UA Biophysics:SysBio Meeting:Journal Watch

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29 September 2015

August 2015

Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network

Search: Computational and Systems Biology

Expression noise facilitates the evolution of gene regulation

Limits on information transduction through amplitude and frequency regulation of transcription factor activity

Nature Reviews of Microbiology

September 2015 Issue 9 Vol 13

Review Highlights: Biofilms: Oscillations relieve the siege

Article Series: Bacterial protein networks: properties and functions

Reviews: The yin and yang of hepatitis C: synthesis and decay of hepatitis C virus RNA

Genome Watch: Looking at Beijing’s skyline

HipBA–promoter structures reveal the basis of heritable multidrug tolerance

August 2015 Issue 8 Vol 13

Research Highlights: Obg controls bacterial persistence

July 2015 Issue 7 Vol 13

Redirected from Nature Research Highlights: Metabolic dependencies drive species co-occurrence in diverse microbial communities

May 2015 Issue 6 Vol 13

Research Highlights: Metalloregulatory riboswitches

Physical Review Letters

Journal Watch Agosto 17 2016

Constraints on Fluctuations in Sparsely Characterized Biological Systems De Paulsson, Limites en el ruido desde lo general usando propiedades matemáticas.

From Quasiperiodic Partial Synchronization to Collective Chaos in Populations of Inhibitory Neurons with Delay De redes neuronales y termodinámica. Caos.

Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness Estudio del feedback negativo.

Heterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module Un motif parecido a lo que se quiere para sistemas TA.

Single-File Escape of Colloidal Particles from Microfluidic Channels De microfluidos.

Emergent Collective Chemotaxis without Single-Cell Gradient Sensing

Information Flows? A Critique of Transfer Entropies Informacion, entropia y sistemas complejos.

Volume 115, Issue 14, 2 Octuber 2015 (Partial)

Volume 115, Issue 11, 11 September 2015

Free Energy Cost of Reducing Noise while Maintaining a High Sensitivity

Volume 115, Issue 12, 18 September 2015

Subdominant Dense Clusters Allow for Simple Learning and High Computational Performance in Neural Networks with Discrete Synapses

Volume 115, Issue 8, 21 August 2015

Generalized Communities in Networks

Aging Wiener-Khinchin Theorem

Wiener-Khinchin Theorem for Nonstationary Scale-Invariant Processes

Volume 115, Issue 7, 14 August 2015

Generalization of Pairwise Models to non-Markovian Epidemics on Networks

Volume 115, Issue 5, 31 July 2015

Multidimensional Langevin Modeling of Nonoverdamped Dynamics

Volume 115, Issue 3, 17 July 2015

Physical Limit to Concentration Sensing Amid Spurious Ligands

Volume 114, Issue 24, 19 June 2015

Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations


Membrane potential regulates growth

Structure of a yeast spliceosome at 3.6-angstrom resolution

Modified yeast produce opiates from sugar

Complete biosynthesis of opioids in yeast

The rhodopsin–guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling

Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics

Emergent genetic oscillations in a synthetic microbial consortium

Synthetic communities, the sum of parts

Engineering cell population behavior

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

Differentiating between nutrient sources

Fitness cost of antibiotic susceptibility during bacterial infection

Biochemical basis of a 24-hour clock

A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

An enhanced view of gene control

PLOS Biology

Biofilm Formation As a Response to Ecological Competition

Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts

Journal Watch Agosto 17 2016

Cooperation and the Fate of Microbial Societies

Cooperation among Microorganisms

The Evolution of Norms

Sperm Sociality: Cooperation, Altruism, and Spite

The Evolution of Quorum Sensing in Bacterial Biofilms

Journal of Mathematical Biology

Theory of a microfluidic serial dilution bioreactor for growth of planktonic and biofilm populations

Microbiology and Molecular Biology Reviews

Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress

Yeast Prions: Structure, Biology, and Prion-Handling Systems

Trends in Microbiology

Collateral sensitivity of antibiotic-resistant microbes

Entry and exit of bacterial outer membrane proteins


Adaptación de microorganismos frente a ambientes cambiantes

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

A mathematical model for adaptive prediction of environmental changes by microorganisms

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Adaptación de levaduras frente a ambientes nutricionales diferentes

Galactose metabolic genes in yeast respond to a ratio of galactose and glucose

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

Sistemas toxina-antitoxina y persistencia

Molecular mechanisms of multiple toxin–antitoxin systems are coordinated to govern the persister phenotype

Large mutational target size for rapid emergence of bacterial persistence

Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases

Teoría de juegos, redes genéticas

Bacterial strategies for chemotaxis response

Phenotypic switching in gene regulatory networks

Intrinsic noise in gene regulatory networks


High-sensitivity microfluidic calorimeters for biological and chemical applications

Molecular Microbiology

Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations

Escherichia coli persister cells suppress translation by selectively disassembling and degrading their ribosomes

A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria

Perturbation of the interaction between Gal4p and Gal80p of the Saccharomyces cerevisiae GAL switch results in altered responses to galactose and glucose


Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics

Biophysical Journal

Isocost Lines Describe the Cellular Economy of Genetic Circuits

Understanding Gene Expression Heterogeneity in Living Cells with Single-Molecule Fluorescence Microscopy

Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems

Information Transmission through Pancreatic Beta Cell Signaling Pathways

Systems Mechanobiology: Tension-Inhibited Protein Turnover Is Sufficient to Physically Control Gene Circuits

Stochastic Control of Intracellular Latency and Transactivation in Human Immunodeficiency Virus Type 1 (HIV-1)

Irreversible Thermodynamics of Transcriptional Regulation

The Engineering of Artificial Cellular Systems using Synthetic Biology Approaches

Microfluidics Assisted Cell Screening


Plasmids in the driving seat: The regulatory RNA Rcd gives plasmid ColE1 control over division and growth of its E. coli host

Transformation of Shewanella baltica with ColE1-like and P1 plasmids and their maintenance during bacterial growth in cultures

Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked?

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

New quantitative methods for measuring plasmid loss rates reveal unexpected stability

Evaluating quantitative methods for measuring plasmid copy numbers in single cells

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