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Rethinking life through digital evolution

In this Journal Club, Chikara Furusawa reflects on a 1991 publication by Tom Ray that presented Tierra, an evolvable computer program that pioneered the use of artificial life to study biological phenomena.

Chikara Furusawa
Research Highlights31 Jul 2025
Nature Reviews Genetics

Volume: 26, P: 740
Repeatability of protein structural evolution following convergent gene fusions

Convergent evolution of proteins has been extensively studied at the levels of amino acid residues and local domain structures. Here, authors unveil a global structural convergence of protein complexes among fusion protein families in nature.

Naoki Konno
Keita Miyake
Wataru Iwasaki
ResearchOpen Access22 Sept 2025
Nature Communications

Volume: 16, P: 1-14
Genetic properties underlying transcriptional variability across different perturbations

Organisms display non-uniform transcriptional variability in response to genetic and environmental perturbations. This study on Escherichia coli reveals how gene regulatory networks shape transcriptional variability shared across different perturbations.

Saburo Tsuru
Chikara Furusawa
ResearchOpen Access21 Mar 2025
Nature Communications

Volume: 16, P: 1-16
High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli

Understanding evolutionary constraints in antibiotic resistance is crucial for prediction and control. Here, the authors use high-throughput laboratory evolution of Escherichia coli alongside machine learning to identify trade-off relationships associated with drug resistance.

Tomoya Maeda
Junichiro Iwasawa
Chikara Furusawa
ResearchOpen Access24 Nov 2020
Nature Communications

Volume: 11, P: 1-13
Prediction of antibiotic resistance by gene expression profiles

The relationship between mutations and phenotypic changes associated with drug resistance in bacteria remains unclear. Here, the authors use antibiotic-resistant E. colistrains, obtained by laboratory evolution, to show that resistance profiles can be predicted by changes in expression of a few genes.

Shingo Suzuki
Takaaki Horinouchi
Chikara Furusawa
ResearchOpen Access17 Dec 2014
Nature Communications

Volume: 5, P: 1-12
Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance

Tomoya Maeda
Hazuki Kotani
Chikara Furusawa
ResearchOpen Access24 Jun 2021
Scientific Reports

Volume: 11, P: 1-9
Congruence between noise and plasticity in protein expression

Saburo Tsuru
Chikara Furusawa
ResearchOpen Access08 Jul 2025
Scientific Reports

Volume: 15, P: 1-13
Suppression of antibiotic resistance evolution by single-gene deletion

Takaaki Horinouchi
Tomoya Maeda
Chikara Furusawa
ResearchOpen Access06 Mar 2020
Scientific Reports

Volume: 10, P: 1-9
Single mutation makes Escherichia coli an insect mutualist

Experimental evolution of Escherichia coli in an insect host reveals that a single mutation in the carbon catabolite repression pathway can transform a non-symbiotic microbial species into an insect mutualist.

Ryuichi Koga
Minoru Moriyama
Takema Fukatsu
ResearchOpen Access04 Aug 2022
Nature Microbiology

Volume: 7, P: 1141-1150
Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro

It is unclear whether strategies involving antibiotic cycling can efficiently control the emergence of antibiotic-resistant bacteria. Here, Yoshidaet al. show that the evolution of multi-drug-resistant bacteria in vitrocan be manipulated by administering pairs of antibiotics and switching between them.

Mari Yoshida
Sabrina Galiñanes Reyes
Leroy Cronin
ResearchOpen Access08 Jun 2017
Nature Communications

Volume: 8, P: 1-11
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mammalian genomes are scattered with repetitive sequences, but their biology remains largely elusive. Here, the authors show that transcription can initiate from short tandem repetitive sequences, and that genetic variants linked to human diseases are preferentially found at repeats with high transcription initiation level.

Mathys Grapotte
Manu Saraswat
Charles-Henri Lecellier
ResearchOpen Access02 Jun 2021
Nature Communications

Volume: 12, P: 1-18
Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli

Techniques for characterizing the mode of action of antibiotic resistance are crucial for developing new antimicrobial drugs. Arno Germond et al. have used Raman spectroscopy combined with gene expression to investigate large metabolic changes that occur when bacteria acquire antibiotic resistance.

Arno Germond
Taro Ichimura
Tomonobu M. Watanabe
ResearchOpen Access02 Jul 2018
Communications Biology

Volume: 1, P: 1-10
Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations

Takaaki Horinouchi
Shingo Suzuki
Chikara Furusawa
ResearchOpen Access25 Oct 2017
Scientific Reports

Volume: 7, P: 1-11
A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape

Masato Tsutsumi
Nen Saito
Chikara Furusawa
ResearchOpen Access06 Jul 2023
npj Systems Biology and Applications

Volume: 9, P: 1-12
Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles

Tomoya Maeda
Masako Kawada
Chikara Furusawa
ResearchOpen Access23 Jul 2021
Scientific Reports

Volume: 11, P: 1-14
Inference of transcriptome signatures of Escherichia coli in long-term stationary phase

Sotaro Takano
Hiromi Takahashi
Saburo Tsuru
ResearchOpen Access06 Apr 2023
Scientific Reports

Volume: 13, P: 1-13
High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds

Tomoya Maeda
Takaaki Horinouchi
Chikara Furusawa
Research21 Feb 2019
The Journal of Antibiotics

Volume: 72, P: 566-573
Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation

Kazuko Okamoto
Arno Germond
Tomonobu M. Watanabe
ResearchOpen Access10 Aug 2018
Scientific Reports

Volume: 8, P: 1-13
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte
Manu Saraswat
Charles-Henri Lecellier
Amendments and CorrectionsOpen Access01 Mar 2022
Nature Communications

Volume: 13, P: 1

Search

Rethinking life through digital evolution

Repeatability of protein structural evolution following convergent gene fusions

Genetic properties underlying transcriptional variability across different perturbations

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli

Prediction of antibiotic resistance by gene expression profiles

Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance

Congruence between noise and plasticity in protein expression

Suppression of antibiotic resistance evolution by single-gene deletion

Single mutation makes Escherichia coli an insect mutualist

Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli

Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations

A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape

Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles

Inference of transcriptome signatures of Escherichia coli in long-term stationary phase

High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds

Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

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