I am currently a postdoc in Søren Brunak's group at the Center for Protein Research, University of Copenhagen. I have a PhD from the Technical University of Denmark under the supervision of associate professor Henrik Nielsen and professor Ole Winther. I got my M.Sc. from the University of Copenhagen supervised by professor Anders Krogh. I am interested in Protein Function Prediction, Deep Learning, Multi-omics Integration and patient disease trajectories.

jose.armenteros@cpr.ku.dk Google Scholar Profile GitHub LinkedIn


Prediction of GPI-anchored proteins with pointer neural networks
M.H. Gislason, H. Nielsen, J.J.A. Armenteros*, A.R. Johansen* (*equal contribution)
Current Research in Biotechnology, 2021
PDF Abstract Bibtex Website

Improved metagenome binning and assembly using deep variational autoencoders
J.N. Nissen, J.Johansen, R.L. Allesøe, C.K Sønderby, J.J.A. Armenteros, C.H. Grønbech, L.J. Jensen, H.B. Nielsen, T.N. Petersen, O. Winther, S. Rasmussen
Nature Biotechnology, 2021
Abstract Bibtex Code

Language modelling for biological sequences curated datasets and baselines
J.J.A. Armenteros*, A.R. Johansen*, O. Winther, H. Nielsen (*equal contribution)
Preprint and website, 2019
PDF Abstract Bibtex Website

Detecting sequence signals in targeting peptides using deep learning
J.J.A. Armenteros*, M. Salvatore*, O. Emanuelsson, O. Winther, G.v. Heijne, A. Elofsson, H. Nielsen (*equal contribution)
Life Science Alliance, 2019
Abstract Bibtex Code Website

SignalP 5.0 improves signal peptide predictions using deep neural networks
J.J.A. Armenteros*, K.D. Tsirigos*, C.K. Sønderby, T.N. Petersen, O. Winther, S. Brunak, G.v. Heijne, H. Nielsen (*equal contribution)
Nature Biotechnology, 2019
Abstract Bibtex Website

An introduction to deep learning on biological sequence data - examples and solutions
V.I. Jurtz, A.R. Johansen, M. Nielsen, J.J.A. Armenteros, H. Nielsen, C.K. Sønderby, O. Winther, S.K. Sønderby
Oxford Bioinformatics, 2017
Abstract Bibtex Code

DeepLoc prediction of protein subcellular localization using deep learning
J.J.A. Armenteros, C.K. Sønderby, S.K. Sønderby, O. Winther, H. Nielsen
Oxford Bionformatics, 2017
Abstract Bibtex Code Website


Below you can find a list over courses I have taught in.

Deep learning
Technical University of Denmark
Final projects supervision and course evaluation
Fall - 2017, 2018 and 2019
Code Website

Bioinformatics and Systems Biology
University of the Chinese Academy of Sciences
Instructor of Introduction to Machine Learning and course evaluation
June - 2018 and 2019

Python and Unix for Bioinformaticians
Technical University of Denmark
Co-intructor and course evaluation
Spring - 2017 and 2018

Next-Generation-Sequencing Analysis
Technical University of Denmark
Co-intructor and course evaluation
June, 2017


Protein language models for signal peptide prediction
Master Thesis, 30 ECTS. Master Thesis,
Autumn, 2020

Multi-label prediction of protein subcellular localization using deep learning
Master Thesis, 30 ECTS. Master Thesis,
Autumn, 2019

Generalized autoregressive pretraining for improved understanding of proteins
Master Thesis, 30 ECTS. Autumn, 2019

Partially autoregressive language modelling and editing of discrete sequences' thesis
Master Thesis, 32.5 ECTS. Autumn, 2019

Prediction of sorting signals in eukaryotic proteins using deep learning
Master Thesis, 35 ECTS. Autumn, 2019

Evaluation of contextual amino acid representations on the prediction of N-terminal targeting peptides based on deep learning
Master Thesis, 30 ECTS. Autumn, 2019

Predicting Recombinant Gene Expression in Bacillus using Deep Learning Techniques
Master Thesis, 35 ECTS. Spring, 2019

Evaluation of Pre-trained Amino Acid Embeddings in Protein Prediction Tasks
Master Thesis, 32.5 ECTS. Spring, 2019

Generative deep learning for codon optimization
Master Thesis, 30 ECTS. Spring, 2019

Prediction of protein sorting in the phylum Apicomplexa
Bachelor Thesis, 20 ECTS. Spring, 2019

Convolutional neural networks for unsupervised learning of patterns in DNA sequences
Bachelor Thesis, 15 ECTS. Spring, 2019

Exploring the biological relevance of the attention function in DeepLoc
Bachelor Thesis, 20 ECTS. Spring, 2018