Mikel Hernaez - Machine Learning for BioMedicine (ML4BM) group

Principal Investigator, Machine Learning for Biomedicine (ML4BM) Group Director, Computational Biology Program CIMA University of Navarra, Spain Adjunct Professor, Department of Physics and Applied Mathematics Adjunct Professor (by courtesy), Department of Biochemistry and genetics University of Navarra, Spain Our group focuses on developing and applying machine learning models, with an emphasis on (graph) representation learning, to solve open biomedical questions in the context of advance lethal diseases. We aim at taking deep learning models to the clinical practice to accelerate the path towards personalize medicine.

Recent Publications

• Uncovering functional lncRNAs by scRNA-seq with ELATUS
  E. Goñi , A. M. Mas , J. Gonzalez, […] , Maite Huarte*, M. Hernaez*
  Nature Communications, 2024

• Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) Myelodysplastic Syndromes and impact of lenalidomide
  G. Serrano, N. Berastegi, A. Diaz-Mazkiaran, […], F. Prosper*, T. Ezponda*, M. Hernaez*
  Nature Communications, 2024

• NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders
  C. Ruiz-Arenas, I. Marin, L. Wang, I. Ochoa, J.L. Perez-Jurado*, M. Hernaez*
  Nucleic Acids Research, 2024

• GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks
  U. Veleiro, J. De la Fuente, G. Serrano, […], I. Ochoa, G. Gevaert*, M. Hernaez*
  Bioinformatics, 2024
  

• Identification of transcriptional network disruptions in drug-resistant metastatic prostate cancer with TraRe
  C. Blatti, J. de la Fuente, H. Gao, I. Marin, Z. Chen, S. D. Zhao, W. Tan, R. Weinshilbaum, K. R. Kalari, L. Wang*, M. Hernaez*
  Cancer Research, 2023
  

• CAR Density Influences Antitumoral Efficacy of BCMA CAR T cells and Correlates with Clinical Outcome
  P. Rodriguez-Marquez, M. E. Calleja-Cervantes, G. Serrano, […], M. Hernaez*, J. R. Rodriguez-Madoz*, F. Prosper*
  Science Advances, 2022 (Oral Presentation at ASH 2022)
  

• JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation
  M. Goyal, G. Serrano, J. Argemi, I. Shomorony, M. Hernaez*, I. Ochoa*
  Bioinformatics, 2022
  

• SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes
  J. Peng, G. Serrano, I. M. Traniello, M. E. Calleja-Cervantes, […], I. Ochoa*, M. Hernaez*
  Communications Biology, 2022
  

• An introduction to MPEG-G: The first open ISO/IEC standard for the compression and exchange of genomic sequencing data
  J. Voges, M. Hernaez, M. Mattavelli, J. Ostermann
  Proceedings of the IEEE, 2021
  

• Towards scalable genomic data access
  M. Hernaez
  Nature Computational Science, 2021