PUBLICATIONS | Kechris Lab

Identification of Plasma Metabolites Responding to Oxycodone Exposure in Rats

Thao Vu, Suneeta Godbole, Lieselot L G Carrette, Lisa Maturin, Olivier George, Laura M Saba, Katerina Kechris

Metabolites 15(2):95 · 04 Feb 2025

DisCo P-ad: Distance-Correlation-Based p-Value Adjustment Enhances Multiple Testing Corrections for Metabolomics

Debmalya Nandy, Debashis Ghosh, Katerina Kechris

Metabolites 15(1):28 · 08 Jan 2025

Prenatal black carbon exposure and DNA methylation in umbilical cord blood

Chloe Friedman, Sierra Niemiec, Dana Dabelea, Katerina Kechris, Ivana V. Yang, John L. Adgate, Deborah H. Glueck, Sheena E. Martenies, Sheryl Magzamen, Anne P. Starling

International Journal of Hygiene and Environmental Health 263:114464. · 01 Jan 2025

Metabolic Aging as an Increased Risk for Chronic Obstructive Pulmonary Disease

Claire J Guo, Suneeta Godbole, Wassim W Labaki, Katherine A Pratte, Jeffrey L Curtis, Robert Paine, Eric Hoffman, Meilan Han, Jill Ohar, Christopher Cooper, Katerina J Kechris, Dawn L DeMeo, Russell P Bowler

Metabolites 14(12):647. · 21 Nov 2024

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics

Alexandria M Jensen, Peter DeWitt, Brianne M Bettcher, Julia Wrobel, Katerina Kechris, Debashis Ghosh

PLoS Computational Biology 20(11):e1012524. · 11 Nov 2024

Death and survival of gut CD4 T cells following HIV-1 infection ex vivo

Kaylee L Mickens, Stephanie M Dillon, Kejun Guo, Ashley N Thompson, Bradley S Barrett, Cheyret Wood, Katerina Kechris, Mario L Santiago, Cara C Wilson

PNAS Nexus 3(11):486. · 29 Oct 2024

The predictive utility of the in utero exposome for childhood adiposity in independent and integrated frameworks

Jonathan VanHawkins, Ryan Peterson, Kylie Harrall, Brandy Moon, Dana Dabelea, Katerina Kechris, Wei Perng

Pediatric Obesity 19(12):e13172. · 26 Sep 2024

Proteomic networks and related genetic variants associated with smoking and chronic obstructive pulmonary disease

Iain R Konigsberg, Thao Vu, Weixuan Liu, Elizabeth M Litkowski, Katherine A Pratte, Luciana B Vargas, Niles Gilmore, Mohamed Abdel-Hafiz, Ani Manichaikul, Michael H Cho, Craig P Hersh, Dawn L DeMeo, Farnoush Banaei-Kashani, Russell P Bowler, Leslie A Lange, Katerina J Kechris

BMC Genomics 25:825 · 02 Sep 2024

Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization

Weixuan Liu, Thao Vu, Iain R Konigsberg, Katherine A Pratte, Yonghua Zhuang, Katerina J Kechris

BMC Bioinformatics 25:276. · 24 Aug 2024

Maternal Serum Metabolomics in Mid-Pregnancy Identifies Lipid Pathways as a Key Link to Offspring Obesity in Early Childhood

Ellen C Francis, Katerina Kechris, Randi K Johnson, Shristi Rawal, Wimal Pathmasiri, Blake R Rushing, Xiuxia Du, Thomas Jansson, Dana Dabelea, Susan J Sumner, Wei Perng

International Journal of Molecular Sciences 25(14):7620. · 11 Jul 2024

Longitudinal changes in DNA methylation during the onset of islet autoimmunity differentiate between reversion versus progression of islet autoimmunity

Patrick M Carry, Lauren A Vanderlinden, Randi K Johnson, Teresa Buckner, Andrea K Steck, Katerina Kechris, Ivana V Yang, Tasha E Fingerlin, Oliver Fiehn, Marian Rewers, Jill M Norris

Frontiers Immunology 10:15:1345494. · 10 Jun 2024

Limitations of clustering with PCA and correlated noise

William Lippitt, Nichole E. Carlson, Jaron Arbet, Tasha E. Fingerlin, Lisa A. Maier, Katerina Kechris

Journal of Statistical Computation and Simulation 94(10):2291-2319. · 05 May 2024

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration

Cecilia Wieder, Juliette Cooke, Clement Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J Kechris, Rachel Pj Lai, Timothy Ebbels

PLoS Computational Biology 20(3):e1011814. · 25 Mar 2024

Differentially methylated regions interrogated for metastable epialleles associate with offspring adiposity

Stephanie W Waldrop, Katherine A Sauder, Sierra S Niemiec, Katerina J Kechris, Ivana V Yang, Anne P Starling, Wei Perng, Dana Dabelea, Sarah J Borengasser

Epigenomics 16(18):1215–1230. · 01 Jan 2024

Sex-based differences in placental DNA methylation profiles related to gestational age: an NIH ECHO meta-analysis

Catherine M Bulka, Todd M Everson, Amber A Burt, Carmen J Marsit, Margaret R Karagas, Kristen E Boyle, Sierra Niemiec, Katerina Kechris, Elizabeth J Davidson, Ivana V Yang, Jason I Feinberg, Heather E Volk, Christine Ladd-Acosta, Carrie V Breton, T Michael O'Shea, Rebecca C Fry, program collaborators for Environmental influences on Child Health Outcomes

Epigenetics 18(1):2179726. · 01 Dec 2023

Accelerated epigenetic age at birth and child emotional and behavioura development in early childhood: a meta-analysis of four prospective cohort studies in ECHO

Ashley Y Song, Catherine M Bulka, Sierra S Niemiec, Katerina Kechris, Kristen E Boyle, Carmen J Marsit, T Michael O'Shea, Rebecca C Fry, Kristen Lyall, M Daniele Fallin, Heather E Volk, Christine Ladd-Acosta

Epigenetics 18(1):2254971. · 01 Dec 2023

TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes

Charlie M Carpenter, Lucas Gillenwater, Russell Bowler, Katerina Kechris, Debashis Ghosh

BMC Bioinformatics 24(1):398. · 25 Oct 2023

Cord blood DNA methylation of immune and lipid metabolism genes is associated with maternal triglycerides and child adiposity

Stephanie W. Waldrop, Sierra Niemiec, Cheyret Wood, Lauren E. Gyllenhammer, Thomas Jansson, Jacob E. Friedman, Jeanie B. Tryggestad, Sarah J. Borengasser, Elizabeth J. Davidson, Ivana V. Yang, Katerina Kechris, Dana Dabelea, Kristen E. Boyle

Obesity 32(1):187-199. · 23 Oct 2023

Quantifying the spatial clustering characteristics of radiographic emphysema explains variability in pulmonary function

Brian E Vestal, Debashis Ghosh, Raúl San José Estépar, Katerina Kechris, Tasha Fingerlin, Nichole E Carlson

Scientific Reports 13(1):13862. · 24 Aug 2023

Prenatal exposures to per- and polyfluoroalkyl substances and epigenetic aging in umbilical cord blood: The Healthy Start study

Sierra S Niemiec, Katerina Kechris, Jack Pattee, Ivana V Yang, John L Adgate, Antonia M Calafat, Dana Dabelea, Anne P Starling

Environmental Research 231(Pt 2):116215. · 15 Aug 2023

Adipocyte hypertrophy in mesenchymal stem cells from infants of mothers with obesity

Madeline Rose Keleher, Shreya Shubhangi, Asya Brown, Allison M Duensing, Manoel E Lixandrão, Kathleen M Gavin, Harry A Smith, Katerina J Kechris, Ivana V Yang, Dana Dabelea, Kristen E Boyle

Obesity 31(8):2090-2102. · 01 Aug 2023

Large scale proteomic studies create novel privacy considerations

Andrew C Hill, Claire Guo, Elizabeth M Litkowski, Ani W Manichaikul, Bing Yu, Iain R Konigsberg, Betty A Gorbet, Leslie A Lange, Katherine A Pratte, Katerina J Kechris, Matthew DeCamp, Marilyn Coors, Victor E Ortega, Stephen S Rich, Jerome I Rotter, Robert E Gerzsten, Clary B Clish, Jeffrey L Curtis, Xiaowei Hu, Ma-En Obeidat, Melody Morris, Joseph Loureiro, Debby Ngo, Wanda K O'Neal, Deborah A Meyers, Eugene R Bleecker, Brian D Hobbs, Michael H Cho, Farnoush Banaei-Kashani, Russell P Bowler

Scientific Reports 13(1):9254. · 07 Jun 2023

Intrauterine Smoke Exposure, microRNA Expression during Human Lung Development, and Childhood Asthma

Lynne Rosenberg, Cuining Liu, Rinku Sharma, Cheyret Wood, Carrie A Vyhlidal, Roger Gaedigk, Alvin T Kho, John P Ziniti, Juan C Celedón, Kelan G Tantisira, Scott T Weiss, Michael J McGeachie, Katerina Kechris, Sunita Sharma

International Journal of Molecular Sciences 24(9):7727. · 23 Apr 2023

Deep learning on graphs for multi-omics classification of COPD

Yonghua Zhuang, Fuyong Xing, Debashis Ghosh, Brian D Hobbs, Craig P Hersh, Farnoush Banaei-Kashani, Russell P Bowler, Katerina Kechris

PLoS One 18(4):e0284563. · 21 Apr 2023

Novel Metabolic Subtypes in Pregnant Women and Risk of Early Childhood Obesity in Offspring

Ellen C Francis, Katerina Kechris, Thomas Jansson, Dana Dabelea, Wei Perng

JAMA Network Open 6(4):e237030. · 03 Apr 2023

Genome-wide analysis of oxylipins and oxylipin profiles in a pediatric population

Teresa Buckner, Randi K Johnson, Lauren A Vanderlinden, Patrick M Carry, Alex Romero, Suna Onengut-Gumuscu, Wei-Min Chen, Soojeong Kim, Oliver Fiehn, Brigitte I Frohnert, Tessa Crume, Wei Perng, Katerina Kechris, Marian Rewers, Jill M Norris

Frontiers in Nutrition 10:1040993. · 28 Mar 2023

Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments

Patrick M Carry, Tim Vigers, Lauren A Vanderlinden, Carson Keeter, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Ivana Yang, Jill M Norris, Katerina Kechris

BMC Bioinformatics 24(1):86. · 07 Mar 2023

Teresa Buckner, Randi K Johnson, Lauren A Vanderlinden, Patrick M Carry, Alex Romero, Suna Onengut-Gumuscu, Wei-Min Chen, Oliver Fiehn, Brigitte I Frohnert, Tessa Crume, Wei Perng, Katerina Kechris, Marian Rewers, Jill M Norris

Nutrients 15(4):945. · 14 Feb 2023

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M Saba, Katerina Kechris

PLoS Computational Biology 19(1):e1010758. · 06 Jan 2023

Fat content in infant mesenchymal stem cells prospectively associates with childhood adiposity and fasting glucose

Lauren E Gyllenhammer, Allison M Duensing, Madeline Rose Keleher, Katerina Kechris, Dana Dabelea, Kristen E Boyle

Obesity 31(1):37-42 · 01 Jan 2023

NetSHy: network summarization via a hybrid approach leveraging topological properties

Thao Vu, Elizabeth M Litkowski, Weixuan Liu, Katherine A Pratte, Leslie Lange, Russell P Bowler, Farnoush Banaei-Kashani, Katerina J Kechris

Bioinformatics 39(1):btac818. · 01 Jan 2023

Effective Subject Representation based on Multi-omics Disease Networks using Graph Embedding

Sundous Hussein, Thao Vu, Leslie Lange, Russell P Bowler, Katerina J Kechris, Farnoush Banaei-Kashani

Proceedings (IEEE Int Conf Bioinformatics Biomed) 2022:1911-1918 · 01 Dec 2022

Ambient air pollution during pregnancy and DNA methylation in umbilical cord blood, with potential mediation of associations with infant adiposity: The Healthy Start study

Anne P. Starling, Cheyret Wood, Cuining Liu, Katerina Kechris, Ivana V. Yang, Chloe Friedman, Deborah S.K. Thomas, Jennifer L. Peel, John L. Adgate, Sheryl Magzamen, Sheena E. Martenies, William B. Allshouse, Dana Dabelea

Environmental Research. 214(Pt 1):113881 · 01 Nov 2022

Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection

Sean T. Jones, Kejun Guo, Emily H. Cooper, Stephanie M. Dillon, Cheyret Wood, David H. Nguyen, Guannan Shen, Bradley S. Barrett, Daniel N. Frank, Miranda Kroehl, Edward N. Janoff, Katerina Kechris, Cara C. Wilson, Mario L. Santiago

Journal of Virology. 96(17):e0097622 · 14 Sep 2022

Predictors of bovine Schistosoma japonicum infection in rural Sichuan, China

Elise Grover, Sara Paull, Katerina Kechris, Andrea Buchwald, Katherine James, Yang Liu, Elizabeth J. Carlton

International Journal for Parasitology. 52(8):485-496 · 01 Jul 2022

Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification

Mohamed Abdel-Hafiz, Mesbah Najafi, Shahab Helmi, Katherine A. Pratte, Yonghua Zhuang, Weixuan Liu, Katerina J. Kechris, Russell P. Bowler, Leslie Lange, Farnoush Banaei-Kashani

Frontiers in Big Data. 5:894632 · 22 Jun 2022

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)

Patrick M. Carry, Kathleen Waugh, Lauren A. Vanderlinden, Randi K. Johnson, Teresa Buckner, Marian Rewers, Andrea K. Steck, Ivana Yang, Tasha E. Fingerlin, Katerina Kechris, Jill M. Norris

Diabetes. 71(9):2048-2057 · 20 Jun 2022

Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics

Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh, Katerina Kechris

BMC Bioinformatics. 16;23(1):179 · 16 May 2022

A Metabolomic Severity Score for Airflow Obstruction and Emphysema

Suneeta Godbole, Wassim W. Labaki, Katherine A. Pratte, Andrew Hill, Matthew Moll, Annette T. Hastie, Stephen P. Peters, Andrew Gregory, Victor E. Ortega, Dawn DeMeo, Michael H. Cho, Surya P. Bhatt, J. Michael Wells, Igor Barjaktarevic, Kathleen A. Stringer, Alejandro Comellas, Wanda O’Neal, Katerina Kechris, Russell P. Bowler

Metabolites. 12(5):368 · 19 Apr 2022

Sex-Specific Differences in MicroRNA Expression During Human Fetal Lung Development

Nancy W. Lin, Cuining Liu, Ivana V. Yang, Lisa A. Maier, Dawn L. DeMeo, Cheyret Wood, Shuyu Ye, Margaret H. Cruse, Vong L. Smith, Carrie A. Vyhlidal, Katerina Kechris, Sunita Sharma

Frontiers in Genetics. 13:762834 · 11 Apr 2022

Metabolomic Profiles in Childhood and Adolescence Are Associated with Fetal Overnutrition

Ellen C. Francis, Katerina Kechris, Catherine C. Cohen, Gregory Michelotti, Dana Dabelea, Wei Perng

Metabolites. 12(3):265 · 19 Mar 2022

Granzyme B⁺ CD4 T cells accumulate in the colon during chronic HIV-1 infection

Stephanie M. Dillon, Kaylee L. Mickens, Tezha A. Thompson, Emily H. Cooper, Sabrina Nesladek, Allison J. Christians, Moriah Castleman, Kejun Guo, Cheyret Wood, Daniel N. Frank, Katerina Kechris, Mario L. Santiago, Cara C. Wilson

Gut Microbes. 14(1):2045852 · 08 Mar 2022

Chronic Marijuana Use Is Associated with Gene Expression Changes in BAL

Cuining Liu, Jeanette Gaydos, Rebecca Johnson-Paben, Katerina Kechris, Ellen L. Burnham, Sunita Sharma

American Journal of Respiratory Cell and Molecular Biology. 66(2):238-239 · 01 Feb 2022

An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning

Yonghua Zhuang, Fuyong Xing, Debashis Ghosh, Farnoush Banaei-Kashani, Russell P. Bowler, Katerina Kechris

Frontiers in Genetics.12:760299 · 27 Jan 2022

Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations

William M. Showers, Sonia M. Leach, Katerina Kechris, Michael Strong

Infection, Genetics and Evolution. 97:105153 · 01 Jan 2022

Epigenome-Wide Association Study of Infant Feeding and DNA Methylation in Infancy and Childhood in a Population at Increased Risk for Type 1 Diabetes

Elizabeth Walker-Short, Teresa Buckner, Timothy Vigers, Patrick Carry, Lauren A Vanderlinden, Fran Dong, Randi K Johnson, Ivana V Yang, Katerina Kechris, Marian Rewers, Jill M Norris

Nutrients. 13(11):4057 · 13 Nov 2021

Identifying miRNA-mRNA Networks Associated With COPD Phenotypes

Yonghua Zhuang, Brian D Hobbs, Craig P Hersh, Katerina Kechris

Frontiers in Genetics. 12:748356 · 28 Oct 2021

PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes

Charlie M. Carpenter, Weiming Zhang, Lucas Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russell Bowler, Katerina Kechris, Debashis Ghosh

PLoS Computational Biology 17(10):e1008986 · 22 Oct 2021

MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools

Jonathan Dekermanjian, Wladimir Labeikovsky, Debashis Ghosh, Katerina Kechris

Metabolites. 11(10):678 · 02 Oct 2021

An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies

Lauren A Vanderlinden, Randi K Johnson, Patrick M Carry, Fran Dong, Dawn L DeMeo, Ivana V Yang, Jill M Norris, Katerina Kechris

BMC Research Notes. 14(1):352 · 08 Sep 2021

Reproducibility of mass spectrometry based metabolomics data

Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina Kechris, Debashis Ghosh

BMC Bioinformatics. 22(1):423 · 07 Sep 2021

Multi-omics subtyping pipeline for chronic obstructive pulmonary disease

Lucas A Gillenwater, Shahab Helmi, Evan Stene, Katherine A Pratte, Yonghua Zhuang, Ronald P Schuyler, Leslie Lange, Peter J Castaldi, Craig P Hersh, Farnoush Banaei-Kashani, Russell P Bowler, Katerina J Kechris

PLoS One 16:e0255337 · 25 Aug 2021

A Mediation Approach to Discovering Causal Relationships between the Metabolome and DNA Methylation in Type 1 Diabetes

Tim Vigers, Lauren A Vanderlinden, Randi K Johnson, Patrick M Carry, Ivana Yang, Brian C DeFelice, Alexander M Kaizer, Laura Pyle, Marian Rewers, Oliver Fiehn, Jill M Norris, Katerina Kechris

Metabolites. 11:542 · 14 Aug 2021

Inverse probability weighting is an effective method to address selection bias during the analysis of high dimensional data

Patrick M. Carry, Lauren A. Vanderlinden, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Timothy Vigers, Jill M. Norris, Katerina Kechris

Genetic Epidemiology. 45(6):593-603 · 15 Jun 2021

Comparing Statistical Tests for Differential Network Analysis of Gene Modules

Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris

Frontiers in Genetics. 12:630215 · 19 May 2021

Semi-Supervised Learning Using Hierarchical Mixture Models: Gene Essentiality Case Study

Michael W. Daniels, Daniel Dvorkin, Rani K. Powers, Katerina Kechris

Mathematical and Computational Applications. 26:40 · 18 May 2021

Soluble receptor for advanced glycation end products (sRAGE) as a biomarker of COPD

Katherine A. Pratte, Jeffrey L. Curtis, Katerina Kechris, David Couper, Michael H. Cho, Edwin K. Silverman, Dawn L. DeMeo, Frank C. Sciurba, Yingze Zhang, Victor E. Ortega, Wanda K. O’Neal, Lucas A. Gillenwater, David A. Lynch, Eric A. Hoffman, John D. Newell, Alejandro P. Comellas, Peter J. Castaldi, Bruce E. Miller, Simon D. Pouwels, Nick H. T. ten Hacken, Rainer Bischoff, Frank Klont, Prescott G. Woodruff, Robert Paine, R. Graham Barr, John Hoidal, Claire M. Doerschuk, Jean-Paul Charbonnier, Ruby Sung, Nicholas Locantore, John G. Yonchuk, Sean Jacobson, Ruth Tal-singer, Debbie Merrill, Russell P. Bowler

Respiratory Research. 22:127 · 27 Apr 2021

The oxylipin profile is associated with development of type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY)

Teresa Buckner, Lauren A. Vanderlinden, Brian C. DeFelice, Patrick M. Carry, Katerina Kechris, Fran Dong, Oliver Fiehn, Brigitte I. Frohnert, Michael Clare-Salzler, Marian Rewers, Jill M. Norris

Diabetologia. 64:1785-1794 · 24 Apr 2021

Phospholipid Levels at Seroconversion Are Associated With Resolution of Persistent Islet Autoimmunity: The Diabetes Autoimmunity Study in the Young

Patrick M. Carry, Lauren A. Vanderlinden, Randi K. Johnson, Teresa Buckner, Oliver Fiehn, Andrea K. Steck, Katerina Kechris, Ivana Yang, Tasha E. Fingerlin, Marian Rewers, Jill M. Norris

Diabetes. 70(7):1592-1601 · 16 Apr 2021

Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

Ryan Lusk, Evan Stene, Farnoush Banaei-Kashani, Boris Tabakoff, Katerina Kechris, Laura M. Saba

Nature Communications. 12:1652 · 12 Mar 2021

Metabolomic Profiling Reveals Sex Specific Associations with Chronic Obstructive Pulmonary Disease and Emphysema

Lucas A. Gillenwater, Katerina J. Kechris, Katherine A. Pratte, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda O’Neal, Jerry A. Krishnan, Victor E. Ortega, Dawn L. DeMeo, Russell P. Bowler

Metabolites. 11:161 · 11 Mar 2021

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R

Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda E. Kroehl

BMC Bioinformatics. 22:41 · 01 Feb 2021

A Practical Guide to Metabolomics Software Development

Hui-Yin Chang, Sean M. Colby, Xiuxia Du, Javier D. Gomez, Maximilian J. Helf, Katerina Kechris, Christine R. Kirkpatrick, Shuzhao Li, Gary J. Patti, Ryan S. Renslow, Shankar Subramaniam, Mukesh Verma, Jianguo Xia, Jamey D. Young

Analytical Chemistry. 93:1912-1923 · 19 Jan 2021

Human Mobility Associated With Risk of Schistosoma japonicum Infection in Sichuan, China

Andrea G Buchwald, Elise Grover, Julia Van Dyke, Katerina Kechris, Ding Lu, Yang Liu, Bo Zhong, Elizabeth J Carlton

American Journal of Epidemiology. 190:1243-1252 · 13 Jan 2021

Placental Insulin/IGF-1 Signaling, PGC-1α, and Inflammatory Pathways Are Associated With Metabolic Outcomes at 4–6 Years of Age: The ECHO Healthy Start Cohort

Madeline Rose Keleher, Kathryn Erickson, Harry A. Smith, Katerina J. Kechris, Ivana V. Yang, Dana Dabelea, Jacob E. Friedman, Kristen E. Boyle, Thomas Jansson

Diabetes. 70:745-751 · 07 Jan 2021

Zachary L. Nikolakis, Nicole R. Hales, Blair W. Perry, Drew R. Schield, Laura E. Timm, Yang Liu, Bo Zhong, Katerina J. Kechris, Elizabeth J. Carlton, David D. Pollock, Todd A. Castoe

PLoS Neglected Tropical Diseases. 15(1):e0009020 · 06 Jan 2021

Prenatal Exposure to Per- and Polyfluoroalkyl Substances, Umbilical Cord Blood DNA Methylation, and Cardio-Metabolic Indicators in Newborns: The Healthy Start Study

Anne P. Starling, Cuining Liu, Guannan Shen, Ivana V. Yang, Katerina Kechris, Sarah J. Borengasser, Kristen E. Boyle, Weiming Zhang, Harry A. Smith, Antonia M. Calafat, Richard F. Hamman, John L. Adgate, Dana Dabelea

Environmental Health Perspectives. 128(12):127014 · 01 Dec 2020

Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules

Lucas A. Gillenwater, Katherine A. Pratte, Brian D. Hobbs, Michael H. Cho, Yonghua Zhuang, Eitan Halper-Stromberg, Charmion Cruickshank-Quinn, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda K. O'Neal, Victor E. Ortega, Dean P. Jones, Karan Uppal, Sean Jacobson, Gregory Michelotti, Christine H. Wendt, Katerina J. Kechris, Russell P. Bowler

Network and Systems Medicine. 3:159-181. · 01 Dec 2020

Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance

Richard A. Radcliffe, Robin Dowell, Aaron T. Odell, Phillip A. Richmond, Beth Bennett, Colin Larson, Katerina Kechris, Laura M. Saba, Pratyaydipta Rudra, Shi Wen

PLoS One. 15(10):e0240253 · 23 Oct 2020

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis

Kejun Guo, Guannan Shen, Jon Kibbie, Tania Gonzalez, Stephanie M. Dillon, Harry A. Smith, Emily H. Cooper, Kerry Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago

PLoS Pathogens. 16(10):e1008986 · 16 Oct 2020

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments

Brian E. Vestal, Camille M. Moore, Elizabeth Wynn, Laura Saba, Tasha Fingerlin, Katerina Kechris

BMC Bioinformatics. (1):375 · 28 Aug 2020

Randi K. Johnson, Lauren A. Vanderlinden, Brian C. DeFelice, Ulla Uusitalo, Jennifer Seifert, Sili Fan, Tessa Crume, Oliver Fiehn, Marian Rewers, Katerina Kechris, Jill M. Norris

Pediatric Diabetes. 21:1202-1209 · 09 Aug 2020

Sex-Specific Metabolite Biomarkers of NAFLD in Youth: A Prospective Study in the EPOCH Cohort

Wei Perng, Ellen C Francis, Harry A Smith, John Carey, Dongqing Wang, Katerina M Kechris, Dana Dabelea

Journal of Clinical Endocrinology & Metabolism. 105(9):e3437-50 · 20 Jul 2020

Alcohol Use Disorders Are Associated With a Unique Impact on Airway Epithelial Cell Gene Expression

Kristina L. Bailey, Harry Smith, Susan K. Mathai, Jonathan Huber, Mark Yacoub, Ivana V. Yang, Todd A. Wyatt, Katerina Kechris, Ellen L. Burnham

Alcoholism Clinical Experimental Research. 44(8):1571-1584 · 01 Jul 2020

Associations between the activity of placental nutrient-sensing pathways and neonatal and postnatal metabolic health: the ECHO Healthy Start cohort

Madeline Rose Keleher, Kathryn Erickson, Katerina Kechris, Ivana V. Yang, Dana Dabelea, Jacob E. Friedman, Kristen E. Boyle, Thomas Jansson

International Journal of Obesity. 44(11):2203-2212 · 23 Apr 2020

Identifying Protein–metabolite Networks Associated with COPD Phenotypes

Emily Mastej, Lucas Gillenwater, Yonghua Zhuang, Katherine A. Pratte, Russell P. Bowler, Katerina Kechris

Metabolites. 10:124 · 25 Mar 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

Patrick M. Carry, Lauren A. Vanderlinden, Randi K. Johnson, Fran Dong, Andrea K. Steck, Brigitte I. Frohnert, Marian Rewers, Ivana V. Yang, Katerina Kechris, Jill M. Norris

Pediatrics Diabetes. 21:597-605 · 28 Feb 2020

Longitudinal DNA methylation differences precede type 1 diabetes

Randi K. Johnson, Lauren A. Vanderlinden, Fran Dong, Patrick M. Carry, Jennifer Seifert, Kathleen Waugh, Hanan Shorrosh, Tasha Fingerlin, Brigitte I. Frohnert, Ivana V. Yang, Katerina Kechris, Marian Rewers, Jill M. Norris

Scientific Reports. 10:3721 · 28 Feb 2020

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis

Yonghua Zhuang, , Kristen Wade, Laura M. Saba, Katerina Kechris, ,

Mathematical Biosciences and Engineering. 17:122-143 · 01 Jan 2020

Predictive Modeling for Metabolomics Data

Tusharkanti Ghosh, Weiming Zhang, Debashis Ghosh, Katerina Kechris

Methods Molecular Biology. 2104:313-336 · 01 Jan 2020

A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence

Wei Perng, Brandy M. Ringham, Harry A. Smith, Gregory Michelotti, Katerina M. Kechris, Dana Dabelea

Diabetologia. 63:296-312 · 13 Nov 2019

Insight into genetic regulation of miRNA in mouse brain

Gordon Kordas, Pratyaydipta Rudra, Audrey Hendricks, Laura Saba, Katerina Kechris

BMC Genomics. 20:849 · 13 Nov 2019

A prospective study of associations between in utero exposure to gestational diabetes mellitus and metabolomic profiles during late childhood and adolescence

Wei Perng, Brandy M. Ringham, Harry A. Smith, Gregory Michelotti, Katerina M. Kechris, Dana Dabelea

Diabetologia. 63:296-312 · 13 Nov 2019

Randi K. Johnson, , Lauren Vanderlinden, Brian C. DeFelice, Katerina Kechris, Ulla Uusitalo, Oliver Fiehn, Marci Sontag, Tessa Crume, Andreas Beyerlein, Åke Lernmark, Jorma Toppari, Anette-G. Ziegler, Jin-Xiong She, William Hagopian, Marian Rewers, Beena Akolkar, Jeffrey Krischer, Suvi M. Virtanen, Jill M. Norris

Scientific Reports. 9:14819 · 15 Oct 2019

Prenatal exposure to per- and polyfluoroalkyl substances and infant growth and adiposity: the Healthy Start Study

Anne P. Starling, John L. Adgate, Richard F. Hamman, Katerina Kechris, Antonia M. Calafat, Dana Dabelea

Environment International. 131:104983 · 01 Oct 2019

Hypertensive Disorders of Pregnancy and DNA Methylation in Newborns

Nabila Kazmi, Gemma C. Sharp, Sarah E. Reese, Florianne O. Vehmeijer, Jari Lahti, Christian M. Page, Weiming Zhang, Sheryl L. Rifas-Shiman, Faisal I. Rezwan, Andrew J. Simpkin, Kimberley Burrows, Tom G. Richardson, Diana L. Santos Ferreira, Abigail Fraser, Quaker E. Harmon, Shanshan Zhao, Vincent W.V. Jaddoe, Darina Czamara, Elisabeth B. Binder, Maria C. Magnus, Siri E. Håberg, Wenche Nystad, Ellen A. Nohr, Anne P. Starling, Katerina J. Kechris, Ivana V. Yang, Dawn L. DeMeo, Augusto A. Litonjua, Andrea Baccarelli, Emily Oken, John W. Holloway, Wilfried Karmaus, Syed H. Arshad, Dana Dabelea, Thorkild I.A. Sørensen, Hannele Laivuori, Katri Raikkonen, Janine F. Felix, Stephanie J. London, Marie-France Hivert, Tom R. Gaunt, Debbie A. Lawlor, Caroline L. Relton

Hypertension. 74:375-383 · 01 Aug 2019

Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma

Eitan Halper-Stromberg, Lucas Gillenwater, Charmion Cruickshank-Quinn, Wanda Kay O’Neal, Nichole Reisdorph, Irina Petrache, Yonghua Zhuang, Wassim W. Labaki, Jeffrey L. Curtis, James Wells, Stephen Rennard, Katherine A. Pratte, Prescott Woodruff, Kathleen A. Stringer, Katerina Kechris, Russell P. Bowler

Metabolites. 9(8) · 25 Jul 2019

A2ML1and otitis media: novel variants, differential expression, and relevant pathways

Eric D. Larson, Jose Pedrito M. Magno, Matthew J. Steritz, Erasmo Gonzalo d.V. Llanes, Jonathan Cardwell, Melquiadesa Pedro, Tori Bootpetch Roberts, Elisabet Einarsdottir, Rose Anne Q. Rosanes, Christopher Greenlee, Rachel Ann P. Santos, Ayesha Yousaf, Sven‐Olrik Streubel, Aileen Trinidad R. Santos, Amanda G. Ruiz, Sheryl Mae Lagrana‐Villagracia, Dylan Ray, Talitha Karisse L. Yarza, Melissa A. Scholes, Catherine B. Anderson, Anushree Acharya, University of Washington Center for , Samuel P. Gubbels, Michael J. Bamshad, Stephen P. Cass, Nanette R. Lee, Rehan S. Shaikh, Deborah A. Nickerson, Karen L. Mohlke, Jeremy D. Prager, Teresa Luisa G. Cruz, Patricia J. Yoon, Generoso T. Abes, David A. Schwartz, Abner L. Chan, Todd M. Wine, Eva Maria Cutiongco‐de la Paz, Norman Friedman, Katerina Kechris, Juha Kere, Suzanne M. Leal, Ivana V. Yang, Janak A. Patel, Ma. Leah C. Tantoco, Saima Riazuddin, Kenny H. Chan, Petri S. Mattila, Maria Rina T. Reyes‐Quintos, Zubair M. Ahmed, Herman A. Jenkins, Tasnee Chonmaitree, Lena Hafrén, Charlotte M. Chiong, Regie Lyn P. Santos‐Cortez

Human Mutation. 40:1156-1171 · 21 May 2019

Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight

Leanne K. Küpers, Claire Monnereau, Gemma C. Sharp, Paul Yousefi, Lucas A. Salas, Akram Ghantous, Christian M. Page, Sarah E. Reese, Allen J. Wilcox, Darina Czamara, Anne P. Starling, Alexei Novoloaca, Samantha Lent, Ritu Roy, Cathrine Hoyo, Carrie V. Breton, Catherine Allard, Allan C. Just, Kelly M. Bakulski, John W. Holloway, Todd M. Everson, Cheng-Jian Xu, Rae-Chi Huang, Diana A. van der Plaat, Matthias Wielscher, Simon Kebede Merid, Vilhelmina Ullemar, Faisal I. Rezwan, Jari Lahti, Jenny van Dongen, Sabine A. S. Langie, Tom G. Richardson, Maria C. Magnus, Ellen A. Nohr, Zongli Xu, Liesbeth Duijts, Shanshan Zhao, Weiming Zhang, Michelle Plusquin, Dawn L. DeMeo, Olivia Solomon, Joosje H. Heimovaara, Dereje D. Jima, Lu Gao, Mariona Bustamante, Patrice Perron, Robert O. Wright, Irva Hertz-Picciotto, Hongmei Zhang, Margaret R. Karagas, Ulrike Gehring, Carmen J. Marsit, Lawrence J. Beilin, Judith M. Vonk, Marjo-Riitta Jarvelin, Anna Bergström, Anne K. Örtqvist, Susan Ewart, Pia M. Villa, Sophie E. Moore, Gonneke Willemsen, Arnout R. L. Standaert, Siri E. Håberg, Thorkild I. A. Sørensen, Jack A. Taylor, Katri Räikkönen, Ivana V. Yang, Katerina Kechris, Tim S. Nawrot, Matt J. Silver, Yun Yun Gong, Lorenzo Richiardi, Manolis Kogevinas, Augusto A. Litonjua, Brenda Eskenazi, Karen Huen, Hamdi Mbarek, Rachel L. Maguire, Terence Dwyer, Martine Vrijheid, Luigi Bouchard, Andrea A. Baccarelli, Lisa A. Croen, Wilfried Karmaus, Denise Anderson, Maaike de Vries, Sylvain Sebert, Juha Kere, Robert Karlsson, Syed Hasan Arshad, Esa Hämäläinen, Michael N. Routledge, Dorret I. Boomsma, Andrew P. Feinberg, Craig J. Newschaffer, Eva Govarts, Matthieu Moisse, M. Daniele Fallin, Erik Melén, Andrew M. Prentice, Eero Kajantie, Catarina Almqvist, Emily Oken, Dana Dabelea, H. Marike Boezen, Phillip E. Melton, Rosalind J. Wright, Gerard H. Koppelman, Letizia Trevisi, Marie-France Hivert, Jordi Sunyer, Monica C. Munthe-Kaas, Susan K. Murphy, Eva Corpeleijn, Joseph Wiemels, Nina Holland, Zdenko Herceg, Elisabeth B. Binder, George Davey Smith, Vincent W. V. Jaddoe, Rolv T. Lie, Wenche Nystad, Stephanie J. London, Debbie A. Lawlor, Caroline L. Relton, Harold Snieder, Janine F. Felix

Nature Communications. 10(1):1893 · 23 Apr 2019

Unsupervised discovery of phenotype-specific multi-omics networks

W Jenny Shi, Yonghua Zhuang, Pamela H Russell, Brian D Hobbs, Margaret M Parker, Peter J Castaldi, Pratyaydipta Rudra, Brian Vestal, Craig P Hersh, Laura M Saba, Katerina Kechris

Bioinformatics. 35:4336-4343 · 08 Apr 2019

Using a spatial point process framework to characterize lung computed tomography scans

Brian E. Vestal, Nichole E. Carlson, Raúl San José Estépar, Tasha Fingerlin, Debashis Ghosh, Katerina Kechris, David Lynch

Spatial Statistic. 29:243-267 · 01 Mar 2019

Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data

Dominik Reinhold, Harrison Pielke-Lombardo, Sean Jacobson, Debashis Ghosh, Katerina Kechris

Methods Molecular Biology. 1978:323-340 · 01 Jan 2019

Bayesian inference of networks across multiple sample groups and data types

Elin Shaddox, Christine B Peterson, Francesco C Stingo, Nicola A Hanania, Charmion Cruickshank-Quinn, Katerina Kechris, Russell Bowler, Marina Vannucci

Biostatistics. 21:561-576 · 26 Dec 2018

Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD

Charmion I. Cruickshank-Quinn, Sean Jacobson, Grant Hughes, Roger L. Powell, Irina Petrache, Katerina Kechris, Russell Bowler, Nichole Reisdorph

Scientific Reports. 8:17132 · 20 Nov 2018

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li

PLoS Computational Biology. 14(9):e1006436 · 21 Sep 2018

Predictive modeling of miRNA-mediated predisposition to alcohol-related phenotypes in mouse

Pratyaydipta Rudra, Wen J. Shi, Pamela Russell, Brian Vestal, Boris Tabakoff, Paula Hoffman, Katerina Kechris, Laura Saba

BMC Genomics. 19(1):639 · 29 Aug 2018

miR-MaGiC improves quantification accuracy for small RNA-seq

Pamela H. Russell, Brian Vestal, Wen Shi, Pratyaydipta D. Rudra, Robin Dowell, Richard Radcliffe, Laura Saba, Katerina Kechris

BMC Research Notes. 11(1):296 · 15 May 2018

miRNA-regulated transcription associated with mouse strains predisposed to hypnotic effects of ethanol

B. Vestal, P. Russell, R.A. Radcliffe, L. Bemis, L.M. Saba, K. Kechris

Brain and Behavior. 8:e00989 · 30 Apr 2018

Epigenetic marks of in utero exposure to gestational diabetes and childhood adiposity outcomes: the EPOCH study

I. V. Yang, W. Zhang, E. J. Davidson, T. E. Fingerlin, K. Kechris, D. Dabelea

Diabetic Medicine. 35(5):612-620 · 13 Mar 2018

Movement decline across lifespan ofCaenorhabditis elegansmutants in the insulin/insulin-like signaling pathway

Breanne L. Newell Stamper, James R. Cypser, Katerina Kechris, David Alan Kitzenberg, Patricia M. Tedesco, Thomas E. Johnson

Aging Cell. 17(1) · 07 Dec 2017

Maternal obesity alters fatty acid oxidation, AMPK activity, and associated DNA methylation in mesenchymal stem cells from human infants

Kristen E. Boyle, Zachary W. Patinkin, Allison L.B. Shapiro, Carly Bader, Lauren Vanderlinden, Katerina Kechris, Rachel C. Janssen, Rebecca J. Ford, Brennan K. Smith, Gregory R. Steinberg, Elizabeth J. Davidson, Ivana V. Yang, Dana Dabelea, Jacob E. Friedman

Molecular Metabolism. 6(11):1503-1516 · 01 Nov 2017

The value of blood cytokines and chemokines in assessing COPD

Eric Bradford, Sean Jacobson, Jason Varasteh, Alejandro P. Comellas, Prescott Woodruff, Wanda O’Neal, Dawn L. DeMeo, Xingnan Li, Victor Kim, Michael Cho, Peter J. Castaldi, Craig Hersh, Edwin K. Silverman, James D. Crapo, Katerina Kechris, Russell P. Bowler

Respiratory Research. 18(1):180 · 24 Oct 2017

Meta-analysis of peripheral blood gene expression modules for COPD phenotypes

Dominik Reinhold, Jarrett D. Morrow, Sean Jacobson, Junxiao Hu, Benjamin Ringel, Max A. Seibold, Craig P. Hersh, Katerina J. Kechris, Russell P. Bowler

PLoS One. 12(10):e0185682 · 09 Oct 2017

Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium

J. Felix, et al.

International Journal of Epidemiology. 47(1):22-23 · 13 Sep 2017

Charmion Cruickshank-Quinn, Roger Powell, Sean Jacobson, Katerina Kechris, Russell P. Bowler, Irina Petrache, Nichole Reisdorph

Scientific Reports. 7(1):5108 · 11 Jul 2017

Perfluoroalkyl Substances during Pregnancy and Offspring Weight and Adiposity at Birth: Examining Mediation by Maternal Fasting Glucose in the Healthy Start Study

Anne P. Starling, John L. Adgate, Richard F. Hamman, Katerina Kechris, Antonia M. Calafat, Xiaoyun Ye, Dana Dabelea

Environmental Health Perspectives. 125(6):067016 · 23 Jun 2017

High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and Represses HLA-E Expression in Human Keratinocytes

Louis Cicchini, Rachel Z. Blumhagen, Joseph A. Westrich, Mallory E. Myers, Cody J. Warren, Charlotte Siska, David Raben, Katerina J. Kechris, Dohun Pyeon

Scientific Reports. 7(1):3633 · 16 Jun 2017

Multiple biomarkers predict disease severity, progression and mortality in COPD

Rachel L. Zemans, Sean Jacobson, Jason Keene, Katerina Kechris, Bruce E. Miller, Ruth Tal-Singer, Russell P. Bowler

Respiratory Research. 18(1):117 · 13 Jun 2017

Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma

Mikaela A. Miller, Thomas Danhorn, Charmion I. Cruickshank-Quinn, Sonia M. Leach, Sean Jacobson, Matthew J. Strand, Nichole A. Reisdorph, Russell P. Bowler, Irina Petrache, Katerina Kechris

PLoS One. 12(6):e0178281 · 02 Jun 2017

Model based heritability scores for high-throughput sequencing data

Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard A. Radcliffe, Laura M. Saba, Katerina Kechris

BMC Bioinformatics. 18:143 · 02 Mar 2017

Biomarkers Predictive of Exacerbations in the SPIROMICS and COPDGene Cohorts

Jason D. Keene, Sean Jacobson, Katerina Kechris, Gregory L. Kinney, Marilyn G. Foreman, Claire M. Doerschuk, Barry J. Make, Jeffrey L. Curtis, Stephen I. Rennard, R. Graham Barr, Eugene R. Bleecker, Richard E. Kanner, Eric C. Kleerup, Nadia N. Hansel, Prescott G. Woodruff, MeiLan K. Han, Robert Paine, Fernando J. Martinez, Russell P. Bowler, Wanda K. O’Neal

American Journal of Respiratory and Critical Care Medicine). 195:473-481 · 15 Feb 2017

Differential correlation for sequencing data

Charlotte Siska, Katerina Kechris

BMC Research Notes. 10:54 · 19 Jan 2017

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD

Elin Shaddox, Francesco C. Stingo, Christine B. Peterson, Sean Jacobson, Charmion Cruickshank-Quinn, Katerina Kechris, Russell Bowler, Marina Vannucci

Statistics in Biosciences. 10:59-85 · 28 Oct 2016

Adaptation of Mycobacterium tuberculosis to Impaired Host Immunity in HIV-Infected Patients

Nicholas D. Walter, Bouke C. de Jong, Benjamin J. Garcia, Gregory M. Dolganov, William Worodria, Patrick Byanyima, Emmanuel Musisi, Laurence Huang, Edward D. Chan, Tran T. Van, Martin Antonio, Abigail Ayorinde, Midori Kato-Maeda, Payam Nahid, Ann M. Leung, Andrew Yen, Tasha E. Fingerlin, Katerina Kechris, Michael Strong, Martin I. Voskuil, J. Lucian Davis, Gary K. Schoolnik

Journal of Infectious Diseases. 214:1205-11 · 17 Aug 2016

Structural and functional characterization of endothelial microparticles released by cigarette smoke

Karina A. Serban, Samin Rezania, Daniela N. Petrusca, Christophe Poirier, Danting Cao, Matthew J. Justice, Milan Patel, Irina Tsvetkova, Krzysztof Kamocki, Andrew Mikosz, Kelly S. Schweitzer, Sean Jacobson, Angelo Cardoso, Nadia Carlesso, Walter C. Hubbard, Katerina Kechris, Bogdan Dragnea, Evgeny V. Berdyshev, Jeanette McClintock, Irina Petrache

Nature Scientific Reports. 6:31596 · 17 Aug 2016

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Wei Sun, Katerina Kechris, Sean Jacobson, M. Bradley Drummond, Gregory A. Hawkins, Jenny Yang, Ting-huei Chen, Pedro Miguel Quibrera, Wayne Anderson, R. Graham Barr, Patricia V. Basta, Eugene R. Bleecker, Terri Beaty, Richard Casaburi, Peter Castaldi, Michael H. Cho, Alejandro Comellas, James D. Crapo, Gerard Criner, Dawn Demeo, Stephanie A. Christenson, David J. Couper, Jeffrey L. Curtis, Claire M. Doerschuk, Christine M. Freeman, Natalia A. Gouskova, MeiLan K. Han, Nicola A. Hanania, Nadia N. Hansel, Craig P. Hersh, Eric A. Hoffman, Robert J. Kaner, Richard E. Kanner, Eric C. Kleerup, Sharon Lutz, Fernando J. Martinez, Deborah A. Meyers, Stephen P. Peters, Elizabeth A. Regan, Stephen I. Rennard, Mary Beth Scholand, Edwin K. Silverman, Prescott G. Woodruff, Wanda K. O’Neal, Russell P. Bowler, ,

PLoS Genetics. 12(8):e1006011 · 17 Aug 2016

Uncovering the liver’s role in immunity through RNA co-expression networks

Kylie K. Harrall, Katerina J. Kechris, Boris Tabakoff, Paula L. Hoffman, Lisa M. Hines, Hidekazu Tsukamoto, Michal Pravenec, Morton Printz, Laura M. Saba

Mammalian Genome. 27:469-84 · 11 Jul 2016

Post-GWAS Prioritization Through Data Integration Provides Novel Insights on Chronic Obstructive Pulmonary Disease

Qiongshi Lu, Chentian Jin, Jiehuan Sun, Russell Bowler, Katerina Kechris, Naftali Kaminski, Hongyu Zhao

Statistics in Biosciences. 2016:1-17 · 13 Jun 2016

The discordant method: a novel approach for differential correlation

Charlotte Siska, Russell Bowler, Katerina Kechris

Bioinformatics. 32:690-6 · 31 Oct 2015

Joint MiRNA/mRNA Expression Profiling Reveals Changes Consistent with Development of Dysfunctional Corpus Luteum after Weight Gain

Andrew P. Bradford, Kenneth Jones, Katerina Kechris, Justin Chosich, Michael Montague, Wesley C. Warren, Margaret C. May, Zain Al-Safi, Satu Kuokkanen, Susan E. Appt, Alex J. Polotsky

PLoS One. 10:e0135163 · 10 Aug 2015

Narrow Band Ultraviolet B Treatment for Human Vitiligo Is Associated with Proliferation, Migration, and Differentiation of Melanocyte Precursors

Nathaniel B. Goldstein, Maranke I. Koster, Laura G. Hoaglin, Nicole S. Spoelstra, Katerina J. Kechris, Steven E. Robinson, William A. Robinson, Dennis R. Roop, David A. Norris, Stanca A. Birlea

Journal of Investigative Dermatology. 135:2068-76 · 01 Aug 2015

Distribution and Ecological Niches of Nitrogenases

Alexander N. Glazer, Katerina Kechris, James B. Howard

Biological Nitrogen Fixation. F.J. deBruijn (ed.), Wiley-Blackwell · 14 Jul 2015

Transcriptional Adaptation of Drug-tolerantMycobacterium tuberculosisDuring Treatment of Human Tuberculosis

Nicholas D. Walter, Gregory M. Dolganov, Benjamin J. Garcia, William Worodria, Alfred Andama, Emmanuel Musisi, Irene Ayakaka, Tran T. Van, Martin I. Voskuil, Bouke C. de Jong, Rebecca M. Davidson, Tasha E. Fingerlin, Katerina Kechris, Claire Palmer, Payam Nahid, Charles L. Daley, Mark Geraci, Laurence Huang, Adithya Cattamanchi, Michael Strong, Gary K. Schoolnik, John Lucian Davis

Journal of Infectious Diseases. 212:990-8 · 11 Mar 2015

Genetic analysis of a murine QTL for diet restriction on chromosome 15

Breanne L. Newell, Katerina Kechris, Matt B. McQueen, Thomas E. Johnson

Age. 37(1):9740 · 01 Feb 2015

Plasma Sphingolipids Associated with Chronic Obstructive Pulmonary Disease Phenotypes

Russell P. Bowler, Sean Jacobson, Charmion Cruickshank, Grant J. Hughes, Charlotte Siska, Daniel S. Ory, Irina Petrache, Jean E. Schaffer, Nichole Reisdorph, Katerina Kechris

American Journal of Respiratory and Critical Care Medicine. 191:275-84 · 01 Feb 2015

The association of plasma biomarkers with computed tomography-assessed emphysema phenotypes

Brendan J Carolan, Grant Hughes, Jarrett Morrow, Craig P Hersh, Wanda K O’Neal, Stephen Rennard, Sreekumar G Pillai, Paula Belloni, Debra A Cockayne, Alejandro P Comellas, Meilan Han, Rachel L Zemans, Katerina Kechris, Russell P Bowler

Respiratory Research. 15:127 · 12 Oct 2014

Genetics of gene expression characterizes response to selective breeding for alcohol preference

P. L. Hoffman, L. M. Saba, S. Flink, N. J. Grahame, K. Kechris, B. Tabakoff

Genes Brain and Behavior. 13:743-57 · 29 Sep 2014

The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

Yuanbin Ru, Katerina J. Kechris, Boris Tabakoff, Paula Hoffman, Richard A. Radcliffe, Russell Bowler, Spencer Mahaffey, Simona Rossi, George A. Calin, Lynne Bemis, Dan Theodorescu

Nucleic Acids Research. 42:e133 · 25 Jul 2014

Integrative Omics Approach Identifies Interleukin-16 as a Biomarker of Emphysema

Russell P. Bowler, Timothy M. Bahr, Grant Hughes, Sharon Lutz, Yu-Il Kim, Christopher D. Coldren, Nichole Reisdorph, Katerina J. Kechris

OMICS, A Journal of Integrative Biology. 17:619-626 · 01 Dec 2013

Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics

Nichole Reisdorph, Robert Stearman, Katerina Kechris, Tzu Lip Phang, Richard Reisdorph, Jessica Prenni, David J. Erle, Christopher Coldren, Kevin Schey, Alexey Nesvizhskii, Mark Geraci

Genomics, Proteomics & Bioinformatics. 11:368-77 · 01 Dec 2013

Biphasic pro-melanogenic and pro-apoptotic effects of all-trans-retinoic acid (ATRA) on human melanocytes: Time-course study

Ioana Baldea, Gertrude-Emilia Costin, Yiqun Shellman, Katerina Kechris, Elena Diana Olteanu, Adriana Filip, Maria Rodica Cosgarea, David Albert Norris, Stanca Ariana Birlea

Journal of Dermatological Science. 72:168-76 · 01 Nov 2013

MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry–based metabolomic data

Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina Kechris

Bioinformatics. 30:133-4 · 29 Oct 2013

Multiple Amino Acid Sequence Alignment Nitrogenase Component 1: Insights into Phylogenetics and Structure-Function Relationships

James B. Howard, Katerina J. Kechris, Douglas C. Rees, Alexander N. Glazer

PLoS One. 8(9):e72751 · 03 Sep 2013

The Association of Adiponectin with Computed Tomography Phenotypes in Chronic Obstructive Pulmonary Disease

Brendan J. Carolan, Yu-il Kim, André A. Williams, Katerina Kechris, Sharon Lutz, Nichole Reisdorph, Russell P. Bowler

American Journal of Respiratory and Critical Care Medicine. 88:561-6 · 01 Sep 2013

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment

S. De, B. S. Pedersen, K. Kechris

Briefings In Bioinformatics. 15:919-28 · 16 Aug 2013

Peripheral Blood Mononuclear Cell Gene Expression in Chronic Obstructive Pulmonary Disease

Timothy M. Bahr, Grant J. Hughes, Michael Armstrong, Rick Reisdorph, Christopher D. Coldren, Michael G. Edwards, Christina Schnell, Ross Kedl, Daniel J. LaFlamme, Nichole Reisdorph, Katerina J. Kechris, Russell P. Bowler

American Journal of Respiratory Cell and Molecular Biology. 49:316-23 · 01 Aug 2013

Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption

Lauren A. Vanderlinden, Laura M. Saba, Katerina Kechris, Michael F. Miles, Paula L. Hoffman, Boris Tabakoff

PLoS One. 8(7):e68878 · 23 Jul 2013

Modeling considerations for using expression data from multiple species

Elizabeth Siewert, Katerina J. Kechris

Statistics in Medicine. 32:4057-4070 · 23 May 2013

Exposure to Maternal Diabetes in Utero and DNA Methylation Patterns in the Offspring

Nancy A West, Katerina Kechris, Dana Dabelea

Immunometabolism. 1:1-9 · 08 Jan 2013

A graphical model method for integrating multiple sources of genome-scale data

Daniel Dvorkin, Brian Biehs, Katerina Kechris

Statistical Applications in Genetics and Molecular Biology. 12:469-87 · 01 Jan 2013

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

B. S. Pedersen, D. A. Schwartz, I. V. Yang, K. J. Kechris

Bioinformatics. 28:2986-8 · 05 Sep 2012

Gene Expression Changes in C57BL/6J and DBA/2J Mice Following Prenatal Alcohol Exposure

Chris Downing, Stephen Flink, Maria L. Florez-McClure, Thomas E. Johnson, Boris Tabakoff, Katerina J. Kechris

Alcoholism, Clinical & Experimental Research. 36:1519-29 · 24 Apr 2012

Bayesian Analysis of High-Throughput Quantitative Measurement of Protein-DNA Interactions

David D. Pollock, A. P. Jason de Koning, Hyunmin Kim, Todd A. Castoe, Mair E. A. Churchill, Katerina J. Kechris

PLoS ONE. 6:e26105 · 01 Nov 2011

A systems genetic analysis of alcohol drinking by mice, rats and men: Influence of brain GABAergic transmission

Laura M. Saba, Beth Bennett, Paula L. Hoffman, Kelsey Barcomb, Takao Ishii, Katerina Kechris, Boris Tabakoff

Neuropharmacology. 60:1269-80 · 01 Jun 2011

Genetical Genomic Analysis of Complex Phenotypes Using the PhenoGen Website

Beth Bennett, Laura M. Saba, Cheryl K. Hornbaker, Katerina J. Kechris, Paula Hoffman, Boris Tabakoff

Behavior Genetics. 41:625-8 · 24 Dec 2010

Hedgehog targets in theDrosophilaembryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling

Brian Biehs, Katerina Kechris, SongMei Liu, Thomas B. Kornberg

Development. 137:3887-98 · 15 Nov 2010

Using the Phenogen website for ‘in silico’ analysis of morphine-induced analgesia: identifying candidate genes

Paula L. Hoffman, Beth Bennett, Laura M. Saba, Sanjiv V. Bhave, Phyllis J. Carosone-Link, Cheryl K. Hornbaker, Katerina J. Kechris, Robert W. Williams, Boris Tabakoff

Addiction Biology. 16:393-404 · 04 Nov 2010

Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics

Katerina J Kechris, Brian Biehs, Thomas B Kornberg

Statistical Applications in Genetics and Molecular Biology. Vol9(No.1). Article 29 · 06 Jan 2010

c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

Katerina Kechris, Hao Li

BMC Bioinformatics. 9:506 · 28 Nov 2008

The genomic determinants of alcohol preference in mice

Boris Tabakoff, Laura Saba, Katherina Kechris, Wei Hu, Sanjiv V. Bhave, Deborah A. Finn, Nicholas J. Grahame, Paula L. Hoffman

Mammalian Genome. 19:352-65 · 01 May 2008

Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays

Katerina Kechris, Yee Yang, Ru-Fang Yeh

BMC Genomics. 9:551(authors contributed equally) · 01 Jan 2008

Hepatitis C virus RNA: Dinucleotide frequencies and cleavage by RNase L

Christopher L. Washenberger, Jian-Qiu Han, Katherina J. Kechris, Babal Kant Jha, Robert H. Silverman, David J. Barton

Virus Research. 130:85-95 · 01 Dec 2007

The PhenoGen Informatics website: tools for analyses of complex traits

Sanjiv V Bhave, Cheryl Hornbaker, Tzu L Phang, Laura Saba, Razvan Lapadat, Katherina Kechris, Jeanette Gaydos, Daniel McGoldrick, Andrew Dolbey, Sonia Leach, Brian Soriano, Allison Ellington, Eric Ellington, Kendra Jones, Jonathan Mangion, John K Belknap, Robert W Williams, Lawrence E Hunter, Paula L Hoffman, Boris Tabakoff

BMC Genetics. 8:59 · 30 Aug 2007

Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study

Katherina J. Kechris, Jason C. Lin, Peter J. Bickel, Alexander N. Glazer

Proceedings of the National Academy of Sciences. 103:9584-9589 · 20 Jun 2006

Regulation of cellular plasticity inDrosophilaimaginal disc cells by the Polycomb group, trithorax group andlamagenes

Ansgar Klebes, Anne Sustar, Katherina Kechris, Hao Li, Gerold Schubiger, Thomas B. Kornberg

Development. 132:3753-3765 · 15 Aug 2005

Estimating Motifs Under Order Restrictions

Erik W van Zwet, Katherina J Kechris, Peter J Bickel, Michael B. Eisen

Statistical Applications in Genetics and Molecular Biology. Vol4(No.1).Article 1 · 10 Jan 2005

Katherina J Kechris, Erik van Zwet, Peter J Bickel, Michael B Eisen

Genome Biology. 5:R50 · 01 Jan 2004

Finding important sites in protein sequences

Peter J. Bickel, Katherina J. Kechris, Philip C. Spector, Gary J. Wedemayer, Alexander N. Glazer

Proceedings of the National Academy of Sciences, USA. 99:14764-14771 · 04 Nov 2002

Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions

Hyunmin Kim, Katherina J. Kechris, Lawrence Hunter

Lecture Notes in Computer Science, International Symposium on Bioinformatics Research and Applications, ISBRA 2007 Proceedings, pg 338-349. · 01 Jan 1900

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