Algorithms on Strings, Trees and Sequences
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dynamic programmingcomputational biologybioinformaticsDNA sequencingedit distancestring matchingsuffix treesalignmentsevolutionary treessequence databases
Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Analysis of algorithms and problem complexity (68Q25) Nonnumerical algorithms (68W05) Introductory exposition (textbooks, tutorial papers, etc.) pertaining to computer science (68-01) Combinatorics on words (68R15) Computing methodologies for text processing; mathematical typography (68U15)
Recommendations
- Algorithms on Strings
- String algorithms. Papers based on the presentations at four meetings, London algorithms workshop, December 2000; London stringology day, February 2003; Rouen sequence algorithmics, June 2002; Patras stringology days, February 2004.
- scientific article; zbMATH DE number 828444
- Algorithmic aspects of bioinformatics. Translated from the German original
Cited in
(only showing first 100 items - show all)- Bioinformatics algorithms. Sequence analysis, genome rearrangements, and phylogenetic reconstruction
- Linear time algorithms for generalizations of the longest common substring problem
- Compact directed acyclic word graphs for a sliding window
- Palindrome pattern matching
- Versatile string kernels
- A probabilistic PTAS for shortest common superstring
- A new method for approximate indexing and dictionary lookup with one error
- Counting distinct palindromes in a word in linear time
- Discovery of stop regions for understanding repeat travel behaviors of moving objects
- Revisiting the parameterized complexity of maximum-duo preservation string mapping
- Palindrome pattern matching
- Speeding up the detection of tandem repeats over the edit distance
- Dynamic 3-sided planar range queries with expected doubly-logarithmic time
- Unbordered pictures: properties and construction
- Global and local sequence alignment with a bounded number of gaps
- Optimal bounds for computing \({\alpha}\)-gapped repeats
- Optimal prefix and suffix queries on texts
- Full-text indexes for high-throughput sequencing
- Searching and indexing circular patterns
- String-matching and alignment algorithms for finding motifs in NGS data
- An efficient approach to merging paired-end reads and incorporation of uncertainties
- Computing the Antiperiod(s) of a String
- Longest substring palindrome after edit
- Approximation guarantees for shortest superstrings: simpler and better
- Prefix sorting DFAs: a recursive algorithm
- Substring complexity in sublinear space
- Algorithms for path-constrained sequence alignment
- On parsing optimality for dictionary-based text compression -- the \texttt{Zip} case
- The structural border array
- Periodicity and Repetitions in Parameterized Strings
- Suffix-sorting via Shannon-Fano-Elias codes
- A comparison of BWT approaches to string pattern matching
- A faster algorithm for computing maximal -gapped repeats in a string
- Fitness landscapes and the Andrews-Curtis conjecture
- Sequential pattern detection: similarities and differences across various fields
- Approximate pattern matching on elastic-degenerate text
- Construction of component tapes for radial placement machines
- Graph traversals, genes and matroids: An efficient case of the travelling salesman problem
- Representing prefix and border tables: results on enumeration
- Parameterized longest previous factor
- Communication-Efficient Private Protocols for Longest Common Subsequence
- Space-efficient representation of truncated suffix trees, with applications to Markov order estimation
- Space-efficient substring occurrence estimation
- Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis
- Polynomial-time approximation algorithms for weighted LCS problem
- Deciding word neighborhood with universal neighborhood automata
- Block-graph width
- Sets of pictures avoiding overlaps
- An algorithm with linear expected running time for string editing with substitutions and substring reversals
- Ask not what stringology can do for you: advances in pattern matching driven by computational biology
- Combinatorics of periods in strings.
- Order-preserving pattern matching indeterminate strings
- Palindromic decompositions with gaps and errors
- scientific article; zbMATH DE number 1754502 (Why is no real title available?)
- Robust variable selection for model-based learning in presence of adulteration
- Clusters of repetition roots: single chains
- Jewels of Stringology
- On new algorithms of mutual transformation of string schemes
- Profile of Tries
- Parallel algorithms to align multiple strings in the context of web data extraction
- Exact matching of RNA secondary structure patterns
- Polynomial-time approximation algorithms for weighted LCS problem
- Approximate symbolic pattern matching for protein sequence data
- DNA combinatorial messages and epigenomics: the case of chromatin organization and nucleosome occupancy in eukaryotic genomes
- Computing longest common extensions in partial words
- Constructing words with high distinct square densities
- On the Suffix Automaton with Mismatches
- Indexing Circular Patterns
- A linear time algorithm for shortest cyclic cover of strings
- On the tiling by translation problem
- Efficient data reconciliation
- Extending maximal perfect haplotype blocks to the realm of pangenomics
- Computing longest single-arm-gapped palindromes in a string
- Ultra-succinct representation of ordered trees with applications
- A subquadratic algorithm for minimum palindromic factorization
- Reverse engineering of compact suffix trees and links: a novel algorithm
- Efficient parameterized string matching
- COMBINATORIAL CHARACTERIZATION OF THE LANGUAGE RECOGNIZED BY FACTOR AND SUFFIX ORACLES
- A similarity measure for graphs with low computational complexity
- Anti-unification for unranked terms and hedges
- On the Structure of Consistent Partitions of Substring Set of a Word
- Fast RSK correspondence by doubling search
- An improved approximation algorithm for the discrete Fréchet distance
- Nonembeddability theorems via Fourier analysis
- Prefix-suffix duplication
- Faster approximate string matching for short patterns
- Content-dependent chunking for differential compression, the local maximum approach
- An impossibility result for phylogeny reconstruction from \(k\)-mer counts
- String inference from longest-common-prefix array
- Clusters of repetition roots forming prefix chains
- Inferring strings from suffix trees and links on a binary alphabet
- General suffix automaton construction algorithm and space bounds
- Practical compressed suffix trees
- Models and algorithms for competitive facility location problems with different customer behavior
- A parallel algorithm for the constrained multiple sequence alignment problem designed for GPUs
- An efficient algorithm for online square detection
- Adaptive memory programming: local search parallel algorithms for phylogenetic tree construc\-tion
- Fast searching in packed strings
- ONLINE AND DYNAMIC RECOGNITION OF SQUAREFREE STRINGS
- Fixed topology alignment with recombination
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