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2020 – today

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2024
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Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa:
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization. Bioinform. 40(3) (2024)
2023
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Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir:
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. PLoS Comput. Biol. 19(10) (2023)
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Jesus de la Fuente, Guillermo Serrano, Uxía Veleiro, Mikel Casals, Laura Vera, Marija Pizurica, Antonio Pineda-Lucena, Idoia Ochoa, Silve Vicent, Olivier Gevaert, Mikel Hernaez:
Towards a more inductive world for drug repurposing approaches. CoRR abs/2311.12670 (2023)
2022
[j22]
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Alba Pagès-Zamora, Idoia Ochoa, Gonzalo Ruiz Cavero, Pol Villalvilla-Ornat:
Unsupervised ensemble learning for genome sequencing. Pattern Recognit. 129: 108721 (2022)
2021
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Felix Hanau, Hannes L. Röst, Idoia Ochoa:
mspack: efficient lossless and lossy mass spectrometry data compression. Bioinform. 37(21): 3923-3925 (2021)
[j20]
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Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo-Silveira, Idoia Ochoa, Álvaro Martín:
RENANO: a REference-based compressor for NANOpore FASTQ files. Bioinform. 37(24): 4862-4864 (2021)
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Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa:
DZip: improved general-purpose loss less compression based on novel neural network modeling. DCC 2021: 153-162
2020
[j19]
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Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez:
GABAC: an arithmetic coding solution for genomic data. Bioinform. 36(7): 2275-2277 (2020)
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Chuanyi Zhang, Idoia Ochoa:
VEF: a variant filtering tool based on ensemble methods. Bioinform. 36(8): 2328-2336 (2020)
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Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol:
ENANO: Encoder for NANOpore FASTQ files. Bioinform. 36(16): 4506-4507 (2020)
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Qingxi Meng, Idoia Ochoa, Mikel Hernaez:
GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form. Bioinform. 36(18): 4810-4812 (2020)
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Albert No, Mikel Hernaez, Idoia Ochoa:
CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores. J. Bioinform. Comput. Biol. 18(6): 2050031:1-2050031:22 (2020)
[c12]
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Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa:
DZip: Improved General-Purpose Lossless Compression Based on Novel Neural Network Modeling. DCC 2020: 372

2010 – 2019

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2019
[j14]
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Shubham Chandak, Kedar Tatwawadi, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
SPRING: a next-generation compressor for FASTQ data. Bioinform. 35(15): 2674-2676 (2019)
[j13]
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Ruochen Yang, Xi Chen, Idoia Ochoa:
MassComp, a lossless compressor for mass spectrometry data. BMC Bioinform. 20(1): 368:1-368:10 (2019)
[c11]
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Idoia Ochoa, Hongyi Li, Florian Baumgarte, Charles Hergenrother, Jan Voges, Mikel Hernaez:
AliCo: A New Efficient Representation for SAM Files. DCC 2019: 93-102
[c10]
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Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa:
DeepZip: Lossless Data Compression Using Recurrent Neural Networks. DCC 2019: 575
[c9]
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Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín:
Compression of Nanopore FASTQ Files. IWBBIO (1) 2019: 36-47
[i4]
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Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa:
DZip: improved general-purpose lossless compression based on novel neural network modeling. CoRR abs/1911.03572 (2019)
2018
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Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman:
QVZ: lossy compression of quality values. Bioinform. 34(1): 179 (2018)
[j11]
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Jianhao Peng, Olgica Milenkovic, Idoia Ochoa:
METHCOMP: a special purpose compression platform for DNA methylation data. Bioinform. 34(15): 2654-2656 (2018)
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Lukasz Roguski, Idoia Ochoa, Mikel Hernaez, Sebastian Deorowicz:
FaStore: a space-saving solution for raw sequencing data. Bioinform. 34(16): 2748-2756 (2018)
[i3]
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Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa:
DeepZip: Lossless Data Compression using Recurrent Neural Networks. CoRR abs/1811.08162 (2018)
2017
[j9]
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Idoia Ochoa, Mikel Hernaez, Rachel L. Goldfeder, Tsachy Weissman, Euan A. Ashley:
Effect of lossy compression of quality scores on variant calling. Briefings Bioinform. 18(2): 183-194 (2017)
[c8]
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Reggy Long, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman:
GeneComp, a New Reference-Based Compressor for SAM Files. DCC 2017: 330-339
2016
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Sebastian Deorowicz, Szymon Grabowski, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
Comment on: 'ERGC: an efficient referential genome compression algorithm'. Bioinform. 32(7): 1115-1117 (2016)
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Kedar Tatwawadi, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman:
GTRAC: fast retrieval from compressed collections of genomic variants. Bioinform. 32(17): 479-486 (2016)
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Idoia Ochoa, Mikel Hernaez, Rachel L. Goldfeder, Tsachy Weissman, Euan A. Ashley:
Denoising of Quality Scores for Boosted Inference and Reduced Storage. DCC 2016: 251-260
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Mikel Hernaez, Idoia Ochoa, Tsachy Weissman:
A Cluster-Based Approach to Compression of Quality Scores. DCC 2016: 261-270
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Idoia Ochoa, Albert No, Mikel Hernaez, Tsachy Weissman:
CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores. ITW 2016: 121-125
2015
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Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
iDoComp: a compression scheme for assembled genomes. Bioinform. 31(5): 626-633 (2015)
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Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman:
QVZ: lossy compression of quality values. Bioinform. 31(19): 3122-3129 (2015)
2014
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Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
Aligned genomic data compression via improved modeling. J. Bioinform. Comput. Biol. 12(6) (2014)
[c4]
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Idoia Ochoa, Amir Ingber, Tsachy Weissman:
Compression Schemes for Similarity Queries. DCC 2014: 332-341
2013
[j3]
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Idoia Ochoa, Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Tsachy Weissman, Golan Yona:
QualComp: a new lossy compressor for quality scores based on rate distortion theory. BMC Bioinform. 14: 187 (2013)
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Idoia Ochoa, Amir Ingber, Tsachy Weissman:
Efficient similarity queries via lossy compression. Allerton 2013: 883-889
2012
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Bobbie Chern, Idoia Ochoa, Alexandros Manolakos, Albert No, Kartik Venkat, Tsachy Weissman:
Reference based genome compression. ITW 2012: 427-431
[i2]
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Bobbie Chern, Idoia Ochoa, Alexandros Manolakos, Albert No, Kartik Venkat, Tsachy Weissman:
Reference Based Genome Compression. CoRR abs/1204.1912 (2012)
[i1]
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  - journals/corr/abs-1207-5184
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Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Idoia Ochoa, Itai Sharon, Tsachy Weissman:
Lossy Compression of Quality Values via Rate Distortion Theory. CoRR abs/1207.5184 (2012)
2010
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Idoia Ochoa, Pedro M. Crespo, Javier Del Ser, Mikel Hernaez:
Turbo joint source-channel coding of non-uniform memoryless sources in the bandwidth-limited regime. IEEE Commun. Lett. 14(4): 336-338 (2010)
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Idoia Ochoa, Pedro M. Crespo, Mikel Hernaez:
LDPC Codes for Non-Uniform Memoryless Sources and Unequal Energy Allocation. IEEE Commun. Lett. 14(9): 794-796 (2010)
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Idoia Ochoa, Pedro M. Crespo, Javier Del Ser, Mikel Hernaez:
Joint Turbo Coding and Source-Controlled Modulation of Cycle-Stationary Sources in the Bandwidth-Limited Regime. MOBILIGHT 2010: 618-625

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