q-gram based database searching using a suffix array (QUASAR)

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

Computing the Threshold for q-Gram Filters

SWAT '02 Proceedings of the 8th Scandinavian Workshop on Algorithm Theory

Text Sparsification via Local Maxima

FST TCS 2000 Proceedings of the 20th Conference on Foundations of Software Technology and Theoretical Computer Science

Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts

COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching

Better Filtering with Gapped q-Grams

CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching

One-Gapped q-Gram Filtersfor Levenshtein Distance

CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching

On Constructing Suffix Arrays in External Memory

ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms

High Similarity Sequence Comparison in Clustering Large Sequence Databases

CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics

Accelerating Approximate Subsequence Search on Large Protein Sequence Databases

CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics

Text sparsification via local maxima

Theoretical Computer Science

Better filtering with gapped q-grams

Fundamenta Informaticae - Special issue on computing patterns in strings

Combinatorics of periods in strings

Journal of Combinatorial Theory Series A

A seriate coverage filtration approach for homology search

Proceedings of the 2004 ACM symposium on Applied computing

Piers: an efficient model for similarity search in DNA sequence databases

ACM SIGMOD Record

Indexing text data under space constraints

Proceedings of the thirteenth ACM international conference on Information and knowledge management

q-Gram Matching Using Tree Models

IEEE Transactions on Knowledge and Data Engineering

siRNA off-target search: a hybrid q-gram based filtering approach

Proceedings of the 5th international workshop on Bioinformatics

A novel filtration method in biological sequence databases

Pattern Recognition Letters

Comparative n-gram analysis of whole-genome protein sequences

HLT '02 Proceedings of the second international conference on Human Language Technology Research

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

Extending q-grams to estimate selectivity of string matching with low edit distance

VLDB '07 Proceedings of the 33rd international conference on Very large data bases

A graph approach to the threshold all-against-all substring matching problem

Journal of Experimental Algorithmics (JEA)

Hardness of optimal spaced seed design

Journal of Computer and System Sciences

Lossless filter for multiple repetitions with Hamming distance

Journal of Discrete Algorithms

Reference-based alignment in large sequence databases

Proceedings of the VLDB Endowment

Efficient and scalable indexing techniques for biological sequence data

BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development

Exhaustive peptide searching using relations

BNCOD'07 Proceedings of the 24th British national conference on Databases

New algorithms for the spaced seeds

FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics

A mining technique using n-grams and motion transcripts for body sensor network data repository

WH '10 Wireless Health 2010

Embedding-based subsequence matching in time-series databases

ACM Transactions on Database Systems (TODS)

Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Hardness of optimal spaced seed design

CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching

Indexing DNA sequences using q-grams

DASFAA'05 Proceedings of the 10th international conference on Database Systems for Advanced Applications

Efficient q-gram filters for finding all ε-matches over a given length

RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology

Lossless filter for finding long multiple approximate repetitions using a new data structure, the bi-factor array

SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval

Better Filtering with Gapped q-Grams

Fundamenta Informaticae - Computing Patterns in Strings

Rime: Repeat identification

Discrete Applied Mathematics