Education

BS Biology UNLV

MS Biology UNLV

PhD Microbiology UW


Contact Information:

David C. Nickle

Seattle, WA


Email:

paste ("dc_nickle", "mac.com", sep = "@")

I currently lead a team of talented bioinformaticians at Monoceros Bio, consulting on projects for biopharma clients. The services we provide range from experimental design to full execution of analyses on high dimensional data. The skill sets encompassed by my team include genetics, genomics and proteomics and involve the application of statistical approaches, including standard R limma models, Machine Learning and Artificial Intelligence. I am truly interested in problems of complex traits and infectious disease and I believe genomic technologies will eventually unravel these complexities. I intend to continue developing tools based on population genetics and molecular evolution that can be applied to the understanding and the control of disease. Although scientific autonomy is important, we are in the day and age where meaningful questions in medical science can be addressed most successfully through a collaborative approach that capitalizes on the synergistic effects of a unified group. In this regard, building collaborations across a diverse array of disciplines to answer the big medical questions is my primary focus.

Publications

© 2021 David Nickle

  1. 136: •    Valette K, Li Z, Bon-Baret V, Chignon A, Bérubé JC, Eslami A, Lamothe J, Gaudreault N, Joubert P, Obeidat M, van den Berge M, Timens W, Sin DD, Nickle DC, Hao K, Labbé C, Godbout K, Côté A, Laviolette M, Boulet LP, Mathieu P, Thériault S, Bossé Y. Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank. Commun Biol. 2021 Jun 8;4(1):700. doi: 10.1038/s42003-021-02227-6. PMID: 34103634; PMCID: PMC8187656.


  3. 135: •    Felt SA, Sun Y, Jozwik A, Paras A, Habibi MS, Nickle D, Anderson L, Achouri E, Feemster KA, Cárdenas AM, Turi KN, Chang M, Hartert TV, Sengupta S, Chiu C, López CB. Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes. Nat Microbiol. 2021 May;6(5):672-681. doi: 10.1038/s41564-021-00882-3. Epub 2021 Apr 1. PMID: 33795879.


  5. 134: •    Zhao H, Nickle DC, Zeng Z, Law PYT, Wilcox MH, Chen L, Peng Y, Meng J, Deng Z, Albright A, Zhong H, Xu X, Zhu S, Shen J, Blanchard RL, Dorr MB, Shaw PM, Li J. Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies. Infect Dis Ther. 2021 Jun;10(2):853-870. doi: 10.1007/s40121-021-00426-6. Epub 2021 Mar 22. PMID: 33751421; PMCID: PMC8116447.


  7. 133: •    Guerrina N, Traboulsi H, Rico de Souza A, Bossé Y, Thatcher TH, Robichaud A, Ding J, Li PZ, Simon L, Pareek S, Bourbeau J, Tan WC, Benedetti A, Obeidat M, Sin DD, Brandsma CA, Nickle DC, Sime PJ, Phipps RP, Nair P, Zago M, Hamid Q, Smith BM, Eidelman DH, Baglole CJ. Aryl hydrocarbon receptor deficiency causes the development of chronic obstructive pulmonary disease through the integration of multiple pathogenic mechanisms. FASEB J. 2021 Mar;35(3):e21376. doi: 10.1096/fj.202002350R. PMID: 33605487.


  9. 132: •    Hernández Cordero AI, Li X, Milne S, Yang CX, Bossé Y, Joubert P, Timens W, van den Berge M, Nickle D, Hao K, Sin DD. Multi-omics highlights ABO plasma protein as a causal risk factor for COVID-19. Hum Genet. 2021 Jun;140(6):969-979. doi: 10.1007/s00439-021-02264-5. Epub 2021 Feb 19. PMID: 33604698; PMCID: PMC7892327.


  11. 131: •    Hernández Cordero AI, Li X, Yang CX, Milne S, Bossé Y, Joubert P, Timens W, van den Berge M, Nickle D, Hao K, Sin DD. Gene expression network analysis provides potential targets against SARS-CoV-2. Sci Rep. 2020 Dec 14;10(1):21863. doi: 10.1038/s41598-020-78818-w. PMID: 33318519; PMCID: PMC7736291.


  13. 130: •    Ortega H, Nickle D, Carter L. Rhinovirus and asthma: Challenges and opportunities. Rev Med Virol. 2020 Nov 20:e2193. doi: 10.1002/rmv.2193. Epub ahead of print. PMID: 33217098.


  15. 129: •    Florez-Sampedro L, Brandsma CA, de Vries M, Timens W, Bults R, Vermeulen CJ, van den Berge M, Obeidat M, Joubert P, Nickle DC, Poelarends GJ, Faiz A, Melgert BN. Genetic regulation of gene expression of MIF family members in lung tissue. Sci Rep. 2020 Oct 12;10(1):16980. doi: 10.1038/s41598-020-74121-w. PMID: 33046825; PMCID: PMC7552402.


  17. 128: •    Habibi MS, Thwaites RS, Chang M, Jozwik A, Paras A, Kirsebom F, Varese A, Owen A, Cuthbertson L, James P, Tunstall T, Nickle D, Hansel TT, Moffatt MF, Johansson C, Chiu C, Openshaw PJM. Neutrophilic inflammation in the respiratory mucosa predisposes to RSV infection. Science. 2020 Oct 9;370(6513):eaba9301. doi: 10.1126/science.aba9301. PMID: 33033192.


  19. 127: •    Ketelaar ME, Portelli MA, Dijk FN, Shrine N, Faiz A, Vermeulen CJ, Xu CJ, Hankinson J, Bhaker S, Henry AP, Billington CK, Shaw DE, Johnson SR, Benest AV, Pang V, Bates DO, Pogson ZEK, Fogarty A, McKeever TM, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Niven R, Simpson A, Tobin MD, Hall IP, Wain LV, Blakey JD, Brightling CE, Obeidat M, Sin DD, Nickle DC, Bossé Y, Vonk JM, van den Berge M, Koppelman GH, Sayers I, Nawijn MC. Phenotypic and functional translation of IL33 genetics in asthma. J Allergy Clin Immunol. 2020 May 19:S0091-6749(20)30680-1. doi: 10.1016/j.jaci.2020.04.051. Epub ahead of print. PMID: 32442646.


  21. 126: •    Ji X, Mukherjee S, Landi MT, Bosse Y, Joubert P, Zhu D, Gorlov I, Xiao X, Han Y, Gorlova O, Hung RJ, Brhane Y, Carreras-Torres R, Christiani DC, Caporaso N, Johansson M, Liu G, Bojesen SE, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Chen C, Byun J, Dragnev KH, Field JK, Kiemeney LF, Lazarus P, Zienolddiny S, Lam S, Schabath MB, Andrew AS, Bertazzi PA, Pesatori AC, Diao N, Su L, Song L, Zhang R, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman C, Wilkens L, Fernandez-Somoano A, Fernandez-Tardon G, Heijden EHFMV, Kim JH, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Goodman GE, Cox A, Taylor F, Woll P, Wichmann E, Muley T, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd F, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Butler LM, Offit K, Srinivasan P, Bandlamudi C, Hellmann MD, Solit DB, Robson ME, Rudin CM, Stadler ZK, Taylor BS, Berger MF, Houlston R, McLaughlin J, Stevens V, Nickle DC, Obeidat M, Timens W, Artigas MS, Shete S, Brenner H, Chanock S, Brennan P, McKay JD, Amos CI. Protein-altering germline mutations implicate novel genes related to lung cancer development. Nat Commun. 2020 May 11;11(1):2220. doi: 10.1038/s41467-020-15905-6. PMID: 32393777; PMCID: PMC7214407.


  23. 125: •    Shen J, Mehrotra DV, Dorr MB, Zeng Z, Li J, Xu X, Nickle D, Holzinger ER, Chhibber A, Wilcox MH, Blanchard RL, Shaw PM. Genetic Association Reveals Protection against Recurrence of Clostridium difficile Infection with Bezlotoxumab Treatment. mSphere. 2020 May 6;5(3):e00232-20. doi: 10.1128/mSphere.00232-20. PMID: 32376702; PMCID: PMC7203456.


  25. 124: •    Portelli MA, Dijk FN, Ketelaar ME, Shrine N, Hankinson J, Bhaker S, Grotenboer NS, Obeidat M, Henry AP, Billington CK, Shaw D, Johnson SR, Pogson ZE, Fogarty A, McKeever TM, Nickle DC, Bossé Y, van den Berge M, Faiz A, Brouwer S, Vonk JM, de Vos P, Brandsma CA, Vermeulen CJ, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Niven R, Simpson A, Blakey JD, Tobin MD, Postma DS, Hall IP, Wain LV, Nawijn MC, Brightling CE, Koppelman GH, Sayers I. Phenotypic and functional translation of IL1RL1 locus polymorphisms in lung tissue and asthmatic airway epithelium. JCI Insight. 2020 Apr 23;5(8):e132446. doi: 10.1172/jci.insight.132446. PMID: 32324168; PMCID: PMC7205441.


  27. 123: •    Douglas CM, Barnard R, Holder D, Leavitt R, Levitan D, Maguire M, Nickle D, Teal V, Wan H, van Alewijk DCJG, van Doorn LJ, Chou S, Strizki J. Letermovir Resistance Analysis in a Clinical Trial of Cytomegalovirus Prophylaxis for Hematopoietic Stem Cell Transplant Recipients. J Infect Dis. 2020 Mar 16;221(7):1117-1126. doi: 10.1093/infdis/jiz577. PMID: 31781762; PMCID: PMC7075417.


  29. 122: •    Allen RJ, Guillen-Guio B, Oldham JM, Ma SF, Dressen A, Paynton ML, Kraven LM, Obeidat M, Li X, Ng M, Braybrooke R, Molina-Molina M, Hobbs BD, Putman RK, Sakornsakolpat P, Booth HL, Fahy WA, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Whyte MKB, Zhang Y, Kaminski N, Adegunsoye A, Strek ME, Neighbors M, Sheng XR, Gudmundsson G, Gudnason V, Hatabu H, Lederer DJ, Manichaikul A, Newell JD Jr, O'Connor GT, Ortega VE, Xu H, Fingerlin TE, Bossé Y, Hao K, Joubert P, Nickle DC, Sin DD, Timens W, Furniss D, Morris AP, Zondervan KT, Hall IP, Sayers I, Tobin MD, Maher TM, Cho MH, Hunninghake GM, Schwartz DA, Yaspan BL, Molyneaux PL, Flores C, Noth I, Jenkins RG, Wain LV. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2020 Mar 1;201(5):564-574. doi: 10.1164/rccm.201905-1017OC. PMID: 31710517; PMCID: PMC7047454.


  31. 121: •    van den Berge M, Brandsma CA, Faiz A, de Vries M, Rathnayake SNH, Paré PD, Sin DD, Bossé Y, Laviolette M, Nickle DC, Hao K, Obeidat M, Dragani TA, Colombo F, Timens W, Postma DS. Differential lung tissue gene expression in males and females: implications for the susceptibility to develop COPD. Eur Respir J. 2019 Jul 18;54(1):1702567. doi: 10.1183/13993003.02567-2017. PMID: 31164434.


  33. 120: •    Shrine N, Portelli MA, John C, Soler Artigas M, Bennett N, Hall R, Lewis J,Henry AP, Billington CK, Ahmad A, Packer RJ, Shaw D, Pogson ZEK, Fogarty A,McKeever TM, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, HollowayJW, Lockett GA, Howarth PH, Djukanovic R, Hankinson J, Niven R, Simpson A, Chung KF, Sterk PJ, Blakey JD, Adcock IM, Hu S, Guo Y, Obeidat M, Sin DD, van den BergeM, Nickle DC, Bossé Y, Tobin MD, Hall IP, Brightling CE, Wain LV, Sayers I.Moderate-to-severe asthma in individuals of European ancestry: a genome-wideassociation study. Lancet Respir Med. 2019 Jan;7(1):20-34. doi:10.1016/S2213-2600(18)30389-8. Epub 2018 Dec 11. PubMed PMID: 30552067; PubMedCentral PMCID: PMC6314966.


  35. 119: •    Zeng X, Vonk JM, van der Plaat DA, Faiz A, Paré PD, Joubert P, Nickle D,Brandsma CA, Kromhout H, Vermeulen R, Xu X, Huo X, de Jong K, Boezen HM.Genome-wide interaction study of gene-by-occupational exposures on respiratorysymptoms. Environ Int. 2019 Jan;122:263-269. doi: 10.1016/j.envint.2018.11.017.Epub 2018 Nov 16. PubMed PMID: 30449631.


  37. 118: •    Ji X, Bossé Y, Landi MT, Gui J, Xiao X, Qian D, Joubert P, Lamontagne M, Li Y,Gorlov I, de Biasi M, Han Y, Gorlova O, Hung RJ, Wu X, McKay J, Zong X,Carreras-Torres R, Christiani DC, Caporaso N, Johansson M, Liu G, Bojesen SE, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G,Chen C, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB,Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, SuL, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman C,Wilkens L, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden EHFM, Kim JH,Dai J, Hu Z, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, MullerDC, Overvad K, Trichopoulou A, Tumino R, Doherty J, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Manz J, Muley T, Risch A, Rosenberger A, Grankvist K, JohanssonM, Shepherd F, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V,Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, SwiatkowskaB, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, GaoYT, Houlston R, McLaughlin J, Stevens V, Nickle DC, Obeidat M, Timens W, Zhu B,Song L, Artigas MS, Tobin MD, Wain LV, Gu F, Byun J, Kamal A, Zhu D, Tyndale RF, Wei WQ, Chanock S, Brennan P, Amos CI. Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk. Nat Commun.2018 Aug 13;9(1):3221. doi: 10.1038/s41467-018-05074-y. PubMed PMID: 30104567;PubMed Central PMCID: PMC6089967.


  39. 117: •    Obeidat M, Dvorkin-Gheva A, Li X, Bossé Y, Brandsma CA, Nickle DC, Hansbro PM,Faner R, Agusti A, Paré PD, Stampfli MR, Sin DD. The Overlap of Lung TissueTranscriptome of Smoke Exposed Mice with Human Smoking and COPD. Sci Rep. 2018Aug 8;8(1):11881. doi: 10.1038/s41598-018-30313-z. PubMed PMID: 30089872; PubMed Central PMCID: PMC6082828.


  41. 116: •    Wyss AB, Sofer T, Lee MK, Terzikhan N, Nguyen JN, Lahousse L, Latourelle JC, Smith AV, Bartz TM, Feitosa MF, Gao W, Ahluwalia TS, Tang W, Oldmeadow C, Duan Q, de Jong K, Wojczynski MK, Wang XQ, Noordam R, Hartwig FP, Jackson VE, Wang T, Obeidat M, Hobbs BD, Huan T, Gui H, Parker MM, Hu D, Mogil LS, Kichaev G, Jin J,  Graff M, Harris TB, Kalhan R, Heckbert SR, Paternoster L, Burkart KM, Liu Y, Holliday EG, Wilson JG, Vonk JM, Sanders JL, Barr RG, de Mutsert R, Menezes AMB,  Adams HHH, van den Berge M, Joehanes R, Levin AM, Liberto J, Launer LJ, Morrison  AC, Sitlani CM, Celedón JC, Kritchevsky SB, Scott RJ, Christensen K, Rotter JI, Bonten TN, Wehrmeister FC, Bossé Y, Xiao S, Oh S, Franceschini N, Brody JA, Kaplan RC, Lohman K, McEvoy M, Province MA, Rosendaal FR, Taylor KD, Nickle DC, Williams LK, Burchard EG, Wheeler HE, Sin DD, Gudnason V, North KE, Fornage M, Psaty BM, Myers RH, O'Connor G, Hansen T, Laurie CC, Cassano PA, Sung J, Kim WJ,  Attia JR, Lange L, Boezen HM, Thyagarajan B, Rich SS, Mook-Kanamori DO, Horta BL, Uitterlinden AG, Im HK, Cho MH, Brusselle GG, Gharib SA, Dupuis J, Manichaikul A, London SJ. Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function. Nat Commun. 2018 Jul 30;9(1):2976. doi: 10.1038/s41467-018-05369-0. PubMed PMID: 30061609; PubMed Central PMCID: PMC6065313.


  43. 115: •    Obeidat M, Dvorkin-Gheva A, Li X, Bossé Y, Brandsma CA, Nickle DC, Hansbro PM, Faner R, Agusti A, Paré PD, Stampfli MR, Sin DD. The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD. Sci Rep. 2018 Aug 8;8(1):11881. doi: 10.1038/s41598-018-30313-z. PubMed PMID: 30089872; PubMed  Central PMCID: PMC6082828.


  45. 114: •    Ji X, Bossé Y, Landi MT, Gui J, Xiao X, Qian D, Joubert P, Lamontagne M, Li Y, Gorlov I, de Biasi M, Han Y, Gorlova O, Hung RJ, Wu X, McKay J, Zong X, Carreras-Torres R, Christiani DC, Caporaso N, Johansson M, Liu G, Bojesen SE, Le  Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Chen C, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, Su L, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman C, Wilkens L, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden EHFM, Kim JH, Dai J, Hu Z, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Doherty J, Goodman GE, Cox A, Taylor F,  Woll P, Brüske I, Manz J, Muley T, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd F, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, Gao YT, Houlston R, McLaughlin J, Stevens V, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Artigas MS, Tobin MD, Wain LV, Gu F, Byun J, Kamal A, Zhu D, Tyndale RF,  Wei WQ, Chanock S, Brennan P, Amos CI. Identification of susceptibility pathways  for the role of chromosome 15q25.1 in modifying lung cancer risk. Nat Commun. 2018 Aug 13;9(1):3221. doi: 10.1038/s41467-018-05074-y. PubMed PMID: 30104567; PubMed Central PMCID: PMC6089967.


  47. 113: •    Zeng X, Vonk JM, van der Plaat DA, Faiz A, Paré PD, Joubert P, Nickle D, Brandsma CA, Kromhout H, Vermeulen R, Xu X, Huo X, de Jong K, Boezen HM. Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms. Environ Int. 2018 Nov 15. pii: S0160-4120(18)31288-1. doi: 10.1016/j.envint.2018.11.017. [Epub ahead of print] PubMed PMID: 30449631.


  49. 112: •    Shrine N, Portelli MA, John C, Soler Artigas M, Bennett N, Hall R, Lewis J, Henry AP, Billington CK, Ahmad A, Packer RJ, Shaw D, Pogson ZEK, Fogarty A, McKeever TM, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Djukanovic R, Hankinson J, Niven R, Simpson A, Chung  KF, Sterk PJ, Blakey JD, Adcock IM, Hu S, Guo Y, Obeidat M, Sin DD, van den Berge M, Nickle DC, Bossé Y, Tobin MD, Hall IP, Brightling CE, Wain LV, Sayers I. Moderate-to-severe asthma in individuals of European ancestry: a genome-wide association study. Lancet Respir Med. 2018 Dec 11. pii: S2213-2600(18)30389-8. doi: 10.1016/S2213-2600(18)30389-8. [Epub ahead of print] PubMed PMID: 30552067.


  51. 111: •    Lamontagne M, Bérubé JC, Obeidat M, Cho MH, Hobbs BD, Sakornsakolpat P, de Jong K, Boezen HM; International COPD Genetics Consortium, Nickle D, Hao K, Timens W, van den Berge M, Joubert P, Laviolette M, Sin DD, Paré PD, Bossé Y. Leveraging lung tissue transcriptome to uncover candidate causal genes in COPD genetic associations. Hum Mol Genet. 2018 Mar 14.


  53. 110: •    Nedeljkovic I, Lahousse L, Carnero-Montoro E, Faiz A, Vonk JM, de Jong K, van  der Plaat DA, van Diemen CC, van den Berge M, Obeidat M, Bossé Y, Nickle DC, Consortium BIOS, Uitterlinden AG, van Meurs JBJ, Stricker BHC, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression. Hum Mol Genet. 2018 Jan 15;27(2):396-405.


  55. 109: •    de Vries M, Faiz A, Woldhuis RR, Postma DS, de Jong TV, Sin DD, Bossé Y, Nickle DC, Guryev V, Timens W, van den Berge M, Brandsma CA. Lung tissue gene-expression signature for the ageing lung in COPD. Thorax. 2017 Dec 6.


  57. 108: •    Obeidat M, Li X, Burgess S, Zhou G, Fishbane N, Hansel NN, Bossé Y, Joubert P, Hao K, Nickle DC, van den Berge M, Timens W, Cho MH, Hobbs BD, de Jong K, Boezen  M, Hung RJ, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Paré PD, Sin  DD; International COPD Genetics Consortium, Lung eQTL Consortium, Lung Health Study. Surfactant protein D is a causal risk factor for COPD: results of Mendelian randomisation. Eur Respir J. 2017 Nov 30;50(5).


  59. 107: •    Allen RJ, Porte J, Braybrooke R, Flores C, Fingerlin TE, Oldham JM, Guillen-Guio B, Ma SF, Okamoto T, John AE, Obeidat M, Yang IV, Henry A, Hubbard RB, Navaratnam V, Saini G, Thompson N, Booth HL, Hart SP, Hill MR, Hirani N, Maher TM, McAnulty RJ, Millar AB, Molyneaux PL, Parfrey H, Rassl DM, Whyte MKB, Fahy WA, Marshall RP, Oballa E, Bossé Y, Nickle DC, Sin DD, Timens W, Shrine N, Sayers I, Hall IP, Noth I, Schwartz DA, Tobin MD, Wain LV, Jenkins RG. Genetic variants associated with susceptibility to idiopathic pulmonary fibrosis in people of European ancestry: a genome-wide association study. Lancet Respir Med.  2017 Nov;5(11):869-880. doi: 10.1016/S2213-2600(17)30387-9. Epub 2017 Oct 20.


  61. 106: •    Nieuwenhuis MA, Vonk JM, Himes BE, Sarnowski C, Minelli C, Jarvis D, Bouzigon  E, Nickle DC, Laviolette M, Sin D, Weiss ST, van den Berge M, Koppelman GH, Postma DS. PTTG1IP and MAML3, novel genomewide association study genes for severity of hyperresponsiveness in adult asthma. Allergy. 2017 May;72(5):792-801.


  63. 105: •    McKay JD, Hung RJ, Han Y, Zong X, Carreras-Torres R, Christiani DC, Caporaso NE, Johansson M, Xiao X, Li Y, Byun J, Dunning A, Pooley KA, Qian DC, Ji X, Liu G, Timofeeva MN, Bojesen SE, Wu X, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, Su L, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman CA, Wilkens LR, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden HFM, Kim JH, Dai J, Hu Z, Davies MPA, Marcus  MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Doherty JA, Barnett MP, Chen C, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Wichmann HE, Manz J, Muley TR, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd FA, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, Gao YT, Houlston RS, McLaughlin J, Stevens VL, Joubert P, Lamontagne M, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Kachuri L, Artigas MS, Tobin MD, Wain LV; SpiroMeta Consortium, Rafnar T, Thorgeirsson TE, Reginsson GW, Stefansson K, Hancock DB, Bierut LJ, Spitz MR, Gaddis NC, Lutz SM, Gu F, Johnson  EO, Kamal A, Pikielny C, Zhu D, Lindströem S, Jiang X, Tyndale RF, Chenevix-Trench G, Beesley J, Bossé Y, Chanock S, Brennan P, Landi MT, Amos CI. Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes. Nat Genet. 2017 Jul;49(7):1126-1132. doi: 10.1038/ng.3892.


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  75. 99: •    Asante-Appiah E, Curry S, McMonagle P, Ingravallo P, Chase R, Nickle D, Qiu P, Howe A, Lahser FC. Antiviral Activity and Resistance Analysis of NS3/4A Protease  Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons. Antimicrob Agents Chemother. 2017 Jun 27;61(7). pii: e00363-17.


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  101. 86: •    van der Plaat DA, de Jong K, Lahousse L, Faiz A, Vonk JM, van Diemen CC, Nedeljkovic I, Amin N, Brusselle GG, Hofman A, Brandsma CA, Bossé Y, Sin DD, Nickle DC, van Duijn CM, Postma DS, Boezen HM. Genome-wide association study on the FEV(1)/FVC ratio in never-smokers identifies HHIP and FAM13A. J Allergy Clin  Immunol. 2016 Sep 6. pii: S0091-6749(16)30895-8.


  103. 85: •    Dore GJ, Altice F, Litwin AH, Dalgard O, Gane EJ, Shibolet O, Luetkemeyer A, Nahass R, Peng CY, Conway B, Grebely J, Howe AY, Gendrano IN, Chen E, Huang HC, Dutko FJ, Nickle DC, Nguyen BY, Wahl J, Barr E, Robertson MN, Platt HL; C-EDGE CO-STAR Study Group.. Elbasvir-Grazoprevir to Treat Hepatitis C Virus Infection in Persons Receiving Opioid Agonist Therapy: A Randomized Trial. Ann Intern Med.  2016 Nov 1;165(9):625-634.


  105. 84: •    Faiz A, Donovan C, Nieuwenhuis MA, van den Berge M, Postma DS, Yao S, Park CY, Hirsch R, Fredberg JJ, Tjin G, Halayko AJ, Rempel KL, Ward JP, Lee T, Bossé Y, Nickle DC, Obeidat M, Vonk JM, Black JL, Oliver BG, Krishnan R, McParland B, Bourke JE, Burgess JK. Latrophilin receptors: novel bronchodilator targets in asthma. Thorax. 2016 Jun 20.


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  109. 82: •    Saferali A, Obeidat M, Bérubé JC, Lamontagne M, Bossé Y, Laviolette M, Hao K, Nickle DC, Timens W, Sin DD, Postma DS, Strug LJ, Gallins PJ, Paré PD, Bingle CD,Sandford AJ. Polymorphisms associated with expression of BPIFA1/BPIFB1 and lungdisease severity in cystic fibrosis. Am J Respir Cell Mol Biol. 2015Nov;53(5):607-14.


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  113. 80: •    Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, Laviolette M, SandfordAJ, Daley DD, Hogg JC, Elliott WM, Fishbane N, Timens W, Hysi PG, Kaprio J,Wilson JF, Hui J, Rawal R, Schulz H, Stubbe B, Hayward C, Polasek O, Järvelin MR, Zhao JH, Jarvis D, Kähönen M, Franceschini N, North KE, Loth DW, Brusselle GG,Smith AV, Gudnason V, Bartz TM, Wilk JB, O'Connor GT, Cassano PA, Tang W, WainLV, Soler Artigas M, Gharib SA, Strachan DP, Sin DD, Tobin MD, London SJ, HallIP, Paré PD. Molecular mechanisms underlying variations in lung function: asystems genetics analysis. Lancet Respir Med. 2015 Oct;3(10):782-95. doi:10.1016/S2213-2600(15)00380-X.


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  117. 78: •    Spanjer AI, Menzen MH, Dijkstra AE, van den Berge M, Boezen HM, Nickle DC, SinDD, Bossé Y, Brandsma CA, Timens W, Postma DS, Meurs H, Heijink IH, Gosens R. Apro-inflammatory role for the Frizzled-8 receptor in chronic bronchitis. Thorax. 2016 Apr;71(4):312-22.


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  123. 75: •    Dijkstra AE, Boezen HM, van den Berge M, Vonk JM, Hiemstra PS, Barr RG,Burkart KM, Manichaikul A, Pottinger TD, Silverman EK, Cho MH, Crapo JD, BeatyTH, Bakke P, Gulsvik A, Lomas DA, Bossé Y, Nickle DC, Paré PD, de Koning HJ,Lammers JW, Zanen P, Smolonska J, Wijmenga C, Brandsma CA, Groen HJ, Postma DS;LifeLines Cohort Study group. Dissecting the genetics of chronic mucushypersecretion in smokers with and without COPD. Eur Respir J. 2015Jan;45(1):60-75.


  125. 74: •    Howe AY, Long J, Nickle DC, Barnard R, Thompson S, Howe J, Alves K, Wahl J.Long-term follow-up of patients receiving boceprevir for treatment of chronichepatitis C. Antiviral Res. 2015 Jan;113:71-8.4: Howe AY, Black S, Curry S, Ludmerer SW, Liu R, Barnard RJ, Newhard W, HwangPM, Nickle D, Gilbert C, Caro L, DiNubile MJ, Mobashery N. Virologic resistanceanalysis from a phase 2 study of MK-5172 combined with pegylatedinterferon/ribavirin in treatment-naive patients with hepatitis C virus genotype 1 infection. Clin Infect Dis. 2014 Dec 15;59(12):1657-65.


  127. 73: •    Dijkstra AE, Postma DS, van Ginneken B, Wielpütz MO, Schmidt M, Becker N,Owsijewitsch M, Kauczor HU, de Koning HJ, Lammers JW, Oudkerk M, Brandsma CA,Bossé Y, Nickle DC, Sin DD, Hiemstra PS, Wijmenga C, Smolonska J, Zanen P, VonkJM, van den Berge M, Boezen HM, Groen HJ. Novel genes for airway wall thicknessidentified with combined genome-wide association and expression analyses. Am JRespir Crit Care Med. 2015 Mar 1;191(5):547-56.


  129. 72: •    Saferali A, Obeidat M, Bérubé JC, Lamontagne M, Bossé Y, Laviolette M, Hao K, Nickle DC, Timens W, Sin DD, Postma DS, Strug LJ, Gallins PJ, Paré PD, Bingle CD,Sandford AJ. Polymorphisms Associated with Expression of BPIFA1/BPIFB1 and LungDisease Severity in Cystic Fibrosis. Am J Respir Cell Mol Biol. 2015 Jan 9.


  131. 71: •    Kurakula K, Vos M, Logiantara A, Roelofs JJ, Nieuwenhuis MA, Koppelman GH, Postma DS, Brandsma CA, Sin DD, Bossé Y, Nickle DC, van Rijt LS, de Vries CJ. Deficiency of FHL2 attenuates airway inflammation in mice and genetic variation associates with human bronchial hyper-responsiveness. Allergy. 2015 Jul 28.


  133. 70: •    Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, Laviolette M, Sandford AJ, Daley DD, Hogg JC, Elliott WM, Fishbane N, Timens W, Hysi PG, Kaprio J, Wilson JF, Hui J, Rawal R, Schulz H, Stubbe B, Hayward C, Polasek O, Järvelin MR, Zhao JH, Jarvis D, Kähönen M, Franceschini N, North KE, Loth DW, Brusselle GG, Smith AV, Gudnason V, Bartz TM, Wilk JB, O'Connor GT, Cassano PA, Tang W, Wain LV, Artigas MS, Gharib SA, Strachan DP, Sin DD, Tobin MD, London SJ, Hall IP, Paré PD. Molecular mechanisms underlying variations in lung function: a systems genetics analysis. Lancet Respir Med. 2015 Sep 21.


  135. 69: •    Nguyen JD, Lamontagne M, Couture C, Conti M, Paré PD, Sin DD, Hogg JC, Nickle DC, Postma DS, Timens W, Laviolette M, Bossé Y. Susceptibility loci for lungcancer are associated with mRNA levels of nearby genes in the lung.Carcinogenesis. 2014 Dec;35(12):2653-9.


  137. 68: •    Lamontagne M, Couture C, Postma DS, Timens W, Sin DD, Paré PD, Hogg JC, Nickle D, Laviolette M, Bossé Y. Refining susceptibility loci of chronic obstructivepulmonary disease with lung eqtls. PLoS One. 2013 Jul 30;8(7)


  139. 67: •    Howe AY, Long J, Nickle D, Barnard R, Thompson S, Howe J, Alves K, Wahl J.Long-term follow-up of patients receiving boceprevir for treatment of chronichepatitis C. Antiviral Res. 2014 Oct 24;113C 71-78.


  141. 66: •    Howe AY, Black S, Curry S, Ludmerer SW, Liu R, Barnard RJ, Newhard W, HwangPM, Nickle D, Gilbert C, Caro L, DiNubile MJ, Mobashery N. Virologic ResistanceAnalysis From a Phase 2 Study of MK-5172 Combined With PegylatedInterferon/Ribavirin in Treatment-Naive Patients With Hepatitis C Virus Genotype 1 Infection. Clin Infect Dis. 2014 Dec 15;59(12) 1657-65.


  143. 65: •    Nguyen JD, Lamontagne M, Couture C, Conti M, Paré PD, Sin DD, Hogg JC, Nickle D, Postma DS, Timens W, Laviolette M, Bossé Y. Susceptibility loci for lungcancer are associated with mRNA levels of nearby genes in the lung.Carcinogenesis. 2014 Dec;35(12)Dijkstra AE, Boezen HM, van den Berge M, Vonk JM, Hiemstra PS, Barr RG,Burkart KM, Manichaikul A, Pottinger TD, Silverman EK, Cho MH, Crapo JD, BeatyTH, Bakke P, Gulsvik A, Lomas DA, Bossé Y, Nickle DC, Paré PD, de Koning HJ,Lammers JW, Zanen P, Smolonska J, Wijmenga C, Brandsma CA, Groen HJ, Postma DS;the LifeLines Cohort Study group. Dissecting the genetics of chronic mucushypersecretion in smokers with and without COPD. Eur Respir J. 2014 Sep 18.


  145. 64: •    Brandsma CA, van den Berge M, Postma DS, Jonker MR, Brouwer S, Paré PD, SinDD, Bossé Y, Laviolette M, Karjalainen J, Fehrmann RS, Nickle DC, Hao K, Spanjer AI, Timens W, Franke L. A large lung gene expression study identifying fibulin-5 as a novel player in tissue repair in COPD. Thorax. 2014 Jul 2.


  147. 63: •    Akhabir L, Bérubé JC, Bossé Y, Laviolette M, Hao K, Nickle DC, Timens W, SinDD, Paré PD, Postma DS, Sandford AJ. Lung expression quantitative trait loci dataset identifies important functional polymorphisms in the asthma-associated IL1RL1region. J Allergy Clin Immunol. 2014 Sep;134(3) 729-31.


  149. 62: •    Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD,Bossé Y, Nickle D, Brandsma CA, Malarstig A, Vangjeli C, Jelinsky SA, John S,Kilty I, McKeever T, Shrine NR, Cook JP, Patel S, Spector TD, Hollox EJ, Hall IP,Tobin MD. Whole exome re-sequencing implicates CCDC38 and cilia structure andfunction in resistance to smoking related airflow obstruction. PLoS Genet. 2014May 1;10(5)


  151. 61: •    Lamontagne M, Timens W, Hao K, Bossé Y, Laviolette M, Steiling K, Campbell JD,Couture C, Conti M, Sherwood K, Hogg JC, Brandsma CA, van den Berge M, SandfordA, Lam S, Lenburg ME, Spira A, Paré PD, Nickle D, Sin DD, Postma DS. Geneticregulation of gene expression in the lung identifies CST3 and CD22 as potentialcausal genes for airflow obstruction. Thorax. 2014 Nov;69(11) 997-1004. 10.1136/thoraxjnl-2014-205630. Epub 2014 Sep 2.


  153. 60: •    Wang IM, Stone DJ, Nickle D, Loboda A, Puig O, Roberts C. Systems biologyapproach for new target and biomarker identification. Curr Top Microbiol Immunol.2013;363 169-99.


  155. 59: •    Bérubé JC, Lamontagne M, Couture C, Nickle D, Timens W, Postma DS, Sin DD, Paré PD, Laviolette M, Bossé Y. Genome-wide genetic ancestry measurements to predict lung function in European populations. Eur Respir J. 2013 Oct;42(4):1144-7.


  157. 58: •    Barnard RJ, McHale CM, Newhard W, Cheney CA, Graham DJ, Himmelberger AL, Strizki J, Hwang PM, Rivera AA, Reeves JD, Nickle D, Dinubile MJ, Hazuda DJ, Mobashery N. Emergence of resistance-associated variants after failed triple therapy with vaniprevir in treatment-experienced non-cirrhotic patients with hepatitis C-genotype 1 infection: a population and clonal analysis. Virology. 2013 Sep 1;443(2):278-84.


  159. 57: •    Nickle DC, Goncharoff LM. Human fist evolution: a critique. J Exp Biol. 2013 Jun 15;216(Pt 12):2359-60.


  161. 56: •    Hao K, Bossé Y, Nickle DC, Paré PD, Postma DS, et al. Nov. 2012. Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma. PLoS Genet 8(11). Co-first author.


  163. 55: •    Rolland M, Frahm N, Nickle DC, Jojic N, Deng W, Allen TM, Brander C, Heckerman DE, Mullins JI. Increased breadth and depth of cytotoxic T lymphocytes responses  against HIV-1-B Nef by inclusion of epitope variant sequences. PLoS One. 2011 Mar 28;6(3).


  165. 54: •    Yang X, Peterson L, Thieringer R, Deignan JL, Wang X, Zhu J, Wang S, Zhong H, Stepaniants S, Beaulaurier J, Wang IM, Rosa R, Cumiskey AM, Luo JM, Luo Q, Shah K, Xiao J, Nickle D, Plump A, Schadt EE, Lusis AJ, Lum PY. Identification and validation of genes affecting aortic lesions in mice. J Clin Invest. 2010 Jul 1;120(7):2414-22. doi: 10.1172/JCI42742. Epub 2010 Jun 23.


  167. 53: •    Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI. DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques. 2010 May;48(5):405-8.


  169. 52: •    Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI. Rare HLA drive additional HIV evolution compared to more frequent alleles. AIDS Res Hum Retroviruses. 2009 Mar;25(3):297-303.


  171. 51: •    Campbell MS, Gottlieb GS, Hawes SE, Nickle DC, Wong KG, Deng W, Lampinen TM, Kiviat NB, Mullins JI. HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk? PLoS One. 2009 May 28;4(5)


  173. 50: •    Balajee SA, Baddley JW, Peterson SW, Nickle D, Varga J, Boey A, Lass-Fl√∂rl C,  Frisvad JC, Samson RA; ISHAM Working Group on A. terreus. Aspergillus alabamensis, a new clinically relevant species in the section Terrei. Eukaryot Cell. 2009 May;8(5):713-22.


  175. 49: •    Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R.  Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol. 2008 Sep 26;4(9):e1000181.


  177. 48: •    Nickle DC, Jojic N, Heckerman D, Jojic V, Kirovski D, Rolland M, Kosakovsky Pond S, Mullins JI.  Comparison of immunogen designs that optimize peptide coverage: reply to Fischer  et al. PLoS Comput Biol. 2008 Jan;4(1):e25. No abstract available.


  179. 47: •    Rousseau CM, Daniels MG, Carlson JM, Kadie C, Crawford H, Prendergast A, Matthews P, Payne R, Rolland M, Raugi DN, Maust BS, Learn GH, Nickle DC, Coovadia H, Ndung'u T, Frahm N, Brander C, Walker BD, Goulder PJ, Bhattacharya T, Heckerman DE, Korber BT, Mullins JI.  HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. J Virol. 2008 Jul;82(13):6434-46. Epub 2008 Apr 23.


  181. 46: •    Diem K, Nickle DC, Motoshige A, Fox A, Ross S, Mullins JI, Corey L, Coombs RW, Krieger JN.  Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses. 2008 Apr;24(4):561-71.


  183. 45: •    Gottlieb GS, Heath L, Nickle DC, Wong KG, Leach SE, Jacobs B, Gezahegne S, van 't Wout AB, Jacobson LP, Margolick JB, Mullins JI.  HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. J Infect Dis. 2008 Apr 1;197(7):1011-5.


  185. 44: •    Sylla M, Chamberland A, Boileau C, Traoré HA, Ag-Aboubacrine S, Cissé M, Koala S, Drabo J, Diallo I, Niamba P, Tremblay-Sher D, Machouf N, Rashed S, Nickle DC,  Nguyen VK, Tremblay CL; ATARAO Group.  Characterization of drug resistance in antiretroviral-treated patients infected with HIV-1 CRF02_AG and AGK subtypes in Mali and Burkina Faso. Antivir Ther. 2008;13(1):141-8.


  187. 43: •    Ngumbela KC, Day CL, Mncube Z, Nair K, Ramduth D, Thobakgale C, Moodley E, Reddy S, de Pierres C, Mkhwanazi N, Bishop K, van der Stok M, Ismail N, Honeyborne I, Crawford H, Kavanagh DG, Rousseau C, Nickle D, Mullins J, Heckerman D, Korber B, Coovadia H, Kiepiela P, Goulder PJ, Walker BD.  Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with  markers of HIV disease progression and lack of selection pressure. AIDS Res Hum Retroviruses. 2008 Jan;24(1):72-82.


  189. 42: •    Frahm N, Nickle DC, Linde CH, Cohen DE, Zuñiga R, Lucchetti A, Roach T, Walker BD, Allen TM, Korber BT, Mullins JI, Brander C.  Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity. AIDS. 2008 Feb 19;22(4):447-56.


  191. 41: •    Chun TW, Nickle DC, Justement JS, Meyers JH, Roby G, Hallahan CW, Kottilil S,  Moir S, Mican JM, Mullins JI, Ward DJ, Kovacs JA, Mannon PJ, Fauci AS.  Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis. 2008 Mar 1;197(5):714-20.


  193. 40: •    Rolland M, Nickle DC, Mullins JI.  HIV-1 group M conserved elements vaccine. PLoS Pathog. 2007 Nov;3(11):e157. Review.


  195. 39: •    Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Kaslow RA, Shepherd JC, Margolick JB, Mullins JI. HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report. Clin Infect Dis. 2007 Aug 15;45(4):501-9.


  197. 38: •    Rolland M, Brander C, Nickle DC, Herbeck JT, Gottlieb GS, Campbell MS, Maust BS, Mullins JI. HIV-1 over time: fitness loss or robustness gain? Nat Rev Microbiol. 2007 Sep;5(9):1-2.


  199. 37: •    Rolland M, Nickle DC, Deng W, Frahm N, Brander C, Learn GH, Heckerman D, Jojic N, Jojic V, Walker BD, Mullins JI. Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PLoS ONE. 2007 Sep 5;2(9):e823.


  201. 36: •    Deng W, Nickle D.C., Learn GH, Maust B, Mullins JI.  ViroBLAST: A standalone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics. 2007 Jun 22.


  203. 35: •    David C. Nickle, L. Heath, M.A. Jensen, P.B. Gilbert, J.I. Mullins and S.L.K. Pond. HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE. 2007 June. Issue 6.


  205. 34: •    Rolland M, Jensen MA, Nickle D.C., Yan J, Learn GH, Heath L, Weiner D, Mullins JI. Reconstruction and function of Ancestral Center-Of-Tree (COT) HIV-I Proteins. J Virol. 2007 May 30.


  207. 33: •    Lie TJ, Dodsworth JA, Nickle D.C., Leigh JA. Diverse homologues of the archaeal repressor NrpR function similarly in nitrogen regulation. FEMS Microbiol Lett. 2007 Apr 24.


  209. 32: •    David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins and Nebosja Jojic. Coping with viral diversity in HIV vaccine design. PLoS Computational Biology. March 2007


  211. 31: •    Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI.  Extensive Intra-subtype Recombination in South African HIV-1 Subtype C Infections. J Virol. 2007 Feb 21; [Epub ahead of print]


  213. 30: •    Gottlieb GS, Hawes SE, Nickle DC, Herbeck JT, Kiviat NB, Mullins JI, Sow PS. Presenting plasma HIV RNA level and rate of CD4 T-cell decline. JAMA. 2007 Feb 28;297(8):805; author reply 806-7.


  215. 29: •    Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Karina Yusim, Ben McMahon, Simon Mallal, James I. Mullins, Gerald Learn, David C. Nickle, Joshua Herbeck, Christine Rousseau, Toshiyuki Miura, Philip J. Goulder, Alasdair Leslie, Photini Kiepiela, Christian Brander, Bruce Walker, and Bette Korber. Founder effects contribute to perceived associations between HIV sequence polymorphisms and HLA class I alleles. Science. 2007 March 16; 315:1586-6


  217. 28: •    Joanne Stekler, Janine Maenza, Claire E. Stevens, Paul D. Swenson, Robert W. Coombs, Robert W. Wood, Mary S. Campbell, David C. Nickle, Ann C. Collier, Matthew R. Golden. Screening for Acute HIV Infection: Lessons Learned. 2007. Clinical Infectious Disease (Feb 1: 44).


  219. 27: •    Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, Bishop K, van der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Frater J, McCarthy N, Brander C, Learn GH, Nickle D, Rousseau C, Coovadia H, Mullins JI, Heckerman D, Walker BD, Goulder P.   CD8(+) T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med. 2007 Jan;13(1):46-53. Epub 2006 Dec 17.


  221. 26: •    Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati,   Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire Stevens, Janine  Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Ann C. Collier, Lawrence  Corey, M. Juliana McElrath, and James I. Mullins.  Selection on the HIV-1 proteome following primary infection. 2006. Journal of Virology.


  223. 25: •    S. Arunmozhi Balajee, David C. Nickle, Janos Varga and Kieren A. Marr. Molecular studies reveal frequent misidentification of A. fumigatus by morphotyping. 2006. Eukaryotic Cell.


  225. 24: •    Shriner D, Liu Y, Nickle DC, Mullins JI. Evolution of Intrahost HIV-1 Genetic Diversity During Chronic Infection. Evolution. 2006: 60, 6, 1165-1176


  227. 23: •    HA Ross, Nickle DC, Liu Y, Heath L, Jensen MA, Rodrigo AG and Mullins JI. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. EBO. 2006: 2 18-41.


  229. 22: •    Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI. Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. J Virol. 2006 Feb;80(4):1637-44.


  231. 21: •    Chun TW, *Nickle DC, Justement JS, Large D, Semerjian A, Curlin ME, O'Shea MA, Hallahan CW, Daucher M, Ward DJ, Moir S, Mullins JI, Kovacs C, Fauci AS. HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J Clin Invest. 2005 Nov;115(11):3250-5.


  233. 20: •    Doria-Rose, N. A., G. H. Learn, A. G. Rodrigo, D. C. Nickle, F. Li, M. Mahalanabis, M. T. Hensel, S. McLaughlin, P. F. Edmonson, D. Montefiori, S. W. Barnett, N. L. Haigwood, and J. I. Mullins. 2005. Human immunodeficiency virus type 1 subtype B ancestral Envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B Envelope. Journal of Virology 79: 11214-11224


  235. 19: •    Gottlieb GS, Nickle DC. Multidrug-resistant, dual-tropic HIV-1 and rapid progression. Lancet. 2005 Jun 21;365(9475):1923-4.


  237. 18: •    Balajee SA, Gribskov JL, Hanley E, Nickle D, Marr KA. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot Cell. 2005 Mar;4(3):625-32.


  239. 17: •    Liu, Y., D. C. Nickle, D. Shriner, M. A. Jensen, G. H. Learn, Jr., J. E. Mittler and J. I. Mullins 2004. Molecular clock-like evolution of human immunodeficiency virus type 1. Virology 329: 101-108.


  241. 16: •    Shriner, D., A. G. Rodrigo, D. C. Nickle and J. I. Mullins. 2004. Pervasive genomic recombination of HIV-1 in vivo. 2004 Genetics 167: 1573-1583.


  243. 15: •    Fulcher JA, Hwangbo Y, Zioni R, Nickle DC, Lin X, Heath L, Mullins JI, CoreyL, Zhu T. Compartmentalization of human immunodeficiency virus type 1 between bloodmonocytes and CD4+ T cells during infection. J Virol. 2004 Aug; 78(15):7883-93.


  245. 14: •    D. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J.E. Mittler, J. B. Margolick and J. I. Mullins. 2004. Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection. Genetics 166: 1155-1164.


  247. 13: •    Gottlieb, G. S., D. C. Nickle, M. A. Jensen, K. G. Wong, J. Grobler, F. Li, S.-L. Liu, C. Rademeyer, G. H. Learn, S. S. Abdool Karim, C. Williamson, L. Corey, J. B. Margolick, J. I. Mullins. 2004. Dual HIV-1 infection associated with rapid disease progression. The Lancet Vol 363, 2004.


  249. 12: •    M. A. Jensen, F. Li, A. B. van 't Wout, D. C. Nickle, D. Shriner, H. X. He, S. McLaughlin, R. Shankarappa, J. B. Margolick, and J. I. Mullins. 2003. Improved Coreceptor Usage Prediction and Genotypic Monitoring of R5-to-X4 Transition by Motif Analysis of Human Immunodeficiency Virus Type 1 env V3 Loop Sequences. Journal of Virology, 77 13376-13388.


  251. 11: •    Shriner, D., Nickle D.C., Jensen, M., Mullins, J.I. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genetical Research, 81: 115-121.


  253. 10: •    Nickle, D.C., M. A. Jensen, G. S. Gottlieb, D. Shriner, G. H. Learn, A. G. Rodrigo, and J. I. Mullins. 2003. Consensus and ancestral state HIV vaccines Science, 299: 1515-1517.


  255. 9: •    Nickle, D.C., M. A. Jensen, D. Shriner, S. J. Brodie, L. M. Frenkel, J. E. Mittler, and J. I. Mullins. 2003. Evolutionary Indicators of Human Immunodeficiency Virus Type 1 Reservoirs and Compartments. Journal of Virology, 77: 5540-5546.


  257. 8: •    Dybul, M., M. Daucher, M. A. Jensen, C. W. Hallahan, T.-W. Chun, M. Belson, B. Hidalgo, D.C. Nickle, C. Yoder, J. A. Metcalf, R. T. Davey, L. Ehler, D. Kress-Rock, E. Nies-Kraske, S. Liu, J. I. Mullins, and A. S. Fauci. 2003. Genetic Characterization of Rebounding Human Immunodeficiency Virus Type 1 in Plasma during Multiple Interruptions of Highly Active Antiretroviral Therapy. Journal of Virology, 77: 3229-3237.


  259. 7: •    Liu, S.-L., J. E. Mittler, D. C. Nickle, T. M. Mulvania, D. Shriner, A. G. Rodrigo, B. Kosloff, X. He, L. Corey, and J. I. Mullins. 2002. Selection for Human Immunodeficiency Virus Type 1 Recombinants in a Patient with Rapid Progression to AIDS. J Virol. 76: 10674-10684


  261. 6: •    Malaspina, A., S. Moir, D. C. Nickle, E. T. Donoghue, K. M. Ogwaro, L. A. Ehler, S. Liu, J. A. Mican, M. Dybul, T. W. Chun, J. I. Mullins, and A. S. Fauci. 2002. Human Immunodeficiency Virus Type 1 Bound to B Cells: Relationship to Virus Replicating in CD4+ T Cells and Circulating in Plasma. J Virol. 15;76: 8855-8863.


  263. 5: •    Zhu T, Muthui D, Holte S, Nickle D, Feng F, Brodie S, Hwangbo Y, Mullins JI, Corey L.  Evidence for Human Immunodeficiency Virus Type 1 Replication In Vivo in CD14(+) Monocytes and Its Potential Role as a Source of Virus in Patients on Highly Active Antiretroviral Therapy. J Virol. 2002 Jan 15;76(2):707-16.


  265. 4: •    Nickle DC, Learn GH, Rain MW, Mullins JI, Mittler JE. Curiously modern DNA for a "250 Million-Year-Old" bacterium. J Mol Evol. 2002 Jan;54(1):134-7.


  267. 3: •    Orange, D.I., B.R. Riddle, and D.C. Nickle: •    1999: •    Phylogeography of a wide-ranging, non-territorial desert lizard, Gambelia wislizenii (Crotaphytidae). Copeia, 1999:267-273.


  269. 2: •    Mochizuki H, Scherer SW, Xi T, Nickle DC, Majer M, Huizenga JJ, Tsui LC, Prochazka M.  Human PON2 gene at 7q21.3: cloning, multiple mRNA forms, and missense polymorphisms in the coding sequence. Gene. 1998 Jun 15;213(1-2):149-57.


  271. 1: •    Rowles, Joie C., Steven W. Scherer, Tina Xi, Martin Majer, David C. Nickle, Kiril Popov, Robert L. Harrris, Nancy Riebow, James Xia, Lap-Chee Tsui, Clifton Bogardus, and Michal Prochazka. Cloning and Characterization of PDK4 on 7q21.3-q22.1 Encoding a Fourth Human Pyruvate Dehydrogenase Kinase Isoenzyme. J. Biol. Chem., Sep 1996; 271: 22376 - 22382