DeepLoc: prediction of protein subcellular localization using deep learning. - José Juan Almagro Armenteros; Casper Kaae Sønderby; Søren Kaae Sønderby; Henrik Nielsen; Ole Winther (Bioinform., 2017)

An introduction to deep learning on biological sequence data: examples and solutions. - Vanessa Isabell Jurtz; Alexander Rosenberg Johansen; Morten Nielsen 001; José Juan Almagro Armenteros; Henrik Nielsen; Casper Kaae Sønderby; Ole Winther; Søren Kaae Sønderby (Bioinform., 2017)

Deep protein representations enable recombinant protein expression prediction. - Hannah-Marie Martiny; José Juan Almagro Armenteros; Alexander Rosenberg Johansen; Jesper Salomon; Henrik Nielsen (Comput. Biol. Chem., 2021)

NetSolP: predicting protein solubility in Escherichia coli using language models. - Vineet Thumuluri; Hannah-Marie Martiny; José Juan Almagro Armenteros; Jesper Salomon; Henrik Nielsen; Alexander Rosenberg Johansen (Bioinform., 2022)

DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. - Vineet Thumuluri; José Juan Almagro Armenteros; Alexander Rosenberg Johansen; Henrik Nielsen; Ole Winther (Nucleic Acids Res., 2022)

SpanSeq: Similarity-based sequence data splitting method for improved development and assessment of deep learning projects. - Alfred Ferrer Florensa; José Juan Almagro Armenteros; Henrik Nielsen; Frank Møller Aarestrup; Philip Thomas Lanken Conradsen Clausen (CoRR, 2024)