Stepwise iterative maximum likelihood clustering approach. - Alok Sharma; Daichi Shigemizu; Keith A. Boroevich; Yosvany López; Yoichiro Kamatani; Michiaki Kubo; Tatsuhiko Tsunoda (BMC Bioinform., 2016)

Arete - candidate gene prioritization using biological network topology with additional evidence types. - Artem Lysenko; Keith A. Boroevich; Tatsuhiko Tsunoda (BioData Min., 2017)

Hierarchical Maximum Likelihood Clustering Approach. - Alok Sharma; Keith A. Boroevich; Daichi Shigemizu; Yoichiro Kamatani; Michiaki Kubo; Tatsuhiko Tsunoda (IEEE Trans. Biomed. Eng., 2017)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

DeepFeature: feature selection in nonimage data using convolutional neural network. - Alok Sharma; Artem Lysenko; Keith A. Boroevich; Edwin Vans; Tatsuhiko Tsunoda (Briefings Bioinform., 2021)

scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning. - Shangru Jia; Artem Lysenko; Keith A. Boroevich; Alok Sharma; Tatsuhiko Tsunoda (Briefings Bioinform., 2023)

VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data. - Tung Dang; Artem Lysenko; Keith A. Boroevich; Tatsuhiko Tsunoda (Briefings Bioinform., 2025)