Graph-based sequence annotation using a data integration approach. - Robert Pesch; Artem Lysenko; Matthew Hindle; Keywan Hassani-Pak; Ralf Thiele; Christopher J. Rawlings; Jacob Köhler; Jan Taubert (J. Integr. Bioinform., 2008)

Linking Life Sciences Data Using Graph-Based Mapping. - Jan Taubert; Matthew Hindle; Artem Lysenko; Jochen Weile; Jacob Köhler; Christopher J. Rawlings (DILS, 2009)

Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. - Artem Lysenko; Matthew Morritt Hindle; Jan Taubert; Mansoor A. S. Saqi; Christopher J. Rawlings (Briefings Bioinform., 2009)

Analysis and Visualisation of RDF Resources in Ondex. - Catherine Canevet; Artem Lysenko; Andrea Splendiani; Matthew R. Pocock; Christopher J. Rawlings (SWAT4LS, 2010)

AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations. - Michael Defoin-Platel; Matthew Morritt Hindle; Artem Lysenko; Stephen J. Powers; Dimah Z. Habash; Christopher J. Rawlings; Mansoor A. S. Saqi (BMC Bioinform., 2011)

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. - Artem Lysenko; Michael Defoin-Platel; Keywan Hassani-Pak; Jan Taubert; Charlie Hodgman; Christopher J. Rawlings; Mansoor A. S. Saqi (BMC Bioinform., 2011)

Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum. - Laura Bennett; Artem Lysenko; Lazaros G. Papageorgiou; Martin Urban; Kim E. Hammond-Kosack; Christopher J. Rawlings; Mansoor A. S. Saqi; Sophia Tsoka (CMSB, 2012)

A Framework for Mining Life Sciences Data on the Semantic Web in an Interactive, Graph-Based Environment. - Artem Lysenko; Jacek Grzebyta; Matthew Morritt Hindle; Christopher J. Rawlings; Andrea Splendiani (CIBB, 2013)

Integrating Multiple Studies of Wheat Microarray Data to Identify Treatment-Specific Regulatory Networks. - Valeria Bo; Artem Lysenko; Mansoor A. S. Saqi; Dimah Z. Habash; Allan Tucker (IDA, 2013)

Representing and querying disease networks using graph databases. - Artem Lysenko; Irina A. Roznovat; Mansoor A. S. Saqi; Alexander Mazein; Christopher J. Rawlings; Charles Auffray (BioData Min., 2016)

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

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. - Irina Balaur; Alexander Mazein; Mansoor A. S. Saqi; Artem Lysenko; Christopher J. Rawlings (Bioinform., 2017)

EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. - Irina Balaur; Mansoor A. S. Saqi; Ana Barat; Artem Lysenko; Alexander Mazein; Christopher J. Rawlings; Heather J. Ruskin; Charles Auffray (J. Comput. Biol., 2017)

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. - Mansoor A. S. Saqi; Artem Lysenko; Yike Guo; Tatsuhiko Tsunoda; Charles Auffray (Briefings Bioinform., 2019)

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)

Optimal normalization in quantum-classical hybrid models for anti-cancer drug response prediction. - Takafumi Ito; Artem Lysenko; Tatsuhiko Tsunoda (CoRR, 2025)