Publications

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2022
 

NetSolP: predicting protein solubility in E. coli using language models

Thumuluri, Vineet ; Martiny, Hannah-Marie ; Armenteros, Jose J. Almagro ; Salomon, Jesper ; Nielsen, Henrik ; Johansen, Alexander R ; Valencia, Alfonso (Editor)
in: Bioinformatics, vol: 38, issue: 4, pages: 941–946

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2022     |    DOI: https://doi.org/10.1093/bioinformatics/btab801

2021
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Deep protein representations enable recombinant protein expression prediction

Martiny, Hannah-Marie ; Armenteros, Jose Juan Almagro ; Johansen, Alexander Rosenberg ; Salomon, Jesper ; Nielsen, Henrik
in: Computational Biology and Chemistry, vol: 95

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1016/j.compbiolchem.2021.107596

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IMLP, a predictor for internal matrix targeting-like sequences in mitochondrial proteins

Schneider, Kevin ; Zimmer, David ; Nielsen, Henrik ; Herrmann, Johannes M. ; Mühlhaus, Timo
in: Biological Chemistry, vol: 402, issue: 8, pages: 937-943

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1515/hsz-2021-0185

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Prediction of GPI-anchored proteins with pointer neural networks

Gíslason, Magnús Halldór ; Nielsen, Henrik ; Almagro Armenteros, Jose Juan ; Johansen, Alexander Rosenberg
in: Current Research in Biotechnology, vol: 3, pages: 6-13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1016/j.crbiot.2021.01.001

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Signal peptide prediction: from plain neural networks to language models

Nielsen, Henrik
Presented at:
Belgrade BioInformatics Conference 2021

Type: Conference abstract for conference

Status: Published     |    Year: 2021

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Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species

Marot-Lassauzaie, Valérie ; Goldberg, Tatyana ; Armenteros, Jose Juan Almagro ; Nielsen, Henrik ; Rost, Burkhard
in: Journal of Molecular Evolution, vol: 89, issue: 8, pages: 544-553

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1007/s00239-021-10022-4

2020
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Landscape of Eukaryotic Transmembrane Beta Barrel Proteins

Roumia, Ahmed F. ; Theodoropoulou, Margarita C. ; Tsirigos, Konstantinos D. ; Nielsen, Henrik ; Bagos, Pantelis G.
in: Journal of Proteome Research, vol: 19, issue: 3, pages: 1209-1221

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1021/acs.jproteome.9b00740

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Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children

Gallardo-Becerra, Luigui ; Cornejo-Granados, Fernanda ; García-López, Rodrigo ; Valdez-Lara, Alejandra ; Bikel, Shirley ; Canizales-Quinteros, Samuel ; López-Contreras, Blanca E. ; Mendoza-Vargas, Alfredo ; Nielsen, Henrik ; Ochoa-Leyva, Adrián
in: Microbial Cell Factories, vol: 19, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1186/s12934-020-01319-y

2019
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A Brief History of Protein Sorting Prediction

Nielsen, Henrik ; Tsirigos, Konstantinos D. ; Brunak, Søren ; von Heijne, Gunnar
in: Protein Journal, vol: 38, issue: 3, pages: 200-216

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s10930-019-09838-3

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Detecting sequence signals in targeting peptides using deep learning

Armenteros, Jose Juan Almagro ; Salvatore, Marco ; Emanuelsson, Olof ; Winther, Ole ; Von Heijne, Gunnar ; Elofsson, Arne ; Nielsen, Henrik
in: Life Science Alliance, vol: 2, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.26508/lsa.201900429