Rodrigo Cánovas

Researcher

Biography

I have always had a great interest in studying new topics and using an interdisciplinary approach to my research. My expertise cover the areas of Algorithms and Data Structures, focusing on Succinct and Compressed Data Structures. Currently, I am working in Bioinformatics, where I apply my knowledge of Computer Science to create tools to solve problems such as motif finding, sequence alignment, and genomic variation analyses amongst others.

For more information on my career, you can find my CV here.

Interests

Design and Analysis of Algorithms
Data Structures and Compression
Bioinformatics
Genomic Data Analysis
Machine Learning

Education

Ph.D. - Engineering, 2015

The University of Melbourne
MSc - Computer Science, 2010

University of Chile
Engineering in Computer Science, 2010

University of Chile
BSc of Engineering, 2007

University of Chile

Selected Publications

CSAM: Compressed SAM format

Next generation sequencing machines produce vast amounts of genomic data. For the data to be useful, it is essential that it can be stored and manipulated efficiently. This work responds to the combined challenge of compressing genomic data, while providing fast access to regions of interest, without necessitating decompression of whole files.

Rodrigo Canovas, Alistair Moffat, Andrew Turpin

Bioinformatics 2016,2016

PDF Code Project

Succinct trees in practice

A general tree of n nodes can be represented in pointer form, requiring O(nlogn) bits, whereas the succinct representations we studied require just 2n+o(n) bits and carry out many sophisticated operations in constant time. Yet, there is no exhaustive study in the literature comparing the practical magnitudes of the o(n)-space and the O(1)-time terms.

Diego Arroyuelo, Rodrigo Canovas, Gonzalo Navarro, Kunihiko Sadakane

In ALENEX’10, 2010

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Some Publications

Diego Arroyuelo, Rodrigo Canovas, Gonzalo Navarro, Rajeev Raman. LZ78 Compression in Low Main Memory Space. SPIRE, 2017.

PDF Code Project

Rodrigo Canovas, Eric Rivals. Full Compressed Affix Tree Representations. In Proc. DCC’17, 2017.

PDF Code Project

Rodrigo Canovas, Alistair Moffat, Andrew Turpin. CSAM: Compressed SAM format. Bioinformatics 2016, 2016.

PDF Code Project

Miguel A Martinez-Prieto, Nieves Brisaboa, Rodrigo Canovas, Francisco Claude, Gonzalo Navarro. Practical compressed string dictionaries. Information Systems, 2016.

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Bastien Cazaux, Rodrigo Canovas, Eric Rivals. Shortest DNA cyclic cover in compressed space. In Proc. DCC’16, 2016.

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Rodrigo Canovas, Alistair Moffat, Andrew Turpin. Lossy compression of quality scores in genomic data. Bioinformatics 2014, 2014.

PDF Code Project

Andres Abeliuk, Rodrigo Canovas, Gonzalo Navarro. Practical compressed suffix trees. Algorithms, 2013.

PDF Code Project

Rodrigo Canovas, Alistair Moffat. Practical compression for multi-alignment genomic files. In Proc. Thirty-Sixth Australasian Computer Science Conference, 2013.

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Miguel A Martinez-Prieto, Javier D Fernandez, Rodrigo Canovas. Compression of RDF dictionaries. In Proc. 27th Annual ACM Symposium on Applied ComputingACM SIGAPP Applied Computing Review, 2012.

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Diego Arroyuelo, Rodrigo Canovas, Gonzalo Navarro, Kunihiko Sadakane. Succinct trees in practice. In ALENEX’10, 2010.

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