Jan Holub

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 22

Top Topics

Pattern Matching

Top Venues

Discret. Appl. Math.

Publications

Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. SEA (2024)
Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests. CoRR (2024)
Petr Procházka, Ondrej Cvacho, Lubos Krcál, Jan Holub
Backward Pattern Matching on Elastic-Degenerate Strings. SN Comput. Sci. 4 (5) (2023)
Lubos Krcál, Shen-Shyang Ho, Jan Holub
Hierarchical Bitmap Indexing for Range Queries on Multidimensional Arrays. DASFAA (1) (2022)
Lubos Krcál, Shen-Shyang Ho, Jan Holub
Hierarchical Bitmap Indexing for Range and Membership Queries on Multidimensional Arrays. CoRR (2021)
Petr Procházka, Ondrej Cvacho, Lubos Krcál, Jan Holub
Backward Pattern Matching on Elastic Degenerate Strings. BIOINFORMATICS (2021)
Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
PFP Compressed Suffix Trees. ALENEX (2021)
Rayan Chikhi, Jan Holub, Paul Medvedev
-long DNA Sequences. ACM Comput. Surv. 54 (1) (2021)
Jan Holub
Preface: Stringology Algorithms. Discret. Appl. Math. 274 (2020)
Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
PFP Data Structures. CoRR (2020)
Petr Procházka, Jan Holub
On-line Searching in IUPAC Nucleotide Sequences. BIOINFORMATICS (2019)
Rayan Chikhi, Jan Holub, Paul Medvedev
Data structures to represent sets of k-long DNA sequences. CoRR (2019)
Aleksander Cislak, Szymon Grabowski, Jan Holub
SOPanG: online text searching over a pan-genome. Bioinform. 34 (24) (2018)
Ondrej Cvacho, Jan Holub
Filtering Invalid Off-Targets in CRISPR/Cas9 Design Tools. DCC (2018)
Jacqueline W. Daykin, Frantisek Franek, Jan Holub, A. S. M. Sohidull Islam, W. F. Smyth
Reconstructing a string from its Lyndon arrays. Theor. Comput. Sci. 710 (2018)
Jorma Tarhio, Jan Holub, Emanuele Giaquinta
Technology beats algorithms (in exact string matching). Softw. Pract. Exp. 47 (12) (2017)
Petr Procházka, Jan Holub
Towards Efficient Positional Inverted Index. Algorithms 10 (1) (2017)
Petr Procházka, Jan Holub
Byte-Aligned Pattern Matching in Encoded Genomic Sequences. WABI (2017)
Jorma Tarhio, Jan Holub, Emanuele Giaquinta
Technology Beats Algorithms (in Exact String Matching). CoRR (2016)
Lukas Hrbek, Jan Holub
Approximate String Matching for Self-Indexes. DCC (2016)
Jan Holub
Editorial: Stringology Algorithms. Discret. Appl. Math. 212 (2016)
Petr Procházka, Jan Holub
Positional Inverted Self-index. DCC (2016)
Petr Procházka, Jan Holub
Compression of a Set of Files with Natural Language Content. Comput. J. 58 (5) (2015)
Lubos Krcál, Jan Holub
Incremental Locality and Clustering-Based Compression. DCC (2015)
Jan Holub
Stringology algorithms. Discret. Appl. Math. 163 (2014)
Petr Procházka, Jan Holub
Compressing Similar Biological Sequences Using FM-Index. DCC (2014)
Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, Kunsoo Park
Suffix Tree of Alignment: An Efficient Index for Similar Data. IWOCA (2013)
Petr Procházka, Jan Holub
ODC: Frame for definition of Dense codes. Eur. J. Comb. 34 (1) (2013)
Petr Procházka, Jan Holub
Natural Language Compression Optimized for Large Set of Files. DCC (2013)
Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, Kunsoo Park
Suffix Tree of Alignment: An Efficient Index for Similar Data CoRR (2013)
Jan Holub
Preface. Int. J. Found. Comput. Sci. 23 (2) (2012)
Jan Holub
The finite automata approaches in stringology. Kybernetika 48 (3) (2012)
Petr Procházka, Jan Holub
Natural Language Compression per Blocks. CCP (2011)
Jan Holub, Jakub Reznicek, Filip Simek
Lossless Data Compression Testbed: ExCom and Prague Corpus. DCC (2011)
Petr Procházka, Jan Holub
Block-Oriented Dense Compressor. DCC (2011)
Tomás Flouri, Jan Holub, Costas S. Iliopoulos, Solon P. Pissis
An algorithm for mapping short reads to a dynamically changing genomic sequence. BIBM (2010)
Branislav Durian, Jan Holub, Hannu Peltola, Jorma Tarhio
Improving practical exact string matching. Inf. Process. Lett. 110 (4) (2010)
Branislav Durian, Jan Holub, Hannu Peltola, Jorma Tarhio
Tuning BNDM with q-Grams. ALENEX (2009)
Petr Procházka, Jan Holub
New Word-Based Adaptive Dense Compressors. IWOCA (2009)
Jan Holub, Stanislav Stekr
On Parallel Implementations of Deterministic Finite Automata. CIAA (2009)
Jan Holub
Preface. Theor. Comput. Sci. 410 (37) (2009)
Jan Holub
Foreword. Int. J. Found. Comput. Sci. 20 (6) (2009)
Jan Holub, William F. Smyth, Shu Wang
Fast pattern-matching on indeterminate strings. J. Discrete Algorithms 6 (1) (2008)
Jan Holub
Foreword. Int. J. Found. Comput. Sci. 19 (1) (2008)
Martin Fiala, Jan Holub
DCA Using Suffix Arrays. DCC (2008)
Pavlos Antoniou, Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Pierre Peterlongo
Finding Common Motifs with Gaps Using Finite Automata. CIAA (2006)
Jan Holub
Foreword. Int. J. Found. Comput. Sci. 17 (6) (2006)
Jan Holub
Editorial. J. Autom. Lang. Comb. 10 (5/6) (2005)
Jan Holub
Foreword. Int. J. Found. Comput. Sci. 16 (6) (2005)
Frantisek Franek, Jan Holub, William F. Smyth, Xiangdong Xiao
Computing Quasi Suffix Arrays. J. Autom. Lang. Comb. 8 (4) (2003)
Jan Holub
Guest Editor's Foreword. Nord. J. Comput. 10 (1) (2003)
Jan Holub
Dynamic Programming - NFA Simulation. CIAA (2002)
Jan Holub, Maxime Crochemore
On the Implementation of Compact DAWG's. CIAA (2002)
Jan Holub
Dynamic programming for reduced NFAs for approximate string and sequence matching. Kybernetika 38 (1) (2002)
Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Laurent Mouchard
Distributed Pattern Matching Using Finite Automata. J. Autom. Lang. Comb. 6 (2) (2001)
Jan Holub
Bit Parallelism - NFA Simulation. CIAA (2001)
Jan Holub, Borivoj Melichar
Approximate string matching using factor automata. Theor. Comput. Sci. 249 (2) (2000)
Jan Holub, Borivoj Melichar
Implementation of Nondeterministic Finite Automata for Approximate Pattern Matching. Workshop on Implementing Automata (1998)
Jan Holub
Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching. Stringology (1998)
Jan Holub
Simulation of NFA in Approximate String and Sequence Matching. Stringology (1997)
Borivoj Melichar, Jan Holub
6D Classification of Pattern Matching Problems. Stringology (1997)
Jan Holub
Reduced Nondeterministic Finite Automata for Approximate String Matching. Stringology (1996)