Predictive biology: modelling, understanding and harnessing microbial complexity

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

(2020) Milenko Tokic et al.   Biotechnology for Biofuels

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

(2020) Pierre Salvy et al.   Nature Communications

Antibiotic collateral sensitivity is contingent on the repeatability of evolution

(2019) Daniel Nichol et al.   Nature Communications

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

(2019) Tim N. Enke et al.   CURRENT BIOLOGY

Designing Metabolic Division of Labor in Microbial Communities

(2019) Meghan Thommes et al.   mSystems

Adapting machine-learning algorithms to design gene circuits

(2019) Tom W. Hiscock   BMC BIOINFORMATICS

Bacterial Metabolism and Antibiotic Efficacy

(2019) Jonathan M. Stokes et al.   Cell Metabolism

Programmable CRISPR-responsive smart materials

(2019) Max A. English et al.   SCIENCE

Rock-paper-scissors: Engineered population dynamics increase genetic stability

(2019) Michael J. Liao et al.   SCIENCE

Microbial Interaction Network Inference in Microfluidic Droplets

(2019) Ryan H. Hsu et al.   Cell Systems

Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate

(2019) Allison J. Lopatkin et al.   Nature Microbiology

Isolating live cells after high-throughput, long-term, time-lapse microscopy

(2019) Scott Luro et al.   NATURE METHODS

Stochastic antagonism between two proteins governs a bacterial cell fate switch

(2019) Nathan D. Lord et al.   SCIENCE

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Cross-feeding modulates antibiotic tolerance in bacterial communities

(2018) Elizabeth M. Adamowicz et al.   ISME Journal

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Designing microbial consortia with defined social interactions

(2018) Wentao Kong et al.   Nature Chemical Biology

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations

(2018) Nela Nikolic et al.   NUCLEIC ACIDS RESEARCH

Metabolic division of labor in microbial systems

(2018) Ryan Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of carbon allocation efficiency in the temperature dependence of autotroph growth rates

(2018) Bernardo García-Carreras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-free prediction of protein expression costs for growing cells

(2018) Olivier Borkowski et al.   Nature Communications

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

(2018) Matthew A. Jackson et al.   PeerJ

Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors

(2018) Ruben Perez-Carrasco et al.   Cell Systems

Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation

(2018) Marios Tomazou et al.   Cell Systems

Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits

(2018) François Bertaux et al.   Royal Society Open Science

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

(2018) Kees C. H. van der Ark et al.   Microbial Biotechnology

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

(2018) Yolanda Schaerli et al.   Molecular Systems Biology

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Physicochemical Factors That Favor Conjugation of an Antibiotic Resistant Plasmid in Non-growing Bacterial Cultures in the Absence and Presence of Antibiotics

(2018) Brendan Headd et al.   Frontiers in Microbiology

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

(2018) Marcus Nguyen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors

(2018) Adam J. Meyer et al.   Nature Chemical Biology

Noise propagation in an integrated model of bacterial gene expression and growth

(2018) Istvan T. Kleijn et al.   PLoS Computational Biology

Scaling from Metabolism to Population Growth Rate to Understand How Acclimation Temperature Alters Thermal Performance

(2017) Thomas M. Luhring et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli

(2017) Karl Kochanowski et al.   Molecular Systems Biology

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

(2017) David W. Erickson et al.   NATURE

Effect of water flow and chemical environment on microbiota growth and composition in the human colon

(2017) Jonas Cremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global transcriptional regulatory network forEscherichia colirobustly connects gene expression to transcription factor activities

(2017) Xin Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Balancing a genetic toggle switch by real-time feedback control and periodic forcing

(2017) Jean-Baptiste Lugagne et al.   Nature Communications

Programming mRNA decay to modulate synthetic circuit resource allocation

(2017) Ophelia S. Venturelli et al.   Nature Communications

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Decoupling Resource-Coupled Gene Expression in Living Cells

(2017) Tatenda Shopera et al.   ACS Synthetic Biology

Resource Competition Shapes the Response of Genetic Circuits

(2017) Yili Qian et al.   ACS Synthetic Biology

A Glucose-Sensing Toggle Switch for Autonomous, High Productivity Genetic Control

(2017) William Bothfeld et al.   ACS Synthetic Biology

Drivers of Bacterial Maintenance and Minimal Energy Requirements

(2017) Christopher P. Kempes et al.   Frontiers in Microbiology

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks

(2017) Enoch Yeung et al.   Cell Systems

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis

(2017) Spencer R. Scott et al.   Nature Microbiology

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics

(2016) Allison J. Lopatkin et al.   BIOESSAYS

Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria

(2016) Yangxiaolu Cao et al.   CELL

Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness

(2016) Bram Cerulus et al.   CURRENT BIOLOGY

Current state and challenges for dynamic metabolic modeling

(2016) Eleni Vasilakou et al.   CURRENT OPINION IN MICROBIOLOGY

Metabolic network architecture and carbon source determine metabolite production costs

(2016) Silvio Waschina et al.   FEBS Journal

Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients

(2016) Breah LaSarre et al.   ISME Journal

Synchronous long-term oscillations in a synthetic gene circuit

(2016) Laurent Potvin-Trottier et al.   NATURE

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

(2016) Asher Brauner et al.   NATURE REVIEWS MICROBIOLOGY

A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes

(2016) Thomas E. Gorochowski et al.   ACS Synthetic Biology

The Cost of Protein Production

(2016) Moshe Kafri et al.   Cell Reports

Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks

(2016) Corentin Briat et al.   Cell Systems

Antibiotics as a selective driver for conjugation dynamics

(2016) Allison J. Lopatkin et al.   Nature Microbiology

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

(2016) Xiongfeng Dai et al.   Nature Microbiology

Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells

(2016) Imane El Meouche et al.   Scientific Reports

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

(2015) Andrea Ocone et al.   BIOINFORMATICS

Isocost Lines Describe the Cellular Economy of Genetic Circuits

(2015) Andras Gyorgy et al.   BIOPHYSICAL JOURNAL

Cell-Size Control and Homeostasis in Bacteria

(2015) Sattar Taheri-Araghi et al.   CURRENT BIOLOGY

Pareto Optimal Design for Synthetic Biology

(2015) Andrea Patane et al.   IEEE Transactions on Biomedical Circuits and Systems

Collateral Resistance and Sensitivity Modulate Evolution of High-Level Resistance to Drug Combination Treatment in Staphylococcus aureus

(2015) Mari Rodriguez de Evgrafov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

A noisy linear map underlies oscillations in cell size and gene expression in bacteria

(2015) Yu Tanouchi et al.   NATURE

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

(2015) Clement T Y Chan et al.   Nature Chemical Biology

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law

(2015) M. Carbonell-Ballestero et al.   NUCLEIC ACIDS RESEARCH

Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

(2015) Ahmad A. Mannan et al.   PLoS One

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments

(2015) Alin Finkelshtein et al.   mBio

Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance

(2015) Guillaume Chevereau et al.   PLOS BIOLOGY

Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment

(2015) Hannah R. Meredith et al.   PLoS Computational Biology

Sources of Variability in a Synthetic Gene Oscillator

(2015) Alan Veliz-Cuba et al.   PLoS Computational Biology

Rapid cell-free forward engineering of novel genetic ring oscillators

(2015) Henrike Niederholtmeyer et al.   eLife

Hierarchy of non-glucose sugars in Escherichia coli

(2014) Guy Aidelberg et al.   BMC Systems Biology

A Constant Size Extension Drives Bacterial Cell Size Homeostasis

(2014) Manuel Campos et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Quorum-Sensing Crosstalk-Driven Synthetic Circuits: From Unimodality to Trimodality

(2014) Fuqing Wu et al.   CHEMISTRY & BIOLOGY

Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect inSaccharomyces cerevisiaeand explaining evolutionary trade-offs of adaptation to galactose through systems biology

(2014) José L. Martínez et al.   FEMS YEAST RESEARCH

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains

(2014) Jasper M. Schuurmans et al.   PLASMID

Bacterial growth laws reflect the evolutionary importance of energy efficiency

(2014) Arijit Maitra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Survival of Bactericidal Antibiotic Treatment by a Persister Subpopulation of Listeria monocytogenes

(2013) Gitte M. Knudsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Promoter activity dynamics in the lag phase of Escherichia coli

(2013) Daniel Madar et al.   BMC Systems Biology

Combined treatment with the antibiotics kanamycin and streptomycin promotes the conjugation ofEscherichia coli

(2013) Peng-Yi Zhang et al.   FEMS MICROBIOLOGY LETTERS

Promoters maintain their relative activity levels under different growth conditions

(2013) L. Keren et al.   Molecular Systems Biology

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

(2013) S. Berthoumieux et al.   Molecular Systems Biology

Characterization of 582 natural and synthetic terminators and quantification of their design constraints

(2013) Ying-Ja Chen et al.   NATURE METHODS

Engineering of regulated stochastic cell fate determination

(2013) M. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

(2013) Alvaro Sanchez et al.   PLOS BIOLOGY

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Contingency and Statistical Laws in Replicate Microbial Closed Ecosystems

(2012) Doeke R. Hekstra et al.   CELL

A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress

(2012) Onn Brandman et al.   CELL

Programming stress-induced altruistic death in engineered bacteria

(2012) Yu Tanouchi et al.   Molecular Systems Biology

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

Mechanism-independent method for predicting response to multidrug combinations in bacteria

(2012) Kevin Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrasensitivity of the Bacillus subtilis sporulation decision

(2012) J. Narula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cost-Benefit Tradeoffs in Engineered lac Operons

(2012) M. Eames et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Interplay between gene expression noise and regulatory network architecture

(2012) Guilhem Chalancon et al.   TRENDS IN GENETICS

Plasmid-mediated horizontal gene transfer is a coevolutionary process

(2012) Ellie Harrison et al.   TRENDS IN MICROBIOLOGY

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

(2012) Dmitry Nevozhay et al.   PLoS Computational Biology

Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate

(2011) Javier Carrera et al.   Biotechnology Journal

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Quantification of metabolic limitations during recombinant protein production in Escherichia coli

(2011) Jan Heyland et al.   JOURNAL OF BIOTECHNOLOGY

The challenges of integrating multi-omic data sets

(2010) Bernhard Palsson et al.   Nature Chemical Biology

Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology

(2010) Philippe Marguet et al.   PLoS One

Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis

(2010) A. Chastanet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies

(2010) Pontus Melke et al.   PLoS Computational Biology

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem

(2009) Hao Song et al.   Nature Chemical Biology

Emergent bistability by a growth-modulating positive feedback circuit

(2009) Cheemeng Tan et al.   Nature Chemical Biology

Deciding fate in adverse times: Sporulation and competence inBacillus subtilis

(2009) Daniel Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

High-throughput screen for small molecules that modulate the ATPase activity of the molecular chaperone DnaK

(2007) Lyra Chang et al.   ANALYTICAL BIOCHEMISTRY