Szymon Grabowski

Bioinform., May, 2023

Space-efficient Huffman codes revisited.

[BibT_eX]

[DOI]

Dominik Köppl

Inf. Process. Lett., 2023

2022

Efficient and compact representations of some non-canonical prefix-free codes.

[BibT_eX]

[DOI]

Alberto Ordóñez Pereira

Theor. Comput. Sci., 2022

2021

Algorithms for all-pairs Hamming distance based similarity.

[BibT_eX]

[DOI]

Softw. Pract. Exp., 2021

2020

SOPanG 2: online searching over a pan-genome without false positives.

[BibT_eX]

[DOI]

CoRR, 2020

PgRC: pseudogenome-based read compressor.

[BibT_eX]

[DOI]

Bioinform., 2020

2019

Revisiting Multiple Pattern Matching.

[BibT_eX]

[DOI]

Comput. Informatics, 2019

Suffix Arrays with a Twist.

[BibT_eX]

[DOI]

Comput. Informatics, 2019

Lightweight Fingerprints for Fast Approximate Keyword Matching Using Bitwise Operations.

[BibT_eX]

[DOI]

Comput. Informatics, 2019

copMEM: finding maximal exact matches via sampling both genomes.

[BibT_eX]

[DOI]

Bioinform., 2019

Whisper: read sorting allows robust mapping of DNA sequencing data.

[BibT_eX]

[DOI]

Adam Gudys

Bioinform., 2019

Viral Genome Deep Classifier.

[BibT_eX]

[DOI]

Anna Fabijanska

IEEE Access, 2019

2018

Faster range minimum queries.

[BibT_eX]

[DOI]

Softw. Pract. Exp., 2018

Rank and select: Another lesson learned.

[BibT_eX]

[DOI]

Inf. Syst., 2018

On Abelian Longest Common Factor with and without RLE.

[BibT_eX]

[DOI]

Tomasz Kociumaka

Jakub Radoszewski

Fundam. Informaticae, 2018

SOPanG: online text searching over a pan-genome.

[BibT_eX]

[DOI]

Jan Holub

Bioinform., 2018

2017

A Bloom filter based semi-index on q-grams.

[BibT_eX]

[DOI]

Softw. Pract. Exp., 2017

Sampled suffix array with minimizers.

[BibT_eX]

[DOI]

Softw. Pract. Exp., 2017

A Practical Index for Approximate Dictionary Matching with Few Mismatches.

[BibT_eX]

[DOI]

Comput. Informatics, 2017

Faster Batched Range Minimum Queries.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2017, 2017

Regular Abelian Periods and Longest Common Abelian Factors on Run-Length Encoded Strings.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2017

FM-index for Dummies.

[BibT_eX]

[DOI]

Proceedings of the Beyond Databases, Architectures and Structures. Towards Efficient Solutions for Data Analysis and Knowledge Representation, 2017

2016

New tabulation and sparse dynamic programming based techniques for sequence similarity problems.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2016

Suffix arrays with a twist.

[BibT_eX]

[DOI]

CoRR, 2016

Comment on: 'ERGC: an efficient referential genome compression algorithm'.

[BibT_eX]

[DOI]

Bioinform., 2016

Longest Common Abelian Factors and Large Alphabets.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2016

2015

A note on the longest common substring with k-mismatches problem.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2015

Indexing arbitrary-length k-mers in sequencing reads.

[BibT_eX]

[DOI]

CoRR, 2015

A Bloom filter based semi-index on q-grams.

[BibT_eX]

[DOI]

CoRR, 2015

A bloated FM-index reducing the number of cache misses during the search.

[BibT_eX]

[DOI]

CoRR, 2015

A note on the longest common Abelian factor problem.

[BibT_eX]

[DOI]

CoRR, 2015

Disk-based compression of data from genome sequencing.

[BibT_eX]

[DOI]

Lukasz Roguski

Bioinform., 2015

KMC 2: fast and resource-frugal k-mer counting.

[BibT_eX]

[DOI]

Marek Kokot

Bioinform., 2015

Sampling the Suffix Array with Minimizers.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2015

OFR: An Efficient Representation of RDF Datasets.

[BibT_eX]

[DOI]

Jakub Swacha

Proceedings of the Languages, Applications and Technologies - 4th International Symposium, 2015

2014

Motif matching using gapped patterns.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

Efficient algorithms for the longest common subsequence in k-length substrings.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2014

Tight and simple Web graph compression for forward and reverse neighbor queries.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2014

Disk-based genome sequencing data compression.

[BibT_eX]

[DOI]

Lukasz Roguski

CoRR, 2014

KMC 2: Fast and resource-frugal k-mer counting.

[BibT_eX]

[DOI]

Marek Kokot

CoRR, 2014

Indexing large genome collections on a PC.

[BibT_eX]

[DOI]

Agnieszka Danek

CoRR, 2014

Multiple Pattern Matching Revisited.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2014, Prague, Czech Republic, 2014

Two Simple Full-Text Indexes Based on the Suffix Array.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2014, Prague, Czech Republic, 2014

Experimental evaluation of selected tree structures for exact and approximate k-nearest neighbor classification.

[BibT_eX]

[DOI]

Proceedings of the 2014 Federated Conference on Computer Science and Information Systems, 2014

2013

Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models.

[BibT_eX]

[DOI]

Esko Ukkonen

J. Comput. Biol., 2013

Approximate pattern matching with k-mismatches in packed text.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2013

New algorithms for binary jumbled pattern matching.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2013

Exploiting word-level parallelism for fast convolutions and their applications in approximate string matching.

[BibT_eX]

[DOI]

Eur. J. Comb., 2013

Disk-based k-mer counting on a PC.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Genome compression: a novel approach for large collections.

[BibT_eX]

[DOI]

Agnieszka Danek

Bioinform., 2013

Data compression for sequencing data.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Motif Matching Using Gapped Patterns.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

Fast and Simple Circular Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the Man-Machine Interactions 3, 2013

Subcubic Algorithms for the Sequence Excluded LCS Problem.

[BibT_eX]

[DOI]

Proceedings of the Man-Machine Interactions 3, 2013

2011

String matching with inversions and translocations in linear average time (most of the time).

[BibT_eX]

[DOI]

Simone Faro

Inf. Process. Lett., 2011

Engineering Relative Compression of Genomes

[BibT_eX]

[DOI]

CoRR, 2011

Robust relative compression of genomes with random access.

[BibT_eX]

[DOI]

Bioinform., 2011

Compression of DNA sequence reads in FASTQ format.

[BibT_eX]

[DOI]

Bioinform., 2011

Merging Adjacency Lists for Efficient Web Graph Compression.

[BibT_eX]

[DOI]

Proceedings of the Man-Machine Interactions 2, 2011

2010

Tight and Simple Web Graph Compression.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2010, Prague, Czech Republic, August 30, 2010

2009

Average-optimal string matching.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2009

Range mode and range median queries in constant time and sub-quadratic space.

[BibT_eX]

[DOI]

Holger Petersen

Inf. Process. Lett., 2009

A hybrid algorithm for the longest common transposition-invariant subsequence problem.

[BibT_eX]

[DOI]

Comput. Informatics, 2009

Nested Counters in Bit-Parallel String Matching.

[BibT_eX]

[DOI]

Proceedings of the Language and Automata Theory and Applications, 2009

Fast Convolutions and Their Applications in Approximate String Matching.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms, 20th International Workshop, 2009

On Two Variants of the Longest Increasing Subsequence Problem.

[BibT_eX]

[DOI]

Proceedings of the Man-Machine Interactions, 2009

2008

Preprocessing for Real-Time Handwritten Character Recognition.

[BibT_eX]

[DOI]

Bartosz Paszkowski

Proceedings of the Computer Recognition Systems 2, 2008

Effective asymmetric XML compression.

[BibT_eX]

[DOI]

Jakub Swacha

Softw. Pract. Exp., 2008

Efficient algorithms for pattern matching with general gaps, character classes, and transposition invariance.

[BibT_eX]

[DOI]

Inf. Retr., 2008

Bit-parallel string matching under Hamming distance in O(n[m/w]) worst case time.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2008

Efficient Algorithms for (delta, gamma, alpha) and (delta, kDelta, alpha)-Matching.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2008

A Highly Efficient XML Compression Scheme for the Web.

[BibT_eX]

[DOI]

Jakub Swacha

Proceedings of the SOFSEM 2008: Theory and Practice of Computer Science, 2008

2006

A general compression algorithm that supports fast searching.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2006

A Simple Alphabet-independent Fm-index.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2006

Efficient Bit-Parallel Algorithms for (delta, alpha)-Matching.

[BibT_eX]

[DOI]

Proceedings of the Experimental Algorithms, 5th International Workshop, 2006

FM-KZ: An even simpler alphabet-independent FM-index.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference, 2006

Efficient algorithms for (delta, gamma, alpha)-matching.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference, 2006

Efficient Algorithms for Pattern Matching with General Gaps and Character Classes.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2006

2005

Revisiting dictionary-based compression.

[BibT_eX]

[DOI]

Softw. Pract. Exp., 2005

A simple alphabet-independent FM-index.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference, 2005

Practical and Optimal String Matching.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2005

2004

First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-Index.

[BibT_eX]

[DOI]

Veli Mäkinen

Gonzalo Navarro

Proceedings of the String Processing and Information Retrieval, 2004

Reducing the Computational Demands for Nearest Centroid Neighborhood Classifiers.

[BibT_eX]

[DOI]

Proceedings of the Artificial Intelligence and Soft Computing, 2004

Variable-length contexts for PPM.

[BibT_eX]

[DOI]