1.4k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- University of TurinIT1.5k papers
- Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali di FrascatiIT1.4k papers
- Istituto Nazionale di Fisica Nucleare, Sezione di TorinoIT1.3k papers
- Joint Institute for Nuclear ResearchRU1.2k papers
- Peking UniversityCN1.1k papers
- Carnegie Mellon UniversityUS1.1k papers
- National Centre for Nuclear ResearchPL1.1k papers
- University of PerugiaIT1.1k papers
- European Organization for Nuclear ResearchCH1k papers
- Institute of High Energy PhysicsCN1k papers
- Panjab UniversityIN956 papers
- The Ohio State UniversityUS953 papers
11 papers · 1 filter
Matching reads to many genomes with the -index
Taher Mun, Alan Kuhnle, Christina Boucher +3
The -index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a gen…
Inducing the Lyndon Array
Felipe A. Louza, Sabrina Mantaci, Giovanni Manzini +2
In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in $O(n…
A New Class of Searchable and Provably Highly Compressible String Transformations
Raffaele Giancarlo, Giovanni Manzini, Giovanna Rosone +1
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have…
Space-efficient merging of succinct de Bruijn graphs
Lavinia Egidi, Felipe A. Louza, Giovanni Manzini
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging app…
Compressing and Indexing Aligned Readsets
Travis Gagie, Garance Gourdel, Giovanni Manzini
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled…
Lyndon Array Construction during Burrows-Wheeler Inversion
Felipe A. Louza, W. F. Smyth, Giovanni Manzini +1
In this paper we present an algorithm to compute the Lyndon array of a string of length as a byproduct of the inversion of the Burrows-Wheeler transform of . Our algorit…
An Encoding for Order-Preserving Matching
Travis Gagie, Giovanni Manzini, Rossano Venturini
Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the fir…
A Compact Index for Order-Preserving Pattern Matching
Gianni Decaroli, Travis Gagie, Giovanni Manzini
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of…
Compressed Spaced Suffix Arrays
Travis Gagie, Giovanni Manzini, Daniel Valenzuela
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches,…
Lightweight Data Indexing and Compression in External Memory
Paolo Ferragina, Travis Gagie, Giovanni Manzini
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are light…
Low-Memory Adaptive Prefix Coding
Travis Gagie, Marek Karpinski, Yakov Nekrich
In this paper we study the adaptive prefix coding problem in cases where the size of the input alphabet is large. We present an online prefix coding algorithm that uses $O(σ^{1 / λ…