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

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

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

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

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

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

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

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

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

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

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

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

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

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

Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. - Lysenko, Artem; Hindle, Matthew Morritt; Taubert, Jan; Saqi, Mansoor A. S.; Rawlings, Christopher J. (Briefings Bioinform., 2010)

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

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

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

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

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