentions: 112     Fields:    Translation:Humans
    35. Gut microbiome is associated with multiple sclerosis activity in children. Ann Clin Transl Neurol. 2021 09; 8(9):1867-1883. Horton MK, McCauley K, Fadrosh D, Fujimura K, Graves J, Ness J, Wheeler Y, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Rodriguez M, Tillema JM, Krupp L, Belman A, Mar S, Rensel M, Chitnis T, Casper TC, Rose J, Hart J, Shao X, Tremlett H, Lynch SV, Barcellos LF, Waubant E, U.S. Network of Pediatric MS Centers. PMID: 34409759; PMCID: PMC8419410.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    36. Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota. Dig Dis Sci. 2022 06; 67(6):2433-2443. Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV. PMID: 34059992.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    37. Fungus fuels mucosal wounds in Crohn's disease. Immunity. 2021 05 11; 54(5):856-858. Magnaye KM, Lynch SV. PMID: 33979584.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    38. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. Res Sq. 2021 Apr 23. Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. PMID: 34013247; PMCID: PMC8132240.
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    40. Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study. Matern Health Neonatol Perinatol. 2020; 6:5. Kassem Z, Sitarik A, Levin AM, Lynch SV, Havstad S, Fujimura K, Kozyrskyj A, Ownby DR, Johnson CC, Yong GJM, Wegienka G, Cassidy-Bushrow AE. PMID: 33101701; PMCID: PMC7576815.
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    42. Distinct lung microbiota associate with HIV-associated chronic lung disease in children. Sci Rep. 2020 09 30; 10(1):16186. Bhadriraju S, Fadrosh DW, Shenoy MK, Lin DL, Lynch KV, McCauley K, Ferrand RA, Majonga ED, McHugh G, Huang L, Lynch SV, Metcalfe JZ. PMID: 32999331; PMCID: PMC7527458.
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    43. Gut Microbial Regulation of Autism Spectrum Disorder Symptoms. Trends Endocrinol Metab. 2020 11; 31(11):809-811. Panzer AR, Lynch SV. PMID: 32972817.
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    44. Association between cesarean delivery types and obesity in preadolescence. Int J Obes (Lond). 2020 10; 44(10):2023-2034. Sitarik AR, Havstad SL, Johnson CC, Jones K, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Yong GJM, Cassidy-Bushrow AE. PMID: 32873910; PMCID: PMC7530127.
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    45. Fetal and early postnatal lead exposure measured in teeth associates with infant gut microbiota. Environ Int. 2020 11; 144:106062. Sitarik AR, Arora M, Austin C, Bielak LF, Eggers S, Johnson CC, Lynch SV, Kyun Park S, Hank Wu KH, Yong GJM, Cassidy-Bushrow AE. PMID: 32871381; PMCID: PMC7572588.
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    46. Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. Lancet Respir Med. 2020 05; 8(5):482-492. Ober C, McKennan CG, Magnaye KM, Altman MC, Washington C, Stanhope C, Naughton KA, Rosasco MG, Bacharier LB, Billheimer D, Gold DR, Gress L, Hartert T, Havstad S, Khurana Hershey GK, Hallmark B, Hogarth DK, Jackson DJ, Johnson CC, Kattan M, Lemanske RF, Lynch SV, Mendonca EA, Miller RL, Naureckas ET, O'Connor GT, Seroogy CM, Wegienka G, White SR, Wood RA, Wright AL, Zoratti EM, Martinez FD, Ownby D, Nicolae DL, Levin AM, Gern JE, Environmental Influences on Child Health Outcomes-Children's Respiratory Research Workgroup. PMID: 32380068; PMCID: PMC7335429.
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    47. Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma. J Allergy Clin Immunol. 2020 11; 146(5):1016-1026. Durack J, Christian LS, Nariya S, Gonzalez J, Bhakta NR, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Peters SP, Rosenberg SR, Sorkness CA, Wechsler ME, Wenzel SE, White SR, Lynch SV, Boushey HA, Huang YJ, National Heart, Lung, and Blood Institute’s ”AsthmaNet“. PMID: 32298699; PMCID: PMC7554083.
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    49. Translating the gut microbiome: ready for the clinic? Nat Rev Gastroenterol Hepatol. 2019 11; 16(11):656-661. Lynch SV, Ng SC, Shanahan F, Tilg H. PMID: 31562390.
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    50. Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. Nat Microbiol. 2019 11; 4(11):1851-1861. Levan SR, Stamnes KA, Lin DL, Panzer AR, Fukui E, McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV. PMID: 31332384; PMCID: PMC6830510.
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    51. Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study. Dig Dis Sci. 2020 04; 65(4):1099-1106. Selvig D, Piceno Y, Terdiman J, Zydek M, Umetsu SE, Balitzer D, Fadrosh D, Lynch K, Lamere B, Leith T, Kassam Z, Beck K, Lewin S, Ma A, Somsouk M, Lynch SV, El-Nachef N. PMID: 31302808.
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    52. A20 in dendritic cells restrains intestinal anti-bacterial peptide expression and preserves commensal homeostasis. PLoS One. 2019; 14(7):e0218999. Talpin A, Kattah MG, Advincula R, Fadrosh D, Lynch K, LaMere B, Fujimura KE, Nagalingam NA, Malynn BA, Lynch SV, Ma A. PMID: 31295268; PMCID: PMC6622485.
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    53. Author Correction: Differences in the fecal microbiota of neonates born at home or in the hospital. Sci Rep. 2019 Jun 18; 9(1):9044. Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG. PMID: 31209226; PMCID: PMC6579757.
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    54. Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma. J Allergy Clin Immunol. 2019 11; 144(5):1187-1197. McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ, Lynch SV, National Institute of Allergy and Infectious Diseases–sponsored Inner-City Asthma Consortium. PMID: 31201890; PMCID: PMC6842413.
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    55. Community ecology as a framework for human microbiome research. Nat Med. 2019 06; 25(6):884-889. Gilbert JA, Lynch SV. PMID: 31133693; PMCID: PMC7410146.
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    56. Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile. United European Gastroenterol J. 2019 07; 7(6):807-814. Gutin L, Piceno Y, Fadrosh D, Lynch K, Zydek M, Kassam Z, LaMere B, Terdiman J, Ma A, Somsouk M, Lynch S, El-Nachef N. PMID: 31316785; PMCID: PMC6620877.
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    57. Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction. Microbiome. 2019 03 11; 7(1):37. Shenoy MK, Fadrosh DW, Lin DL, Worodria W, Byanyima P, Musisi E, Kaswabuli S, Zawedde J, Sanyu I, Chang E, Fong S, McCauley K, Davis JL, Huang L, Lynch SV. PMID: 30857553; PMCID: PMC6413461.
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    58. Longitudinal Phenotypes of Respiratory Health in a High-Risk Urban Birth Cohort. Am J Respir Crit Care Med. 2019 01 01; 199(1):71-82. Bacharier LB, Beigelman A, Calatroni A, Jackson DJ, Gergen PJ, O'Connor GT, Kattan M, Wood RA, Sandel MT, Lynch SV, Fujimura KE, Fadrosh DW, Santee CA, Boushey H, Visness CM, Gern JE, NIAID sponsored Inner-City Asthma Consortium. PMID: 30079758; PMCID: PMC6353010.
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    59. Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease. J Pediatr Gastroenterol Nutr. 2019 01; 68(1):30-36. Fernandes MA, Verstraete SG, Phan TG, Deng X, Stekol E, LaMere B, Lynch SV, Heyman MB, Delwart E. PMID: 30169455; PMCID: PMC6310095.
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    60. Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease. Hepatol Commun. 2019 Jan; 3(1):29-43. Sharpton SR, Yong GJM, Terrault NA, Lynch SV. PMID: 30619992; PMCID: PMC6312661.
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    61. Rules of engagement in the gut microbiome. Nat Med. 2018 11; 24(11):1642-1644. Rackaityte E, Lynch SV. PMID: 30401869.
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    62. Differences in the fecal microbiota of neonates born at home or in the hospital. Sci Rep. 2018 10 23; 8(1):15660. Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG. PMID: 30353125; PMCID: PMC6199260.
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    63. The gut microbiome: Relationships with disease and opportunities for therapy. J Exp Med. 2019 01 07; 216(1):20-40. Durack J, Lynch SV. PMID: 30322864; PMCID: PMC6314516.
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    64. Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments. Gut Microbes. 2019; 10(1):34-44. Ovesen S, Durack J, Kirk KF, Nielsen HL, Nielsen H, Lynch SV. PMID: 30252590; PMCID: PMC6363072.
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    65. Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization. Microbiome. 2018 09 05; 6(1):154. Chang HW, Yan D, Singh R, Liu J, Lu X, Ucmak D, Lee K, Afifi L, Fadrosh D, Leech J, Vasquez KS, Lowe MM, Rosenblum MD, Scharschmidt TC, Lynch SV, Liao W. PMID: 30185226; PMCID: PMC6125946.
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    67. Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation. Front Cell Infect Microbiol. 2018; 8:168. Lee K, Pletcher SD, Lynch SV, Goldberg AN, Cope EK. PMID: 29876323; PMCID: PMC5974464.
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    68. Current understanding of the human microbiome. Nat Med. 2018 04 10; 24(4):392-400. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. PMID: 29634682; PMCID: PMC7043356.
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    69. Dynamics of Bacterial Colonization With Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis During Symptomatic and Asymptomatic Viral Upper Respiratory Tract Infection. Clin Infect Dis. 2018 03 19; 66(7):1045-1053. DeMuri GP, Gern JE, Eickhoff JC, Lynch SV, Wald ER. PMID: 29121208; PMCID: PMC6019034.
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    70. Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients. Am J Respir Crit Care Med. 2018 03 01; 197(5):621-631. Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. PMID: 29035085; PMCID: PMC6005235.
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    71. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat Commun. 2018 02 16; 9(1):707. Durack J, Kimes NE, Lin DL, Rauch M, McKean M, McCauley K, Panzer AR, Mar JS, Cabana MD, Lynch SV. PMID: 29453431; PMCID: PMC5816017.
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    72. Role of the lung microbiome in HIV pathogenesis. Curr Opin HIV AIDS. 2018 Jan; 13(1):45-52. Shenoy MK, Lynch SV. PMID: 29035946.
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    73. Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury. Trauma Surg Acute Care Open. 2017; 2(1):e000108. Howard BM, Kornblith LZ, Christie SA, Conroy AS, Nelson MF, Campion EM, Callcut RA, Calfee CS, Lamere BJ, Fadrosh DW, Lynch S, Cohen MJ. PMID: 29766103; PMCID: PMC5877916.
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    100. Influence and effect of the human microbiome in allergy and asthma. Curr Opin Rheumatol. 2015 Jul; 27(4):373-80. Panzer AR, Lynch SV. PMID: 26002029.
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    101. Does pet-keeping modify the association of delivery mode with offspring body size? Matern Child Health J. 2015 Jun; 19(6):1426-33. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. PMID: 25427878; PMCID: PMC4446256.
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    102. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe. 2015 May 13; 17(5):592-602. Fujimura KE, Lynch SV. PMID: 25974301; PMCID: PMC4443817.
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    103. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. 2015; 10(2):e0117617. Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. PMID: 25658760; PMCID: PMC4319838.
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    104. 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. Lynch SV. PMID: 25546336.
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    105. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci Transl Med. 2014 Sep 03; 6(252):252ra120. Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch SV, Hartigan-O'Connor DJ. PMID: 25186175; PMCID: PMC4362692.
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    106. Fecal microbial therapy: promises and pitfalls. J Pediatr Gastroenterol Nutr. 2014 Aug; 59(2):157-61. Merenstein D, El-Nachef N, Lynch SV. PMID: 24796803; PMCID: PMC4669049.
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    107. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Gut Microbes. 2014 Jul 01; 5(4):494-503. Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch SV. PMID: 25144681.
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    108. 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. 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. PMID: 24908147; PMCID: PMC4151305.
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    109. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014 Aug; 52(8):2813-23. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. PMID: 24850358; PMCID: PMC4136157.
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    110. 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. Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV. PMID: 24752365; PMCID: PMC3994144.
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    111. Viruses and microbiome alterations. Ann Am Thorac Soc. 2014 Jan; 11 Suppl 1:S57-60. Lynch SV. PMID: 24437408.
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    112. 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. Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV. PMID: 24344318; PMCID: PMC3896155.
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    113. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91. 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. PMID: 23843452; PMCID: PMC4094294.
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    114. Probiotic strategies for treatment of respiratory diseases. Trends Microbiol. 2013 Sep; 21(9):485-92. Nagalingam NA, Cope EK, Lynch SV. PMID: 23707554.
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    115. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013 May 15; 187(10):1067-75. 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, Lung HIV Microbiome Project. PMID: 23491408; PMCID: PMC3734620.
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    116. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013 May 15; 187(10):1110-7. 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, Lung HIV Microbiome Project. PMID: 23392441; PMCID: PMC3734615.
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    117. The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med. 2013 Mar 01; 3(3):a009738. Lynch SV, Bruce KD. PMID: 23457293; PMCID: PMC3579208.
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    118. Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Gut Microbes. 2013 Jan-Feb; 4(1):41-7. Lynch SV, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL. PMID: 23060053; PMCID: PMC3555885.
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    119. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med. 2012 Sep 12; 4(151):151ra124. Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, Lynch SV. PMID: 22972842; PMCID: PMC4786373.
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    120. Development of a standardized approach for environmental microbiota investigations related to asthma development in children. J Microbiol Methods. 2012 Nov; 91(2):231-9. 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. PMID: 22975469; PMCID: PMC3615718.
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    121. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol. 2012 Sep; 50(9):2995-3002. Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SV, Huang L. PMID: 22760045; PMCID: PMC3421777.
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    122. Gut dysbiosis in cystic fibrosis. J Cyst Fibros. 2012 Sep; 11(5):454-5. Scanlan PD, Buckling A, Kong W, Wild Y, Lynch SV, Harrison F. PMID: 22538067.
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    123. From microbe to microbiota: considering microbial community composition in infections and airway diseases. Am J Respir Crit Care Med. 2012 Apr 01; 185(7):691-2. Huang YJ, Lynch SV, Wiener-Kronish JP. PMID: 22467799.
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    124. Pseudomonas aeruginosa biofilm-associated homoserine lactone C12 rapidly activates apoptosis in airway epithelia. Cell Microbiol. 2012 May; 14(5):698-709. Schwarzer C, Fu Z, Patanwala M, Hum L, Lopez-Guzman M, Illek B, Kong W, Lynch SV, Machen TE. PMID: 22233488; PMCID: PMC4112999.
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    125. Significance of the microbiome in obstructive lung disease. Thorax. 2012 May; 67(5):456-63. 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. PMID: 22318161; PMCID: PMC3578398.
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    126. 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. 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. PMID: 22312017; PMCID: PMC3360572.
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    127. PcrV antibody-antibiotic combination improves survival in Pseudomonas aeruginosa-infected mice. Eur J Clin Microbiol Infect Dis. 2012 Aug; 31(8):1837-45. Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch SV. PMID: 22187351.
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    128. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med. 2011 Dec; 5(6):809-21. Huang YJ, Lynch SV. PMID: 22082166; PMCID: PMC3359942.
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    129. The potential for probiotic manipulation of the gastrointestinal microbiome. Curr Opin Biotechnol. 2012 Apr; 23(2):192-201. Rauch M, Lynch SV. PMID: 22137452.
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    130. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. J Leukoc Biol. 2012 Feb; 91(2):275-84. Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH. PMID: 22075928; PMCID: PMC3290427.
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    131. Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2012 May; 18(5):968-84. Nagalingam NA, Lynch SV. PMID: 21936031.
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    132. 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. Havstad S, Wegienka G, Zoratti EM, Lynch SV, Boushey HA, Nicholas C, Ownby DR, Johnson CC. PMID: 21820714; PMCID: PMC3185205.
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    133. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. 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. PMID: 21741921; PMCID: PMC3417828.
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    134. 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. Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch SV, Yang K. PMID: 21382698; PMCID: PMC3176759.
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    135. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011 Feb; 127(2):372-381.e1-3. 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, National Heart, Lung, and Blood Institute's Asthma Clinical Research Network. PMID: 21194740; PMCID: PMC3037020.
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    136. 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. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SV. PMID: 20633927; PMCID: PMC2956425.
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    137. 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. Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SV. PMID: 20819463.
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    138. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010 Jun 23; 5(6):e11044. 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. PMID: 20585638; PMCID: PMC2890402.
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    139. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio. 2010 Jun 22; 1(3). Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. PMID: 20802827; PMCID: PMC2925076.
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    140. Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants. Gut Microbes. 2010 Jul; 1(4):243-253. Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, Heimbach JT, Hempel S, Lynch SV, Sanders ME, Tancredi DJ. PMID: 21327031; PMCID: PMC3023606.
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    141. Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration. Microb Pathog. 2010 Oct; 49(4):196-203. Singh G, Wu B, Baek MS, Camargo A, Nguyen A, Slusher NA, Srinivasan R, Wiener-Kronish JP, Lynch SV. PMID: 20570614; PMCID: PMC2935322.
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    142. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther. 2010 Apr; 8(4):435-54. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. PMID: 20377338; PMCID: PMC2881665.
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    143. Polymorphisms in the Pseudomonas aeruginosa type III secretion protein, PcrV - implications for anti-PcrV immunotherapy. Microb Pathog. 2010 Jun; 48(6):197-204. 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. PMID: 20211240; PMCID: PMC2860055.
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    144. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. 2010 May; 12(5):1293-303. 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. PMID: 20192960.
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    145. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010 Feb; 14(1):9-59. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. PMID: 20141328; PMCID: PMC3116451.
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    146. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One. 2010 Jan 18; 5(1):e8745. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV. PMID: 20090909; PMCID: PMC2807455.
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    147. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009 Oct 30; 139(3):485-98. 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. PMID: 19836068; PMCID: PMC2796826.
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    148. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun. 2009 Nov; 77(11):4877-86. Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko T, Lory S, LaBaer J. PMID: 19737893; PMCID: PMC2772540.
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    149. Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia. J Infect. 2009 Jul; 59(1):49-55. El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SV, Wiener-Kronish JP. PMID: 19535150; PMCID: PMC2756421.
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    150. Novel strategies to combat bacterial virulence. Curr Opin Crit Care. 2008 Oct; 14(5):593-9. Lynch SV, Wiener-Kronish JP. PMID: 18787455; PMCID: PMC2859961.
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    151. Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection. Crit Care Med. 2008 Sep; 36(9):2495-503. 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. PMID: 18679122.
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    152. 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. 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. PMID: 18703797; PMCID: PMC2606944.
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    153. Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia. Am J Respir Crit Care Med. 2008 Sep 01; 178(5):513-9. El Solh AA, Akinnusi ME, Wiener-Kronish JP, Lynch SV, Pineda LA, Szarpa K. PMID: 18467510; PMCID: PMC2542430.
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    154. Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa. Infect Immun. 2008 Jun; 76(6):2325-32. 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. PMID: 18378634; PMCID: PMC2423078.
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    155. 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. Wong-Beringer A, Wiener-Kronish J, Lynch S, Flanagan J. PMID: 18190571.
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    156. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob Agents Chemother. 2007 Oct; 51(10):3650-8. Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A. PMID: 17664315; PMCID: PMC2043260.
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    157. Microbial manipulation of immune function for asthma prevention: inferences from clinical trials. Proc Am Thorac Soc. 2007 Jul; 4(3):277-82. Yoo J, Tcheurekdjian H, Lynch SV, Cabana M, Boushey HA. PMID: 17607013; PMCID: PMC2647630.
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    158. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol. 2007 Jun; 45(6):1954-62. Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J. PMID: 17409203; PMCID: PMC1933106.
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    159. Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia. Crit Care Med. 2007 Feb; 35(2):652-3. Song Y, Wiener-Kronish JP, Flanagan J, Lynch SV. PMID: 17251717.
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    160. 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. 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. PMID: 17264718.
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    161. Presence or absence of lipopolysaccharide O antigens affects type III secretion by Pseudomonas aeruginosa. J Bacteriol. 2007 Mar; 189(6):2203-9. Augustin DK, Song Y, Baek MS, Sawa Y, Singh G, Taylor B, Rubio-Mills A, Flanagan JL, Wiener-Kronish JP, Lynch SV. PMID: 17209027; PMCID: PMC1899375.
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    162. Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system. Appl Environ Microbiol. 2006 Dec; 72(12):7701-10. Lynch SV, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A. PMID: 17028231; PMCID: PMC1694224.
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    163. Effect of chromate stress on Escherichia coli K-12. J Bacteriol. 2006 May; 188(9):3371-81. Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A. PMID: 16621832; PMCID: PMC1447458.
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    164. New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution. Mol Cancer Ther. 2006 Jan; 5(1):97-103. Barak Y, Thorne SH, Ackerley DF, Lynch SV, Contag CH, Matin A. PMID: 16432167.
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    165. ChrR, a soluble quinone reductase of Pseudomonas putida that defends against H2O2. J Biol Chem. 2005 Jun 17; 280(24):22590-5. Gonzalez CF, Ackerley DF, Lynch SV, Matin A. PMID: 15840577.
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    166. Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques. Gene. 2004 Dec 08; 343(1):107-15. Carmody M, Byrne B, Murphy B, Breen C, Lynch S, Flood E, Finnan S, Caffrey P. PMID: 15563836.
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    167. 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. Lynch SV, Brodie EL, Matin A. PMID: 15576768; PMCID: PMC532419.
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    168. Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis. Extremophiles. 2003 Apr; 7(2):135-43. Irwin JA, Lynch SV, Coughlan S, Baker PJ, Gudmundsson HM, Alfredsson GA, Rice DW, Engel PC. PMID: 12664266.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    169. Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. Chem Biol. 2001 Jul; 8(7):713-23. Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk M. PMID: 11451671.
      View in: PubMed   Mentions: 78     Fields:    Translation:Cells
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