Phase Conductor on Multi-layered Attentions for Machine Comprehension. - Rui Liu; Wei Wei; Weiguang Mao; Maria Chikina (CoRR, 2017)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. - Boris Simovski; Chakravarthi Kanduri; Sveinung Gundersen; Dmytro Titov; Diana Domanska; Christoph Bock; Lara Bossini-Castillo; Maria Chikina; Alexander V. Favorov; Ryan M. Layer; Andrey A. Mironov; Aaron R. Quinlan; et al. (Nucleic Acids Res., 2018)

RERconverge: an R package for associating evolutionary rates with convergent traits. - Amanda Kowalczyk; Wynn K. Meyer; Raghavendran Partha; Weiguang Mao; Nathan L. Clark; Maria Chikina (Bioinform., 2019)

Causal network perturbations for instance-specific analysis of single cell and disease samples. - Kristina Buschur; Maria Chikina; Panayiotis V. Benos (Bioinform., 2020)

DataRemix: a universal data transformation for optimal inference from gene expression datasets. - Weiguang Mao; Javad Rahimikollu; Ryan Hausler; Maria Chikina (Bioinform., 2021)

Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data. - Weiguang Mao; Maziyar Baran Pouyan; Dennis Kostka; Maria Chikina (Bioinform., 2022)

An intrinsically interpretable neural network architecture for sequence-to-function learning. - Ali Tugrul Balci; Mark Maher Ebeid; Panayiotis V. Benos; Dennis Kostka; Maria Chikina (Bioinform., 2023)

A hybrid constrained continuous optimization approach for optimal causal discovery from biological data. - Yuehua Zhu; Panayiotis V. Benos; Maria Chikina (Bioinform., 2024)

Best holdout assessment is sufficient for cancer transcriptomic model selection. - Jake Crawford; Maria Chikina; Casey S. Greene (Patterns, 2024)