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Ivana Yang

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus

    Collapse Biography 
    Collapse awards and honors
    2013 - 2017Infectious, Reproductive, Asthma and Pulmonary Conditions (IRAP) Study Section , NIH
    2003EU-US Workshop on Molecular Signatures of DNA Damage Induced Stress Response Young Scientist Travel , NIH
    2002Aspen Cancer Conference Young Investigator
    1996Phi Beta Kappa, College of William and Mary
    2014 - 2017Epigenetic marks of in utero exposure to gestational diabetes, NIH-NIDDK: R01-DK100340
    2014 - 2016Regulation of mRNA and miRNA expression in IPF by DNA methylation, NIH-NHLBI: R21-HL121572
    2009 - 2015Determinants of Environmental Airway Disease (Project 3), NIH-NIEHS: P01-ES18181
    2009 - 2012Peripheral Blood Biomarkers for Idiopathic Interstitial Pneumonia, NIH-NHLBI: RC1-HL099571
    2009 - 2015Asthma: An Epidemic Caused by Epigenetics?, NIH-NHLBI: R01-HL101251
    2009 - 2019External Advisory Committee, West Virginia-IDeA Networks of Biomedical Research Excellence, NIH-NIGMS

    Collapse Overview 
    Collapse overview
    I have a broad background in genomics, genetics, and bioinformatics. As a postdoctoral fellow with John Quackenbush, I identified gene expression fingerprints for molecular classification of tumors and outcome prediction in colon cancer. As an Assistant Research Professor at Duke University and then a Staff Scientist at NIEHS, I worked with David Schwartz to identify novel innate immune genes in mice by using genetic and genomic approaches. As the Deputy Director for the Center for Genes, Environment and Health, I provided oversight of next-generation sequencing, expression profiling, genotyping, and epigenomic technologies at National Jewish Health.

    I am currently an Associate Professor in the Division of Pulmonary Sciences and Critical Care Medicine (School of Medicine), Epidemiology (Colorado School of Public Health), and Center for Genes, Environment, and Health (National Jewish Health). The focus of my research at the University of Colorado has largely been on epigenetic regulation and transcriptional profiles in pulmonary fibrosis, asthma, and innate immunity. In this work, we have identified molecular subtypes of pulmonary fibrosis, gene expression profiles of environmental exposures in asthma, and DNA methylation changes associated with the development of asthma and pulmonary fibrosis. I am also collaborating with a number of individuals across campus on epigenetic regulation of gene expression in a variety of diseases including gestational diabetes, maternal health/preterm birth, and chronic beryllium disease.

    I teach a course focused on the immunologic basis of human disease (IMMU 7603), am a member of the Human Molecular Genetics and Genomics Program (HMGGP) and mentor a number of junior faculty, postdoctoral fellows, graduate and undergraduate students both in our laboratory (Schwarz|Yang Lab) and in other Divisions and Departments on the Anschutz Medical Campus.

    Collapse Research 
    Collapse research activities and funding
    R01HL101251     (SCHWARTZ, DAVID ALBERT)Sep 1, 2009 - Jun 30, 2014
    Asthma: An Epidemic Caused by Epigenetics?
    Role: Co-Principal Investigator

    RC1HL099571     (SCHWARTZ, DAVID ALBERT)Sep 30, 2009 - Aug 31, 2012
    Peripheral Blood Biomarkers for Idiopathic Interstitial Pneumonia
    Role: Co-Principal Investigator

    R01DK100340     (DABELEA, DANA)Jul 1, 2014 - Jun 30, 2017
    Epigenetic marks of in utero exposure to gestational diabetes
    Role: Co-Principal Investigator

    R21HL121572     (YANG, IVANA VERONA)Aug 1, 2014 - Apr 30, 2016
    Regulation of mRNA and miRNA Expression in Pulmonary Fibrosis by DNA Methylation
    Role: Principal Investigator

    R01ES023826     (MAIER, LISA A)Apr 1, 2015 - Dec 31, 2019
    Exposure in Epigenetic Regulation of Immune Response in CBD
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Davidson EJ, Yang IV. Role of epigenetics in the development of childhood asthma. Curr Opin Allergy Clin Immunol. 2018 Apr; 18(2):132-138. PMID: 29389731.
      View in: PubMed
    2. Koeppen M, Lee JW, Seo SW, Brodsky KS, Kreth S, Yang IV, Buttrick PM, Eckle T, Eltzschig HK. Hypoxia-inducible factor 2-alpha-dependent induction of amphiregulin dampens myocardial ischemia-reperfusion injury. Nat Commun. 2018 Feb 26; 9(1):816. PMID: 29483579.
      View in: PubMed
    3. Yang IV, Zhang W, Davidson EJ, Fingerlin TE, Kechris K, Dabelea D. GeneticsEpigenetic marks of in utero exposure to gestational diabetes and childhood adiposity outcomes: the EPOCH study. Diabet Med. 2018 Feb 20. PMID: 29461653.
      View in: PubMed
    4. Eyring KR, Pedersen BS, Maclean KN, Stabler SP, Yang IV, Schwartz DA. Methylene-tetrahydrofolate reductase contributes to allergic airway disease. PLoS One. 2018; 13(1):e0190916. PMID: 29329322.
      View in: PubMed
    5. Crouser ED, Fingerlin TE, Yang IV, Maier LA, Nana-Sinkam P, Collman RG, Kaminski N. Application of "Omics" and Systems Biology to Sarcoidosis Research. Ann Am Thorac Soc. 2017 Dec; 14(Supplement_6):S445-S451. PMID: 29053026.
      View in: PubMed
    6. Raghavan S, Zhang W, Yang IV, Lange LA, Lange EM, Fingerlin TE, Dabelea D. Association between gestational diabetes mellitus exposure and childhood adiposity is not substantially explained by offspring genetic risk of obesity. Diabet Med. 2017 Dec; 34(12):1696-1700. PMID: 29048747.
      View in: PubMed
    7. Rudolph MC, Jackman MR, Presby DM, Houck JA, Webb PG, Johnson GC, Soderborg TK, de la Houssaye BA, Yang IV, Friedman JE, MacLean PS. Low Neonatal Plasma N-6/N-3 Pufa Ratios Regulate Offspring Adipogenic Potential and Condition Adult Obesity Resistance. Diabetes. 2017 Nov 14. PMID: 29138256.
      View in: PubMed
    8. 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. PMID: 29066090.
      View in: PubMed
    9. Felix JF, Joubert BR, Baccarelli AA, Sharp GC, Almqvist C, Annesi-Maesano I, Arshad H, Baïz N, Bakermans-Kranenburg MJ, Bakulski KM, Binder EB, Bouchard L, Breton CV, Brunekreef B, Brunst KJ, Burchard EG, Bustamante M, Chatzi L, Cheng Munthe-Kaas M, Corpeleijn E, Czamara D, Dabelea D, Davey Smith G, De Boever P, Duijts L, Dwyer T, Eng C, Eskenazi B, Everson TM, Falahi F, Fallin MD, Farchi S, Fernandez MF, Gao L, Gaunt TR, Ghantous A, Gillman MW, Gonseth S, Grote V, Gruzieva O, Håberg SE, Herceg Z, Hivert MF, Holland N, Holloway JW, Hoyo C, Hu D, Huang RC, Huen K, Järvelin MR, Jima DD, Just AC, Karagas MR, Karlsson R, Karmaus W, Kechris KJ, Kere J, Kogevinas M, Koletzko B, Koppelman GH, Küpers LK, Ladd-Acosta C, Lahti J, Lambrechts N, Langie SAS, Lie RT, Liu AH, Magnus MC, Magnus P, Maguire RL, Marsit CJ, McArdle W, Melén E, Melton P, Murphy SK, Nawrot TS, Nisticò L, Nohr EA, Nordlund B, Nystad W, Oh SS, Oken E, Page CM, Perron P, Pershagen G, Pizzi C, Plusquin M, Raikkonen K, Reese SE, Reischl E, Richiardi L, Ring S, Roy RP, Rzehak P, Schoeters G, Schwartz DA, Sebert S, Snieder H, Sørensen TIA, Starling AP, Sunyer J, Taylor JA, Tiemeier H, Ullemar V, Vafeiadi M, Van Ijzendoorn MH, Vonk JM, Vriens A, Vrijheid M, Wang P, Wiemels JL, Wilcox AJ, Wright RJ, Xu CJ, Xu Z, Yang IV, Yousefi P, Zhang H, Zhang W, Zhao S, Agha G, Relton CL, Jaddoe VWV, London SJ. Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium. Int J Epidemiol. 2017 Sep 13. PMID: 29025028.
      View in: PubMed
    10. Boyle KE, Patinkin ZW, Shapiro ALB, Bader C, Vanderlinden L, Kechris K, Janssen RC, Ford RJ, Smith BK, Steinberg GR, Davidson EJ, Yang IV, Dabelea D, Friedman JE. Maternal obesity alters fatty acid oxidation, AMPK activity, and associated DNA methylation in mesenchymal stem cells from human infants. Mol Metab. 2017 Nov; 6(11):1503-1516. PMID: 29107296.
      View in: PubMed
    11. Monte AA, Sun H, Rapp-Olsson AM, Mohamed F, Gawarammana I, Buckley NA, Evans CM, Yang IV, Schwartz DA. The Plasma Concentration of MUC5B is Associated with Clinical Outcomes in Paraquat Poisoned Patients. Am J Respir Crit Care Med. 2017 Jul 18. PMID: 28719757.
      View in: PubMed
    12. Helling BA, Gerber AN, Kadiyala V, Sasse SK, Pedersen BS, Sparks L, Nakano Y, Okamoto T, Evans CM, Yang IV, Schwartz DA. Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2017 07; 57(1):91-99. PMID: 28272906.
      View in: PubMed
    13. Yang IV, Lozupone CA, Schwartz DA. The environment, epigenome, and asthma. J Allergy Clin Immunol. 2017 Jul; 140(1):14-23. PMID: 28673400.
      View in: PubMed
    14. Wang M, Yang IV, Davidson EJ, Joetham A, Takeda K, O'Connor BP, Gelfand EW. Forkhead box protein 3 demethylation is associated with tolerance induction in peanut-induced intestinal allergy. J Allergy Clin Immunol. 2018 Feb; 141(2):659-670.e2. PMID: 28479331.
      View in: PubMed
    15. Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N, LaSalle JM, Schmidt R, Yousefi P, Perera F, Joubert BR, Wiemels J, Taylor M, Yang IV, Chen R, Hew KM, Freeland DM, Miller R, Murphy SK. Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group. Environ Health Perspect. 2017 04; 125(4):511-526. PMID: 28362264.
      View in: PubMed
    16. Yang IV, Richards A, Davidson EJ, Stevens AD, Kolakowski CA, Martin RJ, Schwartz DA. The Nasal Methylome: A Key to Understanding Allergic Asthma. Am J Respir Crit Care Med. 2017 03 15; 195(6):829-831. PMID: 28294656.
      View in: PubMed
    17. Kusko RL, Brothers JF, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, Geraci M, Yang I, Schwartz DA, Beane J, Spira A, Kaminski N. Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2016 Oct 15; 194(8):948-960. PMID: 27104832.
      View in: PubMed
    18. Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA. The nasal methylome and childhood atopic asthma. J Allergy Clin Immunol. 2017 May; 139(5):1478-1488. PMID: 27745942.
      View in: PubMed
    19. Evans CM, Fingerlin TE, Schwarz MI, Lynch D, Kurche J, Warg L, Yang IV, Schwartz DA. Idiopathic Pulmonary Fibrosis: A Genetic Disease That Involves Mucociliary Dysfunction of the Peripheral Airways. Physiol Rev. 2016 Oct; 96(4):1567-91. PMID: 27630174.
      View in: PubMed
    20. Alper S, Warg LA, De Arras L, Flatley BR, Davidson EJ, Adams J, Smith K, Wohlford-Lenane CL, McCray PB, Pedersen BS, Schwartz DA, Yang IV. Novel Innate Immune Genes Regulating the Macrophage Response to Gram Positive Bacteria. Genetics. 2016 09; 204(1):327-36. PMID: 27356610; PMCID: PMC5012397 [Available on 09/01/17].
    21. Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Murphy E, Smith K, McKean D, Pedersen BS, Talbert J, Powers J, Markin CR, Beckman KB, Lathrop M, Freed B, Langefeld CD, Schwartz DA. Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia. BMC Genet. 2016 06 07; 17(1):74. PMID: 27266705; PMCID: PMC4895966.
    22. Mathai SK, Pedersen BS, Smith K, Russell P, Schwarz MI, Brown KK, Steele MP, Loyd JE, Crapo JD, Silverman EK, Nickerson D, Fingerlin TE, Yang IV, Schwartz DA. Desmoplakin Variants Are Associated with Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2016 May 15; 193(10):1151-60. PMID: 26669357; PMCID: PMC4872666 [Available on 05/15/17].
    23. Yang IV, Pedersen BS, Liu AH, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Gergen P, Togias A, Busse WW, Schwartz DA. DNA Methylation Changes in Nasal Epithelia Are Associated with Allergic Asthma in the Inner City. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S99-S100. PMID: 27027970; PMCID: PMC5015744 [Available on 03/01/17].
    24. Nakano Y, Yang IV, Walts AD, Watson AM, Helling BA, Fletcher AA, Lara AR, Schwarz MI, Evans CM, Schwartz DA. MUC5B Promoter Variant rs35705950 Affects MUC5B Expression in the Distal Airways in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2016 Feb 15; 193(4):464-6. PMID: 26871673; PMCID: PMC4803086 [Available on 02/15/17].
    25. Eyring KR, Pedersen BS, Yang IV, Schwartz DA. In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome. PLoS One. 2015; 10(12):e0144087. PMID: 26642056; PMCID: PMC4671614.
    26. Rosen HR, Golden-Mason L, Daly AK, Yang I, Day CP. Variants in the LGALS9 Gene Are Associated With Development of Liver Disease in Heavy Consumers of Alcohol. Clin Gastroenterol Hepatol. 2016 May; 14(5):762-8.e1. PMID: 26598225.
      View in: PubMed
    27. Julian CG, Pedersen BS, Salmon CS, Yang IV, Gonzales M, Vargas E, Moore LG, Schwartz DA. Unique DNA Methylation Patterns in Offspring of Hypertensive Pregnancy. Clin Transl Sci. 2015 Dec; 8(6):740-5. PMID: 26546417; PMCID: PMC4703563 [Available on 12/01/16].
    28. Yang IV, Fingerlin TE, Evans CM, Schwarz MI, Schwartz DA. MUC5B and Idiopathic Pulmonary Fibrosis. Ann Am Thorac Soc. 2015 Nov; 12 Suppl 2:S193-9. PMID: 26595739; PMCID: PMC4722833 [Available on 11/01/16].
    29. Steele MP, Luna LG, Coldren CD, Murphy E, Hennessy CE, Heinz D, Evans CM, Groshong S, Cool C, Cosgrove GP, Brown KK, Fingerlin TE, Schwarz MI, Schwartz DA, Yang IV. Relationship between gene expression and lung function in Idiopathic Interstitial Pneumonias. BMC Genomics. 2015 Oct 26; 16:869. PMID: 26503507; PMCID: PMC4621862.
    30. Mathai SK, Yang IV, Schwarz MI, Schwartz DA. Incorporating genetics into the identification and treatment of Idiopathic Pulmonary Fibrosis. BMC Med. 2015 Sep 24; 13:191. PMID: 26400796; PMCID: PMC4581155.
    31. Helling BA, Yang IV. Epigenetics in lung fibrosis: from pathobiology to treatment perspective. Curr Opin Pulm Med. 2015 Sep; 21(5):454-62. PMID: 26176965; PMCID: PMC4592772.
    32. Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA. DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol. 2015 Jul; 136(1):69-80. PMID: 25769910; PMCID: PMC4494877.
    33. Liang L, Willis-Owen SAG, Laprise C, Wong KCC, Davies GA, Hudson TJ, Binia A, Hopkin JM, Yang IV, Grundberg E, Busche S, Hudson M, Rönnblom L, Pastinen TM, Schwartz DA, Lathrop GM, Moffatt MF, Cookson WOCM. An epigenome-wide association study of total serum immunoglobulin E concentration. Nature. 2015 Apr 30; 520(7549):670-674. PMID: 25707804; PMCID: PMC4416961.
    34. Peljto AL, Selman M, Kim DS, Murphy E, Tucker L, Pardo A, Lee JS, Ji W, Schwarz MI, Yang IV, Schwartz DA, Fingerlin TE. The MUC5B promoter polymorphism is associated with idiopathic pulmonary fibrosis in a Mexican cohort but is rare among Asian ancestries. Chest. 2015 Feb; 147(2):460-464. PMID: 25275363; PMCID: PMC4314820.
    35. Henao-Martínez AF, Agler AH, Watson AM, Hennessy C, Davidson E, Demos-Davies K, McKinsey TA, Wilson M, Schwartz DA, Yang IV. AKT network of genes and impaired myocardial contractility during murine acute Chagasic myocarditis. Am J Trop Med Hyg. 2015 Mar; 92(3):523-9. PMID: 25582694; PMCID: PMC4350542.
    36. Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA. 2015 Feb; 21(2):164-71. PMID: 25519487; PMCID: PMC4338344.
    37. Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DA. Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2014 Dec 01; 190(11):1263-72. PMID: 25333685; PMCID: PMC4315819.
    38. Meltzer EB, Barry WT, Yang IV, Brown KK, Schwarz MI, Patel H, Ashley A, Noble PW, Schwartz DA, Steele MP. Familial and sporadic idiopathic pulmonary fibrosis: making the diagnosis from peripheral blood. BMC Genomics. 2014 Oct 16; 15:902. PMID: 25318837; PMCID: PMC4288625.
    39. Ito Y, Zemans R, Correll K, Yang IV, Ahmad A, Gao B, Mason RJ. Stanniocalcin-1 is induced by hypoxia inducible factor in rat alveolar epithelial cells. Biochem Biophys Res Commun. 2014 Oct 03; 452(4):1091-7. PMID: 25251473; PMCID: PMC4188510.
    40. Gao Z, Dosman JA, Rennie DC, Schwartz DA, Yang IV, Beach J, Senthilselvan A. NOS3 polymorphism, lung function, and exposure in swine operations: results of 2 studies. J Allergy Clin Immunol. 2014 Aug; 134(2):485-8. PMID: 24865140.
      View in: PubMed
    41. Long H, O'Connor BP, Zemans RL, Zhou X, Yang IV, Schwartz DA. The Toll-like receptor 4 polymorphism Asp299Gly but not Thr399Ile influences TLR4 signaling and function. PLoS One. 2014; 9(4):e93550. PMID: 24695807; PMCID: PMC3973565.
    42. Yang IV, Schwartz DA. Epigenetics of idiopathic pulmonary fibrosis. Transl Res. 2015 Jan; 165(1):48-60. PMID: 24746870; PMCID: PMC4182166.
    43. Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM. Muc5b is required for airway defence. Nature. 2014 Jan 16; 505(7483):412-6. PMID: 24317696; PMCID: PMC4001806.
    44. Julian CG, Yang IV, Browne VA, Vargas E, Rodriguez C, Pedersen BS, Moore LG, Schwartz DA. Inhibition of peroxisome proliferator-activated receptor ?: a potential link between chronic maternal hypoxia and impaired fetal growth. FASEB J. 2014 Mar; 28(3):1268-79. PMID: 24307415; PMCID: PMC3929669.
    45. Das R, Subrahmanyan L, Yang IV, van Duin D, Levy R, Piecychna M, Leng L, Montgomery RR, Shaw A, Schwartz DA, Bucala R. Functional polymorphisms in the gene encoding macrophage migration inhibitory factor are associated with Gram-negative bacteremia in older adults. J Infect Dis. 2014 Mar 01; 209(5):764-8. PMID: 24158957; PMCID: PMC3923543.
    46. Pedersen BS, Yang IV, De S. CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics. 2013 Dec 01; 29(23):3003-6. PMID: 24037212; PMCID: PMC3834799.
    47. Yang IV, Coldren CD, Leach SM, Seibold MA, Murphy E, Lin J, Rosen R, Neidermyer AJ, McKean DF, Groshong SD, Cool C, Cosgrove GP, Lynch DA, Brown KK, Schwarz MI, Fingerlin TE, Schwartz DA. Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis. Thorax. 2013 Dec; 68(12):1114-21. PMID: 23783374.
      View in: PubMed
    48. Jing J, Yang IV, Hui L, Patel JA, Evans CM, Prikeris R, Kobzik L, O'Connor BP, Schwartz DA. Role of macrophage receptor with collagenous structure in innate immune tolerance. J Immunol. 2013 Jun 15; 190(12):6360-7. PMID: 23667110; PMCID: PMC3679202.
    49. Foster MW, Thompson JW, Que LG, Yang IV, Schwartz DA, Moseley MA, Marshall HE. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J Proteome Res. 2013 May 03; 12(5):2194-205. PMID: 23550723.
      View in: PubMed
    50. Henao-Martínez AF, Agler AH, LaFlamme D, Schwartz DA, Yang IV. Polymorphisms in the SUFU gene are associated with organ injury protection and sepsis severity in patients with Enterobacteriacea bacteremia. Infect Genet Evol. 2013 Jun; 16:386-91. PMID: 23538333; PMCID: PMC3669235.
    51. Rosas IO, Yang IV. The promise of epigenetic therapies in treatment of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2013 Feb 15; 187(4):336-8. PMID: 23418324.
      View in: PubMed
    52. Henao-Martínez AF, González-Fontal GR, Castillo-Mancilla JR, Yang IV. Enterobacteriaceae bacteremias among cancer patients: an observational cohort study. Int J Infect Dis. 2013 Jun; 17(6):e374-8. PMID: 23313157; PMCID: PMC3632647.
    53. Gao Z, Dosman JA, Rennie DC, Schwartz DA, Yang IV, Beach J, Senthilselvan A. Association of Toll-like receptor 2 gene polymorphisms with lung function in workers in swine operations. Ann Allergy Asthma Immunol. 2013 Jan; 110(1):44-50.e1. PMID: 23244658.
      View in: PubMed
    54. Yang IV, Schwartz DA. Epigenetic mechanisms and the development of asthma. J Allergy Clin Immunol. 2012 Dec; 130(6):1243-55. PMID: 23026498; PMCID: PMC3518374.
    55. Oakes JL, O'Connor BP, Warg LA, Burton R, Hock A, Loader J, Laflamme D, Jing J, Hui L, Schwartz DA, Yang IV. Ozone enhances pulmonary innate immune response to a Toll-like receptor-2 agonist. Am J Respir Cell Mol Biol. 2013 Jan; 48(1):27-34. PMID: 23002100; PMCID: PMC3547086.
    56. Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics. 2012 Nov 15; 28(22):2986-8. PMID: 22954632; PMCID: PMC3496335.
    57. Yang IV, Schwartz DA. The next generation of complex lung genetic studies. Am J Respir Crit Care Med. 2012 Dec 01; 186(11):1087-94. PMID: 22936355; PMCID: PMC3530203.
    58. Henao-Martínez AF, Schwartz DA, Yang IV. Chagasic cardiomyopathy, from acute to chronic: is this mediated by host susceptibility factors? Trans R Soc Trop Med Hyg. 2012 Sep; 106(9):521-7. PMID: 22819769.
      View in: PubMed
    59. Yang IV, Luna LG, Cotter J, Talbert J, Leach SM, Kidd R, Turner J, Kummer N, Kervitsky D, Brown KK, Boon K, Schwarz MI, Schwartz DA, Steele MP. The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis. PLoS One. 2012; 7(6):e37708. PMID: 22761659; PMCID: PMC3382229.
    60. Warg LA, Oakes JL, Burton R, Neidermyer AJ, Rutledge HR, Groshong S, Schwartz DA, Yang IV. The role of the E2F1 transcription factor in the innate immune response to systemic LPS. Am J Physiol Lung Cell Mol Physiol. 2012 Sep; 303(5):L391-400. PMID: 22707615; PMCID: PMC4587596.
    61. Reynolds SJ, Clark ML, Koehncke N, von Essen S, Prinz L, Keefe TJ, Mehaffy J, Bradford M, Cranmer B, Davidson ME, Yang IV, Burch JB. Pulmonary function reductions among potentially susceptible subgroups of agricultural workers in Colorado and Nebraska. J Occup Environ Med. 2012 May; 54(5):632-41. PMID: 22576462.
      View in: PubMed
    62. Yang IV. Epigenomics of idiopathic pulmonary fibrosis. Epigenomics. 2012 Apr; 4(2):195-203. PMID: 22449190; PMCID: PMC3412586.
    63. De Arras L, Yang IV, Lackford B, Riches DW, Prekeris R, Freedman JH, Schwartz DA, Alper S. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. J Immunol. 2012 Mar 15; 188(6):2905-13. PMID: 22312129; PMCID: PMC3293945.
    64. Yang IV. Sleep, immunology, and epigenetics: tip of an iceberg. Am J Respir Crit Care Med. 2012 Feb 01; 185(3):243-5. PMID: 22298364.
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    65. Yang IV, Tomfohr J, Singh J, Foss CM, Marshall HE, Que LG, McElvania-Tekippe E, Florence S, Sundy JS, Schwartz DA. The clinical and environmental determinants of airway transcriptional profiles in allergic asthma. Am J Respir Crit Care Med. 2012 Mar 15; 185(6):620-7. PMID: 22246175; PMCID: PMC3326287.
    66. Zemans RL, Briones N, Campbell M, McClendon J, Young SK, Suzuki T, Yang IV, De Langhe S, Reynolds SD, Mason RJ, Kahn M, Henson PM, Colgan SP, Downey GP. Neutrophil transmigration triggers repair of the lung epithelium via beta-catenin signaling. Proc Natl Acad Sci U S A. 2011 Sep 20; 108(38):15990-5. PMID: 21880956; PMCID: PMC3179042.
    67. Yang IV, Rutledge HR, Yang J, Warg LA, Sevilla SD, Schwartz DA. A locus on chromosome 9 is associated with differential response of 129S1/SvImJ and FVB/NJ strains of mice to systemic LPS. Mamm Genome. 2011 Oct; 22(9-10):518-29. PMID: 21720866; PMCID: PMC4157901.
    68. Yang IV, Jiang W, Rutledge HR, Lackford B, Warg LA, De Arras L, Alper S, Schwartz DA, Pisetsky DS. Identification of novel innate immune genes by transcriptional profiling of macrophages stimulated with TLR ligands. Mol Immunol. 2011 Sep; 48(15-16):1886-95. PMID: 21665277; PMCID: PMC3163807.
    69. Yang IV, Schwartz DA. Epigenetic control of gene expression in the lung. Am J Respir Crit Care Med. 2011 May 15; 183(10):1295-301. PMID: 21596832; PMCID: PMC3114059.
    70. Seibold MA, Wise AL, Speer MC, Steele MP, Brown KK, Loyd JE, Fingerlin TE, Zhang W, Gudmundsson G, Groshong SD, Evans CM, Garantziotis S, Adler KB, Dickey BF, du Bois RM, Yang IV, Herron A, Kervitsky D, Talbert JL, Markin C, Park J, Crews AL, Slifer SH, Auerbach S, Roy MG, Lin J, Hennessy CE, Schwarz MI, Schwartz DA. A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med. 2011 Apr 21; 364(16):1503-12. PMID: 21506741; PMCID: PMC3379886.
    71. Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, de Villena FP, Churchill GA. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res. 2011 Aug; 21(8):1213-22. PMID: 21406540; PMCID: PMC3149489.
    72. Jin L, Xu LG, Yang IV, Davidson EJ, Schwartz DA, Wurfel MM, Cambier JC. Identification and characterization of a loss-of-function human MPYS variant. Genes Immun. 2011 Jun; 12(4):263-9. PMID: 21248775; PMCID: PMC3107388.
    73. Rutledge HR, Jiang W, Yang J, Warg LA, Schwartz DA, Pisetsky DS, Yang IV. Gene expression profiles of RAW264.7 macrophages stimulated with preparations of LPS differing in isolation and purity. Innate Immun. 2012 Feb; 18(1):80-8. PMID: 21239457.
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    74. Yang IV, Alper S, Lackford B, Rutledge H, Warg LA, Burch LH, Schwartz DA. Novel regulators of the systemic response to lipopolysaccharide. Am J Respir Cell Mol Biol. 2011 Aug; 45(2):393-402. PMID: 21131441; PMCID: PMC3175565.
    75. Yang IV, Wade CM, Kang HM, Alper S, Rutledge H, Lackford B, Eskin E, Daly MJ, Schwartz DA. Identification of novel genes that mediate innate immunity using inbred mice. Genetics. 2009 Dec; 183(4):1535-44. PMID: 19805818; PMCID: PMC2787437.
    76. Huang YC, Li Z, Carter JD, Soukup JM, Schwartz DA, Yang IV. Fine ambient particles induce oxidative stress and metal binding genes in human alveolar macrophages. Am J Respir Cell Mol Biol. 2009 Nov; 41(5):544-52. PMID: 19251948; PMCID: PMC2778161.
    77. Brass DM, Yang IV, Kennedy MP, Whitehead GS, Rutledge H, Burch LH, Schwartz DA. Fibroproliferation in LPS-induced airway remodeling and bleomycin-induced fibrosis share common patterns of gene expression. Immunogenetics. 2008 Jul; 60(7):353-69. PMID: 18553078.
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    78. Brass DM, Tomfohr J, Yang IV, Schwartz DA. Using mouse genomics to understand idiopathic interstitial fibrosis. Proc Am Thorac Soc. 2007 Jan; 4(1):92-100. PMID: 17202297; PMCID: PMC2647620.
    79. Yang IV, Burch LH, Steele MP, Savov JD, Hollingsworth JW, McElvania-Tekippe E, Berman KG, Speer MC, Sporn TA, Brown KK, Schwarz MI, Schwartz DA. Gene expression profiling of familial and sporadic interstitial pneumonia. Am J Respir Crit Care Med. 2007 Jan 01; 175(1):45-54. PMID: 16998095; PMCID: PMC1899261.
    80. Burch LH, Yang IV, Whitehead GS, Chao FG, Berman KG, Schwartz DA. The transcriptional response to lipopolysaccharide reveals a role for interferon-gamma in lung neutrophil recruitment. Am J Physiol Lung Cell Mol Physiol. 2006 Oct; 291(4):L677-82. PMID: 16766576.
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    81. Yang IV. Use of external controls in microarray experiments. Methods Enzymol. 2006; 411:50-63. PMID: 16939785.
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    82. Kwong KY, Bloom GC, Yang I, Boulware D, Coppola D, Haseman J, Chen E, McGrath A, Makusky AJ, Taylor J, Steiner S, Zhou J, Yeatman TJ, Quackenbush J. Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics. 2005 Aug; 86(2):142-58. PMID: 15951154.
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    83. Eschrich S, Yang I, Bloom G, Kwong KY, Boulware D, Cantor A, Coppola D, Kruhøffer M, Aaltonen L, Orntoft TF, Quackenbush J, Yeatman TJ. Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol. 2005 May 20; 23(15):3526-35. PMID: 15908663.
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    84. Bloomston M, Durkin A, Yang I, Rojiani M, Rosemurgy AS, Enkmann S, Yeatman TJ, Zervos EE. Identification of molecular markers specific for pancreatic neuroendocrine tumors by genetic profiling of core biopsies. Ann Surg Oncol. 2004 Apr; 11(4):413-9. PMID: 15070602.
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    85. Sharov V, Kwong KY, Frank B, Chen E, Hasseman J, Gaspard R, Yu Y, Yang I, Quackenbush J. The limits of log-ratios. BMC Biotechnol. 2004 Mar 08; 4:3. PMID: 15113428; PMCID: PMC400743.
    86. Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol. 2004 Jan; 164(1):9-16. PMID: 14695313; PMCID: PMC1602228.
    87. Gore MR, Szalai VA, Ropp PA, Yang IV, Silverman JS, Thorp HH. Detection of attomole quantities [correction of quantitites] of DNA targets on gold microelectrodes by electrocatalytic nucleobase oxidation. Anal Chem. 2003 Dec 01; 75(23):6586-92. PMID: 14640732.
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    88. Chen T, Yang I, Irby R, Shain KH, Wang HG, Quackenbush J, Coppola D, Cheng JQ, Yeatman TJ. Regulation of caspase expression and apoptosis by adenomatous polyposis coli. Cancer Res. 2003 Aug 01; 63(15):4368-74. PMID: 12907606.
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    89. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 05; 420(6915):563-73. PMID: 12466851.
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    90. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol. 2002 Oct 24; 3(11):research0062. PMID: 12429061; PMCID: PMC133446.
    91. Yang IV, Ropp PA, Thorp HH. Toward electrochemical resolution of two genes on one electrode: using 7-deaza analogues of guanine and adenine to prepare PCR products with differential redox activity. Anal Chem. 2002 Jan 15; 74(2):347-54. PMID: 11811407.
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    92. Yang IV, Thorp HH. Modification of indium tin oxide electrodes with repeat polynucleotides: electrochemical detection of trinucleotide repeat expansion. Anal Chem. 2001 Nov 01; 73(21):5316-22. PMID: 11721935.
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    93. Yang IV, Thorp HH. Oxidation of 7-deazaguanine by one-electron and oxo-transfer oxidants: mismatch-dependent electrochemistry and selective strand scission. Inorg Chem. 2001 Mar 26; 40(7):1690-7. PMID: 11261981.
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    94. Weatherly SC, Yang IV, Thorp HH. Proton-coupled electron transfer in duplex DNA: driving force dependence and isotope effects on electrocatalytic oxidation of guanine. J Am Chem Soc. 2001 Feb 14; 123(6):1236-7. PMID: 11456681.
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    95. Yang IV, Thorp HH. Kinetics of metal-mediated one-electron oxidation of guanine in polymeric DNA and in oligonucleotides containing trinucleotide repeat sequences. Inorg Chem. 2000 Oct 16; 39(21):4969-76. PMID: 11196978.
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