Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Katerina Kechris

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentCSPH-Bio Info General Ops
Phone303/724-4363

    Collapse Bibliographic 
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    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.
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    1. Carry PM, Waugh K, Vanderlinden LA, Johnson RK, Buckner T, Rewers M, Steck AK, Yang I, Fingerlin TE, Kechris K, Norris JM. Changes in the Coexpression of Innate Immunity Genes During Persistent Islet Autoimmunity Are Associated With Progression of Islet Autoimmunity: Diabetes Autoimmunity Study in the Young (DAISY). Diabetes. 2022 09 01; 71(9):2048-2057. PMID: 35724268.
      View in: PubMed
    2. Jones ST, Guo K, Cooper EH, Dillon SM, Wood C, Nguyen DH, Shen G, Barrett BS, Frank DN, Kroehl M, Janoff EN, Kechris K, Wilson CC, Santiago ML. Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection. J Virol. 2022 09 14; 96(17):e0097622. PMID: 35938870.
      View in: PubMed
    3. Starling AP, Wood C, Liu C, Kechris K, Yang IV, Friedman C, Thomas DSK, Peel JL, Adgate JL, Magzamen S, Martenies SE, Allshouse WB, Dabelea D. Ambient air pollution during pregnancy and DNA methylation in umbilical cord blood, with potential mediation of associations with infant adiposity: The Healthy Start study. Environ Res. 2022 11; 214(Pt 1):113881. PMID: 35835166.
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    4. Abdel-Hafiz M, Najafi M, Helmi S, Pratte KA, Zhuang Y, Liu W, Kechris KJ, Bowler RP, Lange L, Banaei-Kashani F. Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification. Front Big Data. 2022; 5:894632. PMID: 35811829.
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    5. Grover E, Paull S, Kechris K, Buchwald A, James K, Liu Y, Carlton EJ. Predictors of bovine Schistosoma japonicum infection in rural Sichuan, China. Int J Parasitol. 2022 07; 52(8):485-496. PMID: 35644269.
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    6. Dekermanjian JP, Shaddox E, Nandy D, Ghosh D, Kechris K. Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics. BMC Bioinformatics. 2022 May 16; 23(1):179. PMID: 35578165.
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    7. Godbole S, Labaki WW, Pratte KA, Hill A, Moll M, Hastie AT, Peters SP, Gregory A, Ortega VE, DeMeo D, Cho MH, Bhatt SP, Wells JM, Barjaktarevic I, Stringer KA, Comellas A, O'Neal W, Kechris K, Bowler RP. A Metabolomic Severity Score for Airflow Obstruction and Emphysema. Metabolites. 2022 Apr 19; 12(5). PMID: 35629872.
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    8. Lin NW, Liu C, Yang IV, Maier LA, DeMeo DL, Wood C, Ye S, Cruse MH, Smith VL, Vyhlidal CA, Kechris K, Sharma S. Sex-Specific Differences in MicroRNA Expression During Human Fetal Lung Development. Front Genet. 2022; 13:762834. PMID: 35480332.
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    9. Francis EC, Kechris K, Cohen CC, Michelotti G, Dabelea D, Perng W. Metabolomic Profiles in Childhood and Adolescence Are Associated with Fetal Overnutrition. Metabolites. 2022 03 19; 12(3). PMID: 35323708.
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    10. Liu C, Gaydos J, Johnson-Paben R, Kechris K, Burnham EL, Sharma S. Chronic Marijuana Use Is Associated with Gene Expression Changes in BAL. Am J Respir Cell Mol Biol. 2022 02; 66(2):238-239. PMID: 35103554.
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    11. Zhuang Y, Xing F, Ghosh D, Banaei-Kashani F, Bowler RP, Kechris K. An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning. Front Genet. 2021; 12:760299. PMID: 35154240.
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    12. Dillon SM, Mickens KL, Thompson TA, Cooper EH, Nesladek S, Christians AJ, Castleman M, Guo K, Wood C, Frank DN, Kechris K, Santiago ML, Wilson CC. Granzyme B+ CD4 T cells accumulate in the colon during chronic HIV-1 infection. Gut Microbes. 2022 Jan-Dec; 14(1):2045852. PMID: 35258402.
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    13. Showers WM, Leach SM, Kechris K, Strong M. Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Infect Genet Evol. 2022 01; 97:105153. PMID: 34801754.
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    14. Walker-Short E, Buckner T, Vigers T, Carry P, Vanderlinden LA, Dong F, Johnson RK, Yang IV, Kechris K, Rewers M, Norris JM. Epigenome-Wide Association Study of Infant Feeding and DNA Methylation in Infancy and Childhood in a Population at Increased Risk for Type 1 Diabetes. Nutrients. 2021 Nov 13; 13(11). PMID: 34836312.
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    15. Zhuang Y, Hobbs BD, Hersh CP, Kechris K. Identifying miRNA-mRNA Networks Associated With COPD Phenotypes. Front Genet. 2021; 12:748356. PMID: 34777474.
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    16. Carpenter CM, Zhang W, Gillenwater L, Severn C, Ghosh T, Bowler R, Kechris K, Ghosh D. PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. PLoS Comput Biol. 2021 10; 17(10):e1008986. PMID: 34679079.
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    17. Dekermanjian J, Labeikovsky W, Ghosh D, Kechris K. MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools. Metabolites. 2021 Oct 02; 11(10). PMID: 34677393.
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    18. Vanderlinden LA, Johnson RK, Carry PM, Dong F, DeMeo DL, Yang IV, Norris JM, Kechris K. An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies. BMC Res Notes. 2021 Sep 08; 14(1):352. PMID: 34496950.
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    19. Ghosh T, Philtron D, Zhang W, Kechris K, Ghosh D. Reproducibility of mass spectrometry based metabolomics data. BMC Bioinformatics. 2021 Sep 07; 22(1):423. PMID: 34493210.
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    20. Gillenwater LA, Helmi S, Stene E, Pratte KA, Zhuang Y, Schuyler RP, Lange L, Castaldi PJ, Hersh CP, Banaei-Kashani F, Bowler RP, Kechris KJ. Multi-omics subtyping pipeline for chronic obstructive pulmonary disease. PLoS One. 2021; 16(8):e0255337. PMID: 34432807.
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    21. Vigers T, Vanderlinden LA, Johnson RK, Carry PM, Yang I, DeFelice BC, Kaizer AM, Pyle L, Rewers M, Fiehn O, Norris JM, Kechris K. A Mediation Approach to Discovering Causal Relationships between the Metabolome and DNA Methylation in Type 1 Diabetes. Metabolites. 2021 Aug 14; 11(8). PMID: 34436483.
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    22. Buchwald AG, Grover E, Van Dyke J, Kechris K, Lu D, Liu Y, Zhong B, Carlton EJ. Human Mobility Associated With Risk of Schistosoma japonicum Infection in Sichuan, China. Am J Epidemiol. 2021 07 01; 190(7):1243-1252. PMID: 33438003.
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    23. Carry PM, Vanderlinden LA, Dong F, Buckner T, Litkowski E, Vigers T, Norris JM, Kechris K. Inverse probability weighting is an effective method to address selection bias during the analysis of high dimensional data. Genet Epidemiol. 2021 09; 45(6):593-603. PMID: 34130352.
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    24. Arbet J, Zhuang Y, Litkowski E, Saba L, Kechris K. Comparing Statistical Tests for Differential Network Analysis of Gene Modules. Front Genet. 2021; 12:630215. PMID: 34093641.
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    25. Pratte KA, Curtis JL, Kechris K, Couper D, Cho MH, Silverman EK, DeMeo DL, Sciurba FC, Zhang Y, Ortega VE, O'Neal WK, Gillenwater LA, Lynch DA, Hoffman EA, Newell JD, Comellas AP, Castaldi PJ, Miller BE, Pouwels SD, Hacken NHTT, Bischoff R, Klont F, Woodruff PG, Paine R, Barr RG, Hoidal J, Doerschuk CM, Charbonnier JP, Sung R, Locantore N, Yonchuk JG, Jacobson S, Tal-Singer R, Merrill D, Bowler RP. Soluble receptor for advanced glycation end products (sRAGE) as a biomarker of COPD. Respir Res. 2021 Apr 27; 22(1):127. PMID: 33906653.
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    26. Buckner T, Vanderlinden LA, DeFelice BC, Carry PM, Kechris K, Dong F, Fiehn O, Frohnert BI, Clare-Salzler M, Rewers M, Norris JM. The oxylipin profile is associated with development of type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY). Diabetologia. 2021 08; 64(8):1785-1794. PMID: 33893822.
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    27. Carry PM, Vanderlinden LA, Johnson RK, Buckner T, Fiehn O, Steck AK, Kechris K, Yang I, Fingerlin TE, Rewers M, Norris JM. Phospholipid Levels at Seroconversion Are Associated With Resolution of Persistent Islet Autoimmunity: The Diabetes Autoimmunity Study in the Young. Diabetes. 2021 07; 70(7):1592-1601. PMID: 33863802.
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    28. Lusk R, Stene E, Banaei-Kashani F, Tabakoff B, Kechris K, Saba LM. Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence. Nat Commun. 2021 03 12; 12(1):1652. PMID: 33712618.
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    29. Gillenwater LA, Kechris KJ, Pratte KA, Reisdorph N, Petrache I, Labaki WW, O'Neal W, Krishnan JA, Ortega VE, DeMeo DL, Bowler RP. Metabolomic Profiling Reveals Sex Specific Associations with Chronic Obstructive Pulmonary Disease and Emphysema. Metabolites. 2021 Mar 11; 11(3). PMID: 33799786.
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    30. Carpenter CM, Frank DN, Williamson K, Arbet J, Wagner BD, Kechris K, Kroehl ME. tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R. BMC Bioinformatics. 2021 Feb 01; 22(1):41. PMID: 33526006.
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    31. Chang HY, Colby SM, Du X, Gomez JD, Helf MJ, Kechris K, Kirkpatrick CR, Li S, Patti GJ, Renslow RS, Subramaniam S, Verma M, Xia J, Young JD. A Practical Guide to Metabolomics Software Development. Anal Chem. 2021 02 02; 93(4):1912-1923. PMID: 33467846.
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    32. Keleher MR, Erickson K, Smith HA, Kechris KJ, Yang IV, Dabelea D, Friedman JE, Boyle KE, Jansson T. Placental Insulin/IGF-1 Signaling, PGC-1a, and Inflammatory Pathways Are Associated With Metabolic Outcomes at 4-6 Years of Age: The ECHO Healthy Start Cohort. Diabetes. 2021 03; 70(3):745-751. PMID: 33414248.
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    33. Nikolakis ZL, Hales NR, Perry BW, Schield DR, Timm LE, Liu Y, Zhong B, Kechris KJ, Carlton EJ, Pollock DD, Castoe TA. Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Negl Trop Dis. 2021 01; 15(1):e0009020. PMID: 33406094.
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    34. Starling AP, Liu C, Shen G, Yang IV, Kechris K, Borengasser SJ, Boyle KE, Zhang W, Smith HA, Calafat AM, Hamman RF, Adgate JL, Dabelea D. Prenatal Exposure to Per- and Polyfluoroalkyl Substances, Umbilical Cord Blood DNA Methylation, and Cardio-Metabolic Indicators in Newborns: The Healthy Start Study. Environ Health Perspect. 2020 12; 128(12):127014. PMID: 33356526.
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    35. Gillenwater LA, Pratte KA, Hobbs BD, Cho MH, Zhuang Y, Halper-Stromberg E, Cruickshank-Quinn C, Reisdorph N, Petrache I, Labaki WW, O'Neal WK, Ortega VE, Jones DP, Uppal K, Jacobson S, Michelotti G, Wendt CH, Kechris KJ, Bowler RP. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. Netw Syst Med. 2020 Dec 01; 3(1):159-181. PMID: 33987620.
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    36. Radcliffe RA, Dowell R, Odell AT, Richmond PA, Bennett B, Larson C, Kechris K, Saba LM, Rudra P, Wen S. Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance. PLoS One. 2020; 15(10):e0240253. PMID: 33095786.
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    37. Guo K, Shen G, Kibbie J, Gonzalez T, Dillon SM, Smith HA, Cooper EH, Lavender K, Hasenkrug KJ, Sutter K, Dittmer U, Kroehl M, Kechris K, Wilson CC, Santiago ML. Qualitative Differences Between the IFNa subtypes and IFNß Influence Chronic Mucosal HIV-1 Pathogenesis. PLoS Pathog. 2020 10; 16(10):e1008986. PMID: 33064743.
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    38. Perng W, Francis EC, Smith HA, Carey J, Wang D, Kechris KM, Dabelea D. Sex-Specific Metabolite Biomarkers of NAFLD in Youth: A Prospective Study in the EPOCH Cohort. J Clin Endocrinol Metab. 2020 09 01; 105(9). PMID: 32687159.
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    39. Vestal BE, Moore CM, Wynn E, Saba L, Fingerlin T, Kechris K. MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. BMC Bioinformatics. 2020 Aug 28; 21(1):375. PMID: 32859148.
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    40. Johnson RK, Vanderlinden LA, DeFelice BC, Uusitalo U, Seifert J, Fan S, Crume T, Fiehn O, Rewers M, Kechris K, Norris JM. Metabolomics-related nutrient patterns at seroconversion and risk of progression to type 1 diabetes. Pediatr Diabetes. 2020 11; 21(7):1202-1209. PMID: 32686271.
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    41. Bailey KL, Smith H, Mathai SK, Huber J, Yacoub M, Yang IV, Wyatt TA, Kechris K, Burnham EL. Alcohol Use Disorders Are Associated With a Unique Impact on Airway Epithelial Cell Gene Expression. Alcohol Clin Exp Res. 2020 08; 44(8):1571-1584. PMID: 32524622.
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    42. Shaddox E, Peterson CB, Stingo FC, Hanania NA, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M. Bayesian inference of networks across multiple sample groups and data types. Biostatistics. 2020 07 01; 21(3):561-576. PMID: 30590505.
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    43. Keleher MR, Erickson K, Kechris K, Yang IV, Dabelea D, Friedman JE, Boyle KE, Jansson T. Associations between the activity of placental nutrient-sensing pathways and neonatal and postnatal metabolic health: the ECHO Healthy Start cohort. Int J Obes (Lond). 2020 11; 44(11):2203-2212. PMID: 32327723.
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    44. Mastej E, Gillenwater L, Zhuang Y, Pratte KA, Bowler RP, Kechris K. Identifying Protein-metabolite Networks Associated with COPD Phenotypes. Metabolites. 2020 Mar 25; 10(4). PMID: 32218378.
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    45. Johnson RK, Vanderlinden LA, Dong F, Carry PM, Seifert J, Waugh K, Shorrosh H, Fingerlin T, Frohnert BI, Yang IV, Kechris K, Rewers M, Norris JM. Longitudinal DNA methylation differences precede type 1 diabetes. Sci Rep. 2020 02 28; 10(1):3721. PMID: 32111940.
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    46. Carry PM, Vanderlinden LA, Johnson RK, Dong F, Steck AK, Frohnert BI, Rewers M, Yang IV, Kechris K, Norris JM. DNA methylation near the INS gene is associated with INS genetic variation (rs689) and type 1 diabetes in the Diabetes Autoimmunity Study in the Young. Pediatr Diabetes. 2020 06; 21(4):597-605. PMID: 32061050.
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    47. Ghosh T, Zhang W, Ghosh D, Kechris K. Predictive Modeling for Metabolomics Data. Methods Mol Biol. 2020; 2104:313-336. PMID: 31953824.
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    48. Kordas G, Rudra P, Hendricks A, Saba L, Kechris K. Insight into genetic regulation of miRNA in mouse brain. BMC Genomics. 2019 Nov 13; 20(1):849. PMID: 31722663.
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    49. Perng W, Ringham BM, Smith HA, Michelotti G, Kechris KM, Dabelea D. A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence. Diabetologia. 2020 02; 63(2):296-312. PMID: 31720734.
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    50. Shi WJ, Zhuang Y, Russell PH, Hobbs BD, Parker MM, Castaldi PJ, Rudra P, Vestal B, Hersh CP, Saba LM, Kechris K. Unsupervised discovery of phenotype-specific multi-omics networks. Bioinformatics. 2019 11 01; 35(21):4336-4343. PMID: 30957844.
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    51. Johnson RK, Vanderlinden L, DeFelice BC, Kechris K, Uusitalo U, Fiehn O, Sontag M, Crume T, Beyerlein A, Lernmark Å, Toppari J, Ziegler AG, She JX, Hagopian W, Rewers M, Akolkar B, Krischer J, Virtanen SM, Norris JM. Metabolite-related dietary patterns and the development of islet autoimmunity. Sci Rep. 2019 10 15; 9(1):14819. PMID: 31616039.
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    52. Zhuang YH, Wade K, Saba LM, Kechris K. Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis. Math Biosci Eng. 2019 09 26; 17(1):122-143. PMID: 31731343.
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    53. Halper-Stromberg E, Gillenwater L, Cruickshank-Quinn C, O'Neal WK, Reisdorph N, Petrache I, Zhuang Y, Labaki WW, Curtis JL, Wells J, Rennard S, Pratte KA, Woodruff P, Stringer KA, Kechris K, Bowler RP. Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites. 2019 Jul 25; 9(8). PMID: 31349744.
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    54. Starling AP, Adgate JL, Hamman RF, Kechris K, Calafat AM, Dabelea D. Prenatal exposure to per- and polyfluoroalkyl substances and infant growth and adiposity: the Healthy Start Study. Environ Int. 2019 10; 131:104983. PMID: 31284113.
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    55. Kazmi N, Sharp GC, Reese SE, Vehmeijer FO, Lahti J, Page CM, Zhang W, Rifas-Shiman SL, Rezwan FI, Simpkin AJ, Burrows K, Richardson TG, Santos Ferreira DL, Fraser A, Harmon QE, Zhao S, Jaddoe VWV, Czamara D, Binder EB, Magnus MC, Håberg SE, Nystad W, Nohr EA, Starling AP, Kechris KJ, Yang IV, DeMeo DL, Litonjua AA, Baccarelli A, Oken E, Holloway JW, Karmaus W, Arshad SH, Dabelea D, Sørensen TIA, Laivuori H, Raikkonen K, Felix JF, London SJ, Hivert MF, Gaunt TR, Lawlor DA, Relton CL. Hypertensive Disorders of Pregnancy and DNA Methylation in Newborns. Hypertension. 2019 08; 74(2):375-383. PMID: 31230546.
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    56. Larson ED, Magno JPM, Steritz MJ, Llanes EGDV, Cardwell J, Pedro M, Roberts TB, Einarsdottir E, Rosanes RAQ, Greenlee C, Santos RAP, Yousaf A, Streubel SO, Santos ATR, Ruiz AG, Lagrana-Villagracia SM, Ray D, Yarza TKL, Scholes MA, Anderson CB, Acharya A, Gubbels SP, Bamshad MJ, Cass SP, Lee NR, Shaikh RS, Nickerson DA, Mohlke KL, Prager JD, Cruz TLG, Yoon PJ, Abes GT, Schwartz DA, Chan AL, Wine TM, Cutiongco-de la Paz EM, Friedman N, Kechris K, Kere J, Leal SM, Yang IV, Patel JA, Tantoco MLC, Riazuddin S, Chan KH, Mattila PS, Reyes-Quintos MRT, Ahmed ZM, Jenkins HA, Chonmaitree T, Hafrén L, Chiong CM, Santos-Cortez RLP. A2ML1 and otitis media: novel variants, differential expression, and relevant pathways. Hum Mutat. 2019 08; 40(8):1156-1171. PMID: 31009165.
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    57. Küpers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, Page CM, Reese SE, Wilcox AJ, Czamara D, Starling AP, Novoloaca A, Lent S, Roy R, Hoyo C, Breton CV, Allard C, Just AC, Bakulski KM, Holloway JW, Everson TM, Xu CJ, Huang RC, van der Plaat DA, Wielscher M, Merid SK, Ullemar V, Rezwan FI, Lahti J, van Dongen J, Langie SAS, Richardson TG, Magnus MC, Nohr EA, Xu Z, Duijts L, Zhao S, Zhang W, Plusquin M, DeMeo DL, Solomon O, Heimovaara JH, Jima DD, Gao L, Bustamante M, Perron P, Wright RO, Hertz-Picciotto I, Zhang H, Karagas MR, Gehring U, Marsit CJ, Beilin LJ, Vonk JM, Jarvelin MR, Bergström A, Örtqvist AK, Ewart S, Villa PM, Moore SE, Willemsen G, Standaert ARL, Håberg SE, Sørensen TIA, Taylor JA, Räikkönen K, Yang IV, Kechris K, Nawrot TS, Silver MJ, Gong YY, Richiardi L, Kogevinas M, Litonjua AA, Eskenazi B, Huen K, Mbarek H, Maguire RL, Dwyer T, Vrijheid M, Bouchard L, Baccarelli AA, Croen LA, Karmaus W, Anderson D, de Vries M, Sebert S, Kere J, Karlsson R, Arshad SH, Hämäläinen E, Routledge MN, Boomsma DI, Feinberg AP, Newschaffer CJ, Govarts E, Moisse M, Fallin MD, Melén E, Prentice AM, Kajantie E, Almqvist C, Oken E, Dabelea D, Boezen HM, Melton PE, Wright RJ, Koppelman GH, Trevisi L, Hivert MF, Sunyer J, Munthe-Kaas MC, Murphy SK, Corpeleijn E, Wiemels J, Holland N, Herceg Z, Binder EB, Davey Smith G, Jaddoe VWV, Lie RT, Nystad W, London SJ, Lawlor DA, Relton CL, Snieder H, Felix JF. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun. 2019 04 23; 10(1):1893. PMID: 31015461.
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    58. Reinhold D, Pielke-Lombardo H, Jacobson S, Ghosh D, Kechris K. Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data. Methods Mol Biol. 2019; 1978:323-340. PMID: 31119672.
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    59. Vestal BE, Carlson NE, Estépar RSJ, Fingerlin T, Ghosh D, Kechris K, Lynch D. Using a spatial point process framework to characterize lung computed tomography scans. Spat Stat. 2019 Mar; 29:243-267. PMID: 31750077.
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    60. Cruickshank-Quinn CI, Jacobson S, Hughes G, Powell RL, Petrache I, Kechris K, Bowler R, Reisdorph N. Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD. Sci Rep. 2018 11 20; 8(1):17132. PMID: 30459441.
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    61. Lyu Y, Xue L, Zhang F, Koch H, Saba L, Kechris K, Li Q. Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. PLoS Comput Biol. 2018 09; 14(9):e1006436. PMID: 30240439.
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    62. Rudra P, Shi WJ, Russell P, Vestal B, Tabakoff B, Hoffman P, Kechris K, Saba L. Predictive modeling of miRNA-mediated predisposition to alcohol-related phenotypes in mouse. BMC Genomics. 2018 Aug 29; 19(1):639. PMID: 30157779.
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    63. Russell PH, Vestal B, Shi W, Rudra PD, Dowell R, Radcliffe R, Saba L, Kechris K. miR-MaGiC improves quantification accuracy for small RNA-seq. BMC Res Notes. 2018 May 15; 11(1):296. PMID: 29764489.
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    64. Vestal B, Russell P, Radcliffe RA, Bemis L, Saba LM, Kechris K. miRNA-regulated transcription associated with mouse strains predisposed to hypnotic effects of ethanol. Brain Behav. 2018 06; 8(6):e00989. PMID: 30106247.
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    65. Yang IV, Zhang W, Davidson EJ, Fingerlin TE, Kechris K, Dabelea D. Epigenetic marks of in utero exposure to gestational diabetes and childhood adiposity outcomes: the EPOCH study. Diabet Med. 2018 05; 35(5):612-620. PMID: 29461653.
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    66. 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. 2018 02 01; 47(1):22-23u. PMID: 29025028.
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    67. Newell Stamper BL, Cypser JR, Kechris K, Kitzenberg DA, Tedesco PM, Johnson TE. Movement decline across lifespan of Caenorhabditis elegans mutants in the insulin/insulin-like signaling pathway. Aging Cell. 2018 02; 17(1). PMID: 29214707.
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    68. Bradford E, Jacobson S, Varasteh J, Comellas AP, Woodruff P, O'Neal W, DeMeo DL, Li X, Kim V, Cho M, Castaldi PJ, Hersh C, Silverman EK, Crapo JD, Kechris K, Bowler RP. The value of blood cytokines and chemokines in assessing COPD. Respir Res. 2017 10 24; 18(1):180. PMID: 29065892.
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    69. Reinhold D, Morrow JD, Jacobson S, Hu J, Ringel B, Seibold MA, Hersh CP, Kechris KJ, Bowler RP. Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PLoS One. 2017; 12(10):e0185682. PMID: 29016655.
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    70. 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 11; 6(11):1503-1516. PMID: 29107296.
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    71. Cruickshank-Quinn C, Powell R, Jacobson S, Kechris K, Bowler RP, Petrache I, Reisdorph N. Metabolomic similarities between bronchoalveolar lavage fluid and plasma in humans and mice. Sci Rep. 2017 07 11; 7(1):5108. PMID: 28698669.
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    72. Starling AP, Adgate JL, Hamman RF, Kechris K, Calafat AM, Ye X, Dabelea D. Perfluoroalkyl Substances during Pregnancy and Offspring Weight and Adiposity at Birth: Examining Mediation by Maternal Fasting Glucose in the Healthy Start Study. Environ Health Perspect. 2017 06 26; 125(6):067016. PMID: 28669937.
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    73. Cicchini L, Blumhagen RZ, Westrich JA, Myers ME, Warren CJ, Siska C, Raben D, Kechris KJ, Pyeon D. High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and Represses HLA-E Expression in Human Keratinocytes. Sci Rep. 2017 06 16; 7(1):3633. PMID: 28623356.
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    74. Zemans RL, Jacobson S, Keene J, Kechris K, Miller BE, Tal-Singer R, Bowler RP. Multiple biomarkers predict disease severity, progression and mortality in COPD. Respir Res. 2017 06 13; 18(1):117. PMID: 28610627.
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    75. Miller MA, Danhorn T, Cruickshank-Quinn CI, Leach SM, Jacobson S, Strand MJ, Reisdorph NA, Bowler RP, Petrache I, Kechris K. Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma. PLoS One. 2017; 12(6):e0178281. PMID: 28575117.
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    76. Rudra P, Shi WJ, Vestal B, Russell PH, Odell A, Dowell RD, Radcliffe RA, Saba LM, Kechris K. Model based heritability scores for high-throughput sequencing data. BMC Bioinformatics. 2017 Mar 02; 18(1):143. PMID: 28253840.
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    77. Keene JD, Jacobson S, Kechris K, Kinney GL, Foreman MG, Doerschuk CM, Make BJ, Curtis JL, Rennard SI, Barr RG, Bleecker ER, Kanner RE, Kleerup EC, Hansel NN, Woodruff PG, Han MK, Paine R, Martinez FJ, Bowler RP, O'Neal WK. Biomarkers Predictive of Exacerbations in the SPIROMICS and COPDGene Cohorts. Am J Respir Crit Care Med. 2017 02 15; 195(4):473-481. PMID: 27579823.
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    78. Siska C, Kechris K. Differential correlation for sequencing data. BMC Res Notes. 2017 Jan 19; 10(1):54. PMID: 28103954.
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    79. Siska C, Bowler R, Kechris K. The discordant method: a novel approach for differential correlation. Bioinformatics. 2017 01 01; 33(1):150. PMID: 28034858.
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    80. Shaddox E, Stingo FC, Peterson CB, Jacobson S, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M. A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD. Stat Biosci. 2018; 10(1):59-85. PMID: 33912251.
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    81. Serban KA, Rezania S, Petrusca DN, Poirier C, Cao D, Justice MJ, Patel M, Tsvetkova I, Kamocki K, Mikosz A, Schweitzer KS, Jacobson S, Cardoso A, Carlesso N, Hubbard WC, Kechris K, Dragnea B, Berdyshev EV, McClintock J, Petrache I. Structural and functional characterization of endothelial microparticles released by cigarette smoke. Sci Rep. 2016 08 17; 6:31596. PMID: 27530098.
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    82. Sun W, Kechris K, Jacobson S, Drummond MB, Hawkins GA, Yang J, Chen TH, Quibrera PM, Anderson W, Barr RG, Basta PV, Bleecker ER, Beaty T, Casaburi R, Castaldi P, Cho MH, Comellas A, Crapo JD, Criner G, Demeo D, Christenson SA, Couper DJ, Curtis JL, Doerschuk CM, Freeman CM, Gouskova NA, Han MK, Hanania NA, Hansel NN, Hersh CP, Hoffman EA, Kaner RJ, Kanner RE, Kleerup EC, Lutz S, Martinez FJ, Meyers DA, Peters SP, Regan EA, Rennard SI, Scholand MB, Silverman EK, Woodruff PG, O'Neal WK, Bowler RP. Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD. PLoS Genet. 2016 Aug; 12(8):e1006011. PMID: 27532455.
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    83. Walter ND, de Jong BC, Garcia BJ, Dolganov GM, Worodria W, Byanyima P, Musisi E, Huang L, Chan ED, Van TT, Antonio M, Ayorinde A, Kato-Maeda M, Nahid P, Leung AM, Yen A, Fingerlin TE, Kechris K, Strong M, Voskuil MI, Davis JL, Schoolnik GK. Adaptation of Mycobacterium tuberculosis to Impaired Host Immunity in HIV-Infected Patients. J Infect Dis. 2016 10 15; 214(8):1205-11. PMID: 27534685.
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    84. Harrall KK, Kechris KJ, Tabakoff B, Hoffman PL, Hines LM, Tsukamoto H, Pravenec M, Printz M, Saba LM. Uncovering the liver's role in immunity through RNA co-expression networks. Mamm Genome. 2016 10; 27(9-10):469-84. PMID: 27401171.
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    85. Lu Q, Jin C, Sun J, Bowler R, Kechris K, Kaminski N, Zhao H. Post-GWAS Prioritization Through Data Integration Provides Novel Insights on Chronic Obstructive Pulmonary Disease. Stat Biosci. 2016; 2016:1-17. PMID: 27812370.
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    86. Walter ND, Miller MA, Vasquez J, Weiner M, Chapman A, Engle M, Higgins M, Quinones AM, Rosselli V, Canono E, Yoon C, Cattamanchi A, Davis JL, Phang T, Stearman RS, Datta G, Garcia BJ, Daley CL, Strong M, Kechris K, Fingerlin TE, Reves R, Geraci MW. Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: a Case-Control Study with Systematic Cross-Classifier Evaluation. J Clin Microbiol. 2016 Feb; 54(2):274-82. PMID: 26582831.
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    87. Siska C, Bowler R, Kechris K. The discordant method: a novel approach for differential correlation. Bioinformatics. 2016 03 01; 32(5):690-6. PMID: 26520855.
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    88. Bradford AP, Jones K, Kechris K, Chosich J, Montague M, Warren WC, May MC, Al-Safi Z, Kuokkanen S, Appt SE, Polotsky AJ. Joint MiRNA/mRNA expression profiling reveals changes consistent with development of dysfunctional corpus luteum after weight gain. PLoS One. 2015; 10(8):e0135163. PMID: 26258540.
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    89. Goldstein NB, Koster MI, Hoaglin LG, Spoelstra NS, Kechris KJ, Robinson SE, Robinson WA, Roop DR, Norris DA, Birlea SA. Narrow Band Ultraviolet B Treatment for Human Vitiligo Is Associated with Proliferation, Migration, and Differentiation of Melanocyte Precursors. J Invest Dermatol. 2015 Aug; 135(8):2068-2076. PMID: 25822579.
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    90. Walter ND, Dolganov GM, Garcia BJ, Worodria W, Andama A, Musisi E, Ayakaka I, Van TT, Voskuil MI, de Jong BC, Davidson RM, Fingerlin TE, Kechris K, Palmer C, Nahid P, Daley CL, Geraci M, Huang L, Cattamanchi A, Strong M, Schoolnik GK, Davis JL. Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis. J Infect Dis. 2015 Sep 15; 212(6):990-8. PMID: 25762787.
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    91. Newell BL, Kechris K, McQueen MB, Johnson TE. Genetic analysis of a murine QTL for diet restriction on chromosome 15. Age (Dordr). 2015 Feb; 37(1):9740. PMID: 25651884.
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    92. Bowler RP, Jacobson S, Cruickshank C, Hughes GJ, Siska C, Ory DS, Petrache I, Schaffer JE, Reisdorph N, Kechris K. Plasma sphingolipids associated with chronic obstructive pulmonary disease phenotypes. Am J Respir Crit Care Med. 2015 Feb 01; 191(3):275-84. PMID: 25494452.
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    93. Carolan BJ, Hughes G, Morrow J, Hersh CP, O'Neal WK, Rennard S, Pillai SG, Belloni P, Cockayne DA, Comellas AP, Han M, Zemans RL, Kechris K, Bowler RP. The association of plasma biomarkers with computed tomography-assessed emphysema phenotypes. Respir Res. 2014 Oct 12; 15:127. PMID: 25306249.
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    94. Hoffman PL, Saba LM, Flink S, Grahame NJ, Kechris K, Tabakoff B. Genetics of gene expression characterizes response to selective breeding for alcohol preference. Genes Brain Behav. 2014 Nov; 13(8):743-57. PMID: 25160899.
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    95. Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D. The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Res. 2014; 42(17):e133. PMID: 25063298.
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    96. Reisdorph N, Stearman R, Kechris K, Phang TL, Reisdorph R, Prenni J, Erle DJ, Coldren C, Schey K, Nesvizhskii A, Geraci M. Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics. Genomics Proteomics Bioinformatics. 2013 Dec; 11(6):368-77. PMID: 24316330.
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    97. Hughes G, Cruickshank-Quinn C, Reisdorph R, Lutz S, Petrache I, Reisdorph N, Bowler R, Kechris K. MSPrep--summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. Bioinformatics. 2014 Jan 01; 30(1):133-4. PMID: 24174567.
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    98. Bowler RP, Bahr TM, Hughes G, Lutz S, Kim YI, Coldren CD, Reisdorph N, Kechris KJ. Integrative omics approach identifies interleukin-16 as a biomarker of emphysema. OMICS. 2013 Dec; 17(12):619-26. PMID: 24138069.
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    99. Howard JB, Kechris KJ, Rees DC, Glazer AN. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships. PLoS One. 2013; 8(9):e72751. PMID: 24019874.
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    100. Carolan BJ, Kim YI, Williams AA, Kechris K, Lutz S, Reisdorph N, Bowler RP. The association of adiponectin with computed tomography phenotypes in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2013 Sep 01; 188(5):561-6. PMID: 23777323.
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    101. De S, Pedersen BS, Kechris K. The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Brief Bioinform. 2014 Nov; 15(6):919-28. PMID: 23956260.
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    102. Bahr TM, Hughes GJ, Armstrong M, Reisdorph R, Coldren CD, Edwards MG, Schnell C, Kedl R, LaFlamme DJ, Reisdorph N, Kechris KJ, Bowler RP. Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 2013 Aug; 49(2):316-23. PMID: 23590301.
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    103. Dvorkin D, Biehs B, Kechris K. A graphical model method for integrating multiple sources of genome-scale data. Stat Appl Genet Mol Biol. 2013 Aug; 12(4):469-87. PMID: 23934610.
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    104. Vanderlinden LA, Saba LM, Kechris K, Miles MF, Hoffman PL, Tabakoff B. Whole brain and brain regional coexpression network interactions associated with predisposition to alcohol consumption. PLoS One. 2013; 8(7):e68878. PMID: 23894363.
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    105. Baldea I, Costin GE, Shellman Y, Kechris K, Olteanu ED, Filip A, Cosgarea MR, Norris DA, Birlea SA. Biphasic pro-melanogenic and pro-apoptotic effects of all-trans-retinoic acid (ATRA) on human melanocytes: time-course study. J Dermatol Sci. 2013 Nov; 72(2):168-76. PMID: 23867358.
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    106. Siewert E, Kechris KJ. Modeling considerations for using expression data from multiple species. Stat Med. 2013 Oct 15; 32(23):4057-70. PMID: 23703923.
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    107. West NA, Kechris K, Dabelea D. Exposure to Maternal Diabetes in Utero and DNA Methylation Patterns in the Offspring. Immunometabolism. 2013 Mar; 1:1-9. PMID: 23741625.
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    108. 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.
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    109. Downing C, Flink S, Florez-McClure ML, Johnson TE, Tabakoff B, Kechris KJ. Gene expression changes in C57BL/6J and DBA/2J mice following prenatal alcohol exposure. Alcohol Clin Exp Res. 2012 Sep; 36(9):1519-29. PMID: 22530671.
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    110. Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ. Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS One. 2011; 6(11):e26105. PMID: 22069446.
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    111. Bennett B, Saba LM, Hornbaker CK, Kechris KJ, Hoffman P, Tabakoff B. Genetical genomic analysis of complex phenotypes using the PhenoGen website. Behav Genet. 2011 Jul; 41(4):625-8. PMID: 21184165.
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    112. Saba LM, Bennett B, Hoffman PL, Barcomb K, Ishii T, Kechris K, Tabakoff B. A systems genetic analysis of alcohol drinking by mice, rats and men: influence of brain GABAergic transmission. Neuropharmacology. 2011 Jun; 60(7-8):1269-80. PMID: 21185315.
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    113. Hoffman PL, Bennett B, Saba LM, Bhave SV, Carosone-Link PJ, Hornbaker CK, Kechris KJ, Williams RW, Tabakoff B. Using the Phenogen website for 'in silico' analysis of morphine-induced analgesia: identifying candidate genes. Addict Biol. 2011 Jul; 16(3):393-404. PMID: 21054686.
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    114. Biehs B, Kechris K, Liu S, Kornberg TB. Hedgehog targets in the Drosophila embryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling. Development. 2010 Nov; 137(22):3887-98. PMID: 20978080.
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    115. Kechris KJ, Biehs B, Kornberg TB. Generalizing moving averages for tiling arrays using combined p-value statistics. Stat Appl Genet Mol Biol. 2010; 9:Article29. PMID: 20812907.
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    116. Tabakoff B, Saba L, Printz M, Flodman P, Hodgkinson C, Goldman D, Koob G, Richardson HN, Kechris K, Bell RL, Hübner N, Heinig M, Pravenec M, Mangion J, Legault L, Dongier M, Conigrave KM, Whitfield JB, Saunders J, Grant B, Hoffman PL. Genetical genomic determinants of alcohol consumption in rats and humans. BMC Biol. 2009 Oct 27; 7:70. PMID: 19874574.
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    117. Glazer AN, Kechris KJ. Conserved amino acid sequence features in the alpha subunits of MoFe, VFe, and FeFe nitrogenases. PLoS One. 2009 Jul 03; 4(7):e6136. PMID: 19578539.
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    118. Kechris K, Li H. c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression. BMC Bioinformatics. 2008 Nov 28; 9:506. PMID: 19040743.
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    119. Kechris K, Yang YH, Yeh RF. Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics. 2008 Nov 20; 9:551. PMID: 19021909.
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