Marieke L. Kuijjer

19 papers A* 2Journal 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
Gene regulatory network integration with multi-omics data enhances survival predictions in cancer.
Briefings Bioinform.
Romana T. Pop, Ping-Han Hsieh, Tatiana Belova, Anthony Mathelier, Marieke L. Kuijjer
2025 J jnl
SPONGE: simple prior omics network GEnerator.
Bioinform.
Ladislav Hovan, Marieke L. Kuijjer
2024 J jnl
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data.
CoRR
Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer
2024 J jnl
Improving bioinformatics software quality through teamwork.
Bioinform.
Katalin Ferenc, Ieva Rauluseviciute, Ladislav Hovan, Vipin Kumar, Marieke L. Kuijjer, Anthony Mathelier
2024 J jnl
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.
Nat. Comput. Sci.
Daniel Osório, 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, S. Stephen Yi, Marieke L. Kuijjer
2023 J jnl
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.
Bioinform.
Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
2022 J jnl
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation.
Frontiers Digit. Health
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, Olivier Gevaert, Emily J. Greenspan, Wenrui Hao, Tina Hernandez-Boussard, Pamela R. Jackson, Marieke L. Kuijjer, Adrian Lee, Paul Macklin, Subha Madhavan, Matthew D. McCoy, Navid Mohammad Mirzaei, Talayeh Razzaghi, Heber L. Rocha, Leili Shahriyari, Ilya Shmulevich, Daniel G. Stover, Yi Sun, Tanveer F. Syeda-Mahmood, Jinhua Wang, Qi Wang, Ioannis K. Zervantonakis
2022 J jnl
GRAND: a database of gene regulatory network models across human conditions.
Nucleic Acids Res.
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
2022 J jnl
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.
Bioinform.
Daniel Osório, Marieke L. Kuijjer, James J. Cai
2021 J jnl
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.
Nat. Mach. Intell.
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, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut D. Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig Magne Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve
2020 A* conf
Catalysis Clustering with GAN by Incorporating Domain Knowledge.
KDD
Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
2020 J jnl
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.
IEEE Access
Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
2020 J jnl
PUMA: PANDA Using MicroRNA Associations.
Bioinform.
Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass
2019 J jnl
EndNote: Feature-based classification of networks.
Netw. Sci.
Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela
2019 J jnl
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas.
PLoS Comput. Biol.
David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée
2018 A* conf
Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping.
ICDM
Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding
2017 J jnl
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.
BMC Bioinform.
Joseph N. Paulson, Cho-Yi Chen, Camila Miranda Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
2016 J jnl
Feature-Based Classification of Networks.
CoRR
Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela
2016 J jnl
PyPanda: a Python package for gene regulatory network reconstruction.
Bioinform.
David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer