Publications by Katerina Kechris

2017

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 (to appear PLoS One) (#joint corresponding authors)

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. (to appear Environmental Health Perspectives) (*with post-doc)

E. Shaddox*, F. Stingo, C. Peterson, S. Jacobson, C. Cruickshank-Quinn, K. Kechris, R. Bowler and M. Vannucci (2016) A Bayesian approach for learning gene networks underlying disease severity in COPD. (to appear Statistics in Biosciences) (*with student)

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]

2016

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)

2015

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]

2014

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]

2013

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]

2012

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]

2011

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]

2010

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]

2009

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]

2008

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]

2007

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.

2002-2006

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]