Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder

por Dwivedi, Sanjiv K., Tjärnberg, Andreas, Tegnér, Jesper, Gustafsson, Mika
Publicado 2020

Comparative interactomics with Funcoup 2.0

por Alexeyenko, Andrey, Schmitt, Thomas, Tjärnberg, Andreas, Guala, Dmitri, Frings, Oliver, Sonnhammer, Erik L. L.
Publicado 2012

Functional association networks as priors for gene regulatory network inference

por Studham, Matthew E., Tjärnberg, Andreas, Nordling, Torbjörn E.M., Nelander, Sven, Sonnhammer, Erik L. L.
Publicado 2014

Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

por Tjärnberg, Andreas, Beheler-Amass, Maggie, Jackson, Christopher A, Christiaen, Lionel A, Gresham, David, Bonneau, Richard
Publicado 2023

Knowledge of the perturbation design is essential for accurate gene regulatory network inference

por Seçilmiş, Deniz, Hillerton, Thomas, Tjärnberg, Andreas, Nelander, Sven, Nordling, Torbjörn E. M., Sonnhammer, Erik L. L.
Publicado 2022

Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression

por Jackson, Christopher A, Beheler-Amass, Maggie, Tjärnberg, Andreas, Suresh, Ina, Hickey, Angela Shang-mei, Bonneau, Richard, Gresham, David
Publicado 2023

Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data

por Seçilmiş, Deniz, Hillerton, Thomas, Morgan, Daniel, Tjärnberg, Andreas, Nelander, Sven, Nordling, Torbjörn E. M., Sonnhammer, Erik L. L.
Publicado 2020

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

por Tjärnberg, Andreas, Mahmood, Omar, Jackson, Christopher A., Saldi, Giuseppe-Antonio, Cho, Kyunghyun, Christiaen, Lionel A., Bonneau, Richard A.
Publicado 2021

Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms

por Morgan, Daniel, Studham, Matthew, Tjärnberg, Andreas, Weishaupt, Holger, Swartling, Fredrik J., Nordling, Torbjörn E. M., Sonnhammer, Erik L. L.
Publicado 2020

LASSIM—A network inference toolbox for genome-wide mechanistic modeling

por Magnusson, Rasmus, Mariotti, Guido Pio, Köpsén, Mattias, Lövfors, William, Gawel, Danuta R., Jörnsten, Rebecka, Linde, Jörg, Nordling, Torbjörn E. M., Nyman, Elin, Schulze, Sylvie, Nestor, Colm E., Zhang, Huan, Cedersund, Gunnar, Benson, Mikael, Tjärnberg, Andreas, Gustafsson, Mika
Publicado 2017

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0

por Skok Gibbs, Claudia, Jackson, Christopher A, Saldi, Giuseppe-Antonio, Tjärnberg, Andreas, Shah, Aashna, Watters, Aaron, De Veaux, Nicholas, Tchourine, Konstantine, Yi, Ren, Hamamsy, Tymor, Castro, Dayanne M, Carriero, Nicholas, Gorissen, Bram L, Gresham, David, Miraldi, Emily R, Bonneau, Richard
Publicado 2022

Cancer network activity associated with therapeutic response and synergism

por Serra-Musach, Jordi, Mateo, Francesca, Capdevila-Busquets, Eva, de Garibay, Gorka Ruiz, Zhang, Xiaohu, Guha, Raj, Thomas, Craig J., Grueso, Judit, Villanueva, Alberto, Jaeger, Samira, Heyn, Holger, Vizoso, Miguel, Pérez, Hector, Cordero, Alex, Gonzalez-Suarez, Eva, Esteller, Manel, Moreno-Bueno, Gema, Tjärnberg, Andreas, Lázaro, Conxi, Serra, Violeta, Arribas, Joaquín, Benson, Mikael, Gustafsson, Mika, Ferrer, Marc, Aloy, Patrick, Pujana, Miquel Àngel
Publicado 2016

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

por Gawel, Danuta R., Serra-Musach, Jordi, Lilja, Sandra, Aagesen, Jesper, Arenas, Alex, Asking, Bengt, Bengnér, Malin, Björkander, Janne, Biggs, Sophie, Ernerudh, Jan, Hjortswang, Henrik, Karlsson, Jan-Erik, Köpsen, Mattias, Lee, Eun Jung, Lentini, Antonio, Li, Xinxiu, Magnusson, Mattias, Martínez-Enguita, David, Matussek, Andreas, Nestor, Colm E., Schäfer, Samuel, Seifert, Oliver, Sonmez, Ceylan, Stjernman, Henrik, Tjärnberg, Andreas, Wu, Simon, Åkesson, Karin, Shalek, Alex K., Stenmarker, Margaretha, Zhang, Huan, Gustafsson, Mika, Benson, Mikael
Publicado 2019

Correction to: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

por Gawel, Danuta R., Serra-Musach, Jordi, Lilja, Sandra, Aagesen, Jesper, Arenas, Alex, Asking, Bengt, Bengnér, Malin, Björkander, Janne, Biggs, Sophie, Ernerudh, Jan, Hjortswang, Henrik, Karlsson, Jan-Erik, Köpsen, Mattias, Lee, Eun Jung, Lentini, Antonio, Li, Xinxiu, Magnusson, Mattias, Martínez-Enguita, David, Matussek, Andreas, Nestor, Colm E., Schäfer, Samuel, Seifert, Oliver, Sonmez, Ceylan, Stjernman, Henrik, Tjärnberg, Andreas, Wu, Simon, Åkesson, Karin, Shalek, Alex K., Stenmarker, Margaretha, Zhang, Huan, Gustafsson, Mika, Benson, Mikael
Publicado 2020