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Optimal density of bacterial cells

PLoS computational biology, 2023-06, Vol.19 (6), p.e1011177-e1011177

2023

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Deep learning allows genome-scale prediction of Michaelis constants from structural features

PLoS biology, 2021-10, Vol.19 (10), p.e3001402-e3001402

2021

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Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees

Nucleic acids research, 2019-07, Vol.47 (W1), p.W270

2019

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An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

PLoS genetics, 2021-11, Vol.17 (11), p.e1009939-e1009939

2021

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Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

PLoS computational biology, 2023-06, Vol.19 (6), p.e1011156-e1011156

2023

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On the optimality of the enzyme-substrate relationship in bacteria

PLoS biology, 2021-10, Vol.19 (10), p.e3001416-e3001416

2021

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Synthesis of single-site copper catalysts for methane partial oxidation

Chemical communications (Cambridge, England), 2016-01, Vol.52 (12), p.2553-2556

2016

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An analytical theory of balanced cellular growth

Nature communications, 2020-03, Vol.11 (1), p.1226-1226, Article 1226

2020

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What puzzle are you in?

Genome Biology, 2022-08, Vol.23 (1), p.1-179, Article 179

2022

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A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships

PLoS computational biology, 2024-05, Vol.20 (5), p.e1012100

2024

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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Nature communications, 2018-12, Vol.9 (1), p.5252-10, Article 5252

2018

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EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

Nucleic acids research, 2012-07, Vol.40 (Web Server issue), p.W569

2012

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Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

PLoS computational biology, 2017-04, Vol.13 (4), p.e1005494-e1005494

2017

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The protein translation machinery is expressed for maximal efficiency in Escherichia coli

Nature communications, 2020-10, Vol.11 (1), p.5260-5260, Article 5260

2020

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A general model to predict small molecule substrates of enzymes based on machine and deep learning

Nature communications, 2023-05, Vol.14 (1), p.2787-2787, Article 2787

2023

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Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Nature communications, 2023-07, Vol.14 (1), p.4139-4139, Article 4139

2023

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Impact of the local environment of Brønsted acid sites in ZSM-5 on the catalytic activity in n-pentane cracking

Journal of catalysis, 2014-07, Vol.316, p.93-102

2014

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Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

Nature genetics, 2005-12, Vol.37 (12), p.1372-1375

2005

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Energy efficiency trade-offs drive nucleotide usage in transcribed regions

Nature communications, 2016-04, Vol.7 (1), p.11334-11334, Article 11334

2016

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Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

BioEssays, 2014-01, Vol.36 (1), p.9-20

2014

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Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

Science (American Association for the Advancement of Science), 2013-03, Vol.339 (6124), p.1207-1210

2013

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Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

PLoS computational biology, 2016-08, Vol.12 (8), p.e1005036-e1005036

2016

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Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

Molecular biology and evolution, 2008-03, Vol.25 (3), p.559-567

2008

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Modeling photosynthetic resource allocation connects physiology with evolutionary environments

Scientific reports, 2021-08, Vol.11 (1), p.15979-15979, Article 15979

2021

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Growth‐mediated negative feedback shapes quantitative antibiotic response

Molecular systems biology, 2022-09, Vol.18 (9), p.e10490-n/a

2022

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Optimal density of bacterial cells

Deep learning allows genome-scale prediction of Michaelis constants from structural features

Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees

An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

On the optimality of the enzyme-substrate relationship in bacteria

Synthesis of single-site copper catalysts for methane partial oxidation

An analytical theory of balanced cellular growth

What puzzle are you in?

A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

The protein translation machinery is expressed for maximal efficiency in Escherichia coli

A general model to predict small molecule substrates of enzymes based on machine and deep learning

Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Impact of the local environment of Brønsted acid sites in ZSM-5 on the catalytic activity in n-pentane cracking

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

Modeling photosynthetic resource allocation connects physiology with evolutionary environments

Growth‐mediated negative feedback shapes quantitative antibiotic response

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