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ORCIDMarieke L. Kuijjer
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2020 – today
- 2024
[j12]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): 237-250 (2024)- [i2]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 abs/2405.18655 (2024) - 2023
- [j11]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) - 2022
- [j10]Daniel Osório, 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): 580-582 (2022) - [j9]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:
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers Digit. Health 4 (2022) - [j8]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:
GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 50(D1): 610-621 (2022) - 2021
- [j7]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:
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3(11): 936-944 (2021) - 2020
- [j6]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: 67775-67789 (2020) - [j5]Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass:
PUMA: PANDA Using MicroRNA Associations. Bioinform. 36(18): 4765-4773 (2020) - [c2]Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen:
Catalysis Clustering with GAN by Incorporating Domain Knowledge. KDD 2020: 1344-1352
2010 – 2019
- 2019
- [j4]Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela:
EndNote: Feature-based classification of networks. Netw. Sci. 7(3): 438-444 (2019) - [j3]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) - 2018
- [c1]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: 1079-1084 - 2017
- [j2]Joseph N. Paulson, Cho-Yi Chen, Camila Miranda 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): 437:1-437:10 (2017) - 2016
- [j1]David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer:
PyPanda: a Python package for gene regulatory network reconstruction. Bioinform. 32(21): 3363-3365 (2016) - [i1]Ian Barnett, Nishant Malik, Marieke L. Kuijjer, Peter J. Mucha, Jukka-Pekka Onnela:
Feature-Based Classification of Networks. CoRR abs/1610.05868 (2016)
Coauthor Index
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