Publications by Katerina Kechris

[Publications By Topic]


J. Arbet, Y. Zhuang, E. Litkowski, L. Saba# and K. Kechris# (2021) Comparing statistical tests for differential network analysis of gene modules. Frontiers in Genetics 12:630215. [PubMed] (#joint corresponding authors)

M. Daniels*#, D. Dvorkin*#, R. Powers and K. Kechris (2021) Semi-supervised learning using hierarchical mixture models: Gene essentiality case study. Mathematical and Computational Applications 26:40. [Journal] (*with students, #joint first authors)

P. Carry*, L. Vanderlinden, F. Dong, T. Buckner, E. Litkowski, T. Vigers, J. Norris# and K. Kechris# (2021) Inverse probability weighting is an effective method to address selection bias during the analysis of high dimensional data. Genetic Epidemiology 45(6):593-603. [PubMed] (*with student, #joint corresponding authors)

H. Chang, S. Colby, X. Du, J. Gomez, M. Helf, K. Kechris, C. Kirkpatrick, S. Li, G. Patti, R. Renslow, S. Subramaniam, M. Verma, J. Xia and J. Young (2021) A practical guide to metabolomics software development. Analytical Chemistry 93:1912-1923. [PubMed]

R. Lusk*, E. Stene, F. Banaei-Kashani, B. Tabakoff, K. Kechris and L. Saba (2021) Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence Nature Communications 12:1652. [PubMed] (*with student)

C. Carpenter*, D. Frank, K. Williamson, J. Arbet, B. Wagner, K. Kechris and M. Kroehl (2021) tidyMicro: A pipeline for microbiome data analysis and visualization using the tidyverse in R. BMC Bioinformatics 22:41. [PubMed] (*with student)

K. Pratte, J. Curtis, K. Kechris, .... R. Bowler (2021) Soluble receptor for advanced glycation end products (sRAGE) as a biomarker of COPD. Respiratory Research 22:127. [PubMed]

L. Gillenwater, K. Kechris, K. Pratte, N. Reisdorph, I. Petrache, W. Labaki, W. O'Neal, J. Krishnan, V. Ortega, D. DeMeo and R. Bowler (2021) Metabolomic profiling reveals sex specific associations with chronic obstructive pulmonary disease and emphysema. Metabolites 11:161. [PubMed]

L. Gillenwater*, K. Pratte, B. Hobbs, M. Cho, Y. Zhuang, ..., K. Kechris# and R. Bowler# (2021) Plasma metabolomic signatures of COPD and the impact of genetic variants on phenotype-driven modules. Network and Systems Medicine 3:159-181. [PubMed] (*with student, #joint corresponding authors)

T. Buckner*, L. Vanderlinden, B. DeFelice, P. Carry, K. Kechris, F. Dong, O. Fiehn, B. Frohnert, M. Clare-Salzler, M. Rewers and J. Norris (2021) The oxylipin profile is associated with development of type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY). Diabetologia 64:1785-1794. [PubMed] (*with student)

P. Carry*, L. Vanderlinden, R. Johnson, T. Buckner, O. Fiehn, A. Steck, K. Kechris, I. Yang, T. Fingerlin, M. Rewers and J. Norris (2021) Phospholipid levels at seroconversion are associated With resolution of persistent islet autoimmunity: The Diabetes Autoimmunity Study in the Young. Diabetes 70(7):1592-1601. [PubMed] (*with student)

M. Keleher*, K. Erickson, H. Smith, K. Kechris, I. Yang, D. Dabelea, J. Friedman, K. Boyle and T. Jansson (2021) Placental Insulin/IGF-1 Signaling, PGC1α, and inflammatory pathways are associated With metabolic outcomes at 4-6 years of age: The ECHO Healthy Start cohort. Diabetes 70:745-751. [PubMed] (*with post-doc)

Z. Nikolakis, N. Hales, B. Perry, D. Schield, L. Timm, Y. Liu, B. Zhong, K. Kechris, E. Carlton, D. Pollock, T. Castoe (2021) Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Neglected Tropical Diseases 15(1):e0009020. [PubMed]

A. Buchwald*, E. Grover, J. Van Dyke, K. Kechris, D. Luc, Y. Liu, B. Zhong, E. Carlton (2021) Human mobility associated with risk of Schistosoma japonicum infection in Sichuan, China. American Journal of Epidemiology 190:1243-1252. [PubMed] (*with post-doc)


B. Vestal, C. Moore, E. Wynn, L. Saba, T. Fingerlin, K. Kechris (2020) MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. BMC Bioinformatics (1):375. [PubMed]

E. Mastej*, L. Gillenwater, Y. Zhuang, K. Pratte, R. Bowler and K. Kechris (2020) Identifying protein-metabolite networks associated with COPD phenotypes. Metabolites 10:124. [PubMed] (*with student)

T. Ghosh*, W. Zhang, D. Ghosh and K. Kechris (2020) Predictive modeling for metabolomics Data. Methods Molecular Biology 2104:313-336. [PubMed] (*with post-doc)

E. Shaddox*, C. Peterson, F. Stingo, N. Hanania, C. Cruickshank-Quinn, K. Kechris, R. Bowler and M. Vannucci (2020) Bayesian inference of networks across multiple sample groups and data types. Biostatistics 21:561-576. [PubMed] (*with student)

R. Johnson*, L. Vanderlinden, F. Dong, P. Carry, J. Seifert, K. Waugh, H. Shorrosh, T. Fingerlin, B. Frohnert, I. Yang, K. Kechris, M. Rewers and J. Norris (2020) Longitudinal DNA methylation differences precede type 1 diabetes. Scientific Reports 10:3721. [PubMed] (*with student)

R. Johnson*, L. Vanderlinden, B. DeFelice, U. Uusitalo, J. Seifert, S. Fan, T. Crume, O. Fiehn, M. Rewers, K. Kechris, and J. Norris (2020) Metabolomics-related nutrient patterns at seroconversion and risk of progression to type 1 diabetes. Pediatric Diabetes 21:1202-1209. [PubMed] (*with student)

P. Carry*, L. Vanderlinden, R. Johnson, F. Dong, A. Steck, B. Frohnert, M. Rewers, I. Yang, K. Kechris and J. Norris. (2020) 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. Pediatrics Diabetes 21:597-605. [PubMed] (*with student)

M. Keleher*, K. Erickson, K. Kechris, I. Yang, D. Dabelea, J. Friedman, K. Boyle and T. Jansson (2020) Associations between the activity of placental nutrient-sensing pathways and neonatal and postnatal metabolic health: the ECHO Healthy Start cohort. International Journal of Obesity 44(11):2203-2212. [PubMed] (*with post-doc)

W. Perng, E. Francis, H. Smith, J. Carey, D. Wang, K. Kechris, and D. Dabelea (2020) A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence. Journal of Clinical Endocrinology & Metabolism 105(9):e3437-50. [PubMed]

W. Perng, B. Ringham, H. Smith, G. Michelotti, K. Kechris and D. Dabelea. (2020) A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence. Diabetologia 63:296-312. [PubMed]

A. Starling, C. Liu, G. Shen, I. Yang, K. Kechris, S. Borengasser, K. Boyle, W. Zhang, H. Smith, A. Calafat, R. Hamman, J. Adgate, D. Dabelea (2020) Prenatal Exposure to Per- and Polyfluoroalkyl Substances, Umbilical Cord Blood DNA Methylation, and Cardio-Metabolic Indicators in Newborns: The Healthy Start Study. Environmental Health Perspectives 128(12):127014. [PubMed]

K. Bailey, H. Smith, S. Mathai, J. Huber, M. Yacoub, I. Yang, T. Wyatt, K. Kechris and E. Burnham. (2020) Alcohol use disorders are associated with a unique impact on airways epithelial cell gene expression. Alcoholism Clinical Experimental Research 44(8):1571-1584. [PubMed]

R. Radcliffe, R. Dowell, A. Odell, P. Richmond, B. Bennett, C. Larson, K. Kechris, L. Saba, P. Rudra, S. Wen (2020) Systems genetics analysis of the LXS recombinant inbred mouse strains: Genetic and molecular insights into acute ethanol tolerance. PLoS One 15(10):e0240253. [PubMed]

K. Guo, G. Shen, J. Kibbie, T. Gonzalez, S. Dillon, H. Smith, E. Cooper, K. Lavender, K. Hasenkrug, K. Sutter, U. Dittmer, M. Kroehl, K. Kechris, C. Wilson, M. Santiago (2020) Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis. PLoS Pathogens 16(10):e1008986. [PubMed]


WJ. Shi*#, Y. Zhuang*#, P. Russell, B. Hobbs, M. Parker, P. Castaldi, P. Rudra, B. Vestal, C. Hersh, L. Saba and K. Kechris (2019) Unsupervised discovery of phenotype specific multi-omics networks. Bioinformatics 35:4336-4343. [PubMed] (* with student/post-doc, #joint first authors)

Y. Zhuang*, K. Wade, L. Saba# and K. Kechris# (2019) Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis. Mathematical Biosciences and Engineering 17:122-143. [PubMed] (* with student, #joint corresponding authors)

D. Reinhold, H. Pielke-Lombardo, S. Jacobson, D. Ghosh and K. Kechris (2019) Pre-analytic considerations for mass spectrometry-based untargeted metabolomics data. Methods Molecular Biology 1978:323-340. [PubMed]

B. Vestal*, N. Carlson, R. San Jose Estepar, T. Fingerlin, D. Ghosh, K. Kechris, and D. Lynch. (2019) Using a spatial point process framework to characterize lung computed tomography scans. Spatial Statistic29:243-267. [PubMed] (*with student)

G. Kordas*, P. Rudra, A. Hendricks, L. Saba# and K. Kechris# (2019) Insight into genetic regulation of miRNA in mouse brain. BMC Genomics 20:849. [PubMed] (* with student, #joint corresponding authors)

E. Halper-Stromberg*, L. Gillenwater, C. Cruickshank-Quinn, W. O'Neal, N. Reisdorph, I. Petrache, Y. Zhuang, W. Labaki, J. Curtis, J. Wells, S. Rennard, K. Pratte, P. Woodruff, K. Stringer, K. Kechris#, R. Bowler# (2019) Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites 9(8). [PubMed] (*with student, #joint corresponding authors)

W. Perng, BM. Ringham, HA. Smith, Michelotti G, K. Kechris, and D. Dabelea (2020) A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence. Diabetologia 63:296-312. [PubMed]

R. Johnson*, L. Vanderlinden, B. DeFelice, K. Kechris, U. Uusitalo, O. Fiehn, M. Sontag, T. Crume, A. Beyerlein, Å. Lernmark, J. Toppari, A.-G. Ziegler, J.-X. She, W. Hagopian, M. Rewers, B. Akolkar, J. Krischer, S. Virtanen, J. Norris, and The TEDDY Study Group (2019) Metabolite-related dietary patterns and the development of islet autoimmunity. Scientific Reports 9:14819. [PubMed] (* with student)

A. Starling, J. Adgate, R. Hamman, K. Kechris, A. Calafat, D. Dabelea (2019) Prenatal exposure to per- and polyfluoroalkyl substances and infant growth and adiposity: the Healthy Start Study. Environment International 131:104983. [PubMed]

L. Kupers, ... J. Felix (2019) Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nature Communications 10(1):1893. [PubMed]

N. Kazmi, ... C. Ralton (2019) Hypertensive disorders of pregnancy and DNA methylation in newborns. Hypertension 74:375-383. [PubMed]

E. Larson, ... R. Santos-Cortez (2019) A2ML1 and otitis media: novel variants, differential expression, and relevant pathways. Human Mutation 40:1156-1171. [PubMed]


P. Russell, B. Vestal, W. Shi, P. Rudra, R. Dowell, R. Radcliffe, L. Saba and K. Kechris (2018) miR-MaGiC improves quantification accuracy for small RNA-seq. BMC Research Notes 11(1):296 [PubMed]

Y. Lyu*, L. Xue, F. Zhang, H. Koch, L. Saba, K. Kechris and Q. Li (2018) Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. PLoS Computational Biology 14(9):e1006436 [PubMed] (*with student)

E. Shaddox*, F. Stingo, C. Peterson, S. Jacobson, C. Cruickshank-Quinn, K. Kechris, R. Bowler and M. Vannucci (2018) A Bayesian approach for learning gene networks underlying disease severity in COPD. Statistics in Biosciences 10:59-85 [Link] (*with student)

B. Vestal*, P. Russell, R. Radcliffe, L Bemis, L. Saba and K. Kechris. miRNA regulated transcription associated with mouse strains predisposed to hypnotic effects of ethanol. Brain and Behavior 8:e00989 [PubMed] (*with student)

P. Rudra*, W. Shi, P. Russell, B. Vestal, B. Tabakoff, P. Hoffman, K. Kechris and L. Saba (2018) Predictive modeling of miRNA-mediated predisposition to alcohol-related phenotypes in mouse. BMC Genomics 19(1):639 [PubMed] (*with post-doc)

C. Cruickshank-Quinn*, S. Jacobson, G. Hughes, R. Powell, I. Petrache, K. Kechris, R. Bowler and N.Reisdorph (2018) Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD. Scientific Reports 8:17132. [PubMed] (*with post-doc)

I. Yang, W. Zhang, E. Davidson, T. Fingerlin, K. Kechris and D. Dabelea (2018) Epigenetic marks of in utero exposure to gestational diabetes and childhood adiposity outcomes: the EPOCH study. Diabetic Medicine 35(5):612-620. [PubMed]

J. Felix, et al. (2017) Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium. International Journal of Epidemiology 47(1):22-23 [PubMed]

B. Newell Stamper*, J. Cypser, K. Kechris, D. Kitzenberg, P. Tedesco and T. Johnson (2018) Movement decline across lifespan of Caenorhabditis elegans mutants in the insulin/insulin-like signaling pathway. Aging Cell 17(1) [PubMed] (*with student)


P. Rudra*, W. Shi*, B. Vestal*, P. Russell, A. Odell, R. Dowell-Deen, R. Radcliffe, L. Saba and K. Kechris (2017) Model based heritability scores for high-throughput sequencing data. BMC Bioinformatics 18:143 [PubMed] (*with post-doc, student)

C. Siska* and K. Kechris (2017) Differential correlation for sequencing data. BMC Research Notes 10:54 [PubMed] (*with student)

M. Miller*, T. Danhorn, C. Cruickshank-Quinn, S. Leach, S. Jacobson, M. Strand, N. Reisdorph, R. Bowler#, I. Petrache# and K. Kechris#. (2017) Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma PLoS One 12(6):e0178281 [PubMed] (#joint corresponding authors,*with student)

A. Starling*, J. Adgate, R. Hamman, K. Kechris, A. Calafat, X. Ye and D. Dabelea (2017) Perfluoroalkyl substances during pregnancy and offspring weight and adiposity at birth: examining mediation by maternal fasting glucose in the Healthy Start Study. Environmental Health Perspectives 125(6):067016 [PubMed] (*with post-doc)

J. Keene, S. Jacobson, K. Kechris, G. Kinney, ..., R. Bowler and W. O'Neal; for COPDGene and SPIROMICS Investigators. (2017) Biomarkers predictive of exacerbations in the SPIROMICS and COPDGene Cohorts. American Journal of Respiratory and Critical Care Medicine) 195:473-481. [PubMed]

C. Cruickshank-Quinn*, R. Powell, S. Jacobson, K. Kechris, R. Bowler, I. Petrache and N. Reisdorph. (2017) Metabolomic similarities between bronchoalveolar lavage fluid and plasma in humans and mice. Scientific Reports 7(1):5108 [PubMed] (*with post-doc)

R. Zemans, S. Jacobson, J. Keene, K. Kechris, B. Miller, R. Tal-Singer and R. Bowler. (2017) Multiple biomarkers predict disease severity, progression and mortality in COPD. Respiratory Research 18(1):117. [PubMed]

L. Cicchini*, R. Blumhagen, J. Westrich, M. Myers, C. Warren, C. Siska, D. Raben, K. Kechris and D. Pyeon. (2017) High-risk human papillomavirus E7 alters host DNA methylome and represses HLA-E expression in human keratinocytes. Scientific Reports 7(1):3633 [PubMed](*with student)

E. Bradford, S. Jacobson, J. Varasteh, A. Comellas, P. Woodruff, W. O'Neal, D. DeMeo, X. Li, V. Kim, M. Cho, P. Castaldi, C. Hersh, E. Silverman, J. Crapo, K. Kechris and R. Bowler. (2017) The value of blood cytokines and chemokines in assessing COPD. Respiratory Research 18(1):180 [PubMed]

D. Reinhold, J. Morrow, S. Jacobson, J. Hu, B. Ringel, M. Seibold, C. Hersh, K. Kechris and R. Bowler. (2017) Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PLoS One 12(10):e0185682 [PubMed]

K. Boyle, Z. Patinkin, A. Shapiro, C. Bader, L. Vanderlinden, K. Kechris, R. Janssen, R. Ford, B. Smith, G. Steinberg, E. Davidson, I. Yang, D. Dabelea and J. Friedman. (2017) Maternal obesity alters fatty acid oxidation, AMPK activity, and associated DNA methylation in mesenchymal stem cells from human infants. Molecular Metabolism 6(11):1503-1516 [PubMed]


C. Siska*, R. Bowler, K. Kechris (2016) The discordant method: A novel approach for differential correlation. Bioinformatics 32:690-6 [PubMed] (*with student)

W. Sun', K. Kechris', S. Jacobson', ..., W. O'Neal, R. Bowler (2016) Common genetic polymorphisms influence blood biomarker measurements in COPD. PLoS Genetics 12(8):e1006011. [PubMed] (' authors contributed equally)

Q. Lu*, C. Jin, J. Sun, R. Bowler, K. Kechris, N. Kaminski, H. Zhao (2016) Post-GWAS prioritization through data integration provides novel insights on chronic obstructive pulmonary disease. Statistics in Biosciences 2016:1-17. [PubMed] (*with student)

K. Harrall*, K. Kechris, L. Hines, P. Hoffman, B. Tabakoff, L.M. Saba (2016) Uncovering the liver's role in immunity through RNA co-expression networks. Mammalian Genome 27:469-84 [PubMed] (*with student)

K. Serban, S. Rezania, D. Petrusca, C. Poirier, D. Cao, M. Justice, M. Patel, I. Tsvetkova, K. Kamocki, A. Mikosz, K. Schweitzer, S. Jacobson, A. Cardoso, N. Carlesso, W. Hubbard, K. Kechris, B. Dragnea, E. Berdyshev, J. McClintock, and I. Petrache. (2016) Structural and functional characterization of endothelial microparticles released by cigarette smoke. Nature Scientific Reports 6:31596 [PubMed]

N. Walter*, M. Miller, J. Vasquez, ..., K. Kechris, T. Fingerlin, R. Reves, and M. Geraci (2016) Blood transcriptional biomarkers for active TB among US patients: A case-control study with systematic cross-classifier evaluation. Journal of Clinical Microbiology 54(2): 274-82. [PubMed] (*with student)

N. Walter*, B. de Jong, B. Garcia, ..., T. Fingerlin, K. Kechris, M. Strong, M. Voskuil, J. Davis and G. Schoolnik. (2016) Adaptation of Mycobacterium tuberculosis to impaired host immunity in HIV infected patients. Journal of Infectious Diseases 214:1205-11. [PubMed] (*with student)


R. Bowler, S. Jacobson, C. Cruickshank, G. Hughes, C. Siska, D. Ory, I. Petrache, J. Schaffer, N. Reisdorph and K. Kechris (2015) Plasma sphingolipids associated with COPD phenotypes. American Journal of Respiratory and Critical Care Medicine 191:275-84. [PubMed]

A. Bradford, K. Jones, K. Kechris, J. Chosich, M. Montague, W. Warren, M. May, Z. Al-Safi, S. Kuokkanen, S. Appt and A. Polotsky (2015) Joint miRNA/mRNA expression profiling reveals changes consistent with development of dysfunctional corpus luteum after weight gain. PLoS One 10:e0135163. [PubMed]

B. Newell*, K. Kechris, M. McQueen and T.E. Johnson (2015) Genetic analysis of a murine QTL for diet restriction on chromosome 15. Age 37(1):9740. [PubMed] (*with student)

N. Walter*, G. Dolganov, B. Garcia, W. Worodria, A. Andama, E. Musisi, I. Ayakaka, T. Van, M. Voskuil, B. de Jong, R. Davidson, T. Fingerlin, K. Kechris, C. Palmer, P. Nahid, C. Daley, M. Geraci, L. Huang, A. Cattamanchi, M. Strong, G. Schoolnik and J. Davis (2015) Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis during treatment of human tuberculosis. Journal of Infectious Diseases 212:990-8. [PubMed] (* with student)

N. Goldstein, M. Koster, L. Hoaglin, N. Spoelstra, K. Kechris, S. Robinson, W. Robinson, D. Roop, D. Norris, S. Birlea (2015) Narrow band ultraviolet B treatment for human vitiligo is associated with proliferation, migration and differentiation of melanocyte precursors. Journal of Investigative Dermatology 135:2068-76 [PubMed]

A. Glazer, K. Kechris and J. Howard (2015) Distribution and Ecological Niches of Nitrogenases. Biological Nitrogen Fixation, F.J. deBruijn (ed.), Wiley-Blackwell. [Link]


Y. Ru', K. Kechris', B. Tabakoff, P. Hoffman, R.A. Radcliffe, R. Bowler, S. Mahaffey, S. Rossi, G.A. Calin, L. Bemis and D. Theodorescu (2014) The multiMiR R package: Multiple databases of microRNA-target interactions with their disease and drug associations. Nucleic Acids Research 42:e133. [PubMed] (' authors contributed equally)

G. Hughes*, C. Cruickshank-Quinn, R. Reisdorph, S. Lutz, I. Petrache, N. Reisdorph, R. Bowler and K. Kechris (2014) MSPrep: Summarization, normalization, and diagnostics for processing of mass spectrometry based metabolomic data. Bioinformatics 30:133-4. [PubMed] (*with student)

S. De, B. Pedersen and K. Kechris (2014) The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Briefings In Bioinformatics 15:919-28. [PubMed]

P. Hoffman, L. Saba, S. Flink, N. Grahame, K. Kechris and B. Tabakoff (2014) Genetics of gene expression characterizes response to selective breeding for alcohol preference. Genes Brain and Behavior 13:743-57. [PubMed]

B. Carolan, G. Hughes, J. Morrow, C. Hersh, W. O'Neal, S. Rennard, S. Pillai, P. Belloni, D. Cockayne, A. Comellas, M. Han, R. Zemans, K. Kechris, R. Bowler (2014) The association of plasma biomarkers with computed tomography-assessed emphysema phenotypes. Respiratory Research 15:127. [PubMed]


D. Dvorkin*, B. Biehs and K. Kechris (2013) A graphical model method for integrating multiple sources of genome-scale data. Statistical Applications in Genetics and Molecular Biology 12:469-87. [PubMed] (*with student)

B. Siewert* and K. Kechris (2013) Modeling considerations for using expression data from multiple species. Statistics in Medicine 32:4057-4070. [PubMed] (*with student)

N. Reisdorph, R. Stearman, K. Kechris, T.-L. Phang, R. Reisdorph, J. Prenni, C. Coldren, D. Erle, K. Schey, A. Nesvizhskii and M. Geraci. (2013) Hands on workshops as an effective means of learning advanced technologies including genomics, proteomics, and bioinformatics. Genomics, Proteomics & Bioinformatics 11:368-77. [PubMed]

L. Vanderlinden, L. Saba, K. Kechris, M. Miles, P. Hoffman and B. Tabakoff (2013) Whole brain and brain regional coexpression network interactions associated with predisposition to alcohol consumption. PLoS One, 8(7):e68878. [PubMed]

R. Bowler, T. Bahr, G. Hughes, S. Lutz, Y. Kim, C. Coldren, N. Reisdorph and K. Kechris (2013) Integrative omics approach identifies Interleukin 16 as a biomarker of emphysema. OMICS: A Journal of Integrative Biology 17:619-626 [PubMed]

B.J. Carolan, Y. Kim, A.A. Williams, K. Kechris, S. Lutz, N. Reisdorph and R.P. Bowler (2013) The association of adiponectin with CT phenotypes in chronic obstructive pulmonary disease. American Journal of Respiratory and Critical Care Medicine, 88:561-6. [PubMed]

T. Bahr*, G. Hughes*, M. Armstrong, R. Reisdroph, C. Coldren, M. Edwards, C. Schnell, R. Kedl, D. LaFlamme, N. Reisdorph, K. Kechris# and R. Bowler#. (2013) Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. American Journal of Respiratory Cell and Molecular Biology, 49:316-23. [PubMed] (*with student, #joint corresponding authors)

N. West, K. Kechris and D. Dabelea (2013) Exposure to maternal diabetes in utero and DNA methylation patterns in the offspring. Immunometabolism, 1:1-9. [PubMed]

J. Howard, K. Kechris, D. Rees and A. Glazer. Multiple amino acid sequence alignment of nitrogenase component 1: Insights into phylogenetics and structure-function relationships. PLoS One, 8(9):e72751. [PubMed]

I. Baldea, G. Costin, Y. Shellman, K. Kechris, A. Filip, M. Cosgarea, D.A. Norris and S. Birlea (2013) Biphasic pro-melanogenic and pro-apoptotic effects of all-trans-retinoic acid (ATRA) on human melanocytes: Time-course study. Journal of Dermatological Science 72:168-76. [PubMed]


B. Pedersen, D. Schwartz, I. Yang# and K. Kechris# (2012) Comb-p: software for combining, analyzing, grouping, and correcting spatially correlated p-values. Bioinformatics, 28:2986-8. [PubMed] (#joint corresponding authors)

C. Downing, S. Flink, M. Florez-McClure, B. Tabakoff, T. Johnson and K. Kechris (2012) Gene expression changes in C57BL/6J and DBA/2J mice following prenatal alcohol exposure. Alcoholism: Clinical & Experimental Research, 36:1519-29. [PubMed]


D. Pollock, A.P.J de Koning, H. Kim, T.A. Castoe, M.E.A. Churchill and K. Kechris (2011) Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS ONE, 6:e26105. [PubMed]

T.-L. Phang, W. Feng, R.A. Radcliffe and K. Kechris (2011) Post-processing multi-treatment time-course microarray studies using the Johnson-Neyman procedure. Biostatistics, Bioinformatics and Biomathematics, 2:107-126. [Link]

B. Bennett, L.M. Saba, C.K. Hornbaker, K. Kechris, P. Hoffman and B. Tabakoff (2011) Genetical genomic analysis of complex phenotypes using the PhenoGen website. Behavior Genetics, 41:625-8. [PubMed]

L.M. Saba, B. Bennett, P.L. Hoffman, K. Barcomb, T. Ishii, K. Kechris and B.Tabakoff (2011) A systems genetic analysis of alcohol drinking by mice, rats and men: Influence of brain GABAergic transmission. Neuropharmacology, 60:1269-80 [PubMed]

P. Hoffman, B. Bennett, L. Saba, S. Bhave, P. Carosone-Link, C. Hornbaker, K. Kechris and B. Tabakoff (2011). Using the PhenoGen website for "in silico" analysis of morphine-induced analgesia: Identifying candidate genes. Addiction Biology, 16:393-404. [PubMed]


K. Kechris, B. Biehs and T. Kornberg (2010). Generalizing moving averages for tiling arrays using combined p-value statistics. Statistical Applications in Genetics and Molecular Biology, Vol. 9: No. 1, Article 29. [PubMed]

B. Biehs, K. Kechris, S. Liu and T. Kornberg (2010). Hedgehog targets in the Drosophila embryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling. Development, 137:3887-98. [PubMed]


E. Siewert* and K. Kechris (2009). Prediction of motifs based on a repeated-measures model for integrating cross-species sequence and expression data. Statistical Applications in Genetics and Molecular Biology, Vol. 8: No. 1, Article 36. [PubMed] (*with student)

A. Glazer and K. Kechris (2009). Conserved amino acid sequence features in the α subunits of MoFe, VFe, and FeFe nitrogenases. PLoS ONE, 4(7):e6136. [PubMed]

B. Tabakoff, L. Saba, M. Printz, P. Flodman, C. Hodgkinson, D. Goldman, G. Koob, H. Richardson, K. Kechris, R. Bell, N. Hubner, M. Heinig, M. Pravenec, J. Mangion, L. Legault, M. Dongier, K. Conigrave, J. Whitfield, J. Saunders, B. Grant and P.L. Hoffman, WHO/ISBRA Study on State and Trait Markers of Alcoholism (2009). Genetical genomic determinants of alcohol consumption in rats and humans. BMC Biology, 7:70. [PubMed]


K. Kechris and H. Li (2008). c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression. BMC Bioinformatics, 9:506. [PubMed]

K. Kechris', Y.H. Yang' and R.-F. Yeh (2008). Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics, 9:551. [PubMed] (' authors contributed equally)

W. Hu, L. Saba, K. Kechris, S. Bhave, P. Hoffman and B. Tabakoff (2008). Genomic insights into acute alcohol tolerance. Journal of Pharmacology And Experimental Therapeutics, 326:792-800. [PubMed]

B. Tabakoff, L. Saba, K. Kechris, W. Hu, S. Bhave, D. Finn, N. Grahame and P. Hoffman (2008). The genomic determinants of alcohol preference in mice. Mammalian Genome, 19:352-65. [PubMed]


S. Bhave, C. Hornbaker, T. Phang, L. Saba, R. Lapadat, K. Kechris, J. Gaydos, D. McGoldrick, A. Dolbey, S. Leach, B. Soriano, A. Ellington, E. Ellington, K. Jones, J. Mangion, J. Belknap, R. Williams, L. Hunter, P. Hoffman and B. Tabakoff (2007). The PhenoGen informatics website: Tools for analyses of complex traits. BMC Genetics, 8:59. [PubMed]

C. Washenberger, J. Han, K. Kechris, B. Jha, R. Silverman and D. Barton (2007). Hepatitis C virus RNA: Dinucleotide frequencies and cleavage by RNase L. Virus Research 130:85-95. [PubMed]

H. Kim, K. Kechris and L. Hunter (2007). Mining discriminative distance context of transcription factor binding sites on ChIP enriched regions. Lecture Notes in Computer Science: International Symposium on Bioinformatics Research and Applications, ISBRA 2007 Proceedings, pg 338-349.


K. Kechris, J. Lin, P. Bickel and A. Glazer (2006). Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. Proceedings of the National Academy of Sciences, USA, 103:9584-9589. [PubMed] [Errata]

A. Klebes, A. Sustar, K. Kechris, H. Li, G. Schubiger and T. Kornberg (2005). Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes. Development, 132:3753-3765. [PubMed]

E. van Zwet, K. Kechris, P. Bickel and M. Eisen (2005). Estimating motifs under order restrictions. Statistical Applications in Genetics and Molecular Biology, Vol. 4: No. 1, Article 1. [PubMed]

K. Kechris, E. van Zwet, P. Bickel and M. Eisen (2004). Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biology, 5:R50. [PubMed]

P. Bickel, K. Kechris, P. Spector, G. Wedemayer and A. Glazer (2002). Finding "important" sites in proteins. Proceedings of the National Academy of Sciences, USA, 99:14764-14771. [PubMed]