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Simon J. Puglisi

Simon J. Puglisi

D-Index & Metrics

Computer Science

D-Index
39
Citations
4833
World Ranking
9899
National Ranking
81

Overview

Simon J. Puglisi is affiliated with the University of Helsinki in Finland. Their research spans multiple areas at the intersection of computer science and molecular biology, with a focus on algorithms, data compression, and genomics.

The main fields of study associated with Simon J. Puglisi include:

  • Computer Science
  • Biochemistry, Genetics and Molecular Biology

Their work delves into several specialized subfields, such as:

  • Artificial Intelligence
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Networks and Communications
  • Computer Vision and Pattern Recognition

Key research topics covered in their publications are:

  • Algorithms and Data Compression
  • Genomics and Phylogenetic Studies
  • Natural Language Processing Techniques
  • Semigroups and Automata Theory
  • DNA and Biological Computing
  • Network Packet Processing and Optimization
  • Gene Expression and Cancer Classification

Among the recent papers authored or coauthored by Puglisi are:

  • Data structures based on k-mers for querying large collections of sequencing data sets, 2020, published in Genome Research
  • Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes, 2023, published in Bioinformatics
  • Block trees, 2020, published in Journal of Computer and System Sciences
  • Succinct dynamic de Bruijn graphs, 2020, published in Bioinformatics
  • Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes, 2023, published in bioRxiv (Cold Spring Harbor Laboratory)

Puglisi collaborates frequently with a group of coauthors, including:

  • Jarno Alanko
  • Inge Li Gørtz
  • Leena Salmela
  • Dominik Köppl
  • Martín Farach-Colton

The scientist has contributed extensively to various publication venues, with multiple articles appearing in:

  • Leibniz-Zentrum für Informatik (Schloss Dagstuhl)
  • arXiv (Cornell University)
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Bioinformatics
  • Algorithmica

Best Publications

  • A taxonomy of suffix array construction algorithms

    Simon J. Puglisi;W. F. Smyth;Andrew H. Turpin

  • SHREC: A short-read error correction method

    Jan Schröder;Heiko Schröder;Simon J. Puglisi;Ranjan Sinha

  • Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval

    Shanika Kuruppu;Simon J. Puglisi;Justin Zobel

  • Efficient token based clone detection with flexible tokenization

    Hamid Abdul Basit;Simon J. Puglisi;William F. Smyth;Andrew Turpin

  • Permuted Longest-Common-Prefix Array

    Juha Kärkkäinen;Giovanni Manzini;Simon J. Puglisi

  • Order-preserving matching

    Jinil Kim;Peter Eades;Rudolf Fleischer;Seok-Hee Hong

  • Succinct colored de Bruijn graphs.

    Martin D. Muggli;Alexander Bowe;Noelle R. Noyes;Paul S. Morley

  • New algorithms on wavelet trees and applications to information retrieval

    Travis Gagie;Gonzalo Navarro;Simon J. Puglisi

  • Data structures based on k-mers for querying large collections of sequencing data sets.

    Camille Marchet;Christina Boucher;Simon J. Puglisi;Paul Medvedev

  • Optimized relative Lempel-Ziv compression of genomes

    Shanika Kuruppu;Simon J. Puglisi;Justin Zobel

  • How many runs can a string contain

    Simon J. Puglisi;Jamie Simpson;W. F. Smyth

  • LZ77-Based Self-indexing with Faster Pattern Matching

    Travis Gagie;Pawel Gawrychowski;Juha Kärkkäinen;Yakov Nekrich

  • Range Quantile Queries: Another Virtue of Wavelet Trees

    Travis Gagie;Simon J. Puglisi;Andrew Turpin

  • Top-k ranked document search in general text databases

    J. Shane Culpepper;Gonzalo Navarro;Simon J. Puglisi;Andrew Turpin

  • Colored range queries and document retrieval

    Travis Gagie;Juha Kärkkäinen;Gonzalo Navarro;Simon J. Puglisi

  • Variable-Order de Bruijn Graphs

    Christina Boucher;Alex Bowe;Travis Gagie;Simon J. Puglisi

  • Lempel-Ziv Factorization Using Less Time & Space

    Gang Chen;Simon J. Puglisi;William F. Smyth;William F. Smyth

  • A fast hybrid short read fragment assembly algorithm

    Bertil Schmidt;Ranjan Sinha;Bryan Beresford-Smith;Simon J. Puglisi

  • Linear Time Lempel-Ziv Factorization: Simple, Fast, Small

    Juha Kärkkäinen;Dominik Kempa;Simon J. Puglisi

  • Colored range queries and document retrieval

    Travis Gagie;Gonzalo Navarro;Simon J. Puglisi

Frequent Co-Authors

Juha Kärkkäinen
Juha Kärkkäinen University of Helsinki
gonzalo navarro
gonzalo navarro University of Chile
Andrew Turpin
Andrew Turpin University of Melbourne
William F. Smyth
William F. Smyth McMaster University
Costas S. Iliopoulos
Costas S. Iliopoulos King's College London
Rajeev Raman
Rajeev Raman University of Leicester
Justin Zobel
Justin Zobel University of Melbourne
Veli Mäkinen
Veli Mäkinen University of Helsinki
Falk Scholer
Falk Scholer RMIT University
Keith E. Belk
Keith E. Belk Colorado State University

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