Marieke L. Kuijjer

According to our database, Marieke L. Kuijjer authored at least 15 papers between 2016 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.

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

Nat. Comput. Sci., 2024

2023

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., October, 2023

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

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, 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

Frontiers Digit. Health, 2022

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.

Daniel Osório, Marieke L. Kuijjer, James J. Cai

Bioinform., 2022

2021

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, 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 M. Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve

Nat. Mach. Intell., 2021

2020

PUMA: PANDA Using MicroRNA Associations.

Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass

Bioinform., 2020

Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.

Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen

IEEE Access, 2020

Catalysis Clustering with GAN by Incorporating Domain Knowledge.

Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen

Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020

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

EndNote: Feature-based classification of networks.

Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela

Netw. Sci., 2019

2018

Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping.

Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding

Proceedings of the IEEE International Conference on Data Mining, 2018

2017

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

2016

Feature-Based Classification of Networks.

Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela

CoRR, 2016

PyPanda: a Python package for gene regulatory network reconstruction.

David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer

Bioinform., 2016