52. Takeyuki
Tamura,
MetNetComp: Database for minimal and maximal gene-deletion
strategies for growth-coupled production of genome-scale metabolic networks,
IEEE/ACM
Transactions on Computational Biology and Bioinformatics, in press.
51.
Takeyuki
Tamura, Ai Muto-Fujita,
Yukako Tohsato, Tomoyuki Kosaka,
Gene deletion algorithms for minimum reaction network design by mixed-integer
linear programming for metabolite production in constraint-based models:
gDel_minRN,
Journal of Computational Biology, 30(5):553-568, 2023.
50.
Takeyuki Tamura,
Trimming gene deletion strategies for growth-coupled
production in constraint-based metabolic networks: TrimGdel,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2):1540-1549,
2023.
49.
Yier Ma, Takeyuki Tamura*,
Dynamic solution space division-based methods for calculating reaction deletion
strategies for constraint-based metabolic networks for substance production:
DynCubeProd
Frontiers in Bioinformatics, 1:716112, 2021.
48.
Tatsuya Akutsu, Jesper Jansson,
Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura,
New and improved algorithms for unordered tree inclusion,
Theoretical Computer Science, 883, 83-98, 2021.
47.
Takeyuki Tamura,
L1 norm minimal mode-based methods for listing reaction network designs for
metabolite production,
IEICE Transactions on Information and Systems, 104(5), 679-687, 2021.
46.
Takeyuki Tamura,
Efficient reaction deletion algorithms for redesign of constraint-based
metabolic networks for metabolite production with weak coupling,
IPSJ Transactions on Bioinformatics, 14, 12-21, 2021.
45.
Tatsuya Akutsu, Avraham. A. Melkman
and Takeyuki Tamura,
Improved hardness of maximum common subgraph problems on labeled graphs of
bounded treewidth and bounded degree,
International Journal of Foundations of Computer Science, 31(2), 253-273, 2020.
44.
Y. Bao, S. Marini, Takeyuki
Tamura, M. Kamada, S. Maegawa, H. Hosokawa, J. Song, and T. Akutsu,
Toward more accurate prediction of caspase cleavage sites: a comprehensive
review of current methods, tools and features (Review Article),
Briefings in Bioinformatics, 20(5), 1669-1684, 2019.
43.
S. Itami-Matsumoto, M. Hayakawa, S.
Uchida-Kobayashi, M. Enomoto, A. Tamori, K. Mizuno, H. Toyoda, Takeyuki
Tamura, T. Akutsu, T. Ochiya, N. Kawada, and Y. Murakami,
Circulating exosomal miRNA profiles predict the occurrence and recurrence of
hepatocellular carcinoma in patients with direct-acting antiviral-induced
sustained viral response,
Biomedicines. 7(4), 87, 2019.
42.
Takeyuki Tamura,
Grid-based computational methods for the design of constraint-based
parsimonious chemical reaction networks to simulate metabolite production:
GridProd,
BMC Bioinformatics, 19:325, 2018.
41.
Takeyuki Tamura*,
Wei Lu, Jiangning Song, and Tatsuya Akutsu (* corresponding author)
Computing Minimum Reaction Modifications in a Boolean Metabolic Network,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15:6,
1853-1862, 2018.
40.
Xi Cheng, Takeyuki Tamura,
Wai-Ki Ching and Tatsuya Akutsu.
Discrimination of singleton and periodic attractors in Boolean networks,
Automatica, 84, 205-213, 2017.
39.
Tatsuya Akutsu, Jesper Jansson,
Atsuhiro Takasu, Takeyuki Tamura*, (* corresponding author)
On the parameterized complexity of associative and commutative unification,
Theoretical
Computer Science, Volume 660, Pages 57-74, 2017
Preliminary version has appeared in IPEC 2014.
38.
Wenpin Hou, Takeyuki Tamura,
Wai-Ki. Ching and Tatsuya Akutsu,
Finding and analyzing the minimum set of driver nodes in control of Boolean
networks,
Advances in Complex Systems, 19, 1650006 (32 pages), 2016.
37.
Tomoya Mori, Atsuhiro Takasu, Jesper
Jansson, Jaewook Hwang, Takeyuki Tamura, and Tatsuya Akutsu,
Similar Subtree Search Using Extended Tree Inclusion,
IEEE
Transactions on Knowledge and Data Engineering, Vol. 27, 3360-3373, 2015.
36.
Tatsuya Akutsu, Takeyuki Tamura,
Avraham A. Melkman, and Atsuhiro Takasu,
On the complexity of finding a largest common subtree of bounded degree,
Theoretical
Computer Science, 590, 2-16, 2015.
35.
Takeyuki Tamura,
Wei Lu, and Tatsuya Akutsu,
Computational Methods for Modification of Metabolic Networks (invited mini
review paper),
Computational
and Structural Biotechnology Journal, Volume 13, 376-381, 2015.
34.
Wei Lu, Takeyuki Tamura*,
Jiangning Song, and Tatsuya Akutsu, (* joint first author, and corresponding
author)
Computing smallest intervention strategies for multiple metabolic networks in a
Boolean model,
Journal
of Computational Biology, 22(2), 85-110, 2015.
33.
Chia-Jung Chang, Takeyuki Tamura*,
Kun-Mao Chao and Tatsuya Akutsu, (* corresponding author)
A fixed-parameter algorithm for detecting a singleton attractor in an AND/OR
Boolean network with bounded treewidth,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer Sciences,
E98-A(1), 384-390, 2015.
32.
Rikiya Takeuchi, Takeyuki Tamura,
Toru Nakayashiki, Yuichirou Tanaka, Ai Muto, Barry L. Wanner, and Hirotada
Mori,
Colony-live --a high-throughput method for measuring microbial colony growth
kinetics-- reveals diverse growth effects of gene knockouts in Escherichia
coli,
BMC
Microbiology, 14:171 doi:10.1186/1471-2180-14-171, 2014.
31.
Wei Lu, Takeyuki Tamura*#,
Jiangning Song, and Tatsuya Akutsu#, (* joint first author, # corresponding
authors)
Integer Programming-based Method for Designing Synthetic Metabolic Networks by
Minimum Reaction Insertion in a Boolean Model,
PLoS
ONE 9(3): e92637. doi:10.1371/journal.pone.0092637, 2014.
30.
Yushan Qiu, Takeyuki Tamura,
Wai-Ki Ching, and Tatsuya Akutsu,
On control of singleton attractors in multiple Boolean networks: integer
programming-based method,
BMC Systems Biology, 8
(Suppl for APBC2014):S1:S7, 2014.
29.
Tatsuya Akutsu, Takeyuki Tamura*,
Daiji Fukagawa, Atsuhiro Takasu, (* corresponding author)
Efficient exponential-time algorithms for edit distance between unordered trees,
(Preliminary version has appeared in CPM 2012),
Journal
of Discrete Algorithms, Vol.25, pp.79-93, 2014.
28.
Hao Jiang, Takeyuki Tamura,
Wai-Ki Ching and Tatsuya Akutsu,
On the complexity of inference and completion of Boolean networks from given
singleton attractors,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol.E96-A, No.11, pp. 2265-2274, 2013.
27.
Kazuhiro Takemoto, Takeyuki
Tamura and Tatsuya Akutsu,
Theoretical estimation of metabolic network robustness against multiple
reaction knockouts using branching process approximation,
Physica A, Vol. 392, pp. 5525--5535,
2013.
26.
Yang Zhao, Takeyuki Tamura,
Tatsuya Akutsu and Jean-Philippe Vert,
Flux balance impact degree: A new definition of impact degree to properly treat
reversible reactions in metabolic networks,
Bioinformatics,
Vol. 29(17), pp. 2178--2185, 2013.
25.
Tatsuya Akutsu and Takeyuki
Tamura,
A polynomial-time algorithm for computing the maximum common connected edge
subgraph of outerplanar graphs of bounded degree
(Preliminary version has appeared in MFCS 2012),
Algorithms, Vol.6, pp.119-135,
2013.
24.
Xi Chen, Tatsuya Akutsu, Takeyuki
Tamura and Wai-Ki Ching,
Finding optimal control policy in probabilistic Boolean networks with hard
constraints by using integer programming and dynamic programming
(Preliminary version has appeared in BIBM 2010),
International Journal of
Data Mining and Bioinformatics, Vol.7, No.3, pp.321-343, 2013.
23.
Natsu Nakajima, Takeyuki Tamura,
Yoshihiro Yamanishi, Katsuhisa Horimoto and Tatsuya Akutsu,
Network completion using dynamic programming and least-squares fitting,
The Scientific
World Journal, Volume 2012, Article ID 957620, 8 pages, 2012.
22.
Tatsuya Akutsu, Yang Zhao, Morihiro
Hayashida and Takeyuki Tamura,
Integer programming-based approach to attractor detection and control of
Boolean networks
(Preliminary version has appeared in CDC/CCC 2009),
IEICE
Transactions on Information and Systems, Vol.E95-D, No.12, pp.2960-2970, 2012.
21.
Tomoya Mori, Takeyuki Tamura,
Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita and Tatsuya Akutsu,
A clique-based method using dynamic programming for computing edit distance
between unordered trees,
Journal of
Computational Biology, 19(10): 1089-1104, 2012.
20.
Tatsuya Akutsu, Sven Kosub, Avraham
A. Melkman and Takeyuki Tamura,
Finding a periodic attractor of a Boolean network,
IEEE/ACM
Transactions on Computational Biology and Bioinformatics, Vol. 9,
pp,1410--1421, 2012.
19.
Tatsuya Akutsu, Avraham A. Melkman
and Takeyuki Tamura,
Singleton and 2-periodic attractors of sign-definite Boolean networks,
Information
Processing Letters, Vol.112, Issues 1-2, pp.35--38, 2012.
18.
Kazuhiro Takemoto, Takeyuki
Tamura, Yang Cong, Wai-Ki Ching, Jean-Philippe Vert and Tatsuya Akutsu,
Analysis of the impact degree distribution in metabolic networks using
branching process approximation,
Physica
A, 391, 379, 17pages, 2012.
17.
Takeyuki Tamura*,
Yang Cong, Tatsuya Akutsu and Wai-Ki Ching, (* corresponding author)
An Efficient Method of Computing Impact Degrees for Multiple Reactions in
Metabolic Networks with Cycles,
IEICE
Transactions on Information and Systems, Vol.E94-D, No.12 pp.2393-2399, 2011.
16.
Tatsuya Akutsu, Avraham. A. Melkman,
Takeyuki Tamura and Masaki Yamamoto,
Determining a singleton attractor of a Boolean network with nested canalyzing
functions,
Journal of
Computational Biology, Vol. 18(10), pp. 1--16, 2011.
15.
Daiji Fukagawa, Takeyuki Tamura,
Atsuhiro Takasu, Etsuji Tomita and Tatsuya Akutsu,
A clique-based method for the edit distance between unordered trees and its
application to analysis of glycan structures,
BMC
Bioinformatics (Suppl. for APBC 2011), 12, Suppl 1, S14 (9 pages), 2011.
14.
Tatsuya Akutsu, Daiji Fukagawa,
Atsuhiro Takasu and Takeyuki Tamura,
Exact algorithms for computing tree edit distance between unordered trees,
Theoretical
Computer Science, Vol. 421, pp. 352-364, 2011
13.
J.B. Brown, Takashi Urata, Takeyuki
Tamura, Midori A. Arai, Takeo Kawabata and Tatsuya Akutsu,
Compound analysis via graph kernels incorporating chirality,
Journal
of Bioinformatics and Computational Biology (Suppl. for GIW 2010), Vol. 8,
Suppl. 1, 63-81, 2010.
12.
Takeyuki Tamura*
and Tatsuya Akustu, (* corresponding author)
Exact algorithms for finding a minimum reaction cut under a Boolean model of
metabolic networks,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol. E93-A, pp. 1497-1507, 2010.
11.
Avraham Melkman, Takeyuki Tamura*,
Tatsuya Akutsu, (* corresponding author)
Determining a singleton attractor of an AND/OR Boolean network in O(1.587^n)
time.
Information Processing
Letters, Vol. 110, pp. 565-569, 2010.
10.
Takeyuki Tamura,
Kazuhiro Takemoto and Tatsuya Akutsu,
Finding minimum reaction cuts of metabolic networks under a Boolean model using
integer programming and feedback vertex sets, (PDF)
(Preliminary version has appeared in IIBM2009),
International
Journal of Knowledge Discovery in Bioinformatics, Vol 1, pp. 14-31, 2010.
9.
Morihiro Hayashida, Takeyuki
Tamura, Tatsuya Akutsu, Wai-Ki Ching and Yang Cong,
On distribution and enumeration of attractors in probabilistic Boolean networks
(Preliminary version has appeared in OSB 2008),
IET
Systems Biology, Vol. 3, pp. 465-474, 2009.
8.
Tatsuya Akutsu and Takeyuki
Tamura,
On finding a fixed point in a Boolean network with maximum indegree 2,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol.E92-A, No.8, pp.1771-1778, 2009.
7.
Takeyuki Tamura
and Tatsuya Akutsu,
Algorithms for singleton attractor detection in planar and nonplanar AND/OR
Boolean networks
(Preliminary version has appeared in AB2008),
Mathematics in
Computer Science, Vol. 2, No. 3, pp. 401--420, 2009.
6.
Takeyuki Tamura
and Tatsuya Akutsu,
Detecting a singleton attractor in a Boolean network utilizing SAT algorithms
(Preliminary version has appeared in FCT2007),
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol.E92-A, No.2 pp.493--501, 2009.
5.
Morihiro Hayashida, Takeyuki
Tamura*, Tatsuya Akutsu, Shu-Qin Zhang and Wai-Ki Ching, (* joint first
author)
Algorithms and complexity analyses for control of singleton attractors in
Boolean networks,
EURASIP Journal
on Bioinformatics and Systems Biology, 521407 (16pages), 2008.
4.
Takeyuki Tamura
and Hiro Ito,
Inferring pedigree graphs from genetic distances.
IEICE
Transactions on Information and Systems, Vol. E91-D, No. 2, pp. 162--169, 2008.
3.
Takeyuki Tamura*
and Tatsuya Akutsu, (* corresponding author)
Subcellular location prediction of proteins using support vector machines with
alignment of block sequences utilizing amino acid composition.
BMC Bioinformatics, Vol.
8, No. 466, 2007. - Web server
2.
Takeyuki Tamura
and Tatsuya Akutsu,
Approximation algorithms for optimal RNA secondary structures common to
multiple sequences,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol. E-90A, No.5, pp.917--923, 2007.
1.
Hiro Ito, Kazuo Iwama, and Takeyuki
Tamura,
Efficient methods for determining DNA probe orders,
IEICE
Transactions on Fundamentals of Electronics, Communications and Computer
Sciences, Vol. E89-A, No. 5, pp.1292--1298, 2006.