Reduced Nondeterministic Finite Automata for Approximate String Matching. - Jan Holub 001 (Stringology, 1996)

Simulation of NFA in Approximate String and Sequence Matching. - Jan Holub 001 (Stringology, 1997)

6D Classification of Pattern Matching Problems. - Borivoj Melichar; Jan Holub 001 (Stringology, 1997)

Implementation of Nondeterministic Finite Automata for Approximate Pattern Matching. - Jan Holub 001; Borivoj Melichar (Workshop on Implementing Automata, 1998)

Approximate string matching using factor automata. - Jan Holub 001; Borivoj Melichar (Theor. Comput. Sci., 2000)

Bit Parallelism - NFA Simulation. - Jan Holub 001 (CIAA, 2001)

Distributed Pattern Matching Using Finite Automata. - Jan Holub 001; Costas S. Iliopoulos; Borivoj Melichar; Laurent Mouchard (J. Autom. Lang. Comb., 2001)

Dynamic Programming - NFA Simulation. - Jan Holub 001 (CIAA, 2002)

On the Implementation of Compact DAWG's. - Jan Holub 001; Maxime Crochemore (CIAA, 2002)

Dynamic programming for reduced NFAs for approximate string and sequence matching. - Jan Holub 001 (Kybernetika, 2002)

Computing Quasi Suffix Arrays. - Frantisek Franek; Jan Holub 001; William F. Smyth; Xiangdong Xiao (J. Autom. Lang. Comb., 2003)

Guest Editor's Foreword. - Jan Holub 001 (Nord. J. Comput., 2003)

Editorial. - Jan Holub 001 (J. Autom. Lang. Comb., 2005)

Finding Common Motifs with Gaps Using Finite Automata. - Pavlos Antoniou; Jan Holub 001; Costas S. Iliopoulos; Borivoj Melichar; Pierre Peterlongo (CIAA, 2006)

Foreword. - Jan Holub 001 (Int. J. Found. Comput. Sci., 2006)

DCA Using Suffix Arrays. - Martin Fiala; Jan Holub 001 (DCC, 2008)

Fast pattern-matching on indeterminate strings. - Jan Holub 001; William F. Smyth; Shu Wang (J. Discrete Algorithms, 2008)

Tuning BNDM with q-Grams. - Branislav Durian; Jan Holub 001; Hannu Peltola; Jorma Tarhio (ALENEX, 2009)

New Word-Based Adaptive Dense Compressors. - Petr Procházka; Jan Holub 001 (IWOCA, 2009)

On Parallel Implementations of Deterministic Finite Automata. - Jan Holub 001; Stanislav Stekr (CIAA, 2009)

Preface. - Jan Holub 001 (Theor. Comput. Sci., 2009)

An algorithm for mapping short reads to a dynamically changing genomic sequence. - Tomás Flouri; Jan Holub 001; Costas S. Iliopoulos; Solon P. Pissis (BIBM, 2010)

Improving practical exact string matching. - Branislav Durian; Jan Holub 001; Hannu Peltola; Jorma Tarhio (Inf. Process. Lett., 2010)

Natural Language Compression per Blocks. - Petr Procházka; Jan Holub 001 (CCP, 2011)

Lossless Data Compression Testbed: ExCom and Prague Corpus. - Jan Holub 001; Jakub Reznicek; Filip Simek (DCC, 2011)

Block-Oriented Dense Compressor. - Petr Procházka; Jan Holub 001 (DCC, 2011)

The finite automata approaches in stringology. - Jan Holub 001 (Kybernetika, 2012)

Natural Language Compression Optimized for Large Set of Files. - Petr Procházka; Jan Holub 001 (DCC, 2013)

Suffix Tree of Alignment: An Efficient Index for Similar Data. - Joong Chae Na; Heejin Park; Maxime Crochemore; Jan Holub 001; Costas S. Iliopoulos; Laurent Mouchard; Kunsoo Park (IWOCA, 2013)

ODC: Frame for definition of Dense codes. - Petr Procházka; Jan Holub 001 (Eur. J. Comb., 2013)

Compressing Similar Biological Sequences Using FM-Index. - Petr Procházka; Jan Holub 001 (DCC, 2014)

Stringology algorithms. - Jan Holub 001 (Discret. Appl. Math., 2014)

Incremental Locality and Clustering-Based Compression. - Lubos Krcál; Jan Holub 001 (DCC, 2015)

Compression of a Set of Files with Natural Language Content. - Petr Procházka; Jan Holub 001 (Comput. J., 2015)

Approximate String Matching for Self-Indexes. - Lukas Hrbek; Jan Holub 001 (DCC, 2016)

Positional Inverted Self-index. - Petr Procházka; Jan Holub 001 (DCC, 2016)

Editorial: Stringology Algorithms. - Jan Holub 001 (Discret. Appl. Math., 2016)

Byte-Aligned Pattern Matching in Encoded Genomic Sequences. - Petr Procházka; Jan Holub 001 (WABI, 2017)

Towards Efficient Positional Inverted Index. - Petr Procházka; Jan Holub 001 (Algorithms, 2017)

Technology beats algorithms (in exact string matching). - Jorma Tarhio; Jan Holub 001; Emanuele Giaquinta (Softw. Pract. Exp., 2017)

Filtering Invalid Off-Targets in CRISPR/Cas9 Design Tools. - Ondrej Cvacho; Jan Holub 001 (DCC, 2018)

SOPanG: online text searching over a pan-genome. - Aleksander Cislak; Szymon Grabowski; Jan Holub 001 (Bioinform., 2018)

Reconstructing a string from its Lyndon arrays. - Jacqueline W. Daykin; Frantisek Franek; Jan Holub 001; A. S. M. Sohidull Islam; W. F. Smyth (Theor. Comput. Sci., 2018)

On-line Searching in IUPAC Nucleotide Sequences. - Petr Procházka; Jan Holub 001 (BIOINFORMATICS, 2019)

Data structures to represent sets of k-long DNA sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (CoRR, 2019)

PFP Data Structures. - Christina Boucher 001; Ondrej Cvacho; Travis Gagie; Jan Holub 001; Giovanni Manzini; Gonzalo Navarro 001; Massimiliano Rossi 001 (CoRR, 2020)

Preface: Stringology Algorithms. - Jan Holub 001 (Discret. Appl. Math., 2020)

PFP Compressed Suffix Trees. - Christina Boucher 001; Ondrej Cvacho; Travis Gagie; Jan Holub 001; Giovanni Manzini; Gonzalo Navarro 001; Massimiliano Rossi 001 (ALENEX, 2021)

Hierarchical Bitmap Indexing for Range and Membership Queries on Multidimensional Arrays. - Lubos Krcál; Shen-Shyang Ho; Jan Holub 001 (CoRR, 2021)

Hierarchical Bitmap Indexing for Range Queries on Multidimensional Arrays. - Lubos Krcál; Shen-Shyang Ho; Jan Holub 001 (DASFAA (1), 2022)

Data Structures to Represent a Set of k-long DNA Sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (ACM Comput. Surv., 2022)

Backward Pattern Matching on Elastic-Degenerate Strings. - Petr Procházka; Ondrej Cvacho; Lubos Krcál; Jan Holub 001 (SN Comput. Sci., 2023)

Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. - Dominika Draesslerová; Omar Y. Ahmed; Travis Gagie; Jan Holub 001; Ben Langmead; Giovanni Manzini; Gonzalo Navarro 001 (SEA, 2024)