Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder by Sanjiv K. Dwivedi, Andreas Tjärnberg, Jesper Tegnér, Mika Gustafsson

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Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference by Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A. Jackson, Lionel A. Christiaen, David Gresham, Richard Bonneau

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Knowledge of the perturbation design is essential for accurate gene regulatory network inference by Deniz Seçilmiş, Thomas Hillerton, Andreas Tjärnberg, Sven Nelander, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer

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Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. by Andreas Tjärnberg, Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel A Christiaen, Richard A Bonneau

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LASSIM-A network inference toolbox for genome-wide mechanistic modeling. by Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E M Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson

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Correction to: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases by Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Alex Arenas, Bengt Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan-Erik Karlsson, Mattias Köpsen, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alex K. Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson

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A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases by Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Alex Arenas, Bengt Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan-Erik Karlsson, Mattias Köpsen, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alex K. Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson

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