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2021

Breda, Jérémie and Zavolan, Mihaela and van Nimwegen, Erik. (2021) Bayesian inference of gene expression states from single-cell RNA-seq data. Nature Biotechnology, 39 (8). pp. 1008-1016.

2020

Mukhtar, Tanzila and Breda, Jeremie and Grison, Alice and Karimaddini, Zahra and Grobecker, Pascal and Iber, Dagmar and Beisel, Christian and van Nimwegen, Erik and Taylor, Verdon. (2020) Tead transcription factors differentially regulate cortical development. Scientific Reports, 10 (1). p. 4625.

2018

Rzepiela, Andrzej J. and Ghosh, Souvik and Breda, Jeremie and Vina-Vilaseca, Arnau and Syed, Afzal P. and Gruber, Andreas J. and Eschbach, Katja and Beisel, Christian and van Nimwegen, Erik and Zavolan, Mihaela. (2018) Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Molecular systems biology, 14 (8). e8266.

2017

Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176.

2015

Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2015) Quantifying the strength of miRNA-target interactions. Methods, Vol. 85. pp. 90-99.