Relevant publications by topic

• (*): Corresponding author

• (†): (Co-)First Author

Pre Prints

• Sweetwater: An interpretable and adaptive autoencoder for efficient tissue deconvolution
  J. de la Fuente†, N. Legarra†, G. Serrano, I. Marin-Goni, A. Diaz-Mazkiaran, M. Benito, A. Garcia-Osta, K. R Kalari, C. Fernandez-Granda, I. Ochoa*, M. Hernaez*
  arXiv, 2024

• Towards a more inductive world for drug repurposing approaches
  J. de la Fuente†, G. Serrano†, U. Veleiro†, M. Casals, L. Vera, M. Pizurica, N. Gómez-Cebrián, L. Puchades-Carrasco, A. Pineda-Lucena, I. Ochoa, S. Vicent, O. Gevaert*, M. Hernaez*
  arXiv, 2024

Novel insights into the (patho)physiology of diseases via Machine Learning

• 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

• 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
  

• Optimization of a universal allogeneic CAR-T cells combining CRISPR and transposon-based technologies for treatment of Acute Myeloid Leukemia
  C. Calviño†, C. Ceballos†, A. Alfonso†, P. Jauregui, […], M. Hernaez*, F. Prosper*, J. R. Rodriguez-Madoz*
  Frontiers in Immunology, 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)
  

• Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
  U. V. Chembazhi, S. Bangru, M. Hernaez, A. Kalsotra
  Genome Research, 2021

• Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples
  H. Zheng, K. Brennan, M. Hernaez, O. Gevaert
  GigaScience, 2019
  

(Graph) Representation Learning in biomedicine

• 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
  

• 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
  

• Comparison of single gene and module-based methods for modeling gene regulatory networks
  M. Hernaez*, C. Blatti, O. Gevaert*
  Bioinformatics, 2020
  

Genomic information representation

• 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
  

• GABAC: an arithmetic coding solution for genomic data
  J. Voges, T. Paridaens, F. Müntefering, L. S. Mainzer, B. Bliss, M. Yang, I. Ochoa, J. Fostier, J. Ostermann*, M. Hernaez*
  Bioinformatics, 2020
  

• GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form
  Q. Meng, I. Ochoa, M. Hernaez**
  Bioinformatics, 2020
  

• GABAC: an arithmetic coding solution for genomic data
  J. Voges, T. Paridaens, F. Müntefering, L. S. Mainzer, B. Bliss, M. Yang, I. Ochoa, J. Fostier, J. Ostermann, M. Hernaez*
  Bioinformatics, 2020
  

• Genomic data compression
  M. Hernaez*, D. Pavlichin, T. Weissman, I. Ochoa*
  Annual Review of Biomedical Data Science, 2019
  

• Denoising of Aligned Genomic Data
  I. fischer-Hwang, I. Ochoa, T. Weissman, M. Hernaez*
  Scientific Reports, 2019
  

• AliCo: a new efficient representation for SAM files
  I. Ochoa, H. Li, F. Baumgarte, C. Hergenrother, J. Voges and M. Hernaez* Data Compression Conference (DCC), 2019
  

• SPRING: A next-generation compressor for FASTQ data
  S. Chandak, K. Tatwawadi, I. Ochoa, M. Hernaez* and T. Weissman Bioinformatics, 2018
  

• CALQ: compression of quality values of aligned sequencing data
  J. Voges, J. Ostermann and M. Hernaez*
  Bioinformatics, 2017
  

• GeneComp, a new reference-based compressor for SAM files
  R. Long, M. Hernaez*, I. Ochoa and T. Weissman
  Data Compression Conference (DCC), 2017
  

• Effect of lossy compression of quality scores on variant calling
  I. Ochoa, M. Hernaez*, R. Goldfeder, T. Weissman and E. Ashley
  Briefings in Bioinformatics, 2016
  

• Denoising of Quality Scores for Boosted Inference and Reduced Storage
  I. Ochoa, M. Hernaez*, R. Goldfeder, T. Weissman and E. Ashley
  Data Compression Conference (DCC), 2016
  

• A cluster-based approach to compression of Quality Scores
  M. Hernaez , I. Ochoa and T. Weissman
  Data Compression Conference (DCC), 2016
  

• A An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values
  C. Alberti, N. Daniels, M. Hernaez*, J. Voges, R. L. Goldfeder, A. A. Hernandez-Lopez, M. Mattavelli, B. Berger
  Data Compression Conference (DCC), 2016
  

• QVZ: lossy compression of quality values
  G. Malysa, M. Hernaez*, I. Ochoa, M. Rao, K. Ganesan and T. Weissman
  Bioinformatics, 2015
  

• iDoComp: a compression scheme for assembled genomes
  I. Ochoa, M. Hernaez* and T. Weissman
  Bioinformatics, 2014
  

• Aligned genomic data compression via improved modeling
  I. Ochoa, M. Hernaez(#,$) and T. Weissman
  Journal of bioinformatics and computational biology, 2014 (presented at the GIW ISCB-Asia, 2014)
  

Network Information Theory (PhD Thesis)

• On the Design of a Novel Joint Network-Channel Coding Scheme for the Multiple Access Relay Channel
  M. Hernaez, P. M. Crespo and J. Del Ser
  IEEE Journal on Selected Areas in Communications, 2013
  

• A Decode-and-Forward Scheme for Multihop Wireless Networks
  M. Hernaez, P. M. Crespo and J. Del Ser
  IEEE 78rd Vehicular Technology Conference (VTC Spring), 2013
  

• A Flexible Channel Coding Approach for Short-Length Codewords
  M. Hernaez, P. M. Crespo and J. Del Ser
  IEEE Communications Letters, 2012
  

• A Novel Scheme for Message-Forwarding in Multi-Hop Ad-Hoc Wireless Networks
  M. Hernaez and P. M. Crespo
  IEEE 73rd Vehicular Technology Conference (VTC Spring), 2011
  

• Joint Non-Binary LDPC-BICM and Network Coding with Iterative Decoding for the Multiple Access Relay Channel
  M. Hernaez, P. M. Crespo and J. Del Ser
  IEEE 73rd Vehicular Technology Conference (VTC Spring), 2011
  

• Serially-Concatenated LDGM Codes for Correlated Sources over Gaussian Broadcast Channels
  M. Hernaez, P. M. Crespo, J. Del Ser and J. Garcia-Frias
  IEEE Communications Letters, 2009
  

PhD Thesis

• Joint Network-Channel Coding Schemes for Relay Networks