On the public citation graph
Database indexing for large DNA and protein sequence collections
0 signed · 104 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1097-024x(199911)29:13<1149::aid-spe274>3.0.co;2-oopenalex-snapshot
Reducing the space requirement of suffix trees
inferredcites →https://doi.org/10.1002/spe.395openalex-snapshot
An efficient object promotion algorithm for persistent object systems
inferredcites →https://doi.org/10.1002/spe.4380250203openalex-snapshot
Efficient implementation of suffix trees
inferredcites →https://doi.org/10.1006/jmbi.1990.9999openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1006/jmbi.2000.3576openalex-snapshot
Inferring regulatory elements from a whole genome. an analysis of Helicobacter pyloriσ80 family of promoter signals
inferredcites →https://doi.org/10.1007/3-540-45123-4_27openalex-snapshot
Linear Bidirectional On-Line Construction of Affix Trees
inferredcites →https://doi.org/10.1007/3-540-45123-4_28openalex-snapshot
Using Suffix Trees for Gapped Motif Discovery
inferredcites →https://doi.org/10.1007/3-540-45123-4_29openalex-snapshot
Indexing Text with Approximate q-Grams
inferredcites →https://doi.org/10.1007/3-540-45498-5_3openalex-snapshot
Architecture of the PEVM: A High-Performance Orthogonally Persistent Java™ Virtual Machine
inferredcites →https://doi.org/10.1007/3-540-47849-3_18openalex-snapshot
Factor Oracle: A New Structure for Pattern Matching
inferredcites →https://doi.org/10.1007/3-540-48452-3_13openalex-snapshot
A New Indexing Method for Approximate String Matching
inferredcites →https://doi.org/10.1007/3-540-52846-6_103openalex-snapshot
Boyer-Moore approach to approximate string matching
inferredcites →https://doi.org/10.1007/3-540-60044-2_33openalex-snapshot
Fast approximate matching using suffix trees
inferredcites →https://doi.org/10.1007/3-540-60044-2_48openalex-snapshot
Genome analysis: Pattern search in biological macromolecules
inferredcites →https://doi.org/10.1007/978-3-540-49382-2_17openalex-snapshot
Space Efficient Suffix Trees
inferredcites →https://doi.org/10.1007/978-3-642-59623-0openalex-snapshot
Fully Integrated Data Environments
inferredcites →https://doi.org/10.1007/bf01206331openalex-snapshot
On-line construction of suffix trees
inferredcites →https://doi.org/10.1007/bfb0029808openalex-snapshot
Approximate string-matching over suffix trees
inferredcites →https://doi.org/10.1007/bfb0054100openalex-snapshot
Providing orthogonal persistence for Java
inferredcites →https://doi.org/10.1007/pl00009253openalex-snapshot
Faster Approximate String Matching
inferredcites →https://doi.org/10.1016/0022-2836(81)90087-5openalex-snapshot
Identification of common molecular subsequences
inferredcites →https://doi.org/10.1016/0304-3975(92)90143-4openalex-snapshot
Approximate string-matching with q-grams and maximal matches
inferredcites →https://doi.org/10.1016/s1570-8667(03)00034-0openalex-snapshot
The suffix binary search tree and suffix AVL tree
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1093/bioinformatics/15.2.111openalex-snapshot
A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.
inferredcites →https://doi.org/10.1093/bioinformatics/15.5.426openalex-snapshot
REPuter: fast computation of maximal repeats in complete genomes.
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1101/gr.8.11.1202openalex-snapshot
Predicting Gene Regulatory Elements in Silico on a Genomic Scale
inferredcites →https://doi.org/10.1109/18.259648openalex-snapshot
Asymptotic properties of data compression and suffix trees
inferredcites →https://doi.org/10.1109/sfcs.1998.743441openalex-snapshot
Overcoming the memory bottleneck in suffix tree construction
inferredcites →https://doi.org/10.1109/sfcs.2000.892127openalex-snapshot
Opportunistic data structures with applications
inferredcites →https://doi.org/10.1109/swat.1973.13openalex-snapshot
Linear pattern matching algorithms
inferredcites →https://doi.org/10.1126/science.1058040openalex-snapshot
The Sequence of the Human Genome
inferredcites →https://doi.org/10.1137/0222058openalex-snapshot
Suffix Arrays: A New Method for On-Line String Searches
inferredcites →https://doi.org/10.1145/135239.135243openalex-snapshot
A new approach to text searching
inferredcites →https://doi.org/10.1145/235809.235810openalex-snapshot
Fast text searching for regular expressions or automaton searching on tries
inferredcites →https://doi.org/10.1145/245882.245905openalex-snapshot
An orthogonally persistent Java
inferredcites →https://doi.org/10.1145/28869.28873openalex-snapshot
Complete inverted files for efficient text retrieval and analysis
inferredcites →https://doi.org/10.1145/299432.299460openalex-snapshot
q -gram based database searching using a suffix array (QUASAR)
inferredcites →https://doi.org/10.1145/321941.321946openalex-snapshot
A Space-Economical Suffix Tree Construction Algorithm
inferredcites →https://doi.org/10.1145/332306.332553openalex-snapshot
Extracting structured motifs using a suffix tree—algorithms and application to promoter consensus identification
inferredcites →https://doi.org/10.1145/335191.335434openalex-snapshot
On effective multi-dimensional indexing for strings
inferredcites →https://doi.org/10.1145/375360.375365openalex-snapshot
A guided tour to approximate string matching
inferredcites →https://doi.org/10.19153/cleiej.1.2.3openalex-snapshot
A Practical q -Gram Index for Text Retrieval Allowing Errors
inferredcites →https://doi.org/10.5555/313852.314087openalex-snapshot
Efficient suffix trees on secondary storage
inferredcites →https://doi.org/10.7551/mitpress/2022.001.0001openalex-snapshot
Computational Molecular Biology
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/11425274_25openalex-snapshot
CSI: Clustered Segment Indexing for Efficient Approximate Searching on the Secondary Structure of Protein Sequences
inferred← citeshttps://doi.org/10.1007/11430919_26openalex-snapshot
A Novel Indexing Method for Efficient Sequence Matching in Large DNA Database Environment
inferred← citeshttps://doi.org/10.1007/11602569_8openalex-snapshot
Search-Optimized Suffix-Tree Storage for Biological Applications
inferred← citeshttps://doi.org/10.1007/11670834_19openalex-snapshot
Information Retrieval of Sequential Data in Heterogeneous XML Databases
inferred← citeshttps://doi.org/10.1007/11780441_8openalex-snapshot
Obtaining Provably Good Performance from Suffix Trees in Secondary Storage
inferred← citeshttps://doi.org/10.1007/978-0-387-30162-4_413openalex-snapshot
Suffix Tree Construction in Hierarchical Memory
inferred← citeshttps://doi.org/10.1007/978-1-4939-2864-4_413openalex-snapshot
Suffix Tree Construction in Hierarchical Memory
inferred← citeshttps://doi.org/10.1007/978-1-59745-574-9_6openalex-snapshot
Indexing Protein Structures Using Suffix Trees
inferred← citeshttps://doi.org/10.1007/978-3-030-65847-2_10openalex-snapshot
Relational Text-Type for Biological Sequences
inferred← citeshttps://doi.org/10.1007/978-3-540-71701-0_103openalex-snapshot
A Practical Method for Approximate Subsequence Search in DNA Databases
inferred← citeshttps://doi.org/10.1007/978-3-540-73390-4_3openalex-snapshot
Exhaustive Peptide Searching Using Relations
inferred← citeshttps://doi.org/10.1007/978-3-540-73556-4_27openalex-snapshot
An Experimental Study of Compressed Indexing and Local Alignments of DNA
inferred← citeshttps://doi.org/10.1007/978-3-642-13818-8_22openalex-snapshot
An Indexing Scheme for Fast and Accurate Chemical Fingerprint Database Searching
inferred← citeshttps://doi.org/10.1007/978-3-642-27848-8_413-2openalex-snapshot
Suffix-Tree Construction in Hierarchical Memory
inferred← citeshttps://doi.org/10.1007/s00453-006-1228-8openalex-snapshot
A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays
inferred← citeshttps://doi.org/10.1007/s00779-012-0569-3openalex-snapshot
Efficient techniques on retrieving bio-information for active U-healthcare
inferred← citeshttps://doi.org/10.1007/s10489-010-0233-4openalex-snapshot
A hash trie filter method for approximate string matching in genomic databases
inferred← citeshttps://doi.org/10.1007/s11227-006-0041-0openalex-snapshot
Survey on index based homology search algorithms
inferred← citeshttps://doi.org/10.1016/j.future.2009.08.007openalex-snapshot
VisGenome with CartoonPlus: Supporting large scale genomic analyses via physical space deformation
inferred← citeshttps://doi.org/10.1016/j.jda.2012.01.001openalex-snapshot
On-line suffix tree construction with reduced branching
inferred← citeshttps://doi.org/10.1016/j.jpdc.2007.07.008openalex-snapshot
PSIST: A scalable approach to indexing protein structures using suffix trees
inferred← citeshttps://doi.org/10.1089/cmb.2012.0256openalex-snapshot
Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn032openalex-snapshot
Compressed indexing and local alignment of DNA
inferred← citeshttps://doi.org/10.1093/nar/gks408openalex-snapshot
Prospects and limitations of full-text index structures in genome analysis
inferred← citeshttps://doi.org/10.1109/bibe.2006.253326openalex-snapshot
Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model
inferred← citeshttps://doi.org/10.1109/csb.2005.46openalex-snapshot
PSIST: indexing protein structures using suffix trees
inferred← citeshttps://doi.org/10.1109/ipdps.2008.4536176openalex-snapshot
Supporting high performance bioinformatics flat-file data processing using indices
inferred← citeshttps://doi.org/10.1109/itsim.2010.5561622openalex-snapshot
Enhanced CAFÉ indexing algorithm using hashing function
inferred← citeshttps://doi.org/10.1145/1186810.1186816openalex-snapshot
A data structure for a sequence of string accesses in external memory
inferred← citeshttps://doi.org/10.1145/1723112.1723128openalex-snapshot
High throughput and large capacity pipelined dynamic search tree on FPGA
inferred← citeshttps://doi.org/10.1145/2457317.2457383openalex-snapshot
Trying to outperform a well-known index with a sequential scan
inferred← citeshttps://doi.org/10.1145/2488551.2488579openalex-snapshot
Efficient parallel construction of suffix trees for genomes larger than main memory
inferred← citeshttps://doi.org/10.1145/3388984.3390877openalex-snapshot
Updated index to perform fast regular expression search
inferred← citeshttps://doi.org/10.1145/3589297openalex-snapshot
Exploiting Structure in Regular Expression Queries
inferred← citeshttps://doi.org/10.11606/d.55.2009.tde-19012010-103825openalex-snapshot
Perseus:uma nova técnica para tratar árvores de sufixo persistentes
inferred← citeshttps://doi.org/10.1177/0165551506059229openalex-snapshot
An efficient approach for sequence matching in large DNA databases
inferred← citeshttps://doi.org/10.1177/0165551506062329openalex-snapshot
An efficient DNA sequence searching method using position specific weighting scheme
inferred← citeshttps://doi.org/10.1201/9781420036275-15openalex-snapshot
Lookup Tables, Suffix Trees and Suffix Arrays
inferred← citeshttps://doi.org/10.12988/ces.2014.4684openalex-snapshot
A survey on disk-based genome sequence indexing
inferred← citeshttps://doi.org/10.1587/transinf.2018dap0005openalex-snapshot
The BINDS-Tree: A Space-Partitioning Based Indexing Scheme for Box Queries in Non-Ordered Discrete Data Spaces
inferred← citeshttps://doi.org/10.1587/transinf.e94.d.1369openalex-snapshot
A Fast Divide-and-Conquer Algorithm for Indexing Human Genome Sequences
inferred← citeshttps://doi.org/10.1587/transinf.e94.d.2557openalex-snapshot
A Storage-Efficient Suffix Tree Construction Algorithm for Human Genome Sequences
inferred← citeshttps://doi.org/10.2172/1186981openalex-snapshot
Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale
inferred← citeshttps://doi.org/10.31274/rtd-180813-17140openalex-snapshot
Suffix trees and suffix arrays in primary and secondary storage
inferred← citeshttps://doi.org/10.3390/biotech11030031openalex-snapshot
Bio-Strings: A Relational Database Data-Type for Dealing with Large Biosequences
inferred← citeshttps://doi.org/10.4028/www.scientific.net/amm.733.867openalex-snapshot
Suffix Tree Constructing Algorithm for Datasets with Discrete Contents
inferred← citeshttps://doi.org/10.48550/arxiv.1108.1228openalex-snapshot
An index for regular expression queries: Design and implementation
inferred← citeshttps://doi.org/10.48550/arxiv.1109.6884openalex-snapshot
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings
inferred← citeshttps://doi.org/10.5220/0004143400950102openalex-snapshot
String Searching in Referentially Compressed Genomes
inferred← citeshttps://doi.org/10.5281/zenodo.1328979openalex-snapshot
Fast Database Indexing For Large Protein Sequence Collections Using Parallel N-Gram Transformation Algorithm
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.