Jan Holub

According to our database, Jan Holub authored at least 53 papers between 1996 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.

Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro

CoRR, 2024

2023

Backward Pattern Matching on Elastic-Degenerate Strings.

Petr Procházka, Ondrej Cvacho, Lubos Krcál, Jan Holub

SN Comput. Sci., September, 2023

2022

Data Structures to Represent a Set of <i>k</i>-long DNA Sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

ACM Comput. Surv., 2022

Hierarchical Bitmap Indexing for Range Queries on Multidimensional Arrays.

Lubos Krcál, Shen-Shyang Ho, Jan Holub

Proceedings of the Database Systems for Advanced Applications, 2022

2021

Hierarchical Bitmap Indexing for Range and Membership Queries on Multidimensional Arrays.

Lubos Krcál, Shen-Shyang Ho, Jan Holub

CoRR, 2021

PFP Compressed Suffix Trees.

Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi

Proceedings of the Symposium on Algorithm Engineering and Experiments, 2021

2020

Preface: Stringology Algorithms.

Jan Holub

Discret. Appl. Math., 2020

PFP Data Structures.

Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi

CoRR, 2020

2019

Data structures to represent sets of k-long DNA sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

CoRR, 2019

On-line Searching in IUPAC Nucleotide Sequences.

Petr Procházka, Jan Holub

Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019

2018

Reconstructing a string from its Lyndon arrays.

Jacqueline W. Daykin, Frantisek Franek, Jan Holub, A. S. M. Sohidull Islam, W. F. Smyth

Theor. Comput. Sci., 2018

SOPanG: online text searching over a pan-genome.

Aleksander Cislak, Szymon Grabowski, Jan Holub

Bioinform., 2018

Filtering Invalid Off-Targets in CRISPR/Cas9 Design Tools.

Ondrej Cvacho, Jan Holub

Proceedings of the 2018 Data Compression Conference, 2018

2017

Technology beats algorithms (in exact string matching).

Jorma Tarhio, Jan Holub, Emanuele Giaquinta

Softw. Pract. Exp., 2017

Towards Efficient Positional Inverted Index.

Petr Procházka, Jan Holub

Algorithms, 2017

Byte-Aligned Pattern Matching in Encoded Genomic Sequences.

Petr Procházka, Jan Holub

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016

Editorial: Stringology Algorithms.

Jan Holub

Discret. Appl. Math., 2016

Positional Inverted Self-index.

Petr Procházka, Jan Holub

Proceedings of the 2016 Data Compression Conference, 2016

Approximate String Matching for Self-Indexes.

Lukas Hrbek, Jan Holub

Proceedings of the 2016 Data Compression Conference, 2016

2015

Compression of a Set of Files with Natural Language Content.

Petr Procházka, Jan Holub

Comput. J., 2015

Incremental Locality and Clustering-Based Compression.

Lubos Krcál, Jan Holub

Proceedings of the 2015 Data Compression Conference, 2015

2014

Stringology algorithms.

Jan Holub

Discret. Appl. Math., 2014

Compressing Similar Biological Sequences Using FM-Index.

Petr Procházka, Jan Holub

Proceedings of the Data Compression Conference, 2014

2013

ODC: Frame for definition of Dense codes.

Petr Procházka, Jan Holub

Eur. J. Comb., 2013

Suffix Tree of Alignment: An Efficient Index for Similar Data.

Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, Kunsoo Park

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

Natural Language Compression Optimized for Large Set of Files.

Petr Procházka, Jan Holub

Proceedings of the 2013 Data Compression Conference, 2013

2012

The finite automata approaches in stringology.

Jan Holub

Kybernetika, 2012

2011

Block-Oriented Dense Compressor.

Petr Procházka, Jan Holub

Proceedings of the 2011 Data Compression Conference (DCC 2011), 2011

Lossless Data Compression Testbed: ExCom and Prague Corpus.

Jan Holub, Jakub Reznicek, Filip Simek

Proceedings of the 2011 Data Compression Conference (DCC 2011), 2011

Natural Language Compression per Blocks.

Petr Procházka, Jan Holub

Proceedings of the First International Conference on Data Compression, 2011

2010

Improving practical exact string matching.

Branislav Durian, Jan Holub, Hannu Peltola, Jorma Tarhio

Inf. Process. Lett., 2010

An algorithm for mapping short reads to a dynamically changing genomic sequence.

Tomás Flouri, Jan Holub, Costas S. Iliopoulos, Solon P. Pissis

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

Preface.

Jan Holub

Theor. Comput. Sci., 2009

On Parallel Implementations of Deterministic Finite Automata.

Jan Holub, Stanislav Stekr

Proceedings of the Implementation and Application of Automata, 2009

New Word-Based Adaptive Dense Compressors.

Petr Procházka, Jan Holub

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

Tuning BNDM with q-Grams.

Branislav Durian, Jan Holub, Hannu Peltola, Jorma Tarhio

Proceedings of the Eleventh Workshop on Algorithm Engineering and Experiments, 2009

2008

Fast pattern-matching on indeterminate strings.

Jan Holub, William F. Smyth, Shu Wang

J. Discrete Algorithms, 2008

DCA Using Suffix Arrays.

Martin Fiala, Jan Holub

Proceedings of the 2008 Data Compression Conference (DCC 2008), 2008

2006

Finding Common Motifs with Gaps Using Finite Automata.

Pavlos Antoniou, Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Pierre Peterlongo

Proceedings of the Implementation and Application of Automata, 2006

2005

Editorial.

Jan Holub

J. Autom. Lang. Comb., 2005

Foreword.

Jan Holub

Int. J. Found. Comput. Sci., 2005

2003

Guest Editor's Foreword.

Jan Holub

Nord. J. Comput., 2003

Computing Quasi Suffix Arrays.

Frantisek Franek, Jan Holub, William F. Smyth, Xiangdong Xiao

J. Autom. Lang. Comb., 2003

2002

Dynamic programming for reduced NFAs for approximate string and sequence matching.

Jan Holub

Kybernetika, 2002

On the Implementation of Compact DAWG's.

Jan Holub, Maxime Crochemore

Proceedings of the Implementation and Application of Automata, 2002

Dynamic Programming - NFA Simulation.

Jan Holub

Proceedings of the Implementation and Application of Automata, 2002

2001

Distributed Pattern Matching Using Finite Automata.

Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Laurent Mouchard

J. Autom. Lang. Comb., 2001

Bit Parallelism - NFA Simulation.

Jan Holub

Proceedings of the Implementation and Application of Automata, 2001

2000

Approximate string matching using factor automata.

Jan Holub, Borivoj Melichar

Theor. Comput. Sci., 2000

1998

Implementation of Nondeterministic Finite Automata for Approximate Pattern Matching.

Jan Holub, Borivoj Melichar

Proceedings of the Automata Implementation, 1998

1997

6D Classification of Pattern Matching Problems.

Borivoj Melichar, Jan Holub

Proceedings of the Prague Stringology Club Workshop 1997, 1997

Simulation of NFA in Approximate String and Sequence Matching.

Jan Holub

Proceedings of the Prague Stringology Club Workshop 1997, 1997

1996

Reduced Nondeterministic Finite Automata for Approximate String Matching.

Jan Holub

Proceedings of the Prague Stringology Club Workshop 1996, 1996