Marieke L. Kuijjer

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 15

Top Topics

Domain Specific Knowledge

Mass Spring Model

Top Venues

Publications

Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. CoRR (2024)
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
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. Nat. Comput. Sci. 4 (3) (2024)
Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinform. 39 (10) (2023)
Daniel Osorio, Marieke L. Kuijjer, James J. Cai
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinform. 38 (2) (2022)
Marouen Ben Guebila, Camila M. Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush
GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 50 (D1) (2022)
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
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3 (11) (2021)
Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE Access 8 (2020)
Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
Catalysis Clustering with GAN by Incorporating Domain Knowledge. KDD (2020)
Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass
PUMA: PANDA Using MicroRNA Associations. Bioinform. 36 (18) (2020)
David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. PLoS Comput. Biol. 15 (2) (2019)
Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela
EndNote: Feature-based classification of networks. Netw. Sci. 7 (3) (2019)
Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding
Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping. ICDM (2018)
Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinform. 18 (1) (2017)
David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer
PyPanda: a Python package for gene regulatory network reconstruction. Bioinform. 32 (21) (2016)
Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela
Feature-Based Classification of Networks. CoRR (2016)