Travis Gagie

Research interests

Publications

• SPUMONI 2: improved classification using a pangenome index of minimizer digests

  Genome biology · 2023 · 10.1186/s13059-023-02958-1

• MONI: A Pangenomic Index for Finding Maximal Exact Matches

  Journal of Computational Biology · 2022 · 10.1089/cmb.2021.0290

• Pan-genomic matching statistics for targeted nanopore sequencing

  iScience · 2021 · 10.1016/j.isci.2021.102696

• Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space

  Journal of the ACM · 2020 · 10.1145/3375890

• Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

  CINECA IRIS Institutial research information system (University of Pisa) · 2020 · 10.1089/cmb.2019.0309

• Prefix-free parsing for building big BWTs

  CINECA IRIS Institutial research information system (University of Pisa) · 2019 · 10.1186/s13015-019-0148-5

• Optimal-Time Text Indexing in BWT-runs Bounded Space

  Society for Industrial and Applied Mathematics eBooks · 2018 · 10.1137/1.9781611975031.96

• Succinct colored de Bruijn graphs

  Bioinformatics · 2017 · 10.1093/bioinformatics/btx067

• Wheeler graphs: A framework for BWT-based data structures

  Theoretical Computer Science · 2017 · 10.1016/j.tcs.2017.06.016

• Composite Repetition-Aware Data Structures

  Lecture notes in computer science · 2015 · 10.1007/978-3-319-19929-0_3

• Variable-Order de Bruijn Graphs

  Journal · 2015 · 10.1109/dcc.2015.70

• Queries on LZ-Bounded Encodings

  Journal · 2015 · 10.1109/dcc.2015.69

• Searching and Indexing Genomic Databases via Kernelization

  Frontiers in Bioengineering and Biotechnology · 2015 · 10.3389/fbioe.2015.00012

• A subquadratic algorithm for minimum palindromic factorization

  Journal of Discrete Algorithms · 2014 · 10.1016/j.jda.2014.08.001

• LZ77-Based Self-indexing with Faster Pattern Matching

  Lecture notes in computer science · 2014 · 10.1007/978-3-642-54423-1_63

• Hybrid indexes for repetitive datasets

  Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · 2014 · 10.1098/rsta.2013.0137

• A Faster Grammar-Based Self-index

  Lecture notes in computer science · 2012 · 10.1007/978-3-642-28332-1_21

• Efficient Fully-Compressed Sequence Representations

  Algorithmica · 2012 · 10.1007/s00453-012-9726-3

• Lightweight Data Indexing and Compression in External Memory

  Algorithmica · 2011 · 10.1007/s00453-011-9535-0

• New algorithms on wavelet trees and applications to information retrieval

  Theoretical Computer Science · 2011 · 10.1016/j.tcs.2011.12.002

• Colored Range Queries and Document Retrieval

  Lecture notes in computer science · 2010 · 10.1007/978-3-642-16321-0_7

• Alphabet Partitioning for Compressed Rank/Select and Applications

  Lecture notes in computer science · 2010 · 10.1007/978-3-642-17514-5_27

• Range quantile queries: Another virtue of wavelet trees

  Journal · 2009

• Large alphabets and incompressibility

  Information Processing Letters · 2006 · 10.1016/j.ipl.2006.04.008

Current projects

No projects listed.