PUBLICATIONS

BOOKS

1.     複雑ネットワークと制御理論  (Complex Networks and Control Theory)　　　　　　

       T. Akutsu and J.C. Nacher (216 pages,  森北出版 (2023) (Morikita Editorial) 

PAPERS

83.  Y. Tokuhara , T. Akutsu, J.-M. Schwartz and J.C. Nacher 

         A practically efficient algorithm for identifying critical control proteins in directed probabilistic biological networks

         NPJ Systems Biology and Applications 10(1):87, 1-14, (2024). 

82.   W. Someya, T. Akutsu and J.C. Nacher 

         Target control of linear directed networks based on the path cover problem.

         Scientific Reports, 14:16881, (11 pages), (2024). 

81.  T. Ochiai and J.C. Nacher

Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomics data and volatility-constrained correlation.

BioSystems (Elsevier), 242:105248 (10  pages), (2024)

80.   W. Someya, T. Akutsu, J.-M. Schwartz and J.C. Nacher 

         Measuring criticality in control of complex biological networks.

         NPJ Systems Biology and Applications 10(1):9, 1-16, (2024). 

79.  T. Ochiai and J.C. Nacher

Unveiling the directional network behind the financial statements data using volatility constraint correlation.

Physica A: Statistical mechanics and Its Applications (Elsevier) 600, 127534 (12 pp.) (2022)

78. Y. Shinzawa, T. Akutsu and J.C. Nacher

Uncovering and classifying the role of driven nodes in control of complex networks

Scientific Reports, 11, 9627 (13 pages), (2021). (Nature publishing Group) 

77. E. Yamaguchi, T. Akutsu and J.C. Nacher

Probabilistic critical controllability analysis of protein interaction network integrating normal brain aging gene expression profiles

Int. J. Molecular Sciences, 22(18), 9891 (21 pages), (2021) 

Supplementary Information accompanies the manuscript (40 pages).

76. M. Hayashida, H. Koyano and J.C. Nacher

Measuring the Similarity of Proteomes using Grammar-based Compression via Domain Combinations.

In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems

and Technologies (BIOSTEC 2020), - Volume 3: BIOINFORMATICS , pages 117-122 (2020)  DOI: 10.5220/0008913101170122 

75.  S. Nakashima, J. C. Nacher, J. Son, and T. Akutsu 

An Overview of Bioinformatics Methods for Analyzing Autism Spectrum Disorders

Current Pharmaceutical Design,  25(43), 4552-4559,  (2020).  (Review)

74.  M. Hayashida, J. C. Nacher, H. Koyano, 

Artificial Neural Network Approach to Prediction of Protein-RNA Residue-base Contacts.

In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - 

BIOINFORMATICS, vol.3 pages 163-167 (2019)  DOI: 10.5220/0007348101630167

73.  J-M. Schwartz, H. Otokuni, T. Akutsu and J. C. Nacher, 

Probabilistic controllability approach to metabolic fluxes in normal and cancer tissues.

  Nature Communications, 10, 2725 (9 pages), (2019).

72.   T. Mastubara, T. Ochiai, M. Hayashida, T. Akutsu and J. C. Nacher, 

         Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles,

       Journal of Bioinformatics and Computational Biology, 17(3) (Special Section on CBIM2018), 1940007 (11 pages), (2019).

71.    V. Ravindran, J. C. Nacher, T. Akutsu, M. Ishitsuka, A. Osadcenco, V. Sunitha, G. Bagler, J.-M. Schwartz, D. L. Robertson,

         Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems

         Scientific Reports  9, 2066 (11 pages), (2019)

70.    J.C. Nacher, M. Ishitsuka, S. Miyazaki, T. Akutsu 

        Finding and analysing the minimum set of driver nodes required to control multilayer metabolic networks

        Scientific Reports, 9(1), 576 (12 pages), (2019).

69.   J.C. Nacher and T. Akutsu

     Controllability methods for identifying associations between critical control ncRNAs and human diseases 

        Computational Biology of non-coding RNA:  

         Methods in Molecular Biology, 1912, 289-300, 2019.  Book chapter (Ed. Springer Nature Protocols).

68.  T. Ochiai and J. C. Nacher

     VC correlation analysis on the overnight and daytime return in Japanese stock market

        Physica A: Statistical Mechanics and Its applications (Elsevier), Vol. 515, Pages 537-545, (2019)

67.   Y. Bao, M. Hayashida, P. Liu, M. Ishitsuka, J.C. Nacher and T. Akutsu

        Analysis of critical and redundant vertices in controlling directed biological networks using feedback vertex sets. 

       Journal of  Computational Biology, 25, 1071-1090, 2018.

66.    T. Mori, H. Ngouv, M. Hayashida, T. Akutsu and J. C. Nacher

         ncRNA-disease association prediction based on sequence information and tripartite network.

         BMC Systems Biology 12, Suppl 1 (Supplement for APBC2018), 37 (11 pages), 2018.

65.    K. Wakai, M. Ishitsuka, T. Kishimoto, T. Ochiai and J.C. Nacher 

          Identification of genes and critical control proteins associated with inflammatory breast cancer using network controllability. 

          PLoS ONE 12(11): e0186353 (2017) 

64.    M. Ishitsuka, T. Akutsu and J. C. Nacher 

        Critical controllability analysis of directed biological networks using efficient graph reduction. 

         Scientific Reports (Nature Publishing Group) 7,  14361 (10 pages), 2017.

63.    J. C. Nacher and T. Ochiai

         Analytical solution of minimum dominating set in complex networks

         Int. J. Model. Simul. Sci. Computing, (World Scientific), Vol. 8, 1750005 (16 pages) (2017)

62.    Chi-Hua Tung, Jih-Hsu Chang and J. C. Nacher

         Unveiling disease-protein associations by navigating a structural alphabet-encoded protein network.

         Special Issue for the Int. Conf. on Medical and Health Informatics held in Taiwan (2017),

        Int. Journal of Management and Social Sciences, Vol. 6(S1), pp. 274 – 292, (2017) 

61.   T. Ochiai and J. C. Nacher

         Predicting link directionality in gene regulation from gene expression profiles using volatility-constrained correlation

         BioSystems (Elsevier), 145, 9-18 (2016).

60.      M. Ishitsuka, T. Akutsu and J. C. Nacher

           Critical controllability in proteome-wide protein interaction network integrating transcriptome.

          Nature Scientific Reports, 6, 23541 (13 pp.) (2016)  

          Online Supp. Information (41 pp.)

59.    J. C. Nacher and T. Akutsu

          Minimum dominating set-based Methods for Analyzing Biological Networks

          Methods (Elsevier), 102, 57-63 (2016).

          Issue on Pan-Omics analysis of biological data

58.   H. Kagami, T. Akutsu, S. Maegawa, H. Hosokawa and J. C. Nacher

        Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control

        Nature Scientific Reports, 4, 14577 (11 pp.) (2015).

        Online Supp. Information 30 pp.

57.   J. C. Nacher and T. Akutsu, 

        Structurally Robust Control of Complex Networks

        Physical Review E, 91, 012826 (23 pages) (2015).

 56.   J. C. Nacher and T. Akutsu, 

        Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets,

        Journal of Complex Networks (Oxford Univ. Press) 2, pp. 394-412 (2014).

55.  Yang-Yu Liu, J.C. Nacher, T. Ochiai, Mauro Martino, and Yaniv Altshuler

        Prospect Theory for Online Financial Trading

        PLoS ONE  9(10), e109458 (7 pp.) (2014).

54.   T. Ochiai, H. Takada and J.C. Nacher 

         Quantifying the behavior of price dynamics at opening time in stock market,  

        Physica A: Statistical Mechanics and Its Applications, 413, 534-543 (2014)

 53.   X.-M. Zhao, J. X. Gao and J. C. Nacher, 

        Data Mining in Translational Bioinformatics,

        BioMed Research International, vol. 2014, Article ID 656519 (2014) . 

52.   J.C. Nacher, B. Keith and J.-M. Schwartz,

       Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis,

       Proceedings of the Royal Society B: Biological Sciences, Vol. 281, 20132907 (10 pp.) (2014).

51.   T. Ochiai and J.C. Nacher  

        Volatility-constrained correlation identifies the directionality of the influence between

        Japan's Nikkei 225 and other  financial markets

        Physica A: Statistical Mechanics and Its Applications 393, 364-375 (2014).

50.   J.C. Nacher and T. Akutsu  

       Structural controllability of unidirectional bipartite networks

       Nature Scientific Reports, -Nature Publishing Group-, 3 :1647 (8 pp.) (2013). 

        Supplementary Information:

        http://www.nature.com/srep/2013/130410/srep01647

49.   J.C. Nacher 

       Community structure of noncoding RNA interation network 

       Journal of Integrative Bioinformatics, 10(2), 217 (12 pp.) (2013)

48.   J.C. Nacher and T. Akutsu  

       Dominating scale-free networks with variable scaling-exponent: heterogeneous networks are not difficult to control.

       New Journal of Physics, 14, 073005 (25 pp.) (2012).

47.  J.C. Nacher and T. Ochiai

       Foreign exchange market data analysis revelas statistical features that predict price movement acceleration,

       Physical Review E,  85, 056118 (7 pp.) (2012).                     

46.  Y. Zhao, M. Hayashida, J.C. Nacher, H. Nagamochi and T.Akutsu,

        Protein complex prediction via improved verification methods using constrained domain-domain matching,

        Int. Journal of Bionformatics Research and Applications, 8, 210-227 (2012).

45.   J.C. Nacher and J.-M. Schwartz,

        Modularity in protein complex and drug interactions reveals new polypharmacological properties,

        PLoS ONE, 7, e30028-41 (13 pp.) (2012)

44.   Y. Wang, J.C. Nacher and X.M. Zhao

       Predicting drug targets based on protein domains,

         Molecular BioSystems -The Royal Society of Chemistry- 8, 1528-1534 (2012)

43.  J.C. Nacher and V.B. Ryabov   

      Nonlinear response of gene expression to chemical perturbations: A noise-detector model and its predictions

       BioSystems, 107, 9-17, (2012)

42.  T. Ochiai and J.C. Nacher

       A model for the dynamic behavior of financial assets affected by news: The case of Tohoku-Kanto earthquake

      Physics Letters A, 375, 3552-3556, (2011)

41.  J.C. Nacher and T. Akutsu

       On the degree distribution of projected networks mapped from bipartite networks

       Physica A, 390, 4636-4651, (2011)

40.  J.C. Nacher and T. Ochiai

       Plus-Minus construction leads to perfect invisibility

       Journal of Mathematical Physics, 52, 012903 (17 pp.), (2011)

39.  J.C. Nacher, M. Hayashida and T. Akutsu

     The role of internal duplications in multi-domain proteins

      BioSystems Elsevier, 101, 127-135, (2010). -Supp. Material 31 pp.-

38.  J.C. Nacher and T.Ochiai

       Emergent principles in gene expression dynamics

      The Open Bioinformatics Journal, 5, 34-41 (2011).

37.  J.C. Nacher and N. Araki

      Structural chacterization and modeling of ncRNA-protein interactions

       BioSystems Elsevier, 101, 10-19, (2010).

36.  J.C. Nacher, T. Ochiai, M. Hayashida and T. Akutsu

     A mathematical model for generating bipartite graphs and its application to protein networks,

      Journal of Physics A: Mathematical and Theoretical, 42, 405005 (10 pp.) (2009).

35.  J.C. Nacher, M. Hayashida and T. Akutsu 

       Emergence of scale-free distribution in protein-protein interaction networks based on

       random selection of interacting domain pairs

       BioSystems Elsevier, 95, 155-159, (2009)

34.  T. Ochiai and J.C. Nacher

      On the construction of Complex Networks with optimal Tsallis Entropy

      Physica A, 388, 4887-4892, (2009)

33.  K. Mouri , J.C. Nacher and T. Akutsu

      A Mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation.

      PLoS ONE 4, 5131-5145 (2009)

32.  J.-M. Schwartz and J. C. Nacher

      Local and global modes of drug action in biochemical networks

       BMC Chemical Biology 9, 4-15 (2009).

31.  J.C. Nacher and T. Ochiai.

       Power-law of gene expression fluctuations

       Physics Letters A, 372, 6202-6206, (2008)

30.  J.C. Nacher and J-M. Schwartz

      A global view of drug-therapy interactions

      BMC Pharmacology, 8:5, 1-14, (2008)

29.  J.C. Nacher and T. Ochiai

      Transcription and regulation in negative feed-back loops,

      BioSystems, 91, 1, 76-82 (2008)

28.  T. Ochiai, U. Leonhardt, J.C. Nacher               

       A novel design of dielectric perfect invisibility devices  

       J. Math. Phys. 49, 032903, (2008)

27.  T. Takemoto, J.C. Nacher and T, Akutsu

       Correlation between structure and temperature in prokaryotic metabolic networks

        BMC Bioinformatics, 8 (1): 303, 1-17, (2007)

26.  J.C. Nacher and T. Akutsu

      Recent progress on the analysis of power-law features in complex cellular networks,

      Cell Biochemistry and Biophysics, 49, 37-47, (2007).

25.  T. Ochiai and J.C. Nacher

       Stochastic analysis of autoregulatory gene expression dynamics,

       Mathematical and Computer Modeling of Dynamical Systems, 14(4), 377-388 (2008).

24.  T. Akutsu and J.C. Nacher (Kyoto U, Bioinformatics Ctr.). 

      生体内ネットワーク構造の数理モデルと情報解析,

      Biophysics 47(2), 086-092, (2007).

23.  M. Itoh, J.C. Nacher, K. Kuma, S. Goto and M. Kanehisa

       Evolutionary history and functional implications of protein domains and their combinations in eukaryotes,

      Genome Biology, 8 (6): R121, 1-16 (2007)

22.  J-M. Schwartz, C. Gaugain, J.C. Nacher, A. de Daruvar, M. Kanehisa

       Observing metabolic functions at the genome scale,

       Genome Biology, 8 (6): R123, 1-15 (2007)

21.  T. Ochiai, J.C. Nacher and T. Akutsu

       Emergence of the self-similarity principle in gene expression dynamics,

       Physica A, 382, 739-752 (2007)

20.  J.C. Nacher, J-M. Schwartz, M. Kanehisa and T. Akutsu (Kyoto U)

       Identification of metabolic units induced by environmental signals,

       Bioinformatics (ISMB) 22(14), e375-83, 2006

19.  J.C. Nacher and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

       Sensitivity of the power-law exponent in gene expression distribution to mRNA decay rate,

      Physics Letters A, 360 , 174-178, 2006

18.  J.C. Nacher, T. Ochiai, T. Yamada, M. Kanehisa and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

      The role of log-normal dynamics in the evolution of metabolic pathways,

      BioSystems 83, 26-37, 2006

17.  J.C. Nacher, M. Hayashida and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

      Protein domain networks: scale-free mixing of positive and negative exponents,

      Physica A 367, 538-552, 2006

16.  T. Ochiai, J.C. Nacher,

       Inversible Max-Plus algebras and integrable systems.

       Journal of Mathematical Physics, 46, 063507 (2005).

15.  T. Akutsu, T. Ochiai and J.C. Nacher (Kyoto U, Bioinformatics Ctr.).

      生物情報ネットワークの構造およびダイナミクス解析、

      Protein, Nucleic Acid and Enzyme 50, 16: 2288-2293, 2005

14.  J.C. Nacher, T. Ochiai, and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

      On the relation between fluctuation and scaling-law in gene expression time series from yeast to human.

      Modern Physics Letters B 19, 1169-1177, 2005

13.  T.Ochiai, J.C. Nacher and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

      A stochastic approach to multi-gene expression dynamics,

      Physics Letters A 339, 1-9, 2005

12.  J.C. Nacher, N. Ueda, M. Kanehisa and T. Akutsu (Kyoto U)

      Flexible construction of hierarchical scale-free networks with general exponent,

      Physical Review E 71:036132 (1-7), 2005

11.  T.Ochiai, J.C. Nacher and T. Akutsu (Kyoto U, Bioinformatics Ctr.).

       A constructive approach to gene expression dynamics

       Physics Letters A 330, 313-321, 2004

10.  J.C. Nacher, N. Ueda, T. Yamada, M. Kanehisa and T. Akutsu (Kyoto U)

      Clustering under the line graph transformation: Application to enzymes network.

      BMC Bioinformatics, 5, 207:1-17, 2004

9.   J.C. Nacher, T. Yamada, S. Goto, M. Kanehisa and T. Akutsu (Kyoto U)

     Two complementary representations of a scale-free network,

     Physica A 349, 349-363, 2005

8.  D. Jido, A. Ramos, J.C. Nacher, A. Hosaka, E.Oset (Osaka U)

     Magnetic moments of the lambda(1405) and lambda(1670) resonances

     Physical Review C 66, 025203 (1-9) (2002).

7.   J.C. Nacher and E.Oset

     Study of polarization observables in double pion photo-production on the proton

     Nuclear Physics A 697, 372-387 (2002)

6.   J.C. Nacher, L. Roca, M.J. Vicente and E. Oset

     The role of Delta (1700) excitation and Rho production in double pion photoproduction”

     Nuclear Physics A 695, 295-327 (2001)

5.   M. Wolf, J. Ahrens, R. Beck, V. Hejny, J.D. Kellie, J.C. Nacher, B. Krusche and V. Metag (Mainz, Glasgow, Gottingen U.)

      Photoproduction of neutral pion pairs from the proton

     The European Physical Journal A, 9, 5-8 (2000) EDP Sciences

4.   J.C. Nacher, A. Parreno, E. Oset，A. Hosaka and M. Oka  (Osaka U. & Tokyo Inst. of Tech.)

     Chiral unitary approach to the N*N*PI, N*N*ETA couplings for the N*(1535) resonance”

     Nuclear Physics A 678, 187-211 (2000)

3.   J.C. Nacher, A. Ramos, E. Oset and H. Toki (Osaka U)

      Radiative production of the lambda(1405) resonance in K-collisions on protons and nuclei

      Physics Letters B 461, 299-306 (1999)

2.   J.C. Nacher, A. Ramos, E. Oset and H. Toki (Osaka U)

     Photoproduction of the lambda(1405) on the proton and nuclei

     Physics Letters B 455, 55-61 (1999)

1.   J.C. Nacher and E. Oset

      A model for the delta(1232)-pion reaction

      Nuclear Physics A 674, 205-228 (2000)

CONFERENCE PROCEEDINGS

(Under construction)