Aita, Takuyo: search on Z-Library

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1

Biophysical connection between evolutionary dynamics and thermodynamics in in vitro evolution

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

2012

Language:

english

File:

PDF, 364 KB

english, 2012

2

A visualization of 3D proteome universe: Mapping of a proteome ensemble into 3D space based on the protein-structure composition

Takuyo Aita, Koichi Nishigaki

Journal:

Molecular Phylogenetics and Evolution

Year:

2011

Language:

english

File:

PDF, 873 KB

english, 2011

3

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II

Takuyo Aita, Shunichi Morinaga, Yuzuru Husimi

Journal:

Bulletin of Mathematical Biology

Year:

2005

Language:

english

File:

PDF, 885 KB

english, 2005

4

Biomolecular information gained throughin vitroevolution

Takuyo Aita, Yuzuru Husimi

Journal:

Biophysical Reviews

Year:

2010

Language:

english

File:

PDF, 759 KB

english, 2010

5

3P-077 Systematic P2P interaction analysis realized by the demonstrable concept of epitope-like protein area (epa)(The 46th Annual Meeting of the Biophysical Society of Japan)

Yoshida, Chuya, Kitamura, Koichiro, Biyani, Madhu, Futakami, Masae, Aita, Takuyo, Nishigaki, Koichi

Journal:

Seibutsu Butsuri

Year:

2008

Language:

english

File:

PDF, 286 KB

english, 2008

6

In Vitro Selection of DNA Aptamers on Chips Using a Method for Generating Point Mutations

Asai, Ryoichi, Nishimura, Shin I., Aita, Takuyo, Takahashi, Katsutoshi

Journal:

Analytical Letters

Year:

2005

Language:

english

File:

PDF, 224 KB

english, 2005

7

Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing

Aita, Takuyo, Ichihashi, Norikazu, Yomo, Tetsuya

Journal:

Computational Biology and Chemistry

Year:

2013

Language:

english

File:

PDF, 850 KB

english, 2013

8

Periodic Pattern of Genetic and Fitness Diversity during Evolution of an Artificial Cell-Like System

Ichihashi, Norikazu, Aita, Takuyo, Motooka, Daisuke, Nakamura, Shota, Yomo, Tetsuya

Journal:

Molecular Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

9

Fitness Spectrum Among Random Mutants on Mt. Fuji-Type Fitness Landscape

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

1996

Language:

english

File:

PDF, 405 KB

english, 1996

10

Hierarchical distribution of ascending slopes, nearly neutral networks, highlands, and local optima at the dth order in an NK fitness landscape

Journal:

Journal of Theoretical Biology

Year:

2008

Language:

english

File:

PDF, 546 KB

english, 2008

11

3P-281 Prediction of the protein translation activity values by estimating Bahadur coefficients from a small number of experimental data set(The 46th Annual Meeting of the Biophysical Society of Japan)

Kazuta, Yasuaki, Matsuura, Tomoaki, Aita, Takuyo, Adachi, Jiro, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Year:

2008

Language:

english

File:

PDF, 297 KB

english, 2008

12

Thermodynamical interpretation of an adaptive walk on a Mt. Fuji-type fitness landscape: Einstein relation-like formula holds in a stochastic evolution

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 259 KB

english, 2003

13

2P301 Visualization of genome space by mapping into 3D-space(The 48th Annual Meeting of the Biophysical Society of Japan)

Nishigaki, Koichi, Aita, Takuyo

Journal:

Seibutsu Butsuri

Year:

2010

Language:

english

File:

PDF, 226 KB

english, 2010

14

Adaptive walks by the fittest among finite random mutants on a Mt. Fuji-type fitness landscape II. Effect of small non-additivity

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Mathematical Biology

Year:

2000

Language:

english

File:

PDF, 315 KB

english, 2000

15

Estimation of statistical binding properties of ligand population during in vitro selection based on population dynamics theory

Aita, Takuyo, Nishigaki, Koichi, Husimi, Yuzuru

Journal:

Mathematical Biosciences

Year:

2014

Language:

english

File:

PDF, 1.69 MB

english, 2014

16

Y-ligation: An efficient method for ligating single-stranded DNAs and RNAs with T4 RNA ligase

Koichi Nishigaki, Katsuya Taguchi, Yasunori Kinoshita, Takuyo Aita, Yuzuru Husimi

Journal:

Molecular Diversity

Year:

1998

Language:

english

File:

PDF, 58 KB

english, 1998

17

2P264 Global clustering of whole organisms enabled by the GP method(21A. Genome biology:Genome analysis,Poster)

Sharma, Harshita, Ohtani, Fumihito, Kumari, Parmila, Diwan, Deepti, Suzuki, Miho, Nemoto, Naoto, Aita, Takuyo, Nishigaki, Koichi

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 730 KB

english, 2014

18

Inference of fitness values and putative appearance time points for evolvable self-replicating molecules from time series of occurrence frequencies in an evolution reactor

Aita, Takuyo, Ichihashi, Norikazu, Yomo, Tetsuya

Journal:

Journal of Theoretical Biology

Year:

2016

Language:

english

File:

PDF, 428 KB

english, 2016

19

2P138 A novel biased mutation assembling method for evolutionary protein engineering(32. Evolutionary molecular engineering,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Suzuki, Takeru, Aita, Takuyo, Futatsugi, Rui, Husimi, Yuzuru

Journal:

Seibutsu Butsuri

Year:

2006

Language:

english

File:

PDF, 156 KB

english, 2006

20

A fitness model with a significant epistatic term : analysis of sequence-fitness relationship for mutants from Biased Mutation Scrambiling.

Aita, Takuyo, Hamamatsu, Norio, Nomiya, Yukiko, Uchiyama, Hidefumi, Shibanaka, Yasuhiko, Husimi, Yuzuru

Journal:

Seibutsu Butsuri

Year:

2001

File:

PDF, 261 KB

2001

21

1P-235 Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential(Bioinformatics:Structural genomics, The 47th Annual Meeting of the Biophysical Society of Japan)

Aita, Takuyo, Nisigaki, Koichi, Husimi, Yuzuru

Journal:

Seibutsu Butsuri

Year:

2009

Language:

english

File:

PDF, 462 KB

english, 2009

22

1P-072 Versatile techniques in making of a protein Hamming library for the fast systematic directed evolution(Protein:Engineering, The 47th Annual Meeting of the Biophysical Society of Japan)

Miyazawa, Yosuke, Aita, Takuyo, Husimi, Yuzuru

Journal:

Seibutsu Butsuri

Year:

2009

Language:

english

File:

PDF, 237 KB

english, 2009

23

Experimental Rugged Fitness Landscape in Protein Sequence Space

Hayashi, Yuuki, Aita, Takuyo, Toyota, Hitoshi, Husimi, Yuzuru, Urabe, Itaru, Yomo, Tetsuya, Rutherford, Suzannah

Journal:

Year:

2006

Language:

english

File:

PDF, 213 KB

english, 2006

24

Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin

Takuyo Aita, Hidefumi Uchiyama, Tetsuya Inaoka, Motowo Nakajima, Toshio Kokubo, Yuzuru Husimi

Journal:

Year:

2000

Language:

english

File:

PDF, 322 KB

english, 2000

25

Period Dependent Selection in Continuous Culture of Viruses in a Periodic Environment

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

1994

File:

PDF, 417 KB

1994

26

Theory of Evolutionary Molecular Engineering through Simultaneous Accumulation of Advantageous Mutations

TAKUYO AITA, YUZURU HUSIMI

Journal:

Journal of Theoretical Biology

Year:

2000

Language:

english

File:

PDF, 334 KB

english, 2000

27

Adaptive Walks by the Fittest among Finite Random Mutants on a Mt. Fuji-type Fitness Landscape

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

1998

Language:

english

File:

PDF, 563 KB

english, 1998

28

A trade-off relationship between energetic cost and entropic cost for in vitro evolution

Journal:

Year:

2010

Language:

english

File:

PDF, 192 KB

english, 2010

29

Systematic genome sequence differences among leaf cells within individual trees

Diwan, Deepti, Komazaki, Shun, Suzuki, Miho, Nemoto, Naoto, Aita, Takuyo, Satake, Akiko, Nishigaki, Koichi

Journal:

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

30

3P269 Conformational Free Energy Landscapes in Sequence Space for a Certain Protein Conformation(The genesis of life, and biological evolution,Poster Presentations)

Aita, Takuyo, Husimi, Yuzuru

Journal:

Seibutsu Butsuri

Year:

2007

File:

PDF, 238 KB

2007

31

3P-280 Quantifying contributions of inter-component interactions on the activity of protein translation system(The 46th Annual Meeting of the Biophysical Society of Japan)

Kawamura, Atsushi, Matsuura, Tomoaki, Kazuta, Yasuaki, Aita, Takuyo, Adachi, Jiro, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Year:

2008

Language:

english

File:

PDF, 557 KB

english, 2008

32

A mathematical consideration of the word-composition vector method in comparison of biological sequences

Takuyo Aita, Yuzuru Husimi, Koichi Nishigaki

Journal:

Year:

2011

Language:

english

File:

PDF, 2.40 MB

english, 2011

33

Theoretical consideration of selective enrichment in in vitro selection: Optimal concentration of target molecules

Aita, Takuyo, Nishigaki, Koichi, Husimi, Yuzuru

Journal:

Mathematical Biosciences

Year:

2012

Language:

english

File:

PDF, 644 KB

english, 2012

34

Extracting characteristic properties of fitness landscape from in vitro molecular evolution: A case study on infectivity of fd phage to E.coli

Takuyo Aita, Yuuki Hayashi, Hitoshi Toyota, Yuzuru Husimi, Itaru Urabe, Tetsuya Yomo

Journal:

Journal of Theoretical Biology

Year:

2007

Language:

english

File:

PDF, 357 KB

english, 2007

35

Evolutionary dynamics of a polymorphic self-replicator population with a finite population size and hyper mutation rate

Aita, Takuyo, Yomo, Tetsuya

Journal:

Journal of Theoretical Biology

Year:

2015

Language:

english

File:

PDF, 855 KB

english, 2015

36

2TA3-05 Exploring the fitness landscape of the protein translation system(The 47th Annual Meeting of the Biophysical Society of Japan)

Matsuura, Tomoaki, Kazuta, Yasuaki, Aita, Takuyo, Adachi, Jiro, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Year:

2009

Language:

english

File:

PDF, 220 KB

english, 2009

37

3P278 Fitness landscape in protein sequence space based on in vitro molecular evolution experiment.(Proteins- protein engineering, and evolutionary engineering,Poster Presentations)

Hayashi, Yuuki, Aita, Takuyo, Toyota, Hitoshi, Husimi, Yuzuru, Urabe, Itaru, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Year:

2007

Language:

english

File:

PDF, 240 KB

english, 2007

38

Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution

Takuyo Aita, Norio Hamamatsu, Yukiko Nomiya, Hidefumi Uchiyama, Yasuhiko Shibanaka, Yuzuru Husimi

Journal:

Year:

2002

Language:

english

File:

PDF, 223 KB

english, 2002

39

Protein Tyrosine Phosphatases from Amphioxus, Hagfish, and Ray: Divergence of Tissue-Specific Isoform Genes in the Early Evolution of Vertebrates

Takuyo Aita, Satoshi Urata, Yuzuru Husimi

Journal:

Journal of Molecular Evolution

Year:

2000

Language:

english

File:

PDF, 895 KB

english, 2000

40

Toward an evolutionary containment of evolving pathogen-receptors by using an ensemble of multiple mutant ligands: From the viewpoint of fitness landscape in sequence space

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

2012

Language:

english

File:

PDF, 438 KB

english, 2012

41

A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition

Aita, Takuyo, Nishigaki, Koichi

Journal:

Molecular Phylogenetics and Evolution

Year:

2012

Language:

english

File:

PDF, 1.73 MB

english, 2012

42

Modified substrate specificity of pyrroloquinoline quinone glucose dehydrogenase by biased mutation assembling with optimized amino acid substitution

Norio Hamamatsu, Akitoshi Suzumura, Yukiko Nomiya, Masaaki Sato, Takuyo Aita, Motowo Nakajima, Yuzuru Husimi, Yasuhiko Shibanaka

Journal:

Applied Microbiology and Biotechnology

Year:

2006

Language:

english

File:

PDF, 385 KB

english, 2006

43

Statistical Formulae of the Energy Distribution among a Globular Protein Structure Ensemble

TAKUYO AITA, YUZURU HUSIMI

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 547 KB

english, 2003

44

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I

Takuyo Aita, Shunichi Morinaga, Yuzuru Husimi

Journal:

Bulletin of Mathematical Biology

Year:

2004

Language:

english

File:

PDF, 1.22 MB

english, 2004

45

Rapid and efficient screening of mutants with multi amino-acid substitutions by biased mutation scrambling

Hamamatsu, Norio, Aita, Takuyo, Nomiya, Yukiko, Uchiyama, Hidefumi, Shibanaka, Yasuhiko

Journal:

Seibutsu Butsuri

Year:

2001

File:

PDF, 278 KB

2001

46

Fitness Landscape of a Biopolymer Participating in a Multi-step Reaction

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

1998

Language:

english

File:

PDF, 376 KB

english, 1998

47

An in silico Exploration of the Neutral Network in Protein Sequence Space

TAKUYO AITA, MOTONORI OTA, YUZURU Husimi

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 315 KB

english, 2003

48

Modes of Population Changeovers in Continuous Culture of Bacterial and Viral Mutants Spectrum

Yuzuru Husimi, Takuya Mori, Shinobu Ushijima, Takuyo Aita

Journal:

Journal of Theoretical Biology

Year:

1993

File:

PDF, 400 KB

1993

49

Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential

Takuyo Aita, Koichi Nishigaki, Yuzuru Husimi

Journal:

Computational Biology and Chemistry

Year:

2010

Language:

english

File:

PDF, 1.61 MB

english, 2010

50

Fitting protein-folding free energy landscape for a certain conformation to an NK fitness landscape

Takuyo Aita, Yuzuru Husimi

Journal:

Journal of Theoretical Biology

Year:

2008

Language:

english

File:

PDF, 520 KB

english, 2008

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