Joint Turbo Coding and Source-Controlled Modulation of Cycle-Stationary Sources in the Bandwidth-Limited Regime. - Idoia Ochoa; Pedro M. Crespo; Javier Del Ser; Mikel Hernaez (MOBILIGHT, 2010)

LDPC Codes for Non-Uniform Memoryless Sources and Unequal Energy Allocation. - Idoia Ochoa; Pedro M. Crespo; Mikel Hernaez (IEEE Commun. Lett., 2010)

Turbo joint source-channel coding of non-uniform memoryless sources in the bandwidth-limited regime. - Idoia Ochoa; Pedro M. Crespo; Javier Del Ser; Mikel Hernaez (IEEE Commun. Lett., 2010)

Reference based genome compression. - Bobbie Chern; Idoia Ochoa; Alexandros Manolakos; Albert No; Kartik Venkat; Tsachy Weissman (ITW, 2012)

Lossy Compression of Quality Values via Rate Distortion Theory - Himanshu Asnani; Dinesh Bharadia; Mainak Chowdhury; Idoia Ochoa; Itai Sharon; Tsachy Weissman (CoRR, 2012)

Efficient similarity queries via lossy compression. - Idoia Ochoa; Amir Ingber; Tsachy Weissman (Allerton, 2013)

QualComp: a new lossy compressor for quality scores based on rate distortion theory. - Idoia Ochoa; Himanshu Asnani; Dinesh Bharadia; Mainak Chowdhury; Tsachy Weissman; Golan Yona (BMC Bioinform., 2013)

Compression Schemes for Similarity Queries. - Idoia Ochoa; Amir Ingber; Tsachy Weissman (DCC, 2014)

Aligned genomic data compression via improved modeling. - Idoia Ochoa; Mikel Hernaez; Tsachy Weissman (J. Bioinform. Comput. Biol., 2014)

iDoComp: a compression scheme for assembled genomes. - Idoia Ochoa; Mikel Hernaez; Tsachy Weissman (Bioinform., 2015)

A Cluster-Based Approach to Compression of Quality Scores. - Mikel Hernaez; Idoia Ochoa; Tsachy Weissman (DCC, 2016)

Denoising of Quality Scores for Boosted Inference and Reduced Storage. - Idoia Ochoa; Mikel Hernaez; Rachel L. Goldfeder; Tsachy Weissman; Euan A. Ashley (DCC, 2016)

CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores. - Idoia Ochoa; Albert No; Mikel Hernaez; Tsachy Weissman (ITW, 2016)

Comment on: 'ERGC: an efficient referential genome compression algorithm'. - Sebastian Deorowicz; Szymon Grabowski; Idoia Ochoa; Mikel Hernaez; Tsachy Weissman (Bioinform., 2016)

GTRAC: fast retrieval from compressed collections of genomic variants. - Kedar Tatwawadi; Mikel Hernaez; Idoia Ochoa; Tsachy Weissman (Bioinform., 2016)

GeneComp, a New Reference-Based Compressor for SAM Files. - Reggy Long; Mikel Hernaez; Idoia Ochoa; Tsachy Weissman (DCC, 2017)

Effect of lossy compression of quality scores on variant calling. - Idoia Ochoa; Mikel Hernaez; Rachel L. Goldfeder; Tsachy Weissman; Euan A. Ashley (Briefings Bioinform., 2017)

QVZ: lossy compression of quality values. - Greg Malysa; Mikel Hernaez; Idoia Ochoa; Milind Rao; Karthik Ganesan 001; Tsachy Weissman (Bioinform., 2018)

METHCOMP: a special purpose compression platform for DNA methylation data. - Jianhao Peng; Olgica Milenkovic; Idoia Ochoa (Bioinform., 2018)

FaStore: a space-saving solution for raw sequencing data. - Lukasz Roguski; Idoia Ochoa; Mikel Hernaez; Sebastian Deorowicz (Bioinform., 2018)

DeepZip: Lossless Data Compression Using Recurrent Neural Networks. - Mohit Goyal; Kedar Tatwawadi; Shubham Chandak; Idoia Ochoa (DCC, 2019)

AliCo: A New Efficient Representation for SAM Files. - Idoia Ochoa; Hongyi Li; Florian Baumgarte; Charles Hergenrother; Jan Voges; Mikel Hernaez (DCC, 2019)

Compression of Nanopore FASTQ Files. - Guillermo Dufort y Álvarez; Gadiel Seroussi; Pablo Smircich; José Sotelo; Idoia Ochoa; Álvaro Martín (IWBBIO (1), 2019)

SPRING: a next-generation compressor for FASTQ data. - Shubham Chandak; Kedar Tatwawadi; Idoia Ochoa; Mikel Hernaez; Tsachy Weissman (Bioinform., 2019)

MassComp, a lossless compressor for mass spectrometry data. - Ruochen Yang; Xi Chen 076; Idoia Ochoa (BMC Bioinform., 2019)

DZip: Improved General-Purpose Lossless Compression Based on Novel Neural Network Modeling. - Mohit Goyal; Kedar Tatwawadi; Shubham Chandak; Idoia Ochoa (DCC, 2020)

ENANO: Encoder for NANOpore FASTQ files. - Guillermo Dufort y Álvarez; Gadiel Seroussi; Pablo Smircich; José Sotelo; Idoia Ochoa; Álvaro Martín; Inanç Birol (Bioinform., 2020)

GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form. - Qingxi Meng; Idoia Ochoa; Mikel Hernaez (Bioinform., 2020)

GABAC: an arithmetic coding solution for genomic data. - Jan Voges; Tom Paridaens; Fabian Müntefering; Liudmila S. Mainzer; Brian Bliss; Mingyu Yang; Idoia Ochoa; Jan Fostier; Jörn Ostermann; Mikel Hernaez (Bioinform., 2020)

VEF: a variant filtering tool based on ensemble methods. - Chuanyi Zhang; Idoia Ochoa (Bioinform., 2020)

CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores. - Albert No; Mikel Hernaez; Idoia Ochoa (J. Bioinform. Comput. Biol., 2020)

DZip: improved general-purpose loss less compression based on novel neural network modeling. - Mohit Goyal; Kedar Tatwawadi; Shubham Chandak; Idoia Ochoa (DCC, 2021)

RENANO: a REference-based compressor for NANOpore FASTQ files. - Guillermo Dufort y Álvarez; Gadiel Seroussi; Pablo Smircich; José Sotelo-Silveira; Idoia Ochoa; Álvaro Martín (Bioinform., 2021)

mspack: efficient lossless and lossy mass spectrometry data compression. - Felix Hanau; Hannes L. Röst; Idoia Ochoa (Bioinform., 2021)

JIND: joint integration and discrimination for automated single-cell annotation. - Mohit Goyal; Guillermo Serrano; Josepmaria Argemi; Ilan Shomorony; Mikel Hernaez; Idoia Ochoa (Bioinform., 2022)

Unsupervised ensemble learning for genome sequencing. - Alba Pagès-Zamora; Idoia Ochoa; Gonzalo Ruiz Cavero; Pol Villalvilla-Ornat (Pattern Recognit., 2022)

Towards a more inductive world for drug repurposing approaches. - 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 (CoRR, 2023)

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. - Leah L. Weber; Chuanyi Zhang; Idoia Ochoa; Mohammed El-Kebir (PLoS Comput. Biol., 2023)

EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization. - Guillermo Dufort y Álvarez; Martí Xargay-Ferrer; Alba Pagès-Zamora; Idoia Ochoa (Bioinform., 2024)

Interpretable Causal Representation Learning for Biological Data in the Pathway Space. - Jesus de la Fuente Cedeño; Robert Lehmann 002; Carlos Ruiz-Arenas; Jan Voges; Irene Marín-Goñi; Xabier Martinez de Morentin; David Gomez-Cabrero; Idoia Ochoa; Jesper Tegnér; Vincenzo Lagani; Mikel Hernaez (ICLR, 2025)

Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. - Leah L. Weber; Anna Hart; Idoia Ochoa; Mohammed El-Kebir (RECOMB, 2025)

RAT-CC: A Recurrent Autoencoder for Time-Series Compression and Classification. - Giacomo Chiarot; Sebastiano Vascon; Claudio Silvestri; Idoia Ochoa (IEEE Access, 2025)

Towards a more inductive world for drug repurposing approaches. - 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; et al. (Nat. Mac. Intell., 2025)

REX: Causal Discovery based on Machine Learning and Explainability techniques. - Jesus Renero; Idoia Ochoa; Roberto Maestre (CoRR, 2025)