Idoia Ochoa-Alvarez

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Research Output

2020

DZip: Improved general-purpose lossless compression based on novel neural network modeling

Goyal, M., Tatwawadi, K., Chandak, S. & Ochoa, I., Mar 2020, Proceedings - DCC 2020: Data Compression Conference. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., 1 p. 9105846. (Data Compression Conference Proceedings; vol. 2020-March).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

GABAC: An arithmetic coding solution for genomic data

Voges, J., Paridaens, T., Müntefering, F., Mainzer, L. S., Bliss, B., Yang, M., Ochoa, I., Fostier, J., Ostermann, J., Hernaez, M. & Hancock, J., Apr 1 2020, In : Bioinformatics. 36, 7, p. 2275-2277 3 p.

Research output: Contribution to journalArticle

Open Access

VEF: A variant filtering tool based on ensemble methods

Zhang, C. & Ochoa, I., Apr 15 2020, In : Bioinformatics. 36, 8, p. 2328-2336 9 p.

Research output: Contribution to journalArticle

2019

AliCo: A New Efficient Representation for SAM Files

Ochoa, I., Li, H., Baumgarte, F., Hergenrother, C., Voges, J. & Hernaez, M., May 10 2019, Proceedings - DCC 2019: 2019 Data Compression Conference. Storer, J. A., Bilgin, A., Serra-Sagrista, J. & Marcellin, M. W. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 93-102 10 p. 8712770. (Data Compression Conference Proceedings; vol. 2019-March).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Compression of Nanopore FASTQ Files

Dufort y Álvarez, G., Seroussi, G., Smircich, P., Sotelo, J., Ochoa, I. & Martín, Á., Jan 1 2019, Bioinformatics and Biomedical Engineering - 7th International Work-Conference, IWBBIO 2019, Proceedings. Ortuño, F., Rojas, I., Rojas, F., Valenzuela, O. & Ortuño, F. (eds.). Springer-Verlag Berlin Heidelberg, p. 36-47 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11465 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

DeepZip: Lossless Data Compression Using Recurrent Neural Networks

Goyal, M., Tatwawadi, K., Chandak, S. & Ochoa, I., May 10 2019, Proceedings - DCC 2019: 2019 Data Compression Conference. Bilgin, A., Storer, J. A., Marcellin, M. W. & Serra-Sagrista, J. (eds.). Institute of Electrical and Electronics Engineers Inc., 1 p. 8712659. (Data Compression Conference Proceedings; vol. 2019-March).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Denoising of Aligned Genomic Data

Fischer-Hwang, I., Ochoa, I., Weissman, T. & Hernaez, M., Dec 1 2019, In : Scientific reports. 9, 1, 15067.

Research output: Contribution to journalArticle

Open Access

MassComp, a lossless compressor for mass spectrometry data

Yang, R., Chen, X. & Ochoa, I., Jul 1 2019, In : BMC bioinformatics. 20, 1, 368.

Research output: Contribution to journalArticle

Open Access

SPRING: A next-generation compressor for FASTQ data

Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M. & Weissman, T., Aug 1 2019, In : Bioinformatics. 35, 15, p. 2674-2676 3 p., bty1015.

Research output: Contribution to journalArticle

Open Access
2018

FaStore: A space-saving solution for raw sequencing data

Roguski, L., Ochoa, I., Hernaez, M. & Deorowicz, S., Jan 1 2018, In : Bioinformatics. 34, 16, p. 2748-2756 9 p.

Research output: Contribution to journalArticle

METHCOMP: A special purpose compression platform for DNA methylation data

Peng, J., Milenkovic, O. & Ochoa, I., Jan 1 2018, In : Bioinformatics. 34, 15, p. 2654-2656 3 p.

Research output: Contribution to journalArticle

2017

Effect of lossy compression of quality scores on variant calling

Ochoa, I., Hernaez, M., Goldfeder, R., Weissman, T. & Ashley, E., Jan 1 2017, In : Briefings in bioinformatics. 18, 2, p. 183-194 12 p.

Research output: Contribution to journalArticle

GeneComp, a New Reference-Based Compressor for SAM Files

Long, R., Hernaez, M., Ochoa, I. & Weissman, T., May 8 2017, Proceedings - DCC 2017, 2017 Data Compression Conference. Bilgin, A., Serra-Sagrista, J., Marcellin, M. W. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 330-339 10 p. 7923646. (Data Compression Conference Proceedings; vol. Part F127767).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2016

A Cluster-Based Approach to Compression of Quality Scores

Hernaez, M., Ochoa, I. & Weissman, T., Dec 15 2016, Proceedings - DCC 2016: 2016 Data Compression Conference. Marcellin, M. W., Bilgin, A., Serra-Sagrista, J. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 261-270 10 p. 7786170. (Data Compression Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Comment on: 'ERGC: an efficient referential genome compression algorithm'

Deorowicz, S., Grabowski, S., Ochoa, I., Hernaez, M. & Weissman, T., Apr 1 2016, In : Bioinformatics. 32, 7, p. 1115-1117 3 p.

Research output: Contribution to journalArticle

CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores

Ochoa, I., No, A., Hernaez, M. & Weissman, T., Oct 21 2016, 2016 IEEE Information Theory Workshop, ITW 2016. Institute of Electrical and Electronics Engineers Inc., p. 121-125 5 p. 7606808. (2016 IEEE Information Theory Workshop, ITW 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Denoising of Quality Scores for Boosted Inference and Reduced Storage

Ochoa, I., Hernaez, M., Goldfeder, R., Weissman, T. & Ashley, E., Dec 15 2016, Proceedings - DCC 2016: 2016 Data Compression Conference. Marcellin, M. W., Bilgin, A., Serra-Sagrista, J. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 251-260 10 p. 7786169. (Data Compression Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

GTRAC: Fast retrieval from compressed collections of genomic variants

Tatwawadi, K., Hernaez, M., Ochoa, I. & Weissman, T., Sep 1 2016, In : Bioinformatics. 32, 17, p. i479-i486

Research output: Contribution to journalArticle

2015

IDoComp: A compression scheme for assembled genomes

Ochoa, I., Hernaez, M. & Weissman, T., Mar 1 2015, In : Bioinformatics. 31, 5, p. 626-633 8 p.

Research output: Contribution to journalArticle

QVZ: Lossy compression of quality values

Malysa, G., Hernaez, M., Ochoa, I., Rao, M., Ganesan, K. & Weissman, T., Oct 1 2015, In : Bioinformatics. 31, 19, p. 3122-3129 8 p.

Research output: Contribution to journalArticle

2014

Aligned genomic data compression via improved modeling

Ochoa, I., Hernaez, M. & Weissman, T., Dec 29 2014, In : Journal of Bioinformatics and Computational Biology. 12, 6, 1442002.

Research output: Contribution to journalArticle

CaMoDi: A new method for cancer module discovery

Manolakos, A., Ochoa, I., Venkat, K., Goldsmith, A. J. & Gevaert, O., Jan 1 2014, In : BMC genomics. 15, S8.

Research output: Contribution to journalArticle

Compression schemes for similarity queries

Ochoa, I., Ingber, A. & Weissman, T., Jan 1 2014, Proceedings - DCC 2014: 2014 Data Compression Conference. Institute of Electrical and Electronics Engineers Inc., p. 332-341 10 p. 6824441. (Data Compression Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2013

Efficient similarity queries via lossy compression

Ochoa, I., Ingber, A. & Weissman, T., Jan 1 2013, 2013 51st Annual Allerton Conference on Communication, Control, and Computing, Allerton 2013. IEEE Computer Society, p. 883-889 7 p. 6736618. (2013 51st Annual Allerton Conference on Communication, Control, and Computing, Allerton 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

QualComp: A new lossy compressor for quality scores based on rate distortion theory

Ochoa, I., Asnani, H., Bharadia, D., Chowdhury, M., Weissman, T. & Yona, G., Jun 8 2013, In : BMC bioinformatics. 14, 1, 187.

Research output: Contribution to journalArticle

2012

Reference based genome compression

Chern, B. G., Ochoa-Alvarez, I., Manolakos, A., No, A., Venkat, K. & Weissman, T., Dec 1 2012, 2012 IEEE Information Theory Workshop, ITW 2012. p. 427-431 5 p. 6404708. (2012 IEEE Information Theory Workshop, ITW 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2010

Joint Turbo coding and source-controlled modulation of cycle-stationary sources in the bandwidth-limited regime

Ochoa-Alvarez, I., Crespo, P. M., Del Ser, J. & Hernaez, M., Dec 1 2010, Mobile Lightweight Wireless Systems - Second International ICST Conference, MOBILIGHT 2010, Revised Selected Papers. p. 618-625 8 p. (Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering; vol. 45 LNICST).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

LDPC codes for non-uniform memoryless sources and unequal energy allocation

Ochoa, I., Crespo, P. M. & Hernaez, M., Sep 1 2010, In : IEEE Communications Letters. 14, 9, p. 794-796 3 p., 5572892.

Research output: Contribution to journalArticle

Turbo joint source-channel coding of non-uniform memoryless sources in the bandwidth-limited regime

Ochoa, I., Crespo, P., Ser, J. D. & Hernaez, M., Apr 1 2010, In : IEEE Communications Letters. 14, 4, p. 336-338 3 p., 5439357.

Research output: Contribution to journalArticle