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

Song of the Day

本來想選農村武裝青年最新專輯裡的歌，
畢竟過去這一年是土地意識大回歸，
而且主唱彰化田中將大，啊不是，
我的同鄉彰化田中阿達真的唱出了對田中、彰化、台灣的情感與熱愛，
此外大提琴手俐君是台大保育社出來的XD
但考慮良久，
還是決定今年以加選年度音樂創作人／專輯來推廣農村武裝青年！

# 農村武裝青年新專輯《幸福在哪裡？》
有興趣的朋友可以出點錢支持，
不過其實幾乎所有曲目在 youtube 都找得到現場演出的錄影錄音。

接下來，
年度新認識的有趣人物／鄉民／部落格毋庸置疑是張紹中（男子漢），
他的 p2 隱版文章曾在幾個月前讓我決定封筆過一次。
這世界有太多深刻、深邃的人事物，
以違背大眾認知、認可、認同的形態，
潛藏在不為人知、黑暗的角落邊緣閃耀著光芒。

# 張紹中公開部落格 《未央歌》
張紹中公開版面上的神作很多，
不過為了呼應農村武裝青年新專輯《幸福在哪裡？》及今年的生日選歌，
摘一篇〈那些（不）幸福的種種〉跟有緣的朋友分享

Anyway, 今年的生日選歌是李宗盛唱他自己詞曲的〈我是一隻小小鳥〉 :)

今天想說的、想祝福的，
都在大哥的歌聲中與下面這些大概是出自原本趙傳專輯小冊的文字了。
感謝這個世界與大家。

----------------------------------------

選兩個意境有細微差異的版本——
% 版本一：理性與感性作品音樂會
https://www.youtube.com/watch?v=SLIu37eNGSg
% 版本二：天下三十美麗台灣音樂晚會
https://www.youtube.com/watch?v=wLKT_vN2TqM

⋯⋯

每一條路都似乎艱辛而漫長
每一種生活都有難言的隱痛
有的人生來就是翱翔的飛鷹
有的人注定只是枝頭奔波的小鳥

⋯⋯

紅塵鳥低飛
飛過人性的善惡和褪色的夢想
這無奇不有的世界
你注定在笑容和淚水之間
飛來飛去

⋯⋯

我想了又想：
實現自己心底的願望，
是不是每一個曾在玻璃窗前仰望蒼天傢伙的夢？
也許我們的夢都一樣美麗而單純——

只要一個可供棲息的溫暖懷抱。

我走過每一天、每一個地方，
那個機車青年穿梭在陽光風雨裡載著他破碎的愛情，
那個抱著書本苦讀的中學生想著一座美麗殿堂，
那個在東區雨中流浪在櫥窗前的少女，
那個俱樂部裡走向麥克風的先生，
他們正在每一條路上摸索著未來⋯⋯

我舉杯敬那些——

在生命裡跌倒後又爬起來向前走，
在風雨中哭喊後又重新展現笑容，
最後終於飛上青天的人！

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

Song of the Day

又到一年一度可以選 Song of the Day 的日子了。
（雖說今年已經在退伍的時候
破例選了 Proud of You 給陪我渡過七個月空軍生涯的弟兄XD）

Anyway,
今年的生日選歌是馬修連恩《Orchid Island》專輯裡頭的 Water Taro :)

已經有好些年沒有花時間用心聽馬修連恩的音樂，
部份原因應該是對音樂的 taste 跟隨著個性一起變得更加內斂，
較難再和馬修連恩樂音裡頭那種句句情感滿溢的表達方式共鳴；
但最近幾個月花了一些時間回頭檢視過往幾年的日子、
仔細聆聽自己心底深處的聲音後，
驚覺根本是我對在台灣這塊土地上生湠的生命們感情越來越淡卻不自知。
最明顯的證據--
即使是中科四期、國光石化…近年在自己家鄉上的環境議題，
除了點連署填信託認股支持外，幾乎沒有更積極的作為跟行動。

真的很慶幸去年在政校抽到 304 小政這隻籤，
讓我有機會在台灣最南端的兩個縣，
台東跟屏東，分別待了四個月和三個月，
慢慢把對土地的感情找回來；
出國前跟老共衝花東縱谷南段、
（大部份時間）一個人用雙腳走騎平溪／雙溪／花蓮，
在這兩次旅途中，
就像《月亮忘記了》裡頭的月亮那樣，記起許多往事，
從小一路積累的那股熱血跟衝勁都回來了。

離開台灣來米國之後的這一百多天，
看到好幾個令人不解、擔憂、心痛的消息，
特別是先詠 po 的蘭嶼核廢料問題。

想起高中時說服自己不唸環工唸生物最大的理由是，
更瞭解生命運作的法則才有辦法做好環境經營和保育工作，
所以今年生日最大的願望，
在有生之年研究主題能往上回到或應用到 EEB 層級，
像謝志豪老師現在那樣XD
小小心願則是還有機會回台灣跟小朋友講〈重新看見海洋〉，
好歹我也上過荒野的推廣講師培訓，
但竟然到現在都還沒講過一場真正的！

謝謝大家今年的祝福，
也衷心希望心中還有一點的熱血的朋友們，
即使大家都在喊"鬼島"跟"塊陶"，
還能繼續為台灣這塊土地努力 :)

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)

Song of the Day [Special Edition]

第一次在非生日選 Song of the Day

挑了一天，決定把這首 Proud of You 送給陪我走過這七個月的空軍弟兄姊妹們，真心希望你們 open your mind and love with heart ;) 志願役的還要繼續面對這個體系中的眾多荒謬與不合理，但願你們至少還能保有一點點理想；義務役的大家，你們或許比我見過更多世間險惡與人心黑暗，不過無論如何，真正的無畏來自於無私的愛。一起加油，展翅高飛！

Love in your eyes
Sitting silent by my side
Going on
Holding hands
Walking through the nights

Hold me up
Hold me tight
Lift me up to touch the sky
Teaching me to love with heart
Helping me open my mind
I can fly
I'm proud that I can fly
To give the best of mine
Till the end of the time
Believe me I can fly
I'm proud that I can fly
To give the best of mine
The heaven in the sky

Stars in the sky
Wishing once upon a time
Give me love
Make me smile
Till the end of life

Hold me up
Hold me tight
Lift me up to touch the sky
Teaching me to love with heart
Helping me open my mind
I can fly
I'm proud that I can fly
To give the best of mine
Till the end of the time
Believe me I can fly
I'm proud that I can fly
To give the best of mine
The heaven in the sky

Can't you believe that you light up my way
No matter how that ease my path
I'll never lose my faith
See me fly
I'm proud to fly up high
Show you the best of mine
Till the end of the time
Believe me I can fly
I'm singing in the sky
Show you the best of mine
The heaven in the sky

Nothing can stop me
Spread my wings so wide

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