| A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases DR Gawel, J Serra-Musach, S Lilja, J Aagesen, A Arenas, B Asking, ... Genome medicine 11, 1-25, 2019 | 82 | 2019 |
| Comparative interactomics with Funcoup 2.0 A Alexeyenko, T Schmitt, A Tjärnberg, D Guala, O Frings, ... Nucleic acids research 40 (D1), D821-D828, 2012 | 67 | 2012 |
| Functional association networks as priors for gene regulatory network inference ME Studham, A Tjärnberg, TEM Nordling, S Nelander, ELL Sonnhammer Bioinformatics 30 (12), i130-i138, 2014 | 51 | 2014 |
| Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder SK Dwivedi, A Tjärnberg, J Tegnér, M Gustafsson Nature communications 11 (1), 856, 2020 | 43 | 2020 |
| High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 CS Gibbs, CA Jackson, GA Saldi, A Tjärnberg, A Shah, A Watters, ... Bioinformatics 38 (9), 2519, 2022 | 38 | 2022 |
| Optimal tuning of weighted kNN-and diffusion-based methods for denoising single cell genomics data A Tjärnberg, O Mahmood, CA Jackson, GA Saldi, K Cho, LA Christiaen, ... PLoS computational biology 17 (1), e1008569, 2021 | 35 | 2021 |
| High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 C Skok Gibbs, CA Jackson, GA Saldi, A Tjärnberg, A Shah, A Watters, ... Bioinformatics 38 (9), 2519-2528, 2022 | 29 | 2022 |
| Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data D Seçilmiş, T Hillerton, D Morgan, A Tjärnberg, S Nelander, TEM Nordling, ... NPJ systems biology and applications 6 (1), 37, 2020 | 19 | 2020 |
| Optimal sparsity criteria for network inference A Tjärnberg, TEM Nordling, M Studham, ELL Sonnhammer Journal of Computational Biology 20 (5), 398-408, 2013 | 18 | 2013 |
| GeneSPIDER–gene regulatory network inference benchmarking with controlled network and data properties A Tjärnberg, DC Morgan, M Studham, TEM Nordling, ELL Sonnhammer Molecular BioSystems 13 (7), 1304-1312, 2017 | 17 | 2017 |
| Avoiding pitfalls in L 1-regularised inference of gene networks A Tjärnberg, TEM Nordling, M Studham, S Nelander, ELL Sonnhammer Molecular Biosystems 11 (1), 287-296, 2015 | 16 | 2015 |
| A generalized framework for controlling FDR in gene regulatory network inference D Morgan, T Nordling, A Tjarnberg Bioinformatics, 2018 | 15 | 2018 |
| Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms D Morgan, M Studham, A Tjärnberg, H Weishaupt, FJ Swartling, ... Scientific reports 10 (1), 14149, 2020 | 11 | 2020 |
| LASSIM—A network inference toolbox for genome-wide mechanistic modeling R Magnusson, GP Mariotti, M Köpsén, W Lövfors, DR Gawel, R Jörnsten, ... PLoS computational biology 13 (6), e1005608, 2017 | 11 | 2017 |
| Cancer network activity associated with therapeutic response and synergism J Serra-Musach, F Mateo, E Capdevila-Busquets, GR de Garibay, ... Genome medicine 8, 1-12, 2016 | 10 | 2016 |
| Knowledge of the perturbation design is essential for accurate gene regulatory network inference D Seçilmiş, T Hillerton, A Tjärnberg, S Nelander, TEM Nordling, ... Scientific reports 12 (1), 16531, 2022 | 9 | 2022 |
| Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference A Tjärnberg, M Beheler-Amass, CA Jackson, LA Christiaen, D Gresham, ... Genome biology 25 (1), 24, 2024 | 3 | 2024 |
| Correction to: a validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases DR Gawel, J Serra-Musach, S Lilja, J Aagesen, A Arenas, B Asking, ... Genome Medicine 12, 2020 | 3 | 2020 |
| Exploring the boundaries of gene regulatory network inference A Tjärnberg Department of Biochemistry and Biophysics, Stockholm University, 2015 | 1 | 2015 |
| Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression CA Jackson, M Beheler-Amass, A Tjärnberg, I Suresh, AS Hickey, ... bioRxiv, 2023 | | 2023 |
Erik SonnhammerProfessor of Bioinformatics, DBB Stockholm University, Science for Life LaboratoryVerified email at scilifelab.se
