Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions. - Hyunmin Kim; Katherina J. Kechris; Lawrence Hunter (ISBRA, 2007)

c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression. - Katerina J. Kechris; Hao Li (BMC Bioinform., 2008)

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. - Brent S. Pedersen; David A. Schwartz; Ivana V. Yang; Katerina J. Kechris (Bioinform., 2012)

Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics. - Nichole Reisdorph; Robert Stearman; Katerina J. Kechris; Tzu Lip Phang; Richard Reisdorph; Jessica E. Prenni; David J. Erle; Christopher Coldren; Kevin L. Schey; Alexey I. Nesvizhskii; Marc Geraci (Genom. Proteom. Bioinform., 2013)

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. - Subhajyoti De; Brent S. Pedersen; Katerina J. Kechris (Briefings Bioinform., 2014)

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 J. Kechris (Bioinform., 2014)

The discordant method: a novel approach for differential correlation. - Charlotte Siska; Russell Bowler; Katerina J. Kechris (Bioinform., 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 Radcliffe; Laura M. Saba; Katerina J. Kechris (BMC Bioinform., 2017)

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 M. Saba; Katerina J. Kechris; Qunhua Li (PLoS Comput. Biol., 2018)

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 J. Kechris (Bioinform., 2019)

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. - Brian Vestal; Camille M. Moore; Elizabeth Wynn; Laura M. Saba; Tasha Fingerlin; Katerina J. Kechris (BMC Bioinform., 2020)

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 J. Kechris; Miranda Kroehl (BMC Bioinform., 2021)

Reproducibility of mass spectrometry based metabolomics data. - Tusharkanti Ghosh; Daisy Philtron; Weiming Zhang; Katerina J. Kechris; Debashis Ghosh (BMC Bioinform., 2021)

PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. - Charlie M. Carpenter; Weiming Zhang; Lucas A. Gillenwater; Cameron Severn; Tusharkanti Ghosh; Russell Bowler; Katerina J. Kechris; Debashis Ghosh (PLoS Comput. Biol., 2021)

Effective Subject Representation based on Multi-omics Disease Networks using Graph Embedding. - Sundous Hussein; Thao Vu; Leslie Lange; Russell Bowler; Katerina J. Kechris; Farnoush Banaei Kashani (BIBM, 2022)

Semi-supervised Embedding for Scalable and Accurate Time Series Clustering. - Andrew Hill; Russell Bowler; Katerina J. Kechris; Farnoush Banaei Kashani (IEEE Big Data, 2022)

Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics. - Jonathan P. Dekermanjian; Elin Shaddox; Debmalya Nandy; Debashis Ghosh; Katerina J. Kechris (BMC Bioinform., 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 Bowler; Leslie Lange; Farnoush Banaei Kashani (Frontiers Big Data, 2022)

NetSHy: network summarization via a hybrid approach leveraging topological properties. - Thao Vu; Elizabeth Litkowski; Weixuan Liu; Katherine A. Pratte; Leslie Lange; Russell Bowler; Farnoush Banaei Kashani; Katerina J. Kechris (Bioinform., 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 J. Kechris (PLoS Comput. Biol., 2023)

TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes. - Charlie M. Carpenter; Lucas A. Gillenwater; Russell Bowler; Katerina J. Kechris; Debashis Ghosh (BMC Bioinform., 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; Katherina J. Kechris (BMC Bioinform., 2023)

Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach. - Sundous Hussein; Vicente Ramos; Weixuan Liu; Katerina J. Kechris; Leslie Lange; Russell P. Bowler; Farnoush Banaei Kashani (BIBM, 2024)

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics. - Alexandria M. Jensen; Peter Dewitt; Brianne M. Bettcher; Julia Wrobel; Katerina J. Kechris; Debashis Ghosh (PLoS Comput. Biol., 2024)

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. - Cecilia Wieder; Juliette Cooke; Clément Frainay; Nathalie Poupin; Russell Bowler; Fabien Jourdan; Katerina J. Kechris; Rachel P. J. Lai; Timothy M. D. Ebbels (PLoS Comput. Biol., 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 Bioinform., 2024)

A generalized higher-order correlation analysis framework for multi-omics network inference. - Weixuan Liu; Katherine A. Pratte; Peter J. Castaldi; Craig P. Hersh; Russell P. Bowler; Farnoush Banaei Kashani; Katerina J. Kechris (PLoS Comput. Biol., 2025)

BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool. - Vicente Ramos; Sundous Hussein; Mohamed Abdel-Hafiz; Arunangshu Sarkar; Weixuan Liu; Katerina J. Kechris; Russell P. Bowler; Leslie Lange; Farnoush Banaei Kashani (CoRR, 2025)