Selected Paperes 123113

biophysics
Emergence of Macroscopic Directed Motion in Populations of Motile Colloids

cell biology
An Excitable Signal Integrator Couples to an Idling Cytoskeletal Oscillator to Drive Cell Migration
The Autophagosome: Origins Unknown, Biogenesis Complex [review]
The Biophysics and Cell Biology of Lipid Droplets [review]
Peroxisomes Take Shape [review]
Changes in Cytoplasmic Volume Are Sufficient to Drive Spindle Scaling
Cytoplasmic Volume Modulates Spindle Size During Embryogenesis
Memory and Modularity in Cell-fate Decision Making
Rho GTPases Orient Directional Sensing in Chemotaxis
KaiC Intersubunit Communication Facilitates Robustness of Circadian Rhythms in Cyanobacteria
The Bacterial Cell Division Proteins FtsA and FtsZ Self-organize into Dynamic Cytoskeletal Patterns
Apart from Its Known Function, the Plasma Membrane Ca2+ ATPase can Regulate Ca2+ Signaling by Controlling Phosphatidylinositol 4,5-bisphosphate Levels

developmental biology
ERK as a Model for Systems Biology of Enzyme Kinetics in Cells [review]
Directional Tissue Migration through a Self-generated Chemokine Gradient

cancer biology
Emergence of Spatial Structure in the Tumor Microenvironment due to the Warburg Effect

ecology
The Hidden Geometry of Complex, Network-Driven Contagion Phenomena

imaging
Single-molecule Superresolution Imaging Allows Quantitative Analysis of RAF Multimer Formation and Signaling
Intracellular Mini-binders [perspective]
Resolution Doubling in Fluorescence Microscopy with Confocal Spinning-disk Image Scanning Microscopy

synthetic biology
Tuning the Range and Stability of Multiple Phenotypic States with Coupled Positive–negative Feedback Loops

Selected Papers 103113

calcium, ER, plasma membrane
Ca2+ Release-activated Ca2+ Channel Blockade as a Potential Tool in Antipancreatitis Therapy
hGAAP Promotes Cell Adhesion and Migration via the Stimulation of Store-operated Ca2+ Entry and Calpain 2
An ER‐peroxisome Tether Exerts Peroxisome Population Control in Yeast
Ca2+ Channel Nanodomains Boost Local Ca2+ Amplitude
Wnt5a Directs Polarized Calcium Gradients by Recruiting Cortical Endoplasmic Reticulum to the Cell Trailing Edge

autophagy
Bit-by-bit Autophagic Removal of Parkin-labelled Mitochondria
Diverse Autophagosome Membrane Sources Coalesce in Recycling Endosomes

genetics
Statistical Mechanics of Pluripotency [perspective]

cell biology
Cytoplasmic Streaming in Plant Cells Emerges Naturally by Microfilament Self-organization
A Cost–benefit Analysis of the Physical Mechanisms of Membrane Curvature
Membrane-Sculpting BAR Domains Generate Stable Lipid Microdomains
Analysis of the Local Organization and Dynamics of Cellular Actin Networks
Robustness and Compensation of Information Transmission of Signaling Pathways

developmental biology
Positional Information, in Bits

ecology
Emergence of Structural and Dynamical Properties of Ecological Mutualistic Networks
Resource Heterogeneity can Facilitate Cooperation
Bounded Population Sizes, Fluctuating Selection and the Tempo and Mode of Coexistence

imaging
Quantifying Spatial Structure in Experimental Observations and Agent-based Simulations Using Pair-correlation Functions
Counting Molecules in Single Organelles with Superresolution Microscopy Allows Tracking of the Endosome Maturation Trajectory

synthetic biology
Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers
Self-organized Optical Device Driven by Motor Proteins

Selected Papers 073113

calcium, ER & plasma membrane
PI(4,5)P2-Dependent and Ca2+-Regulated ER-PM Interactions Mediated by the Extended Synaptotagmins
Intramolecular Shielding Maintains the ER Ca2+ Sensor STIM1 in an Inactive Conformation
The STIM1 CTID Domain Determines Access of SARAF to SOAR to Regulate Orai1 Channel Function
An siRNA Screen for NFAT Activation Identifies Septins as Coordinators of Store-Operated Ca2+ Entry
Spatiotemporal Control of Endocytosis by Phosphatidylinositol-3,4-bisphosphate
Stacked Endoplasmic Reticulum Sheets Are Connected by Helicoidal Membrane Motifs
Initial Activation of STIM1, the Regulator of Store-Operated Calcium Entry

cell polarity
Identifying Network Motifs that Buffer Front-to-Back Signaling in Polarized Neutrophils
Daughter Cell Identity Emerges from the Interplay of Cdc42, Septins, and Exocytosis

cell biology
Chase-and-Run between Adjacent Cell Populations Promotes Directional Collective Migration
Matrix Geometry Determines Optimal Cancer Cell Migration Strategy and Modulates Response to Interventions
Neutrophil Swarms Require LTB4 and Integrins at Sites of Cell Death in Vivo
Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei
Direct Imaging Reveals Stable, Micrometer-Scale Lipid Domains That Segregate Proteins in Live Cells
OPA1 Promotes pH Flashes That Spread between Contiguous Mitochondria without Matrix Protein Exchange
Spatiotemporally Controlled Induction of Autophagy-mediated Lysosome Turnover

plant physiology
Balanced Nucleocytosolic Partitioning Defines a Spatial Network to Coordinate Circadian Physiology in Plants

plant physiology, evolution
Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

ecology
An Adaptive Response to Uncertainty Generates Positive and Negative Contrast Effects
Spatial Population Expansion Promotes the Evolution of Cooperation in an Experimental Prisoner’s Dilemma
Phase Separation Explains a New Class of Self-organized Spatial Patterns in Ecological Systems

synthetic biology
A Design Principle of Group-level Decision Making in Cell Populations
Synthetic Analog Computation in Living Cells

imaging
Stimulated Emission Depletion-Based Raster Image Correlation Spectroscopy Reveals Biomolecular Dynamics in Live Cells
Far-red Light Photoactivatable Near-infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome

Selected Papers 050813

biochemistry
Evolutionary Conservation of Codon Optimality Reveals Hidden Signatures of Cotranslational Folding
Non-optimal Codon Usage Affects Expression, Structure and Function of Clock Protein FRQ
Non-optimal Codon Usage Is a Mechanism to Achieve Circadian Clock Conditionality

cell polarity
The Role of Microtubules in Neutrophil Polarity and Migration in Live Zebrafish
A Safeguard Mechanism Regulates Rho GTPases to Coordinate Cytokinesis with the Establishment of Cell Polarity
Rab11 Regulates Cell–Cell Communication during Collective Cell Movements
Actin Cytoskeleton of Chemotactic Amoebae Operates Close to the Onset of Oscillations
Electrophoresis of Cellular Membrane Components Creates the Directional Cue Guiding Keratocyte Galvanotaxis
Keratocyte Fragments and Cells Utilize Competing Pathways to Move in Opposite Directions in an Electric Field
Mitochondrial Localization and the Persistent Migration of Epithelial Cancer cells

cell biology
Systematic Identification of Signal-Activated Stochastic Gene Regulation
Endoplasmic Reticulum-Associated Mitochondria–Cortex Tether Functions in the Distribution and Inheritance of Mitochondria
Cell Shape Can Mediate the Spatial Organization of the Bacterial Cytoskeleton
Cyclic GMP-AMP Is an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA
Cyclic GMP-AMP Synthase Is a Cytosolic DNA Sensor That Activates the Type I Interferon Pathway
Correlative Live-Cell and Superresolution Microscopy Reveals Cargo Transport Dynamics at Microtubule Intersections
Dynamics Extracted from Fixed Cells Reveal Feedback Linking Cell Growth to Cell Cycle
Rate of Environmental Change Determines Stress Response Specificity
Lysosomes Shape Ins(1,4,5)P3-evoked Ca2+ Signals by Selectively Sequestering Ca2+ Released from the Endoplasmic Reticulum
Autophagosomes Form at ER–mitochondria Contact Sites
Binding to F-actin Guides Cadherin Cluster Assembly, Stability, and Movement
The ER Ca2+ Sensor STIM1 Regulates Actomyosin Contractility of Migratory Cells
Downregulation of Store-operated Ca2+ Entry during Mammalian Meiosis Is Required for the Egg-to-Embryo Transition

developmental biology
How Cells Know Where They Are [review]
Phase Transition in the Economically Modeled Growth of a Cellular Nervous System

plant physiology
Regulation of Flowering by Trehalose-6-Phosphate Signaling in Arabidopsis thaliana

ecology
Caffeine in Floral Nectar Enhances a Pollinator's Memory of Reward
Slower Recovery in Space before Collapse of Connected Populations

synthetic biology
Optogenetic Protein Clustering and Signaling Activation in Mammalian Cells

imaging
Quantifying Spatial Organization in Point-localization Superresolution Images Using Pair Correlation Analysis
Single-molecule Imaging of Transcription Factor Binding to DNA in Live Mammalian Cells

Selected Papers 013113

biochemistry
Spontaneous Network Formation among Cooperative RNA Replicators
Cellular Crowding Imposes Global Constraints on the Chemistry and Evolution of Proteomes

calcium, ER & plasma membrane
Sub-resolution Lipid Domains Exist in the Plasma Membrane and Regulate Protein Diffusion and Distribution
ER-to-Plasma Membrane Tethering Proteins Regulate Cell Signaling and ER Morphology
Rab10 GTPase Regulates ER Dynamics and Morphology
Coordinated Oscillations in Cortical Actin and Ca2+ Correlate with Cycles of Vesicle Secretion
Calcium Oscillations-coupled Conversion of Actin Travelling Waves to Standing oscillations
Crystal Structure of the Calcium Release–Activated Calcium Channel Orai
Orai-STIM–mediated Ca2+ Release from Secretory Granules Revealed by a Targeted Ca2+ and pH Probe
Ca2+ Regulates T-cell Receptor Ativation by Modulating the Charge Property of Lipids
Single-molecule Analysis of Fluorescently Labeled G-protein–coupled Receptors Reveals Complexes with Distinct Dynamics and Organization
Mitochondrial Colocalization with Ca2+ Release Sites is Crucial to Cardiac Metabolism

cell polarity
Synthetic Spatially Graded Rac Activation Drives Cell Polarization and Movement
Modeling the Self-organized Phosphatidylinositol Lipid Signaling System in Chemotactic Cells Using Quantitative Image Analysis
Tracking Shallow Chemical Gradients by Actin-Driven Wandering of the Polarization Site
Non-uniform Membrane Diffusion Enables Steady-state Cell Polarization via Vesicular Trafficking

cell biology
Building Complexity: Insights into Self-Organized Assembly of Microtubule-Based Architectures [review]
The Problem of Colliding Networks and its Relation to Cell Fusion and Cancer
Predicting Rates of Cell State Change Caused by Stochastic Fluctuations Using a Data-driven Landscape Model
Force Fluctuations within Focal Adhesions Mediate ECM-Rigidity Sensing to Guide Directed Cell Migration
Guidance of Cell Migration by Substrate Dimension
An Actin-Dependent Step in Mitochondrial Fission Mediated by the ER-Associated Formin INF2
Tunable Signal Processing Through Modular Control of Transcription Factor Translocation

developmental biology
A Cell-Level Biomechanical Model of Drosophila Dorsal Closure

plant physiology, evolution
A Critical Transition in Leaf Evolution Facilitated the Cretaceous Angiosperm Revolution
Physical Limits to Leaf Size in Tall Trees

ecology
Different Types of Synchrony in Chaotic and Cyclic Communities
Recurrent Jellyfish Blooms Are a Consequence of Global Oscillations
The Ghost of Nestedness in Ecological Networks

evolution
Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
Predictability of Evolution Depends Nonmonotonically on Population Size

computational biology
Geometric Origin of Scaling in Large Traffic Networks

synthetic biology
Bottom-up Construction of in Vitro Switchable Memories
Towards a Bottom-up Reconstitution of Bacterial Cell Division [review]
Designing Biological Compartmentalization [review]
Directed Cytoskeleton Self-organization [review]
Directing the Assembly of Spatially Organized Multicomponent Tissues from the Bottom Up [review]
Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell [review]

imaging
Optical Control of Protein Activity by Fluorescent Protein Domains
Ultrabright Photoactivatable Fluorophores Created by Reductive Caging

Selected Papers 103112

biophysics
Energetic Costs of Cellular Computation

biophysics, cytoskeleton
Intermittent Depolymerization of Actin Filaments Is Caused by Photo-induced Dimerization of Actin Protomers
Deformations Within Moving Kinetochores Reveal Different Sites of Active and Passive Force Generation
Geometry Sensing by Self-organized Protein Patterns

genetics
Chromatin Organization Is a Major Influence on Regional Mutation Rates in Human Cancer Cells

signaling
Noise and Correlations in Parallel Perceptual Decision Making
Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification

signaling, synthetic biology
Adaptive Mutations that Prevent Crosstalk Enable the Expansion of Paralogous Signaling Protein Families

calcium signaling & ER-PM junction
STIM Proteins: Dynamic Calcium Signal Transducers

autophagy
Atg9 Vesicles Are an Important Membrane Source during Early Steps of Autophagosome Formation

cell polarity
Oscillatory Dynamics of Cdc42 GTPase in the Control of Polarized Growth
Class II Formin Targeting to the Cell Cortex by Binding PI(3,5)P2 Is Essential for Polarized Growth
Weakly Nonlinear Analysis of Symmetry Breaking in Cell Polarity Models
Initiation of Cell Wall Pattern by a Rho- and Microtubule-Driven Symmetry Breaking
PIP3 Waves and PTEN Dynamics in the Emergence of Cell Polarity
Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization

cell biology
A General Theoretical Framework to Infer Endosomal Network Dynamics from Quantitative Image Analysis
Plasma Membrane Reshaping during Endocytosis Is Revealed by Time-Resolved Electron Tomography
The Critical Size Is Set at a Single-cell Level by Growth Rate to Attain Homeostasis and Adaptation
Spatial Ordering of Chromosomes Enhances the Fidelity of Chromosome Partitioning in Cyanobacteria
Mitochondrial Fission, Fusion, and Stress [review]
Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics
Interaction Landscape of Membrane-protein Complexes in Saccharomyces cerevisiae

cancer biology
Defining the Mode of Tumour Growth by Clonal Analysis

plant physiology, biophysics
How the Cucumber Tendril Coils and Overwinds

neuroscience
Neural Population Dynamics during Reaching
Theory and Simulation in Neuroscience [review]

ecology, theoretical biology
The Dynamics of Coordinated Group Hunting and Collective Information Transfer among Schooling Prey
Identifying Influential and Susceptible Members of Social Networks
Diversity of Interaction Types and Ecological Community Stability
Spontaneously Broken Neutral Symmetry in an Ecological System
Sensing and Decision-making in Random Search
Emergence of Diversity in a Model Ecosystem
Unifying the Spatial Epidemiology and Molecular Evolution of Emerging Epidemics
Bacterial Quorum Sensing and Metabolic Incentives to Cooperate
Detecting Causality in Complex Ecosystems
Slime Mold Uses an Externalized Spatial "Memory" to Navigate in Complex Environments

computational biology
Studying and Modelling Dynamic Biological Processes Using Time-series Gene Expression Data [review]

theoretical biology
First Passage Time for Random Walks in Heterogeneous Networks
From Networks to Time Series
Anticipating Critical Transitions

synthetic biology
Synthetic Memory Circuits for Tracking Human Cell Fate
A Design Principle for a Posttranslational Biochemical Oscillator

single-molecule techniques
A Single-Molecule Hershey-Chase Experiment
Force Probing of Individual Molecules Inside the Living Cell Is Now a Reality

imaging
Widely Accessible Method for Superresolution Fluorescence Imaging of Living Systems
Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms
Super-resolution Fluorescence Imaging of Organelles in Live Cells with Photoswitchable Membrane Probes
Counting Single Photoactivatable Fluorescent Molecules by Photoactivated Localization Microscopy (PALM)

Selected Papers 063012

biophysics
Spatial-temporal Dynamics of Collective Chemosensing
Robust Classification of Salient Links in Complex Networks
Active Remodeling of Cortical Actin Regulates Spatiotemporal Organization of Cell Surface Molecules
Generalized Lévy Walks and the Role of Chemokines in Migration of Effector CD8+ T Cells
The lac Repressor Displays Facilitated Diffusion in Living Cells

biochemistry
Rethinking Glycolysis: On the Biochemical Logic of Metabolic Pathways [review]
Identifying Sources of Variation and the Flow of Information in Biochemical Networks
Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

cell polarity
Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway
Planar Polarity Specification through Asymmetric Subcellular Localization of Fat and Dachsous
Network Crosstalk Dynamically Changes during Neutrophil Polarization
Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation

cell biology
Cost-Benefit Tradeoffs in Engineered lac Operons
FtsA Forms Actin-like Protofilaments
Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging
Spatial Positive Feedback at the Onset of Mitosis
p53 Dynamics Control Cell Fate
Adaptation to Optimal Cell Growth through Self-Organized Criticality
Cell Size Control in Yeast [review]
A Motor-Driven Mechanism for Cell-Length Sensing
Bistability, Bifurcations, and Waddington's Epigenetic Landscape [review]

synthetic biology
Foundations for the Design and Implementation of Synthetic Genetic Circuits [review]

immunology
A Decade of Imaging Cellular Motility and Interaction Dynamics in the Immune System [review]

ecology
Developmentally Based Scaling of Leaf Venation Architecture Explains Global Ecological Patterns
Foraging Success of Biological Lévy Flights Recorded in Situ
Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse

evolution
Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
Emergence of Stable Polymorphisms Driven by Evolutionary Games between Mutants

imaging
Statistical Deconvolution for Superresolution Fluorescence Microscopy
Focus on Bioimage Informatics [special issue]

Selected Papers 050812

biophysics
Statistical Mechanics for Natural Flocks of Birds
Optimizing Information Flow in Small Genetic Networks
Optimizing Information Flow in Small Genetic Networks. II. Feed-forward Interactions
Optimizing Information Flow in Small Genetic Networks. III. A Self-interacting Gene

biochemistry
Phase Transitions in the Assembly of Multivalent Signalling Proteins
A Single Vesicle-vesicle Fusion Assay for in Vitro Studies of SNAREs and Accessory Proteins

cell polarity
Noise Reduction in the Intracellular Pom1p Gradient by a Dynamic Clustering Mechanism
Nonpolarized Signaling Reveals Two Distinct Modes of 3D Cell Migration
Negative Feedback Enhances Robustness in the Yeast Polarity Establishment Circuit
Centrosomes Can Initiate a Polarity Axis from Any Position within One-Cell C. elegans Embryos
Segregation of Molecules at Cell Division Reveals Native Protein Localization

cell biology
(Re)inventing the Circadian Feedback Loop [review]
Large-scale Vortex Lattice Emerging from Collectively Moving Microtubules
A Link between Mitotic Entry and Membrane Growth Suggests a Novel Model for Cell Size Control
ParA-like Protein Uses Nonspecific Chromosomal DNA Binding to Partition Protein Complexes
Robustness and Accuracy of Cell Division in Escherichia coli in Diverse Cell Shapes

cancer biology
Intra-tumour Heterogeneity: A Looking Glass for Cancer? [review]

developmental biology
Geometry, Epistasis, and Developmental Patterning

ecology
Stability Criteria for Complex Ecosystems
Power Laws Reveal Phase Transitions in Landscape Controls of Fire Regimes
A Universal Model for Mobility and Migration Patterns

evolution
Negative Feedback Confers Mutational Robustness in Yeast Transcription Factor Regulation
Multidimensional Optimality of Microbial Metabolism

computational biology
Asymmetric Positive Feedback Loops Reliably Control Biological Responses

imaging
Live-Cell Fluorescence Microscopy with Molecular Biosensors: What Are We Really Measuring?
Correlative 3D Superresolution Fluorescence and Electron Microscopy Reveal the Relationship of Mitochondrial Nucleoids to Membranes

Selected Papers 022812

biophysics
Nonlinear Material Behaviour of Spider Silk Yields Robust Webs

biochemistry
Identifying Dynamical Bottlenecks of Stochastic Transitions in Biochemical Networks
Protein-Binding Dynamics Imaged in a Living Cell
Single-Molecule Pull-Down for Studying Protein Interactions

autophagy
Autophagosomes Initiate Distally and Mature during Transport toward the Cell Soma in Primary Neurons
Arf6 Promotes Autophagosome Formation via Effects on Phosphatidylinositol 4,5-Bisphosphate and pPhospholipase D

cell polarity
Asymmetric Segregation of Polarized Antigen on B Cell Division Shapes Presentation Capacity
Organelle segregation during mitosis: Lessons from asymmetrically dividing cells [review]
Identification of F-actin as the Dynamic Hub in a Microbial-Induced GTPase Polarity Circuit

cell biology
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
Pulsed Feedback Defers Cellular Differentiation
Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
Genes Adopt Non-Optimal Codon Usage to Generate Cell Cycle-Dependent Oscillations in Protein Levels
Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

developmental biology
Optimality in the Development of Intestinal Crypts
Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo
Generation of Leaf Shape Through Early Patterns of Growth and Tissue Polarity
Elastic Domains Regulate Growth and Organogenesis in the Plant Shoot Apical Meristem
Noise and Robustness in Phyllotaxis

ecology
Social Networks and Cooperation in Hunter-Gatherers
Spatiotemporal Dynamics of Bumblebees Foraging under Predation Risk
The Robustness and Restoration of a Network of Ecological Networks
Spread of Social Information and Dynamics of Social Transmission within Drosophila Groups

evolution
Experimental Evolution of Multicellularity
The Molecular Diversity of Adaptive Convergence
Stochastic Signalling Rewires the Interaction Map of a Multiple Feedback Network during Yeast Evolution

computaional biology
A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser
Adjusting Phenotypes by Noise Control
Network Physiology Reveals Relations between Network Topology and Physiological Function

imaging
A Multispectral Optical Illumination System with Precise Spatiotemporal Control for the Manipulation of Optogenetic Reagents
Dual-Objective STORM Reveals Three-Dimensional Filament Organization in the Actin Cytoskeleton

Selected Papers 013112

biochemistry
Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit

signaling
Trafficking Coordinate Description of Intracellular Transport Control of Signaling Networks
Substrate-Dependent Control of ERK Phosphorylation Can Lead to Oscillations

autophagy
Mechanisms of Autophagosome Biogenesis [review]

cell polarity
Phosphatidylserine Is Polarized and Required for Proper Cdc42 Localization and for Development of Cell Polarity
Asymmetric B Cell Division in the Germinal Center Reaction
Membrane Tension Maintains Cell Polarity by Confining Signals to the Leading Edge during Neutrophil Migration

cell biology
The Competitive Advantage of a Dual-Transporter System
Collective and Single Cell Behavior in Epithelial Contact Inhibition
Mechanical Compression Drives Cancer Cells toward Invasive Phenotype
Activation-Induced B Cell Fates Are Selected by Intracellular Stochastic Competition
The Origin of Phragmoplast Asymmetry
Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments
Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast
Local Zones of Endoplasmic Reticulum Complexity Confine Cargo in Neuronal Dendrites

developmental biology
Polarization of PAR Proteins by Advective Triggering of a Pattern-Forming System
Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

neuroscience
Locally Synchronized Synaptic Inputs
Spectral Fingerprints of Large-Scale Neuronal Interactions

plant physiology
How do Plants Achieve Immunity? Defence without Specialized Immune Cells

psychology
Rational Choice, Context Dependence, and the Value of Information in European Starlings (Sturnus vulgaris)

ecology
Evolutionary and Population Dynamics: A Coupled Approach
Stop Signals Provide Cross Inhibition in Collective Decision-Making by Honeybee Swarms
Computational Modeling of Pancreatic Cancer Reveals Kinetics of Metastasis Suggesting Optimum Treatment Strategies

computational biology
Complexity [special issue]
Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits

imaging
Evaluation of Fluorophores for Optimal Performance in Localization-Based Super-Resolution Imaging
Determining the Number of Specific Proteins in Cellular Compartments by Quantitative Microscopy
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
Nonlinear Structured-Illumination Microscopy with a Photoswitchable Protein Reveals Cellular Structures at 50-nm Resolution

Selected Papers 121711

biochemistry
How Fast-Folding Proteins Fold
A Mechanism for the Evolution of Phosphorylation Sites

biophysics
Chemically Mediated Mechanical Expansion of the Pollen Tube Cell Wall
Nonequilibrium Candidate Monte Carlo Is an Efficient Tool for Equilibrium Simulation

autophagy
Autophagy: Renovation of Cells and Tissues
Autophagy [special issue]
Canonical and Non-canonical Autophagy: Variations on a Common Theme of Self-eating? [perspective]
Atg8 Transfer from Atg7 to Atg3: A Distinctive E1-E2 Architecture and Mechanism in the Autophagy Pathway
Structural Basis of Atg8 Activation by a Homodimeric E1, Atg7
Microtubule-associated Protein 1 Light Chain 3 Alpha (LC3)-associated Phagocytosis Is Required for the Efficient Clearance of Dead Cells

cell biology
ER Tubules Mark Sites of Mitochondrial Division
Extracting a Cellular Hierarchy from High-Dimensional Cytometry Data with SPADE
Linking Flickering to Waves and Whole-Cell Oscillations in a Mitochondrial Network Model
Physical Limits of Cells and Proteomes
A Quantitative Model for Ordered Cdk Substrate Dephosphorylation during Mitotic Exit
A Highly Dynamic ER-Derived Phosphatidylinositol-Synthesizing Organelle Supplies Phosphoinositides to Cellular Membranes

developmental biology
Measurement and Perturbation of Morphogen Lifetime: Effects on Gradient Shape

developmental biology, computational biology
Dynamics and Control of State-dependent Networks for Probing Genomic Organization

ecology, computational biology
Bayesian Modeling to Unmask and Predict Influenza A/H1N1pdm Dynamics in London
Temporal Dynamics of Bacterial Aging and Rejuvenation

evolution, computational biology
Predictability of Evolutionary Trajectories in Fitness Landscapes

imaging
Single-Molecule Transcript Counting of Stem-Cell Markers in the Mouse Intestine
A Reversibly Photoswitchable GFP-like Protein with Fluorescence Excitation Decoupled from Switching
Probing Protein Heterogeneity in the Plasma Membrane Using PALM and Pair Correlation Analysis

Selected Papers 101511

synthetic biology
Entrainment of a Population of Synthetic Genetic Oscillators

autophagy
The WD40 Repeat PtdIns(3)P-Binding Protein EPG-6 Regulates Progression of Omegasomes to Autophagosomes
p62/SQSTM1 in autophagic clearance of a non-ubiquitylated substrate

cell biology
Reconstructing Regulatory Network Transitions [review]
Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change
Distinct Interactions Select and Maintain a Specific Cell Fate
The Min Oscillator Uses MinD-Dependent Conformational Changes in MinE to Spatially Regulate Cytokinesis
Divergent Strategies for Controlling the Nuclear Membrane Satisfy Geometric Constraints during Nuclear Division
Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria
The Spatial Arrangement of Chromosomes during Prometaphase Facilitates Spindle Assembly
Rapid Microtubule Self-Assembly Kinetics
In Vitro Centromere and Kinetochore Assembly on Defined Chromatin Templates

cell biology, quantitative biology
Random Partitioning of Molecules at Cell Division
Integrating Multiple Signals into Cell Decisions by Networks of Protein Modification Cycles

developmental biology
Generation of Spatial Patterns Through Cell Polarity Switching

developmental biology, modeling
Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?

evolution
Signalling and the Evolution of Cooperative Foraging in Dynamic Environments

evolution, cancer biology, theoretical biology
Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

ecology
A Unifying Approach for Food Webs, Phylogeny, Social Networks, and Statistics

imaging
An Expanded Palette of Genetically Encoded Ca2+ Indicators
Superresolution Imaging of Multiple Fluorescent Proteins with Highly Overlapping Emission Spectra in Living Cells
Quantifying Spatial Correlations of Fluorescent Markers Using Enhanced Background Reduction with Protein Proximity Index and Correlation Coefficient Estimations

Selected Papers 073011

biochemistry
A Synthetic Prestin Reveals Protein Domains and Molecular Operation of Outer Hair Cell Piezoelectricity

genetics
Fundamental Relationship between Operon Organization and Gene Expression

autophagy
SNARE Proteins Are Required for Macroautophagy
Autophagosome Precursor Maturation Requires Homotypic Fusion
Mitochondria Regulate Autophagy by Conserved Signalling Pathways
Distinct Autophagosomal-Lysosomal Fusion Mechanism Revealed by Thapsigargin-Induced Autophagy Arrest

cell biology
On a Bender—BARs, ESCRTs, COPs, and Finally Getting Your Coat [review]
The Nucleoplasmic Reticulum: Form and Function [review]
Metazoan Operons Accelerate Recovery from Growth-Arrested States
Feedback Control in Sensing Chromosome Biorientation by the Aurora B Kinase
Dynamics of Cdk1 Substrate Specificity during the Cell Cycle
Temporal and Spatial Oscillations in Bacteria [review]
Modularity of the Bacterial Cell Cycle Enables Independent Spatial and Temporal Control of DNA Replication
Micropatterned Mammalian Cells Exhibit Phenotype-specific Left-right Asymmetry

cell biology, evolution
Evolution of the Mitochondrial Fusion–Fission Cycle and Its Role in Aging
Non-adaptive Origins of Interactome Complexity

cell biology, modeling
Turing's Next Steps: The Mechanochemical Basis of Morphogenesis [perspective]

developmental biology
Scales of Understanding in Biological Development [special issue]
A Decade of Developmental Cell [special issue]

neuroscience
Perceiving Spatial Relations via Attentional Tracking and Shifting
The Human Visual System's Assumption That Light Comes from Above Is Weak

neuroscience, modeling
Using Theoretical Models to Analyse Neural Development [review]

ecology
How Social Influence can Undermine the Wisdom of Crowd Effect
Gene Flow Increases Fitness at the Warm Edge of a Species’ Range
Aerosol–cloud–precipitation System as a Predator-prey Problem

evolution
Chaos and Unpredictability in Evolutionary Dynamics in Discrete Time

imaging
Fast, Three-dimensional Super-resolution Imaging of Live Cells

Selected Papers 051411

biophysics, plant physiology
Growth, Geometry, and Mechanics of a Blooming Lily
Universal Rule for the Symmetric Division of Plant Cells

biochemistry, membrane biology
A 3D Analysis of Yeast ER Structure Reveals How ER Domains Are Organized by Membrane Curvature

synthetic biology, evolution
A System for the Continuous Directed Evolution of Biomolecules

autophagy
Atg1-mediated Myosin II Activation Regulates Autophagosome Formation during Starvation-induced Autophagy
Microautophagy of Cytosolic Proteins by Late Endosomes
Lysosomal Positioning Coordinates Cellular Nutrient Responses
LC3 and GATE-16 N Termini Mediate Membrane Fusion Processes Required for Autophagosome Biogenesis
During Autophagy Mitochondria Elongate, Are Spared from Degradation and Sustain Cell Viability
Autophagosome Targeting and Membrane Curvature Sensing by Barkor/Atg14(L)

cell biology
Influence of Cell Geometry on Division-Plane Positioning

cell biology, computational biology
Review Issue: Systems Biology [special issue]
Modeling Vesicle Traffic Reveals Unexpected Consequences for Cdc42p-Mediated Polarity Establishment
Topology of Protein Interaction Network Shapes Protein Abundances and Strengths of Their Functional and Nonspecific Interactions
Modular Coherence of Protein Dynamics in Yeast Cell Polarity System

developmental biology
Intronic Delay is Essential for Oscillatory Expression in the Segmentation Clock
Local Kinetics of Morphogen Gradients

neuroscience
Non-Bayesian Contour Synthesis

plant physiology
Timing of Plant Immune Responses by a Central Circadian Regulator
Model for the Regulation of Arabidopsis thaliana Leaf Margin Development

plant physiology, computational biology
Computational Morphodynamics of Plants: Integrating Development over Space and Time [perspective]

ecology, theoretical biology
Compartmentalization Increases Food-web Persistence
A Competitive Network Theory of Species Diversity

evolution
Gene Clustering Pattern, Promoter Architecture, and Gene Expression Stability in Eukaryotic Genomes
An Evolutionary Process That Assembles Phenotypes through Space Rather Than through Time
Experimental Illumination of a Fitness Landscape

mathematical biology
Topology-free Stability of a Steady State in Network Systems with Dynamic Connections

mathematical biology, evolution
The Noisy Edge of Traveling Waves
Multiple Strategies in Structured Populations

imaging
Confined Activation and Subdiffractive Localization Enables Whole-cell PALM with Genetically Expressed Probes

Selected Papers 012111

biophysics
Mitotic Membrane Helps to Focus and Stabilize the Mitotic Spindle

biochemistry
Membrane Curvature during Peroxisome Fission Requires Pex11
Cell-free Fusion of Bacteria-containing Phagosomes with Endocytic Compartments
Tracking and Visualizing the Circadian Ticking of the Cyanobacterial Clock Protein KaiC in Solution
Nonspecific Binding Limits the Number of Proteins in a Cell and Shapes Their Interaction Networks

autophagy
p62 Targeting to the Autophagosome Formation Site Requires Self-oligomerization but not LC3 Binding
Autophagic Substrate Clearance Requires Activity of the Syntaxin-5 SNARE Complex
Mechanisms of Mitophagy [review]

cell biology
Mechanisms Determining the Morphology of the Peripheral ER
Cdc42 Localization and Cell Polarity Depend on Membrane Traffic
Spatial Gradient of Protein Phosphorylation Underlies Replicative Asymmetry in a Bacterium
Driving the Cell Cycle with a Minimal CDK Control Network
Mitochondrial Fusion and Fission in Cell Life and Death [review]
Membrane Budding [review]
Asymmetric Cell Division: Recent Developments and Their Implications for Tumour Biology [review]

cell biology, modeling
Bimodal Gene Expression in Noncooperative Regulatory Systems
Robust Circadian Clocks from Coupled Protein-modification and Transcription–translation Cycles
Stochastic Reaction-diffusion Kinetics in the Microscopic Limit
A Computational Model Predicts Xenopus Meiotic Spindle Organization

evolution, modeling
Dynamical Phase Transition in a Model for Evolution with Migration

imaging
Single-molecule Imaging Reveals Mechanisms of Protein Disruption by a DNA Translocase
Single SNARE-Mediated Vesicle Fusion Observed In Vitro by Polarized TIRFM
Protein Localization in Electron Micrographs Using Fluorescence Nanoscopy

Selected Papers 111610

biophysics
Continuum Electromechanical Modeling of Protein-Membrane Interactions
Crowding and Hydrodynamic Interactions Likely Dominate in Vivo Macromolecular Motion
Phospholipid Bilayers Are Viscoelastic

biochemistry
Appropriation of the MinD Protein-interaction Motif by the Dimeric Interface of the Bacterial Cell Division Regulator MinE

autophagy
Cdc48/p97 and Shp1/p47 Regulate Autophagosome Biogenesis in Concert with Ubiquitin-like Atg8
An Atg9-containing Compartment That Functions in the Early Steps of Autophagosome Biogenesis
p53-dependent Regulation of Autophagy Protein LC3 Supports Cancer Cell Survival under Prolonged Starvation
Autophagy Protein Microtubule-associated Protein 1 Light Chain-3B (LC3B) Activates Extrinsic Apoptosis during Cigarette Smoke-induced Emphysema

cell biology
Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
Imaging-Based Identification of a Critical Regulator of FtsZ Protofilament Curvature in Caulobacter
Direct Dynamin–Actin Interactions Regulate the Actin Cytoskeleton
Nuclear Membrane: Nuclear Envelope PORosity in Fission Yeast Meiosis [commentary]
Nuclear Compartmentalization Is Abolished during Fission Yeast Meiosis
Virtual Breakdown of the Nuclear Envelope in Fission Yeast Meiosis
Multisubunit Tethering Complexes and Their Role in Membrane Fusion [review]
TRAPP Complexes in Membrane Traffic: Convergence through a Common Rab [perspective]

evolution
Molecular and Regulatory Properties of a Public Good Shape the Evolution of Cooperation

mathematical biology
Calcium Wave Propagation in Chains of Endothelial Cells with Nonlinear Reaction Dynamics: Green's Function Approach

theoretical biology
Stochastic Models for Large Interacting Systems and Related Correlation Inequalities
Accumulation of Driver and Passenger Mutations during Tumor Progression

imaging
A Quantitative Approach to Analyze Binding Diffusion Kinetics by Confocal FRAP

Selected Papers 091110

biochemistry
A Red-Shifted Chlorophyll

biophysics
Polar Patterns of Driven Filaments

autophagy
Focus on Autophagy [Special Issue]
Plasma Membrane Contributes to the Formation of Pre-autophagosomal Structures
Autophagy Requires Endoplasmic Reticulum Targeting of the PI3-kinase Complex via Atg14L
Regulation of the Autophagy Protein LC3 by Phosphorylation
ATG12 Conjugation to ATG3 Regulates Mitochondrial Homeostasis and Cell Death

cell biology
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Caulobacter Chromosome Segregation Is an Ordered Multistep Process
MEC-17 Is an α-Tubulin Acetyltransferase
Self-Assembly of Filopodia-Like Structures on Supported Lipid Bilayers
Spindle Position Is Coordinated with Cell-Cycle Progression through Establishment of Mitotic Exit-Activating and -Inhibitory Zones
Intermolecular Associations Determine the Dynamics of the Circadian KaiABC Oscillator
Phosphatidic Acid Is a pH Biosensor That Links Membrane Biogenesis to Metabolism
Aquaporin-3 Mediates Hydrogen Peroxide Uptake to Regulate Downstream Intracellular Signaling

plant physiology, cell biology
Oscillating Gene Expression Determines Competence for Periodic Arabidopsis Root Branching

ecology
Bacterial Charity Work Leads to Population-wide Resistance

theoretical biology
Functional Roles for Noise in Genetic Circuits [review]
Fundamental Limits on the Suppression of Molecular Fluctuations

theoretical biology, ecology
Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks
Statistical Inference for Noisy Nonlinear Ecological Dynamic Systems

imaging
Time-resolved Luminescence Resonance Energy Transfer Imaging of Protein–Protein Interactions in Living Cells

The ParA Year...

我之前在研究的prokaryotic cytoskeletal system
在Caulobacter crescentus異常的成功啊XD
這個暑假出了兩篇research articles──
A Nat Cell Biol:
A Spindle-like Apparatus Guides Bacterial Chromosome Segregation
A PNAS:
Caulobacter Chromosome Segregation Is an Ordered Multistep Process

回頭看六月在"道阻且長"提到的
累計今年已經有一篇Science、一篇Nat Cell Biol、兩篇PNAS
外加一篇Cell Leading Edge Review

事實上在我決定做那麼大的改變的時候
手邊的實驗結果也已經露出了一線曙光
跟近來幾個大頭提的看法相符
Nat Cell Biol那篇做了大部分我能力所及而且有希望完成的實驗
然而他們沒有做某個重要的assay！
假如我之前在這個assay的結果可以apply到Caulobacter crescentus
他們的model有相當關鍵的一點可能需要修正

真的是天時地利缺人和啊XD

Selected Papers 073110

biophysics
Understanding Phase Behavior of Plant Cell Cortex Microtubule Organization
Protein Folded States Are Kinetic Hubs

prokaryotic cytoskeleton
Membrane Potential Is Important for Bacterial Cell Division
Dynamic SpoIIIE Assembly Mediates Septal Membrane Fission during Bacillus subtilis Sporulation
Crystal Structure of Helicobacter pylori MinE, a Cell Division Topological Specificity Factor
Actin-like Cytoskeleton Filaments Contribute to Cell Mechanics in Bacteria
Plasmid Protein TubR Uses a Distinct Mode of HTH-DNA Binding and Recruits the Prokaryotic Tubulin Homolog TubZ to Effect DNA Partition
Pushing and Pulling in Prokaryotic DNA Segregation [review]

cell biology
Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection
Asymmetrical Distribution of the Second Messenger c-di-GMP upon Bacterial Cell Division
Robust Growth of Escherichia coli
Imaging Interorganelle Contacts and Local Calcium Dynamics at the ER-Mitochondrial Interface
Cell Division Intersects with Cell Geometry [perspective]

cell biology, signaling
Aurora B and 14-3-3 Coordinately Regulate Clustering of Centralspindlin during Cytokinesis
Aurora B Phosphorylates Spatially Distinct Targets to Differentially Regulate the Kinetochore-Microtubule Interface
Fourier Analysis and Systems Identification of the p53 Feedback Loop

developmental biology
Intercellular Coupling Regulates the Period of the Segmentation Clock

neuroscience
Astrocytes Control Breathing Through pH-Dependent Release of ATP

evolution
A Generalization of Hamilton’s Rule for the Evolution of Microbial Cooperation
Population Robustness Arising from Cellular Heterogeneity
Genetic Flexibility of Regulatory Networks
Individual Histories and Selection in Heterogeneous Populations

imaging
Biophotonic Probing of Macromolecular Transformations during Apoptosis
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

theoretical biology
Community Structure in Time-Dependent, Multiscale, and Multiplex Networks
Arrested Phase Separation in Reproducing Bacteria Creates a Generic Route to Pattern Formation
Inferring Individual Rules from Collective Behavior
Stability of Graph Communities across Time Scales

Selected Papers 061210

biophysics
Dynamic Sorting of Lipids and Proteins in Membrane Tubes with a Moving Phase Boundary
Steric Confinement of Proteins on Lipid Membranes Can Drive Curvature and Tubulation

prokaryotic cytoskeleton, theoretical biology
Mesoscale Spatial Patterning in the Escherichia coli Min System: Reaction–Diffusion versus Mechanical Communication [perspective]
Multiple Modes of Interconverting Dynamic Pattern Formation by Bacterial Cell Division Proteins

cell biology
The Palmitoylation Machinery Is a Spatially Organizing System for Peripheral Membrane Proteins

cell biology, theoretical biology
Potential and Flux Landscapes Quantify the Stability and Robustness of Budding Yeast Cell Cycle Network

developmental biology, modeling
Scaling of Morphogen Gradients by an Expansion-Repression Integral Feedback Control

plant physiology, physics
Foldable Structures and the Natural Design of Pollen Grains

ecology
The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science

ecology, theoretical biology
Complexity and Diversity
Disentangling Collective Trends from Local Dynamics
Self-Similarity and Scaling in Forest Communities

evolution, cell biology
Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination
Imprints of the Genetic Code in the Ribosome

imaging, biophysics
Stoichiometry and Architecture of Active DNA Replication Machinery in Escherichia coli