Publications

Journal Publications

• FaStore – a space-saving solution for raw sequencing data
  Bioinformatics, 2018 (to appear)
  L. Roguski, I. Ochoa, M. Hernaez, and S. Deorowicz

• METHCOMP: A Special Purpose Compression Platform for DNA Methylation Data
  Bioinformatics, bty143, 2018
  J. Peng, O. Milenkovic, and I. Ochoa

• GTRAC: fast retrieval from compressed collections of genomic variants (PDF, Supp. Data)
  Bioinformatics, btw437, 2016
  K. Tatwawadi, M. Hernaez, I. Ochoa, and T. Weissman

• Effect of lossy compression of quality scores on variant calling (PDF, Supp. Data)
  Briefings in Bioinformatics, bbw011, 2016
  I. Ochoa, M. Hernaez, R. Goldfeder, T. Weissman and E. Ashley

• Comment on: 'ERGC: An efficient referential genome compression algorithm’ (PDF, Supp. Data)
  Bioinformatics, btv704, 2015
  S. Deorowicz, S. Grabowski, I. Ochoa, M. Hernaez and T. Weissman

• QVZ: lossy compression of quality values (PDF, Supp. Data)
  Bioinformatics, btv330, 2015
  G. Malysa, M. Hernaez, I. Ochoa, M. Rao, K. Ganesan and T. Weissman

• Aligned genomic data compression via improved modeling (PDF, Supp. Data)
  Journal of bioinformatics and computational biology, Vol. 12, No. 6, 2014
  I. Ochoa, M. Hernaez and T. Weissman

• CaMoDi: a new method for cancer module discovery (PDF, Supp. Data)
  BMC genomics, Vol. 15, No. Sup. 10, 2014 (Highly Accessed)
  A. Manolakos, I. Ochoa, K. Venkat, A. Goldsmith and O. Gevaert

• iDoComp: a compression scheme for assembled genomes (PDF, Supp. Data)
  Bioinformatics, btu698, 2014
  I. Ochoa, M. Hernaez and T. Weissman

• QualComp: a new Lossy Compression Algorithm of Quality Scores based on Rate Distortion Theory (PDF, Supp. Data)
  BMC Bioinformatics, Vol. 14, No. 1, 2013 (Highly Accessed)
  I. Ochoa, H. Asnani, D. Bharadia, M. Chowdhury, T. Weissman and G. Yona

• LDPC Codes for Non-Uniform Memoryless Sources and Unequal Energy Allocation (PDF)
  IEEE Communications Letters, Vol. 14, No. 9, 2010
  I. Ochoa, P. Crespo and M. Hernaez

• Turbo Joint Source-Channel Coding of NonUniform Memoryless Sources in the Bandwidth-Limited Regime (PDF)
  IEEE Communications Letters, Vol. 14, No. 4, 2010
  I. Ochoa, P. Crespo, J. Del Ser and M. Hernaez

Conference Presentations

• Universal Denoising of Aligned Genomic Sequences (PDF, Supp. Data)
  International Society for Computational Biology (ISMB), 2017 (Submitted)
  I. Fischer-Hwang, M. Hernaez, I. Ochoa and Tsachy Weissman

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

• GTRAC: fast retrieval from compressed collections of genomic variants (PDF, Supp. Data)
  European Conference on Computational Biology (ECCB), Netherlands, 2016
  K. Tatwawadi, M. Hernaez, I. Ochoa, and T. Weissman

• CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores (PDF)
  IEEE Information Theory Workshop (ITW), UK, September, 2016
  I. Ochoa, A. No, M. Hernaez, and T. Weissman

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

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

• Aligned genomic data compression via improved modeling (PDF, Supp. Data)
  GIW ISCB-Asia, Japan, December 2014
  I. Ochoa, M. Hernaez and T. Weissman

• CaMoDi: a new method for cancer module discovery (PDF, Supp. Data)
  GIW ISCB-Asia, Japan, December 2014
  A. Manolakos, I. Ochoa, K. Venkat, A. Goldsmith and O. Gevaert

• Compression Schemes for Similarity Queries (PDF)
  Data Compression Conference (DCC), USA, March 2014
  I. Ochoa, A. Ingber and T. Weissman

• Efficient Similarity Queries via Lossy Compression (PDF)
  Allerton Conference on Communication, Control, and Computing, USA, October 2013
  I. Ochoa, A. Ingber and T. Weissman

• Reference Based Genome Compression (PDF)
  IEEE Information Theory Workshop (ITW), Switzerland, September, 2012
  B. G. Chern, I. Ochoa, A. Manolakos, A. No, K. Venkat and T. Weissman

• Turbo Joint Source-Channel Coding of Cycle-Stationary Sources in the Bandwidth-Limited Regime (PDF)
  The 2nd International Conference on Mobile Lightweight Wireless Systems (MOBILIGHT), Spain, May 2010
  I. Ochoa, P. Crespo, J. Del Ser and M. Hernaez

• Codigos LDGM concatenados para la transmision de fuentes correlacionadas para canales de difusion (PDF)
  XXIV National Assembly of the International Union of Radio Science (URSI), Spain, September 2009
  M. Hernaez, P. Crespo, J. Del Ser and I. Ochoa

PhD Thesis

• Genomic Data Compression and Processing: Theory, Models, Algorithms, and Experiments

Master Thesis

• Iterative Decoding Techniques for the Relay Channel