PyPanda: a Python package for gene regulatory network reconstruction. - David G. P. van IJzendoorn; Kimberly Glass; John Quackenbush; Marieke L. Kuijjer (Bioinform., 2016)

Feature-Based Classification of Networks. - Ian Barnett; Nishant Malik; Marieke L. Kuijjer; Peter J. Mucha; Jukka-Pekka Onnela (CoRR, 2016)

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. - Joseph N. Paulson; Cho-Yi Chen; Camila Miranda Lopes-Ramos; Marieke L. Kuijjer; John Platig; Abhijeet R. Sonawane; Maud Fagny; Kimberly Glass; John Quackenbush (BMC Bioinform., 2017)

Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping. - Tianyu Kang; Kourosh Zarringhalam; Marieke L. Kuijjer; Ping Chen 001; John Quackenbush; Wei Ding 003 (ICDM, 2018)

EndNote: Feature-based classification of networks. - Ian Barnett; Nishant Malik; Marieke L. Kuijjer; Peter J. Mucha; Jukka-Pekka Onnela (Netw. Sci., 2019)

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. - David G. P. van IJzendoorn; Karoly Szuhai; Inge H. Briaire-de Bruijn; Marie Kostine; Marieke L. Kuijjer; Judith V. M. G. Bovée (PLoS Comput. Biol., 2019)

Catalysis Clustering with GAN by Incorporating Domain Knowledge. - Olga Andreeva; Wei Li 121; Wei Ding 003; Marieke L. Kuijjer; John Quackenbush; Ping Chen 001 (KDD, 2020)

Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. - Jipeng Qiang; Wei Ding 003; Marieke L. Kuijjer; John Quackenbush; Ping Chen 001 (IEEE Access, 2020)

PUMA: PANDA Using MicroRNA Associations. - Marieke L. Kuijjer; Maud Fagny; Alessandro Marin; John Quackenbush; Kimberly Glass (Bioinform., 2020)

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. - Milena Pavlovic; Lonneke Scheffer; Keshav Motwani; Chakravarthi Kanduri; Radmila Kompova; Nikolay Vazov; Knut Waagan; Fabian L. M. Bernal; Alexandre Almeida Costa; Brian Corrie; Rahmad Akbar; Ghadi S. Al Hajj; et al. (Nat. Mach. Intell., 2021)

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. - Daniel Osório 004; Marieke L. Kuijjer; James J. Cai (Bioinform., 2022)

Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. - Eric A. Stahlberg; Mohamed Abdel-Rahman; Boris Aguilar; Alireza Asadpoure; Robert A. Beckman; Lynn L. Borkon; Jeffrey N. Bryan; Colleen M. Cebulla; Young Hwan Chang; Ansu Chatterjee; Jun Deng; Sepideh Dolatshahi; et al. (Frontiers Digit. Health, 2022)

GRAND: a database of gene regulatory network models across human conditions. - Marouen Ben Guebila; Camila Miranda Lopes-Ramos; Deborah A. Weighill; Abhijeet Rajendra Sonawane; Rebekka Burkholz; Behrouz Shamsaei; John Platig; Kimberly Glass; Marieke L. Kuijjer; John Quackenbush (Nucleic Acids Res., 2022)

Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. - Ping-Han Hsieh; Camila Miranda Lopes-Ramos; Manuela Zucknick; Geir Kjetil Sandve; Kimberly Glass; Marieke L. Kuijjer (Bioinform., 2023)

CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. - Ping-Han Hsieh; Ru-Xiu Hsiao; Katalin Ferenc; Anthony Mathelier; Rebekka Burkholz; Chien-Yu Chen 001; Geir Kjetil Sandve; Tatiana Belova; Marieke L. Kuijjer (CoRR, 2024)

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. - Daniel Osório 004; Anna Capasso; S. Gail Eckhardt; Uma Giri; Alexander Somma; Todd M. Pitts; Christopher H. Lieu; Wells A. Messersmith; Stacey M. Bagby; Harinder Singh; Jishnu Das; Nidhi Sahni; et al. (Nat. Comput. Sci., 2024)

Gene regulatory network integration with multi-omics data enhances survival predictions in cancer. - Romana T. Pop; Ping-Han Hsieh; Tatiana Belova; Anthony Mathelier; Marieke L. Kuijjer (Briefings Bioinform., 2025)