José Juan Almagro Armenteros
José Juan Almagro Armenteros
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SignalP 5.0 improves signal peptide predictions using deep neural networks
JJ Almagro Armenteros, KD Tsirigos, CK Sønderby, TN Petersen, ...
Nature biotechnology 37 (4), 420-423, 2019
DeepLoc: prediction of protein subcellular localization using deep learning
JJ Almagro Armenteros, CK Sønderby, SK Sønderby, H Nielsen, ...
Bioinformatics 33 (21), 3387-3395, 2017
Detecting sequence signals in targeting peptides using deep learning
JJA Armenteros, M Salvatore, O Emanuelsson, O Winther, G Von Heijne, ...
Life science alliance 2 (5), 2019
SignalP 6.0 predicts all five types of signal peptides using protein language models
F Teufel, JJ Almagro Armenteros, AR Johansen, MH Gíslason, SI Pihl, ...
Nature biotechnology 40 (7), 1023-1025, 2022
An introduction to deep learning on biological sequence data: examples and solutions
VI Jurtz, AR Johansen, M Nielsen, JJ Almagro Armenteros, H Nielsen, ...
Bioinformatics 33 (22), 3685-3690, 2017
Improved metagenome binning and assembly using deep variational autoencoders
JN Nissen, J Johansen, RL Allesøe, CK Sønderby, JJA Armenteros, ...
Nature biotechnology 39 (5), 555-560, 2021
DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks
J Hallgren, KD Tsirigos, MD Pedersen, JJ Almagro Armenteros, ...
BioRxiv, 2022.04. 08.487609, 2022
Modeling of waning immunity after SARS-CoV-2 vaccination and influencing factors
L Pérez-Alós, JJA Armenteros, JR Madsen, CB Hansen, I Jarlhelt, ...
Nature communications 13 (1), 1614, 2022
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
V Thumuluri, JJ Almagro Armenteros, AR Johansen, H Nielsen, O Winther
Nucleic acids research 50 (W1), W228-W234, 2022
Prediction of GPI-anchored proteins with pointer neural networks
MH Gíslason, H Nielsen, JJA Armenteros, AR Johansen
Current Research in Biotechnology 3, 6-13, 2021
Language modelling for biological sequences–curated datasets and baselines
JJ Almagro Armenteros, AR Johansen, O Winther, H Nielsen
BioRxiv, 2020.03. 09.983585, 2020
Decline in antibody concentration 6 months after two doses of SARS-CoV-2 BNT162b2 vaccine in solid organ transplant recipients and healthy controls
SR Hamm, DL Møller, L Pérez-Alós, CB Hansen, MM Pries-Heje, ...
Frontiers in immunology 13, 2022
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
KH Iversen, LH Rasmussen, K Al-Nakeeb, JJA Armenteros, CS Jensen, ...
Scientific Reports 10 (1), 2728, 2020
NetSolP: predicting protein solubility in Escherichia coli using language models
V Thumuluri, HM Martiny, JJ Almagro Armenteros, J Salomon, H Nielsen, ...
Bioinformatics 38 (4), 941-946, 2022
Deep protein representations enable recombinant protein expression prediction
HM Martiny, JJA Armenteros, AR Johansen, J Salomon, H Nielsen
Computational Biology and Chemistry 95, 107596, 2021
Antibody responses and risk factors associated with impaired immunological outcomes following two doses of BNT162b2 COVID-19 vaccination in patients with chronic pulmonary diseases
ZB Harboe, SR Hamm, L Pérez-Alós, P Sivapalan, H Priemé, T Wilcke, ...
BMJ Open Respiratory Research 9 (1), e001268, 2022
Spectrum of protein location in proteomes captures evolutionary relationship between species
V Marot-Lassauzaie, T Goldberg, JJA Armenteros, H Nielsen, B Rost
Journal of molecular evolution 89 (8), 544-553, 2021
Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning
JJ Almagro Armenteros, M Salvatore, O Emanuelsson, O Winther, ...
bioRxiv, 639203, 2019
Temporal patterns of multi-morbidity in 570157 ischemic heart disease patients: a nationwide cohort study
AD Haue, JJA Armenteros, PC Holm, R Eriksson, PL Moseley, LV Køber, ...
Cardiovascular Diabetology 21 (1), 87, 2022
Waning humoral and cellular immunity after COVID-19 vaccination in patients with psoriasis treated with methotrexate and biologics: a cohort study
A Kvist-Hansen, L Pérez-Alós, RF Al-Sofi, LD Heftdal, SR Hamm, ...
British Journal of Dermatology, ljad023, 2023
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