T. Aita

发表

Experimental Rugged Fitness Landscape in Protein Sequence Space

T. Yomo, I. Urabe, Yuuki Hayashi, 2006, PloS one.

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

Katsutoshi Takahashi, Takuyo Aita, Katsutoshi Takahashi, 2004 .

Biomolecular Information Gained through In Vitro Evolution on a Fitness Landscape in Sequence Space

Y. Husimi, T. Aita, 2014 .

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

T. Aita, K. Nishigaki, 2012, Molecular phylogenetics and evolution.

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

T. Yomo, N. Ichihashi, T. Aita, 2016, Journal of theoretical biology.

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

Y. Husimi, T. Aita, 2003, Journal of theoretical biology.

An in silico exploration of the neutral network in protein sequence space.

M. Ota, Y. Husimi, T. Aita, 2003, Journal of Theoretical Biology.

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

T. Yomo, T. Aita, 2015, Journal of theoretical biology.

Biomolecular information gained through in vitro evolution

Y. Husimi, T. Aita, 2010, Biophysical Reviews.

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

T. Aita, K. Nishigaki, 2011, Molecular phylogenetics and evolution.

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

Y. Husimi, T. Aita, Shunichi Morinaga, 2004, Bulletin of mathematical biology.

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

Y. Husimi, T. Aita, 1998 .

Quantifying epistatic interactions among the components constituting the protein translation system

Tetsuya Yomo, Tomoaki Matsuura, Takuyo Aita, 2009, Molecular systems biology.

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

Tetsuya Yomo, Norikazu Ichihashi, Takuyo Aita, 2013, Comput. Biol. Chem..

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

Yuzuru Husimi, Takuyo Aita, Y. Husimi, 2008, Journal of theoretical biology.

From Amino Acid Landscape to Protein Landscape: Analysis of Genetic Codes in Terms of Fitness Landscape

Yuzuru Husimi, Takuyo Aita, Y. Husimi, 2000, Journal of Molecular Evolution.

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

Koichi Nishigaki, Yuzuru Husimi, Takuyo Aita, 2012, Mathematical biosciences.

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

Y Husimi, M. Nakajima, Y. Husimi, 2000, Biopolymers.

Statistical formulae of the energy distribution among a globular protein structure ensemble.

T. Aita, Y. Husimi, 2003, Journal of theoretical biology.

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

Yuzuru Husimi, Takuyo Aita, Y. Husimi, 2000, Journal of mathematical biology.

Fitness spectrum among random mutants on Mt. Fuji-type fitness landscape.

Y Husimi, Y. Husimi, T. Aita, 1996, Journal of theoretical biology.

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

Yasuhiko Shibanaka, Yuzuru Husimi, Takuyo Aita, 2002, Biopolymers.

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

T. Yomo, D. Motooka, N. Ichihashi, 2015, Molecular biology and evolution.

Experimental Approach for Early Evolution of Protein Function

T. Yomo, Yuuki Hayashi, T. Aita, 2011 .

A cross-section of the fitness landscape of dihydrofolate reductase.

Y Husimi, M. Iwakura, Y. Husimi, 2001, Protein engineering.

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.

Y. Husimi, T. Aita, 2012, Journal of theoretical biology.

Systematic genome sequence differences among leaf cells within individual trees

Miho Suzuki, A. Satake, T. Aita, 2014, BMC Genomics.

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

Takuyo Aita, T. Aita, 2008, Journal of theoretical biology.

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

Tetsuya Yomo, Itaru Urabe, Yuuki Hayashi, 2007, Journal of theoretical biology.

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

Y. Husimi, T. Aita, K. Taguchi, 2004, Molecular Diversity.

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

Takuyo Aita, T. Aita, 2010, Biosyst..

Biased mutation-assembling: an efficient method for rapid directed evolution through simultaneous mutation accumulation.

Motowo Nakajima, Yasuhiko Shibanaka, Yuzuru Husimi, 2005, Protein engineering, design & selection : PEDS.

Theory of evolutionary molecular engineering through simultaneous accumulation of advantageous mutations.

Y. Husimi, T. Aita, 2000, Journal of theoretical biology.

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

Yuzuru Husimi, Takuyo Aita, Koichi Nishigaki, 2010, Comput. Biol. Chem..

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

Koichi Nishigaki, Yuzuru Husimi, Takuyo Aita, 2014, Mathematical biosciences.

Modes of population changeovers in continuous culture of bacterial and viral mutants spectrum.

T. Mori, Y. Husimi, T. Aita, 1993, Journal of theoretical biology.

Biophysical connection between evolutionary dynamics and thermodynamics in in vitro evolution.

Y. Husimi, T. Aita, 2012, Journal of theoretical biology.

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

Y. Husimi, T. Aita, Shunichi Morinaga, 2004, Bulletin of mathematical biology.

Y. Husimi, T. Aita, I. Tabuchi, 2002, Journal of biological physics.

An Interpretation of Evolutionary Dynamics in in vitro Molecular Evolution from Thermodynamical and Informational View Point

Y. Husimi, T. Aita, 2006 .

On-chip selection of DNA ligands using a method for generating point mutations

Katsutoshi Takahashi, S. Nishimura, T. Aita, 2004 .

Directed evolution by accumulating tailored mutations: thermostabilization of lactate oxidase with less trade-off with catalytic activity.

Motowo Nakajima, Yasuhiko Shibanaka, Yuzuru Husimi, 2006, Protein engineering, design & selection : PEDS.

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

Motowo Nakajima, Yasuhiko Shibanaka, Yuzuru Husimi, 2006, Applied Microbiology and Biotechnology.

Detection of ultra-low levels of DNA changes by drinking water: epidemiologically important finding.

Miho Suzuki, T. Aita, N. Nemoto, 2015, Journal of biochemistry.

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

T. Aita, K. Nishigaki, 2011, Molecular phylogenetics and evolution.

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

Koichi Nishigaki, Yuzuru Husimi, Takuyo Aita, 2011, Biosyst..

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

T. Yomo, D. Motooka, N. Ichihashi, 2015, Molecular biology and evolution.

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

Y. Husimi, T. Aita, Aita, 1998, Journal of theoretical biology.

Contributory presentations/posters

Diederichs, Bosco K. Ho, Hironori K. Nakamura, 1999, Journal of Biosciences.