Idoia Ochoa

55 papers A* 1B 11Journal 39Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors.
J. Comput. Biol.
Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir
2026 J jnl
ReX: Causal discovery based on machine learning and explainability techniques.
Pattern Recognit.
Jesus Renero, Roberto Maestre, Idoia Ochoa
2025 J jnl
A Compact and Low-Cost Hybrid Reader for Chipless RFID Systems.
IEEE Trans. Instrum. Meas.
Pablo García-Cardarelli, Jafait Junior Fodop Sokoudjou, Paul Aramberri Araiz, Javier D. Diaz, Idoia Ochoa, Daniel Valderas, Ainhoa Rezola
2025 — conf
AI for Chipless RFID Tag Detection: Generalization and Deployability on Embedded Digital Signal Processors.
RFID-TA
Jafait Junior Fodop Sokoudjou, Pablo Garcia-Cardarelli, Ainhoa Rezola, E. Perret, Idoia Ochoa
2025 A* conf
Interpretable Causal Representation Learning for Biological Data in the Pathway Space.
ICLR
Jesus de la Fuente Cedeño, Robert Lehmann, Carlos Ruiz-Arenas, Jan Voges, Irene Marín-Goñi, Xabier Martinez de Morentin, David Gomez-Cabrero, Idoia Ochoa, Jesper Tegnér, Vincenzo Lagani, Mikel Hernaez
2025 J jnl
Interpretable Causal Representation Learning for Biological Data in the Pathway Space.
CoRR
Jesus de la Fuente, Robert Lehmann, Carlos Ruiz-Arenas, Jan Voges, Irene Marín-Goñi, Xabier Martinez de Morentin, David Gomez-Cabrero, Idoia Ochoa, Jesper Tegnér, Vincenzo Lagani, Mikel Hernaez
2025 B conf
Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors.
RECOMB
Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir
2025 J jnl
RAT-CC: A Recurrent Autoencoder for Time-Series Compression and Classification.
IEEE Access
Giacomo Chiarot, Sebastiano Vascon, Claudio Silvestri, Idoia Ochoa
2025 J jnl
REX: Causal Discovery based on Machine Learning and Explainability techniques.
CoRR
Jesus Renero, Idoia Ochoa, Roberto Maestre
2025 J jnl
Towards a more inductive world for drug repurposing approaches.
Nat. Mac. Intell.
Jesus de la Fuente Cedeño, Guillermo Serrano, Uxía Veleiro, Mikel Casals, Laura Vera, Marija Pizurica, Nuria Gómez-Cebrián, Leonor Puchades-Carrasco, Antonio Pineda-Lucena, Idoia Ochoa, Silve Vicent, Olivier Gevaert, Mikel Hernaez
2024 J jnl
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization.
Bioinform.
Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa
2024 J jnl
Ge N Nius : an ultrafast drug-target interaction inference method based on graph neural networks.
Bioinform.
Uxía Veleiro, Jesus de la Fuente, Guillermo Serrano, Marija Pizurica, Mikel Casals, Antonio Pineda-Lucena, Silve Vicent, Idoia Ochoa, Olivier Gevaert, Mikel Hernaez
2024 J jnl
gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python.
Bioinform.
Carlos J. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis Vitores Valcarcel, Francisco J. Planes
2023 J jnl
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.
PLoS Comput. Biol.
Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir
2023 J jnl
Towards a more inductive world for drug repurposing approaches.
CoRR
Jesus de la Fuente Cedeño, Guillermo Serrano, Uxía Veleiro, Mikel Casals, Laura Vera, Marija Pizurica, Antonio Pineda-Lucena, Idoia Ochoa, Silve Vicent, Olivier Gevaert, Mikel Hernaez
2022 J jnl
JIND: joint integration and discrimination for automated single-cell annotation.
Bioinform.
Mohit Goyal, Guillermo Serrano, Josepmaria Argemi, Ilan Shomorony, Mikel Hernaez, Idoia Ochoa
2022 J jnl
Unsupervised ensemble learning for genome sequencing.
Pattern Recognit.
Alba Pagès-Zamora, Idoia Ochoa, Gonzalo Ruiz Cavero, Pol Villalvilla-Ornat
2021 B conf
DZip: improved general-purpose loss less compression based on novel neural network modeling.
DCC
Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
2021 J jnl
RENANO: a REference-based compressor for NANOpore FASTQ files.
Bioinform.
Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo-Silveira, Idoia Ochoa, Álvaro Martín
2021 J jnl
mspack: efficient lossless and lossy mass spectrometry data compression.
Bioinform.
Felix Hanau, Hannes L. Röst, Idoia Ochoa
2020 J jnl
CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores.
J. Bioinform. Comput. Biol.
Albert No, Mikel Hernaez, Idoia Ochoa
2020 B conf
DZip: Improved General-Purpose Lossless Compression Based on Novel Neural Network Modeling.
DCC
Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
2020 J jnl
ENANO: Encoder for NANOpore FASTQ files.
Bioinform.
Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol
2020 J jnl
GABAC: an arithmetic coding solution for genomic data.
Bioinform.
Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
2020 J jnl
GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form.
Bioinform.
Qingxi Meng, Idoia Ochoa, Mikel Hernaez
2020 J jnl
VEF: a variant filtering tool based on ensemble methods.
Bioinform.
Chuanyi Zhang, Idoia Ochoa
2019 B conf
AliCo: A New Efficient Representation for SAM Files.
DCC
Idoia Ochoa, Hongyi Li, Florian Baumgarte, Charles Hergenrother, Jan Voges, Mikel Hernaez
2019 — conf
Compression of Nanopore FASTQ Files.
IWBBIO (1)
Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín
2019 J jnl
DZip: improved general-purpose lossless compression based on novel neural network modeling.
CoRR
Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
2019 B conf
DeepZip: Lossless Data Compression Using Recurrent Neural Networks.
DCC
Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
2019 J jnl
MassComp, a lossless compressor for mass spectrometry data.
BMC Bioinform.
Ruochen Yang, Xi Chen, Idoia Ochoa
2019 J jnl
SPRING: a next-generation compressor for FASTQ data.
Bioinform.
Shubham Chandak, Kedar Tatwawadi, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman
2018 J jnl
DeepZip: Lossless Data Compression using Recurrent Neural Networks.
CoRR
Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
2018 J jnl
FaStore: a space-saving solution for raw sequencing data.
Bioinform.
Lukasz Roguski, Idoia Ochoa, Mikel Hernaez, Sebastian Deorowicz
2018 J jnl
METHCOMP: a special purpose compression platform for DNA methylation data.
Bioinform.
Jianhao Peng, Olgica Milenkovic, Idoia Ochoa
2018 J jnl
QVZ: lossy compression of quality values.
Bioinform.
Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman
2017 J jnl
Effect of lossy compression of quality scores on variant calling.
Briefings Bioinform.
Idoia Ochoa, Mikel Hernaez, Rachel L. Goldfeder, Tsachy Weissman, Euan A. Ashley
2017 B conf
GeneComp, a New Reference-Based Compressor for SAM Files.
DCC
Reggy Long, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman
2016 B conf
A Cluster-Based Approach to Compression of Quality Scores.
DCC
Mikel Hernaez, Idoia Ochoa, Tsachy Weissman
2016 B conf
CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.
ITW
Idoia Ochoa, Albert No, Mikel Hernaez, Tsachy Weissman
2016 J jnl
Comment on: 'ERGC: an efficient referential genome compression algorithm'.
Bioinform.
Sebastian Deorowicz, Szymon Grabowski, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman
2016 B conf
Denoising of Quality Scores for Boosted Inference and Reduced Storage.
DCC
Idoia Ochoa, Mikel Hernaez, Rachel L. Goldfeder, Tsachy Weissman, Euan A. Ashley
2016 J jnl
GTRAC: fast retrieval from compressed collections of genomic variants.
Bioinform.
Kedar Tatwawadi, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman
2015 J jnl
QVZ: lossy compression of quality values.
Bioinform.
Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman
2015 J jnl
iDoComp: a compression scheme for assembled genomes.
Bioinform.
Idoia Ochoa, Mikel Hernaez, Tsachy Weissman
2014 J jnl
Aligned genomic data compression via improved modeling.
J. Bioinform. Comput. Biol.
Idoia Ochoa, Mikel Hernaez, Tsachy Weissman
2014 B conf
Compression Schemes for Similarity Queries.
DCC
Idoia Ochoa, Amir Ingber, Tsachy Weissman
2013 — conf
Efficient similarity queries via lossy compression.
Allerton
Idoia Ochoa, Amir Ingber, Tsachy Weissman
2013 J jnl
QualComp: a new lossy compressor for quality scores based on rate distortion theory.
BMC Bioinform.
Idoia Ochoa, Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Tsachy Weissman, Golan Yona
2012 J jnl
Lossy Compression of Quality Values via Rate Distortion Theory
CoRR
Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Idoia Ochoa, Itai Sharon, Tsachy Weissman
2012 J jnl
Reference Based Genome Compression
CoRR
Bobbie Chern, Idoia Ochoa, Alexandros Manolakos, Albert No, Kartik Venkat, Tsachy Weissman
2012 B conf
Reference based genome compression.
ITW
Bobbie Chern, Idoia Ochoa, Alexandros Manolakos, Albert No, Kartik Venkat, Tsachy Weissman
2010 — conf
Joint Turbo Coding and Source-Controlled Modulation of Cycle-Stationary Sources in the Bandwidth-Limited Regime.
MOBILIGHT
Idoia Ochoa, Pedro M. Crespo, Javier Del Ser, Mikel Hernaez
2010 J jnl
LDPC Codes for Non-Uniform Memoryless Sources and Unequal Energy Allocation.
IEEE Commun. Lett.
Idoia Ochoa, Pedro M. Crespo, Mikel Hernaez
2010 J jnl
Turbo joint source-channel coding of non-uniform memoryless sources in the bandwidth-limited regime.
IEEE Commun. Lett.
Idoia Ochoa, Pedro M. Crespo, Javier Del Ser, Mikel Hernaez