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Research Output 1999 2019

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Article
2019

Dynamic index and LZ factorization in compressed space

Nishimoto, T., Tomohiro, I., Inenaga, S., Bannai, H. & Takeda, M., Jan 1 2019, In : Discrete Applied Mathematics.

Research output: Contribution to journalArticle

Factorization
Deletion
Insertion
Encoding
Signature

On the size of the smallest alphabet for Lyndon trees

Nakashima, Y., Takagi, T., Inenaga, S., Bannai, H. & Takeda, M., Nov 5 2019, In : Theoretical Computer Science. 792, p. 131-143 13 p.

Research output: Contribution to journalArticle

Binary trees
Ordered Trees
Strings
Binary Tree
Leaves

Refining the r-index

Bannai, H., Gagie, T. & I, T., Jan 1 2019, (Accepted/In press) In : Theoretical Computer Science.

Research output: Contribution to journalArticle

Refining
Genes
Genome
Burrows-Wheeler Transform
Run Length
2018
1 Citation (Scopus)

Algorithms and combinatorial properties on shortest unique palindromic substrings

Inoue, H., Nakashima, Y., Mieno, T., Inenaga, S., Bannai, H. & Takeda, M., Sep 1 2018, In : Journal of Discrete Algorithms. 52-53, p. 122-132 11 p.

Research output: Contribution to journalArticle

Strings
Interval
Query
Palindrome
Optimal Solution
1 Citation (Scopus)

Diverse Palindromic Factorization is NP-Complete

Bannai, H., Gagie, T., Inenaga, S., Kärkkäinen, J., Kempa, D., Piakowski, M. & Sugimoto, S., Feb 1 2018, In : International Journal of Foundations of Computer Science. 29, 2, p. 143-163 21 p.

Research output: Contribution to journalArticle

Factorization
2017
1 Citation (Scopus)

Efficient Computation of Substring Equivalence Classes with Suffix Arrays

Narisawa, K., Hiratsuka, H., Inenaga, S., Bannai, H. & Takeda, M., Oct 1 2017, In : Algorithmica. 79, 2, p. 291-318 28 p.

Research output: Contribution to journalArticle

Suffix Array
Equivalence classes
Equivalence class
Strings
Text Indexing
1 Citation (Scopus)

Inferring strings from Lyndon factorization

Nakashima, Y., Okabe, T., I, T., Inenaga, S., Bannai, H. & Takeda, M., Aug 15 2017, In : Theoretical Computer Science. 689, p. 147-156 10 p.

Research output: Contribution to journalArticle

Factorization
Strings
p.m.
Lyndon Words
Unique factorisation
20 Citations (Scopus)

The "runs" theorem

Bannai, H., I, T., Inenaga, S., Nakashima, Y., Takeda, M. & Tsuruta, K., Jan 1 2017, In : SIAM Journal on Computing. 46, 5, p. 1501-1514 14 p.

Research output: Contribution to journalArticle

Strings
Theorem
Linear-time Algorithm
Lyndon Words
Factorization
2016
5 Citations (Scopus)

Closed factorization

Badkobeh, G., Bannai, H., Goto, K., I, T., Iliopoulos, C. S., Inenaga, S., Puglisi, S. J. & Sugimoto, S., Oct 30 2016, In : Discrete Applied Mathematics. 212, p. 23-29 7 p.

Research output: Contribution to journalArticle

Factorization
Strings
Closed
Sturmian Words
Factorise
9 Citations (Scopus)

Faster Lyndon factorization algorithms for SLP and LZ78 compressed text

I, T., Nakashima, Y., Inenaga, S., Bannai, H. & Takeda, M., Dec 20 2016, In : Theoretical Computer Science. 656, p. 215-224 10 p.

Research output: Contribution to journalArticle

Straight-line Programs
Factorization
Data structures
Preprocessing
Data Structures
4 Citations (Scopus)

Generalized pattern matching and periodicity under substring consistent equivalence relations

Matsuoka, Y., Aoki, T., Inenaga, S., Bannai, H. & Takeda, M., Dec 20 2016, In : Theoretical Computer Science. 656, p. 225-233 9 p.

Research output: Contribution to journalArticle

Pattern matching
Pattern Matching
Equivalence relation
Periodicity
Strings
2015
5 Citations (Scopus)

Compressed automata for dictionary matching

I, T., Nishimoto, T., Inenaga, S., Bannai, H. & Takeda, M., May 1 2015, In : Theoretical Computer Science. 578, p. 30-41 12 p.

Research output: Contribution to journalArticle

Glossaries
Automata
Straight-line Programs
Matching Problem
Dictionary
5 Citations (Scopus)

Constructing LZ78 tries and position heaps in linear time for large alphabets

Nakashima, Y., I, T., Inenaga, S., Bannai, H. & Takeda, M., Sep 1 2015, In : Information Processing Letters. 115, 9, p. 655-659 5 p.

Research output: Contribution to journalArticle

Heap
Linear Time
Strings
Factorization
Suffix Tree
7 Citations (Scopus)

Detecting regularities on grammar-compressed strings

I, T., Matsubara, W., Shimohira, K., Inenaga, S., Bannai, H., Takeda, M., Narisawa, K. & Shinohara, A., Feb 1 2015, In : Information and Computation. 240, p. 74-89 16 p.

Research output: Contribution to journalArticle

Straight-line Programs
Grammar
Strings
Regularity
Context free grammars
2014
9 Citations (Scopus)

Inferring strings from suffix trees and links on a binary alphabet

I, T., Inenaga, S., Bannai, H. & Takeda, M., Jan 30 2014, In : Discrete Applied Mathematics. 163, PART 3, p. 316-325 10 p.

Research output: Contribution to journalArticle

Suffix Tree
Reverse engineering
Strings
Binary
Information retrieval
6 Citations (Scopus)

On the existence of tight relative 2-designs on binary Hamming association schemes

Bannai, E., Bannai, E. & Bannai, H., Jan 1 2014, In : Discrete Mathematics. 314, 1, p. 17-37 21 p.

Research output: Contribution to journalArticle

Association Scheme
T-designs
Binary
Shell
Weight Function
2013
11 Citations (Scopus)

Fast q-gram mining on SLP compressed strings

Goto, K., Bannai, H., Inenaga, S. & Takeda, M., Jan 1 2013, In : Journal of Discrete Algorithms. 18, p. 89-99 11 p.

Research output: Contribution to journalArticle

Straight-line Programs
Mining
Strings
Data Classification
Computational Experiments
2012
4 Citations (Scopus)

An efficient algorithm to test square-freeness of strings compressed by straight-line programs

Bannai, H., Gagie, T., I, T., Inenaga, S., Landau, G. M. & Lewenstein, M., Oct 15 2012, In : Information Processing Letters. 112, 19, p. 711-714 4 p.

Research output: Contribution to journalArticle

Straight-line Programs
Efficient Algorithms
Strings
Square free
Arbitrary
3 Citations (Scopus)

Finding characteristic substrings from compressed texts

Inenaga, S. & Bannai, H., Feb 1 2012, In : International Journal of Foundations of Computer Science. 23, 2, p. 261-280 20 p.

Research output: Contribution to journalArticle

Equivalence classes
Computer science
Polynomials
2011
11 Citations (Scopus)

Verifying and enumerating parameterized border arrays

I, T., Inenaga, S., Bannai, H. & Takeda, M., Nov 25 2011, In : Theoretical Computer Science. 412, 50, p. 6959-6981 23 p.

Research output: Contribution to journalArticle

Pattern matching
Pattern Matching
Matching Problem
Linear-time Algorithm
Binary
2009
9 Citations (Scopus)

Linear-Time text compression by longest-first substitution

Nakamura, R., Inenaga, S., Bannai, H., Funamoto, T., Takeda, M. & Shinohara, A., Dec 1 2009, In : Algorithms. 2, 4, p. 1429-1448 20 p.

Research output: Contribution to journalArticle

Text Compression
Substitution
Linear Time
Substitution reactions
Linear-time Algorithm
8 Citations (Scopus)

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

Yashiro, Y., Bannai, H., Minowa, T., Yabiku, T., Miyano, S., Osawa, M., Iwama, A. & Nakauchi, H., Jan 1 2009, In : International journal of hematology. 89, 1, p. 24-33 10 p.

Research output: Contribution to journalArticle

Hematopoietic Stem Cells
Genes
Microarray Analysis
Gene Library
Transcriptome
2008

Reachability on suffix tree graphs

Higa, Y., Bannai, H., Inenaga, S. & Takeda, M., Feb 1 2008, In : International Journal of Foundations of Computer Science. 19, 1, p. 147-162 16 p.

Research output: Contribution to journalArticle

Merging
Labeling
5 Citations (Scopus)

Uniqueness of certain association schemes

Bannai, E., Bannai, E. & Bannai, H., Aug 1 2008, In : European Journal of Combinatorics. 29, 6, p. 1379-1395 17 p.

Research output: Contribution to journalArticle

Association Scheme
Uniqueness
Spherical Codes
Optimal Codes
Henry
2007
1 Citation (Scopus)

On the complexity of deriving position specific score matrices from positive and negative sequences

Akutsu, T., Bannai, H., Miyano, S. & Ott, S., Apr 1 2007, In : Discrete Applied Mathematics. 155, 6-7, p. 676-685 10 p.

Research output: Contribution to journalArticle

Molecular biology
Computational Molecular Biology
Computational complexity
Hardness
Polynomials
2006
22 Citations (Scopus)

Contribution of comparative fish studies to general endocrinology: Structure and function of some osmoregulatory hormones

Takei, Y., Kawakoshi, A., Tsukada, T., Yuge, S., Ogoshi, M., Inoue, K., Hyodo, S., Bannai, H. & Miyano, S., Sep 1 2006, In : Journal of Experimental Zoology Part A: Comparative Experimental Biology. 305, 9, p. 787-798 12 p.

Research output: Contribution to journalArticle

endocrinology
hormones
fish
body fluids
natriuretic peptides
2005
9 Citations (Scopus)

Estimating gene networks from expression data and binding location data via boolean networks

Hirose, O., Nariai, N., Tamada, Y., Bannai, H., Imoto, S. & Miyano, S., 2005, In : Unknown Journal. 3482, III, p. 349-356 8 p.

Research output: Contribution to journalArticle

Gene expression
Genes
gene
gene expression
Microarrays
23 Citations (Scopus)

Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models

Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M. & Miyano, S., Dec 1 2005, In : Journal of bioinformatics and computational biology. 3, 6, p. 1295-1313 19 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Bayesian networks
Gene expression
Genes
Gene Expression
2004
7 Citations (Scopus)

An O(N2) algorithm for discovering optimal Boolean pattern pairs

Bannai, H., Hyyrö, H., Shinohara, A., Takeda, M., Nakai, K. & Miyano, S., Oct 1 2004, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 1, 4, p. 159-170 12 p.

Research output: Contribution to journalArticle

Strings
Boolean functions
RNA Stability
Numerics
Messenger RNA
19 Citations (Scopus)

Efficiently finding regulatory elements using correlation with gene expression

Bannai, H., Inenaga, S., Shinohara, A., Takeda, M. & Miyano, S., Jun 1 2004, In : Journal of bioinformatics and computational biology. 2, 2, p. 273-288 16 p.

Research output: Contribution to journalArticle

Gene expression
Gene Expression
Microarrays
Genes
DNA sequences
10 Citations (Scopus)
Strings
Efficient Algorithms
Denote
Form
Class
4 Citations (Scopus)

Finding optimal pairs of patterns

Bannai, H., Hyyrö, H., Shinohara, A., Takeda, M., Nakai, K. & Miyano, S., 2004, In : Lecture Notes in Computer Science. 3240, p. 450-462 13 p.

Research output: Contribution to journalArticle

Strings
Microarrays
Nucleotides
Numerics
Gene expression
215 Citations (Scopus)

Identification of novel adrenomedullin in mammals: A potent cardiovascular and renal regulator

Takei, Y., Inoue, K., Ogoshi, M., Kawahara, T., Bannai, H. & Miyano, S., Jan 2 2004, In : FEBS Letters. 556, 1-3, p. 53-58 6 p.

Research output: Contribution to journalArticle

Adrenomedullin
Mammals
Kidney
Tetraodontiformes
Synteny
2003
14 Citations (Scopus)
Pattern matching
Strings
Pattern Matching
Pruning
Class
137 Citations (Scopus)

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection

Tamada, Y., Kim, S. Y., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S. & Miyano, S., Dec 1 2003, In : Bioinformatics. 19, SUPPL. 2

Research output: Contribution to journalArticle

Gene Networks
Gene Regulatory Networks
DNA sequences
Bayesian networks
Bayesian Model
39 Citations (Scopus)
Strings
Graph in graph theory
Suffix Array
Subsequence
benzoylprop-ethyl
8 Citations (Scopus)

Intrasplicing--analysis of long intron sequences.

Ott, S., Tamada, Y., Bannai, H., Nakai, K. & Miyano, S., Jan 1 2003, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 339-350 12 p.

Research output: Contribution to journalArticle

Introns
DNA Sequence Analysis
Sequence Analysis
2002
17 Citations (Scopus)
Introns
Zebrafish
Diptera
Gene Expression
Datasets
532 Citations (Scopus)

Extensive feature detection of N-terminal protein sorting signals

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K. & Miyano, S., Jan 1 2002, In : Bioinformatics. 18, 2, p. 298-305 8 p.

Research output: Contribution to journalArticle

Intuition
Feature Detection
Protein Sorting Signals
Sorting
Molecular Biology
2 Citations (Scopus)

Fast algorithm for extracting multiple unordered short motifs using bit operations

Maruyama, O., Bannai, H., Tamada, Y., Kuhara, S. & Miyano, S., Oct 1 2002, In : Information sciences. 146, 1-4, p. 115-126 12 p.

Research output: Contribution to journalArticle

Unordered
Fast Algorithm
Genes
Gene
Gene Expression Profile
2001
98 Citations (Scopus)

Yeast [PSI+] "prions" that are crosstransmissible and susceptible beyond a species barrier through a quasi-prion state

Nakayashiki, T., Ebihara, K., Bannai, H. & Nakamura, Y., Jan 1 2001, In : Molecular Cell. 7, 6, p. 1121-1130 10 p.

Research output: Contribution to journalArticle

Prions
Yeasts
Proteins
Yarrowia
Kluyveromyces