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List of works by Daniel Segrè

A comparative whole-genome approach identifies bacterial traits for marine microbial interactions

scientific article published on 28 March 2022

A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells

scientific article published on 20 August 2018

A multidimensional perspective on microbial interactions

scientific article published on 01 June 2019

A system-level approach for deciphering the transcriptional response to prion infection

scientific article

A thermodynamic atlas of carbon redox chemical space

scientific article published on 21 December 2020

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

scientific article published in 2021

Analysis of optimality in natural and perturbed metabolic networks

scientific article

BowSaw: Inferring Higher-Order Trait Interactions Associated With Complex Biological Phenotypes

scientific article published in 2021

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

scientific article

Chromosomal periodicity of evolutionarily conserved gene pairs

scholarly article

Co-evolution of metabolism and protein sequences

scientific article published on 01 January 2010

Comparative determination of biomass composition in differentially active metabolic States

scientific article published on January 2008

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

scientific article (publication date: 26 September 2012)

Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine

scientific article published in 2022

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

scientific article published on 09 January 2019

Deep sequencing of the oral microbiome reveals signatures of periodontal disease

scientific article

Designing Metabolic Division of Labor in Microbial Communities

scientific article published on 01 March 2019

Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.

scientific article

Diminishing returns epistasis among beneficial mutations decelerates adaptation

scientific article

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus

scientific article published in 2021

Ecosystems biology of microbial metabolism

scientific article

Emergent Simplicity in Microbial Community Assembly

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Diauxic Growth

scientific article published on 15 January 2019

Emergent simplicity in microbial community assembly

scientific article published in Science

Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism

scientific article published on 11 November 2019

Environments that induce synthetic microbial ecosystems

scientific article

Epistasis from functional dependence of fitness on underlying traits

scientific article published on 15 August 2012

Epistatic interaction maps relative to multiple metabolic phenotypes

scientific article

Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species.

scientific article published in January 2007

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools

scientific article (publication date: 2013)

From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting ⬇️

scientific article published on January 1, 2003

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

scientific article published on September 2017

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

scientific article

Growth instabilities shape morphology and genetic diversity of microbial colonies

scientific article published in 2022

Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

scientific article

Introduction to focus issue: genetic interactions

scientific article published on June 2010

Invariance and optimality in the regulation of an enzyme

scientific article

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

scholarly article published in mSystems

Mapping the landscape of metabolic goals of a cell

scientific article published on 23 May 2016

Metabolic network model of a human oral pathogen.

scientific article published on 17 October 2008

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

scientific article published on 13 June 2019

Metabolic proximity in the order of colonization of a microbial community

scientific article

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

scientific article

Microbial carbon use efficiency predicted from genome-scale metabolic models

scientific article published on 08 August 2019

Microbial metabolites in the marine carbon cycle

scientific article published in 2022

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

scientific article published on 22 September 2008

Modeling the complex dynamics of enzyme-pathway coevolution

scientific article published on 01 December 2010

Modular epistasis in yeast metabolism.

scientific article published on 12 December 2004

Non-additive microbial community responses to environmental complexity

scientific article published on 22 April 2021

On the stability of metabolic cycles

scientific article

Optimal metabolic regulation using a constraint-based model

scientific article published on January 2008

Optimality criteria for the prediction of metabolic fluxes in yeast mutants.

scientific article published in January 2008

Organization principles in genetic interaction networks

scientific article published on January 2012

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli

scientific article published on 12 December 2014

Protein cost minimization promotes the emergence of coenzyme redundancy

scientific article published in 2022

Remnants of an Ancient Metabolism without Phosphate.

scientific article published on 2 March 2017

Resource competition may lead to effective treatment of antibiotic resistant infections

scientific article (publication date: 2013)

Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor

scientific article published in February 2011

Signatures of arithmetic simplicity in metabolic network architecture

scientific article

Species interactions differ in their genetic robustness

scientific article published on 14 April 2015

Synthetic Ecology of Microbes: Mathematical Models and Applications

scientific article

Temporal expression-based analysis of metabolism

scientific article

The COMBREX project: design, methodology, and initial results

scientific article

The average enzyme principle

scientific article

The cost of efficiency in energy metabolism

scientific article (publication date: 11 June 2013)

The dynamics of hybrid metabolic-genetic oscillators

scientific article

The effect of oxygen on biochemical networks and the evolution of complex life

scientific article

The importance of compartmentalization in metabolic flux models: yeast as an ecosystem of organelles

scientific article published on 01 January 2010

The regulatory software of cellular metabolism

scientific article published in June 2004

Toward FAIR Representations of Microbial Interactions

scientific article published in 2022

Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor

scientific article

Twenty Years of "Lipid World": A Fertile Partnership with David Deamer

scientific article published on 20 September 2019

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

scientific article published in April 2023

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

scientific article

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

scientific article

animalcules: interactive microbiome analytics and visualization in R

scientific article published on 28 March 2021

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