Sebastian Deorowicz

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 25

Top Topics

Protein Families

Compression Algorithm

Collection Selection

Sequence Alignment

Top Venues

Publications

Sebastian Deorowicz, Adam Gudys
Efficient protein structure archiving using ProteStAr. Bioinform. 40 (7) (2024)
Sebastian Deorowicz, Agnieszka Danek, Heng Li
AGC: compact representation of assembled genomes with fast queries and updates. Bioinform. 39 (3) (2023)
Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
-mers. Bioinform. 38 (18) (2022)
Andrzej Zielezinski, Sebastian Deorowicz, Adam Gudys
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences. Bioinform. 38 (5) (2022)
Sebastian Deorowicz, Adam Gudys
Whisper 2: Indel-sensitive short read mapping. SoftwareX 14 (2021)
Sebastian Deorowicz, Agnieszka Danek, Marek Kokot
VCFShark: how to squeeze a VCF file. Bioinform. 37 (19) (2021)
Sebastian Deorowicz, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz
CoMSA: compression of protein multiple sequence alignment files. Bioinform. 35 (2) (2019)
Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys, Szymon Grabowski
Whisper: read sorting allows robust mapping of DNA sequencing data. Bioinform. 35 (12) (2019)
Sebastian Deorowicz, Adam Gudys, Maciej Dlugosz, Marek Kokot, Agnieszka Danek
Kmer-db: instant evolutionary distance estimation. Bioinform. 35 (1) (2019)
Sebastian Deorowicz, Agnieszka Danek
GTShark: genotype compression in large projects. Bioinform. 35 (22) (2019)
Agnieszka Danek, Sebastian Deorowicz
GTC: how to maintain huge genotype collections in a compressed form. Bioinform. 34 (11) (2018)
Lukasz Roguski, Idoia Ochoa, Mikel Hernaez, Sebastian Deorowicz
FaStore: a space-saving solution for raw sequencing data. Bioinform. 34 (16) (2018)
Marek Kokot, Maciej Dlugosz, Sebastian Deorowicz
KMC 3: counting and manipulating k-mer statistics. Bioinform. 33 (17) (2017)
Marek Kokot, Sebastian Deorowicz, Maciej Dlugosz
Even faster sorting of (not only) integers. CoRR (2017)
Maciej Dlugosz, Sebastian Deorowicz, Marek Kokot
Improvements in DNA Reads Correction. ICMMI (2017)
Marek Kokot, Sebastian Deorowicz, Maciej Dlugosz
Even Faster Sorting of (Not Only) Integers. ICMMI (2017)
Marek Kokot, Maciej Dlugosz, Sebastian Deorowicz
KMC 3: counting and manipulating k-mer statistics. CoRR (2017)
Marek Kokot, Sebastian Deorowicz, Agnieszka Debudaj-Grabysz
Sorting Data on Ultra-Large Scale with RADULS - New Incarnation of Radix Sort. BDAS (2017)
Maciej Dlugosz, Sebastian Deorowicz, Marek Kokot
Even better correction of genome sequencing data. CoRR (2017)
Szymon Grabowski, Marcin Raniszewski, Sebastian Deorowicz
FM-index for Dummies. BDAS (2017)
Maciej Dlugosz, Sebastian Deorowicz
RECKONER: read error corrector based on KMC. Bioinform. 33 (7) (2017)
Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys
Aligning 415 519 proteins in less than two hours on PC. CoRR (2016)
Marek Kokot, Sebastian Deorowicz, Agnieszka Debudaj-Grabysz
Sorting Data on Ultra-Large Scale with RADULS. New Incarnation of Radix Sort. CoRR (2016)
Maciej Dlugosz, Sebastian Deorowicz
RECKONER: Read Error Corrector Based on KMC. CoRR (2016)
Sebastian Deorowicz, Szymon Grabowski, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman
Comment on: 'ERGC: an efficient referential genome compression algorithm'. Bioinform. 32 (7) (2016)
Szymon Grabowski, Marcin Raniszewski, Sebastian Deorowicz
FM-index for dummies. CoRR (2015)
Tomasz Marek Kowalski, Szymon Grabowski, Sebastian Deorowicz
Indexing arbitrary-length k-mers in sequencing reads. CoRR (2015)
Adam Gudys, Sebastian Deorowicz
QuickProbs 2: towards rapid construction of high-quality alignments of large protein families. CoRR (2015)
Szymon Grabowski, Sebastian Deorowicz, Lukasz Roguski
Disk-based compression of data from genome sequencing. Bioinform. 31 (9) (2015)
Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
-mer counting. Bioinform. 31 (10) (2015)
Sebastian Deorowicz, Agnieszka Danek, Marcin Niemiec
GDC 2: Compression of large collections of genomes. CoRR (2015)
Jolanta Kawulok, Sebastian Deorowicz
An Improved Algorithm for Fast and Accurate Classification of Sequences. BDAS (2014)
Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
KMC 2: Fast and resource-frugal k-mer counting. CoRR (2014)
Bozena Wieczorek, Marcin Polomski, Piotr Pecka, Sebastian Deorowicz
An Effective Way of Storing and Accessing Very Large Transition Matrices Using Multi-core CPU and GPU Architectures. BDAS (2014)
Agnieszka Danek, Sebastian Deorowicz, Szymon Grabowski
Indexing large genome collections on a PC. CoRR (2014)
Szymon Grabowski, Sebastian Deorowicz, Lukasz Roguski
Disk-based genome sequencing data compression. CoRR (2014)
Sebastian Deorowicz, Szymon Grabowski
Efficient algorithms for the longest common subsequence in k-length substrings. Inf. Process. Lett. 114 (11) (2014)
Lukasz Roguski, Sebastian Deorowicz
DSRC 2 - Industry-oriented compression of FASTQ files. Bioinform. 30 (15) (2014)
Robert Susik, Szymon Grabowski, Sebastian Deorowicz
Fast and Simple Circular Pattern Matching. ICMMI (2013)
Sebastian Deorowicz, Szymon Grabowski
Efficient algorithms for the longest common subsequence in $k$-length substrings. CoRR (2013)
Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Szymon Grabowski
Disk-based k-mer counting on a PC. BMC Bioinform. 14 (2013)
Sebastian Deorowicz, Agnieszka Danek, Szymon Grabowski
Genome compression: a novel approach for large collections. Bioinform. 29 (20) (2013)
Agnieszka Danek, Sebastian Deorowicz
Bit-Parallel Algorithm for the Block Variant of the Merged Longest Common Subsequence Problem. ICMMI (2013)
Sebastian Deorowicz, Szymon Grabowski
Data compression for sequencing data. Algorithms Mol. Biol. 8 (2013)
Sebastian Deorowicz, Szymon Grabowski
Subcubic Algorithms for the Sequence Excluded LCS Problem. ICMMI (2013)
Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys
Kalign-LCS - A More Accurate and Faster Variant of Kalign2 Algorithm for the Multiple Sequence Alignment Problem. ICMMI (2013)
Sebastian Deorowicz, Agnieszka Danek
Bit-Parallel Algorithms for the Merged Longest Common Subsequence Problem. Int. J. Found. Comput. Sci. 24 (8) (2013)
Michal Wojciech Szczesniak, Sebastian Deorowicz, Jakub Gapski, Lukasz Kaczynski, Izabela Makalowska
miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res. 40 (Database-Issue) (2012)
Sebastian Deorowicz
Quadratic-time algorithm for a string constrained LCS problem. Inf. Process. Lett. 112 (11) (2012)
Sebastian Deorowicz
A Cover-Merging-Based Algorithm for the Longest Increasing Subsequence in a Sliding Window Problem. Comput. Informatics 31 (6) (2012)
Adam Gudys, Sebastian Deorowicz
A Parallel Algorithm for the Constrained Multiple Sequence Alignment Problem Designed for GPUs. Int. J. Found. Comput. Sci. 23 (4) (2012)
Sebastian Deorowicz, Szymon Grabowski
Compression of DNA sequence reads in FASTQ format. Bioinform. 27 (6) (2011)
Szymon Grabowski, Sebastian Deorowicz
Engineering Relative Compression of Genomes CoRR (2011)
Sebastian Deorowicz
Quadratic-time Algorithm for the String Constrained LCS Problem CoRR (2011)
Adam Gudys, Sebastian Deorowicz
A Parallel GPU-Designed Algorithm for the Constrained Multiple Sequence Alignment Problem. ICMMI (2011)
Piotr Pecka, Sebastian Deorowicz, Mateusz Nowak
Efficient Representation of Transition Matrix in the Markov Process Modeling of Computer Networks. ICMMI (2011)
Sebastian Deorowicz, Szymon Grabowski
Robust relative compression of genomes with random access. Bioinform. 27 (21) (2011)
Sebastian Deorowicz
Solving longest common subsequence and related problems on graphical processing units. Softw. Pract. Exp. 40 (8) (2010)
Sebastian Deorowicz, J. Obstoj
Constrained Longest Common Subsequence Computing Algorithms in Practice. Comput. Informatics 29 (3) (2010)
Sebastian Deorowicz
Bit-Parallel Algorithm for the Constrained Longest Common Subsequence Problem. Fundam. Informaticae 99 (4) (2010)
Sebastian Deorowicz, Szymon Grabowski
A hybrid algorithm for the longest common transposition-invariant subsequence problem. Comput. Informatics 28 (5) (2009)
Sebastian Deorowicz, Szymon Grabowski
On Two Variants of the Longest Increasing Subsequence Problem. ICMMI (2009)
Sebastian Deorowicz
An algorithm for solving the longest increasing circular subsequence problem. Inf. Process. Lett. 109 (12) (2009)
Sebastian Deorowicz
Computing the Longest Common Transposition-Invariant Subsequence with GPU. ICMMI (2009)
Sebastian Deorowicz, Szymon Grabowski
Efficient Preprocessing for Web Log Compression. Int. J. Comput. 7 (1) (2008)
Sebastian Deorowicz
Speeding up transposition-invariant string matching. Inf. Process. Lett. 100 (1) (2006)
Przemyslaw Skibinski, Szymon Grabowski, Sebastian Deorowicz
Revisiting dictionary-based compression. Softw. Pract. Exp. 35 (15) (2005)
Sebastian Deorowicz
Context exhumation after the Burrows-Wheeler transform. Inf. Process. Lett. 95 (1) (2005)
Sebastian Deorowicz
Second step algorithms in the Burrows-Wheeler compression algorithm. Softw. Pract. Exp. 32 (2) (2002)
Marcin Ciura, Sebastian Deorowicz
How to squeeze a lexicon. Softw. Pract. Exp. 31 (11) (2001)
Sebastian Deorowicz
Improvements to Burrows-Wheeler compression algorithm. Softw. Pract. Exp. 30 (13) (2000)