Katerina J. Kechris

27 papers B 1Journal 24Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
A generalized higher-order correlation analysis framework for multi-omics network inference.
PLoS Comput. Biol.
Weixuan Liu, Katherine A. Pratte, Peter J. Castaldi, Craig P. Hersh, Russell P. Bowler, Farnoush Banaei Kashani, Katerina J. Kechris
2025 J jnl
BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool.
CoRR
Vicente Ramos, Sundous Hussein, Mohamed Abdel-Hafiz, Arunangshu Sarkar, Weixuan Liu, Katerina J. Kechris, Russell P. Bowler, Leslie Lange, Farnoush Banaei Kashani
2024 J jnl
Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics.
PLoS Comput. Biol.
Alexandria M. Jensen, Peter Dewitt, Brianne M. Bettcher, Julia Wrobel, Katerina J. Kechris, Debashis Ghosh
2024 — conf
Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach.
BIBM
Sundous Hussein, Vicente Ramos, Weixuan Liu, Katerina J. Kechris, Leslie Lange, Russell P. Bowler, Farnoush Banaei Kashani
2024 J jnl
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.
PLoS Comput. Biol.
Cecilia Wieder, Juliette Cooke, Clément Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J. Kechris, Rachel P. J. Lai, Timothy M. D. Ebbels
2024 J jnl
Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization.
BMC Bioinform.
Weixuan Liu, Thao Vu, Iain R. Konigsberg, Katherine A. Pratte, Yonghua Zhuang, Katerina J. Kechris
2023 J jnl
NetSHy: network summarization via a hybrid approach leveraging topological properties.
Bioinform.
Thao Vu, Elizabeth Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell Bowler, Farnoush Banaei Kashani, Katerina J. Kechris
2023 J jnl
RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks.
PLoS Comput. Biol.
Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina J. Kechris
2023 J jnl
TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes.
BMC Bioinform.
Charlie M. Carpenter, Lucas A. Gillenwater, Russell Bowler, Katerina J. Kechris, Debashis Ghosh
2022 — conf
Effective Subject Representation based on Multi-omics Disease Networks using Graph Embedding.
BIBM
Sundous Hussein, Thao Vu, Leslie Lange, Russell Bowler, Katerina J. Kechris, Farnoush Banaei Kashani
2022 J jnl
Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics.
BMC Bioinform.
Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh, Katerina J. Kechris
2022 B conf
Semi-supervised Embedding for Scalable and Accurate Time Series Clustering.
IEEE Big Data
Andrew Hill, Russell Bowler, Katerina J. Kechris, Farnoush Banaei Kashani
2022 J jnl
Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification.
Frontiers Big Data
Mohamed Abdel-Hafiz, Mesbah Najafi, Shahab Helmi, Katherine A. Pratte, Yonghua Zhuang, Weixuan Liu, Katerina J. Kechris, Russell Bowler, Leslie Lange, Farnoush Banaei Kashani
2021 J jnl
PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes.
PLoS Comput. Biol.
Charlie M. Carpenter, Weiming Zhang, Lucas A. Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russell Bowler, Katerina J. Kechris, Debashis Ghosh
2021 J jnl
Reproducibility of mass spectrometry based metabolomics data.
BMC Bioinform.
Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina J. Kechris, Debashis Ghosh
2021 J jnl
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R.
BMC Bioinform.
Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina J. Kechris, Miranda Kroehl
2020 J jnl
MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments.
BMC Bioinform.
Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura M. Saba, Tasha Fingerlin, Katerina J. Kechris
2019 J jnl
Unsupervised discovery of phenotype-specific multi-omics networks.
Bioinform.
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
2018 J jnl
Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network.
PLoS Comput. Biol.
Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura M. Saba, Katerina J. Kechris, Qunhua Li
2017 J jnl
Model based heritability scores for high-throughput sequencing data.
BMC Bioinform.
Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard Radcliffe, Laura M. Saba, Katerina J. Kechris
2017 J jnl
The discordant method: a novel approach for differential correlation.
Bioinform.
Charlotte Siska, Russell Bowler, Katerina J. Kechris
2016 J jnl
The discordant method: a novel approach for differential correlation.
Bioinform.
Charlotte Siska, Russell Bowler, Katerina J. Kechris
2014 J jnl
MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data.
Bioinform.
Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina J. Kechris
2014 J jnl
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.
Briefings Bioinform.
Subhajyoti De, Brent S. Pedersen, Katerina J. Kechris
2013 J jnl
Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics.
Genom. Proteom. Bioinform.
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
2012 J jnl
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated
Bioinform.
Brent S. Pedersen, David A. Schwartz, Ivana V. Yang, Katerina J. Kechris
2008 J jnl
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression.
BMC Bioinform.
Katerina J. Kechris, Hao Li