Universal Data Compression Based on the Burrows-Wheeler Transformation: Theory and Practice
IEEE Transactions on Computers
Succinct representations of lcp information and improvements in the compressed suffix arrays
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Suffix vector: space- and time-efficient alternative to suffix trees
ACSC '02 Proceedings of the twenty-fifth Australasian conference on Computer science - Volume 4
Compactly encoding unstructured inputs with differential compression
Journal of the ACM (JACM)
Database indexing for large DNA and protein sequence collections
The VLDB Journal — The International Journal on Very Large Data Bases
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
The Enhanced Suffix Array and Its Applications to Genome Analysis
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Suffix Vector: A Space-Efficient Suffix Tree Representation
ISAAC '01 Proceedings of the 12th International Symposium on Algorithms and Computation
Optimal Exact Strring Matching Based on Suffix Arrays
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
Efficient Implementation of Lazy Suffix Trees
WAE '99 Proceedings of the 3rd International Workshop on Algorithm Engineering
Space-Economical Algorithms for Finding Maximal Unique Matches
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Engineering a Lightweight Suffix Array Construction Algorithm
ESA '02 Proceedings of the 10th Annual European Symposium on Algorithms
Searching large text collections
Handbook of massive data sets
Rapid Large-Scale Oligonucleotide Selection for Microarrays
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
The suffix binary search tree and suffix AVL tree
Journal of Discrete Algorithms
Constructing chromosome scale suffix trees
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
SPINE: Putting Backbone into String Indexing
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
Engineering a Fast Online Persistent Suffix Tree Construction
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
When indexing equals compression: experiments with compressing suffix arrays and applications
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
New text indexing functionalities of the compressed suffix arrays
Journal of Algorithms
Computing all repeats using suffix arrays
Journal of Automata, Languages and Combinatorics - Special issue: Selected papers of the 13th Australasian workshop on combinatorial algorithms
Efficient Phrase-Based Document Indexing for Web Document Clustering
IEEE Transactions on Knowledge and Data Engineering
Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory
IEEE Transactions on Knowledge and Data Engineering
Antisequential Suffix Sorting for BWT-Based Data Compression
IEEE Transactions on Computers
Journal of the ACM (JACM)
Practical methods for constructing suffix trees
The VLDB Journal — The International Journal on Very Large Data Bases
Processing comparable corpora with Bilingual Suffix Trees
EMNLP '02 Proceedings of the ACL-02 conference on Empirical methods in natural language processing - Volume 10
Software—Practice & Experience
An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A suffix tree approach to anti-spam email filtering
Machine Learning
When indexing equals compression: Experiments with compressing suffix arrays and applications
ACM Transactions on Algorithms (TALG)
Constructing large suffix trees on a computational grid
Journal of Parallel and Distributed Computing
Computing suffix links for suffix trees and arrays
Information Processing Letters
Compressed indexes for dynamic text collections
ACM Transactions on Algorithms (TALG)
On-line construction of compact directed acyclic word graphs
Discrete Applied Mathematics - 12th annual symposium on combinatorial pattern matching (CPM)
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Multi-factor clustering for a marketplace search interface
Proceedings of the 16th international conference on World Wide Web
Indexing schemes for similarity search in datasets of short protein fragments
Information Systems
OASIS: an online and accurate technique for local-alignment searches on biological sequences
VLDB '03 Proceedings of the 29th international conference on Very large data bases - Volume 29
Practical suffix tree construction
VLDB '04 Proceedings of the Thirtieth international conference on Very large data bases - Volume 30
Text document clustering based on frequent word meaning sequences
Data & Knowledge Engineering
International Journal of Bioinformatics Research and Applications
Improving suffix array locality for fast pattern matching on disk
Proceedings of the 2008 ACM SIGMOD international conference on Management of data
Fast profile matching algorithms – A survey
Theoretical Computer Science
An(other) Entropy-Bounded Compressed Suffix Tree
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Efficient String Mining under Constraints Via the Deferred Frequency Index
ICDM '08 Proceedings of the 8th industrial conference on Advances in Data Mining: Medical Applications, E-Commerce, Marketing, and Theoretical Aspects
Fast and Adaptive Variable Order Markov Chain Construction
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
On-line construction of compact suffix vectors and maximal repeats
Theoretical Computer Science
A new method for indexing genomes using on-disk suffix trees
Proceedings of the 17th ACM conference on Information and knowledge management
Indexed Hierarchical Approximate String Matching
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
B-tries for disk-based string management
The VLDB Journal — The International Journal on Very Large Data Bases
Compressing and indexing labeled trees, with applications
Journal of the ACM (JACM)
Finding Similarities in Source Code Through Factorization
Electronic Notes in Theoretical Computer Science (ENTCS)
Faster entropy-bounded compressed suffix trees
Theoretical Computer Science
AS-index: a structure for string search using n-grams and algebraic signatures
Proceedings of the 18th ACM conference on Information and knowledge management
Information Processing Letters
On-line construction of compact directed acyclic word graphs
Discrete Applied Mathematics
Suffix tree construction algorithms on modern hardware
Proceedings of the 13th International Conference on Extending Database Technology
Algorithms for memory hierarchies: advanced lectures
Algorithms for memory hierarchies: advanced lectures
CIAA'02 Proceedings of the 7th international conference on Implementation and application of automata
On the implementation of compact DAWG's
CIAA'02 Proceedings of the 7th international conference on Implementation and application of automata
Fast lightweight suffix array construction and checking
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Efficient and scalable indexing techniques for biological sequence data
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Optimal self-adjusting trees for dynamic string data in secondary storage
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Approximate string matching with Lempel-Ziv compressed indexes
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
An experimental study of compressed indexing and local alignments of DNA
COCOA'07 Proceedings of the 1st international conference on Combinatorial optimization and applications
Post BWT stages of the Burrows–Wheeler compression algorithm
Software—Practice & Experience
Sampled longest common prefix array
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Indexing methods for approximate dictionary searching: Comparative analysis
Journal of Experimental Algorithmics (JEA)
Space-efficient construction of Lempel-Ziv compressed text indexes
Information and Computation
Proceedings of the 11th ACM symposium on Document engineering
Inverted files versus suffix arrays for locating patterns in primary memory
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
An efficient algorithm for finding long conserved regions between genes
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Practical compressed suffix trees
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
A modification of the landau-vishkin algorithm computing longest common extensions via suffix arrays
BSB'05 Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
Parallel construction of large suffix trees on a PC cluster
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
On-line suffix tree construction with reduced branching
Journal of Discrete Algorithms
Computing regularities in strings: A survey
European Journal of Combinatorics
A Lempel-Ziv text index on secondary storage
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Fast and practical algorithms for computing all the runs in a string
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Optimal lightweight construction of suffix arrays for constant alphabets
WADS'07 Proceedings of the 10th international conference on Algorithms and Data Structures
Viewing functions as token sequences to highlight similarities in source code
Science of Computer Programming
A Compressed Suffix Tree Based Implementation With Low Peak Memory Usage
Electronic Notes in Theoretical Computer Science (ENTCS)
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