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- Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira
- ACM Trans. Algorithms
- 2008

Suffix trees are by far the most important data structure in stringology, with a myriad of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require Θ(<i>n</i> log <i>n</i>) bits of space, for a string of size <i>n</i>. This is considerably more than the <i>n</i> log<sub>2</sub> σ… (More)

- Francisco Fernandes, Paulo G. S. da Fonseca, Luís M. S. Russo, Arlindo L. Oliveira, Ana T. Freitas
- BMC Bioinformatics
- 2010

Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific… (More)

- Luís M. S. Russo, Alexandre P. Francisco
- J. Heuristics
- 2016

- Luís M. S. Russo, Arlindo L. Oliveira
- Information Retrieval
- 2006

A compressed full-text self-index for a text T, of size u, is a data structure used to search for patterns P, of size m, in T, that requires reduced space, i.e. space that depends on the empirical entropy (H k or H 0) of T, and is, furthermore, able to reproduce any substring of T. In this paper we present a new compressed self-index able to locate the… (More)

- Gonzalo Navarro, Luís M. S. Russo
- ISAAC
- 2011

We consider various data-analysis queries on two-dimensional points. We give new space/time tradeoffs over previous work on geometric queries such as dominance and rectangle visibility, and on semigroup and group queries such as sum, average, variance, minimum and maximum. We also introduce new solutions to queries less frequently considered in the… (More)

- Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira, Pedro Morales
- Algorithms
- 2009

Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics, data compression and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is considerably more than the n log 2 σ bits needed for the string itself,… (More)

- Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo, Jonas S. Almeida
- Algorithms for Molecular Biology
- 2012

Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L… (More)

- Luís M. S. Russo, Alexandre P. Francisco
- IEEE Trans. Evolutionary Computation
- 2014

—We present a new algorithm to calculate exact hy-pervolumes. Given a set of d-dimensional points, it computes the hypervolume of the dominated space. Determining this value is an important subroutine of Multiobjective Evolutionary Algorithms (MOEAs). We analyze the " Quick Hypervolume " (QHV) algorithm theoretically and experimentally. The theoretical… (More)

We study parallel and distributed compressed indexes. Compressed indexes are a new and functional way to index text strings. They exploit the compressibility of the text, so that their size is a function of the compressed text size. Moreover, they support a considerable amount of functions, more than many classical indexes. We make use of this extended… (More)