Comparative interactomics with Funcoup 2.0. - Andrey Alexeyenko; Thomas Schmitt 003; Andreas Tjärnberg; Dimitri Guala; Oliver Frings; Erik L. L. Sonnhammer (Nucleic Acids Res., 2012)

Optimal Sparsity Criteria for Network Inference. - Andreas Tjärnberg; Torbjörn E. M. Nordling; Matthew Studham; Erik L. L. Sonnhammer (J. Comput. Biol., 2013)

Functional association networks as priors for gene regulatory network inference. - Matthew Studham; Andreas Tjärnberg; Torbjörn E. M. Nordling; Sven Nelander; Erik L. L. Sonnhammer (Bioinform., 2014)

Exploring the Boundaries of Gene Regulatory Network Inference. - Andreas Tjärnberg (2015)

LASSIM - A network inference toolbox for genome-wide mechanistic modeling. - 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; et al. (PLoS Comput. Biol., 2017)

A generalized framework for controlling FDR in gene regulatory network inference. - Daniel Morgan; Andreas Tjärnberg; Torbjörn E. M. Nordling; Erik L. L. Sonnhammer (Bioinform., 2019)

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. - Andreas Tjärnberg; Omar Mahmood; Christopher A. Jackson; Giuseppe-Antonio Saldi; Kyunghyun Cho; Lionel A. Christiaen; Richard A. Bonneau (PLoS Comput. Biol., 2021)

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. - Claudia Skok Gibbs; Christopher A. Jackson; Giuseppe-Antonio Saldi; Andreas Tjärnberg; Aashna Shah; Aaron Watters; Nicholas De Veaux; Konstantine Tchourine; Ren Yi; Tymor Hamamsy; Dayanne M. Castro; Nicholas Carriero; et al. (Bioinform., 2022)