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October 2008, Volume 4, Issue 10
- 1-13 Cell Groups Reveal Structure of Stimulus Space
by Carina Curto & Vladimir Itskov - 1-14 Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
by Duncan Hull & Steve R Pettifer & Douglas B Kell - 1-15 Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development
by Szymon Stoma & Mikael Lucas & Jérôme Chopard & Marianne Schaedel & Jan Traas & Christophe Godin - 1-16 The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation
by David M Santucci & Sridhar Raghavachari - 1-18 Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation
by Steven A Prescott & Yves De Koninck & Terrence J Sejnowski
September 2008, Volume 4, Issue 9
- 1-10 Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
by Ji-Ping Wang & Yvonne Fondufe-Mittendorf & Liqun Xi & Guei-Feng Tsai & Eran Segal & Jonathan Widom - 1-11 A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction
by Patrick Flaherty & Mala L Radhakrishnan & Tuan Dinh & Robert A Rebres & Tamara I Roach & Michael I Jordan & Adam P Arkin - 1-13 Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
by Kai Wang & Jeremy A Horst & Gong Cheng & David C Nickle & Ram Samudrala - 1-14 Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo
by Francisco J P Lopes & Fernando M C Vieira & David M Holloway & Paulo M Bisch & Alexander V Spirov - 1-16 Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
by Roeland M H Merks & Erica D Perryn & Abbas Shirinifard & James A Glazier - 1-18 Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2
by Klaus Wimmer & K Jannis Hildebrandt & R Matthias Hennig & Klaus Obermayer - 1-21 Probabilistic Phylogenetic Inference with Insertions and Deletions
by Elena Rivas & Sean R Eddy
August 2008, Volume 4, Issue 8
- 1-6 Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach
by Alessandro Ambrosi & Claudia Cattoglio & Clelia Di Serio - 1-8 Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif
by Yu Tanouchi & Dennis Tu & Jungsang Kim & Lingchong You - 1-8 Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory
by James V Stone & Peter E Jupp - 1-9 A Novel Three-Phase Model of Brain Tissue Microstructure
by Jana L Gevertz & Salvatore Torquato - 1-10 Modeling ChIP Sequencing In Silico with Applications
by Zhengdong D Zhang & Joel Rozowsky & Michael Snyder & Joseph Chang & Mark Gerstein - 1-11 Cooperative Transition between Open and Closed Conformations in Potassium Channels
by Turkan Haliloglu & Nir Ben-Tal - 1-12 The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau
by Austin Huang & Collin M Stultz - 1-12 Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways
by Sangjo Han & Dongsup Kim - 1-13 Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin
by V V Krishnan & Edmond Y Lau & Justin Yamada & Daniel P Denning & Samir S Patel & Michael E Colvin & Michael F Rexach - 1-14 Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System
by Michael Capalbo & Eric Postma & Rainer Goebel - 1-15 Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress
by Ronald C Taylor & George Acquaah-Mensah & Mudita Singhal & Deepti Malhotra & Shyam Biswal - 1-15 Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics
by Philip G McQueen & F Ellis McKenzie - 1-17 A Feature-Based Approach to Modeling Protein–DNA Interactions
by Eilon Sharon & Shai Lubliner & Eran Segal - 1-17 Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules
by Giancarlo La Camera & Barry J Richmond - 1-35 The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields
by Gustavo Deco & Viktor K Jirsa & Peter A Robinson & Michael Breakspear & Karl Friston
July 2008, Volume 4, Issue 7
- 1-3 Computational Biology Resources Lack Persistence and Usability
by Stella Veretnik & J Lynn Fink & Philip E Bourne - 1-9 Optimal Compensation for Temporal Uncertainty in Movement Planning
by Todd E Hudson & Laurence T Maloney & Michael S Landy - 1-9 The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
by Namiko Mitarai & Ian B Dodd & Michael T Crooks & Kim Sneppen - 1-9 Memory Switches in Chemical Reaction Space
by Naren Ramakrishnan & Upinder S Bhalla - 1-9 Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development
by Anthony Randal McIntosh & Natasa Kovacevic & Roxane J Itier - 1-10 Circadian Phase Resetting via Single and Multiple Control Targets
by Neda Bagheri & Jörg Stelling & Francis J Doyle III - 1-10 Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
by Morten Nielsen & Claus Lundegaard & Thomas Blicher & Bjoern Peters & Alessandro Sette & Sune Justesen & Søren Buus & Ole Lund - 1-11 Intrinsic Gain Modulation and Adaptive Neural Coding
by Sungho Hong & Brian Nils Lundstrom & Adrienne L Fairhall - 1-12 Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology
by Karthik Devarajan - 1-13 Local Function Conservation in Sequence and Structure Space
by Nils Weinhold & Oliver Sander & Francisco S Domingues & Thomas Lengauer & Ingolf Sommer - 1-13 Similarity Queries for Temporal Toxicogenomic Expression Profiles
by Adam A Smith & Aaron Vollrath & Christopher A Bradfield & Mark Craven - 1-13 Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions
by Denise G Teotico & Monica L Frazier & Feng Ding & Nikolay V Dokholyan & Brenda R S Temple & Matthew R Redinbo
June 2008, Volume 4, Issue 6
- 1-2 How To Advance Open International Scientific Exchange
by Barbara Bryant - 1-3 Ten Simple Rules for Organizing a Scientific Meeting
by Manuel Corpas & Nils Gehlenborg & Sarath Chandra Janga & Philip E Bourne - 1-5 ISMB 2008 Toronto
by Michal Linial & Jill P Mesirov & B J Morrison McKay & Burkhard Rost - 1-10 Model-Based Hypothesis Testing of Key Mechanisms in Initial Phase of Insulin Signaling
by Gunnar Cedersund & Jacob Roll & Erik Ulfhielm & Anna Danielsson & Henrik Tidefelt & Peter Strålfors - 1-12 Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data
by Joseph Schlecht & Matthew E Kaplan & Kobus Barnard & Tatiana Karafet & Michael F Hammer & Nirav C Merchant - 1-12 Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins
by Jason W Locasale & Arup K Chakraborty - 1-15 A Comparative Computer Simulation of Dendritic Morphology
by Duncan E Donohue & Giorgio A Ascoli - 1-18 Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework
by David Balduzzi & Giulio Tononi - 1-20 CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
by Pradipta Ray & Suyash Shringarpure & Mladen Kolar & Eric P Xing
May 2008, Volume 4, Issue 5
- 1-2 Ten Simple Rules for Aspiring Scientists in a Low-Income Country
by Edgardo Moreno & José-María Gutiérrez - 1-6 Why Are Computational Neuroscience and Systems Biology So Separate?
by Erik De Schutter - 1-9 Transient Cognitive Dynamics, Metastability, and Decision Making
by Mikhail I Rabinovich & Ramón Huerta & Pablo Varona & Valentin S Afraimovich - 1-9 Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing
by John Porrill & Paul Dean - 1-10 Uncovering Interactions in the Frequency Domain
by Shuixia Guo & Jianhua Wu & Mingzhou Ding & Jianfeng Feng - 1-10 Context-Specific Metabolic Networks Are Consistent with Experiments
by Scott A Becker & Bernhard O Palsson - 1-10 An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism
by Tatyana K Korendyaseva & Denis N Kuvatov & Vladimir A Volkov & Michael V Martinov & Victor M Vitvitsky & Ruma Banerjee & Fazoil I Ataullakhanov - 1-12 Discovering Sequence Motifs with Arbitrary Insertions and Deletions
by Martin C Frith & Neil F W Saunders & Bostjan Kobe & Timothy L Bailey - 1-12 Measuring Global Credibility with Application to Local Sequence Alignment
by Bobbie-Jo M Webb-Robertson & Lee Ann McCue & Charles E Lawrence - 1-13 The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures
by Diego U Ferreiro & Aleksandra M Walczak & Elizabeth A Komives & Peter G Wolynes - 1-13 Viral Population Estimation Using Pyrosequencing
by Nicholas Eriksson & Lior Pachter & Yumi Mitsuya & Soo-Yon Rhee & Chunlin Wang & Baback Gharizadeh & Mostafa Ronaghi & Robert W Shafer & Niko Beerenwinkel - 1-14 A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
by Sean R Eddy
April 2008, Volume 4, Issue 4
- 1-6 Translational Systems Biology of Inflammation
by Yoram Vodovotz & Marie Csete & John Bartels & Steven Chang & Gary An - 1-8 Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
by Sourav Bandyopadhyay & Ryan Kelley & Nevan J Krogan & Trey Ideker - 1-8 Distinct Timing Mechanisms Produce Discrete and Continuous Movements
by Raoul Huys & Breanna E Studenka & Nicole L Rheaume & Howard N Zelaznik & Viktor K Jirsa - 1-9 Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
by Jon Bohlin & Eystein Skjerve & David W Ussery - 1-10 Dimensionality and Dynamics in the Behavior of C. elegans
by Greg J Stephens & Bethany Johnson-Kerner & William Bialek & William S Ryu - 1-10 Predicting Co-Complexed Protein Pairs from Heterogeneous Data
by Jian Qiu & William Stafford Noble - 1-10 A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach
by Peng Wang & John Sidney & Courtney Dow & Bianca Mothé & Alessandro Sette & Bjoern Peters - 1-11 Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth
by Lubomir Kostal & Petr Lansky & Jean-Pierre Rospars - 1-11 The Statistical Neuroanatomy of Frontal Networks in the Macaque
by Bruno B Averbeck & Moonsang Seo
March 2008, Volume 4, Issue 3
- 1-3 Open Access: Taking Full Advantage of the Content
by Philip E Bourne & J Lynn Fink & Mark Gerstein - 1-10 Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
by Thomas Manke & Helge G Roider & Martin Vingron - 1-10 Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity
by Yonatan Loewenstein - 1-11 The Dynamics of Human Body Weight Change
by Carson C Chow & Kevin D Hall - 1-11 Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation
by Bin Kang & Yuan-Yuan Li & Xiao Chang & Lei Liu & Yi-Xue Li - 1-12 Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution
by Ilya Nemenman & Geoffrey D Lewen & William Bialek & Rob R de Ruyter van Steveninck - 1-13 Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation
by Alex Roxin & Anders Ledberg - 1-14 Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
by Sichun Yang & Benoît Roux
February 2008, Volume 4, Issue 2
- 1-3 On the Process of Becoming a Great Scientist
by Morgan C Giddings - 1-6 Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
by Dennis Kostka & Rainer Spang - 1-7 Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes
by Ivan Coluzza & Alfonso De Simone & Franca Fraternali & Daan Frenkel - 1-8 Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding
by Adrian W R Serohijos & Tamás Hegedűs & John R Riordan & Nikolay V Dokholyan - 1-8 Accurate Structural Correlations from Maximum Likelihood Superpositions
by Douglas L Theobald & Deborah S Wuttke - 1-8 Predicting the Receptive Range of Olfactory Receptors
by Rafi Haddad & Liran Carmel & Noam Sobel & David Harel - 1-10 Stimulus Design for Model Selection and Validation in Cell Signaling
by Joshua F Apgar & Jared E Toettcher & Drew Endy & Forest M White & Bruce Tidor - 1-11 Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability
by Antti Saarinen & Marja-Leena Linne & Olli Yli-Harja - 1-12 Computational Methods for Protein Identification from Mass Spectrometry Data
by Leo McHugh & Jonathan W Arthur - 1-13 Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences
by Li Zhaoping & Li Jingling - 1-15 Statistical Resolution of Ambiguous HLA Typing Data
by Jennifer Listgarten & Zabrina Brumme & Carl Kadie & Gao Xiaojiang & Bruce Walker & Mary Carrington & Philip Goulder & David Heckerman - 1-15 The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks
by Derek Ruths & Melissa Muller & Jen-Te Tseng & Luay Nakhleh & Prahlad T Ram - 1-16 Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment
by Avner Wallach & Danny Eytan & Shimon Marom & Ron Meir - 1-16 A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
by Naomi Habib & Tommy Kaplan & Hanah Margalit & Nir Friedman
January 2008, Volume 4, Issue 1
- 1-1 Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation
by Clinton H Hansen & Robert G Endres & Ned S Wingreen - 1-2 Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al
by David C Nickle & Nebojsa Jojic & David Heckerman & Vladimir Jojic & Darko Kirovski & Morgane Rolland & Sergei Kosakovsky Pond & James I Mullins - 1-6 Why is Real-World Visual Object Recognition Hard?
by Nicolas Pinto & David D Cox & James J DiCarlo - 1-7 Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
by Gil Hornung & Naama Barkai - 1-11 Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor
by Xinli Liu & Yechun Xu & Honglin Li & Xicheng Wang & Hualiang Jiang & Francisco J Barrantes - 1-11 Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
by Guo-Cheng Yuan & Jun S Liu - 1-12 Matt: Local Flexibility Aids Protein Multiple Structure Alignment
by Matthew Menke & Bonnie Berger & Lenore Cowen
December 2007, Volume 3, Issue 12
- 1-1 The Long and Thorny Road to Publication in Quality Journals
by Thomas C Erren - 1-5 Getting Started in Probabilistic Graphical Models
by Edoardo M Airoldi - 1-10 The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
by Antonio del Sol & Pablo Carbonell - 1-11 Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering
by Carlos Gomez-Uribe & George C Verghese & Leonid A Mirny - 1-13 Social Interactions in Myxobacterial Swarming
by Yilin Wu & Yi Jiang & Dale Kaiser & Mark Alber
November 2007, Volume 3, Issue 11
- 1-1 Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
by Kevin P Keegan & Suraj Pradhan & Ji-Ping Wang & Ravi Allada - 1-2 Ten Simple Rules for Graduate Students
by Jenny Gu & Philip E Bourne - 1-5 Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country
by Tirso Pons & Luis A Montero & Juan P Febles - 1-7 Predicting Gene Expression from Sequence: A Reexamination
by Yuan Yuan & Lei Guo & Lei Shen & Jun S Liu - 1-9 In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
by Lei Xie & Jian Wang & Philip E Bourne - 1-9 Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust
by Jongrae Kim & Pat Heslop-Harrison & Ian Postlethwaite & Declan G Bates - 1-10 Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection
by Xiaohong Li & Steven G Self & Patricia C Galipeau & Thomas G Paulson & Brian J Reid - 1-10 A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast
by Leelavati Narlikar & Raluca Gordân & Alexander J Hartemink - 1-11 A Dynamical Systems Hypothesis of Schizophrenia
by Marco Loh & Edmund T Rolls & Gustavo Deco - 1-12 Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites
by Kaoru Sugimura & Kohei Shimono & Tadashi Uemura & Atsushi Mochizuki - 1-15 MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
by Saurabh Sinha & Xin He - 1-15 CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
by Oliver C Redfern & Andrew Harrison & Tim Dallman & Frances M G Pearl & Christine A Orengo - 1-15 From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses
by Sven Zenker & Jonathan Rubin & Gilles Clermont - 1-20 Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
by Hailiang Huang & Bruno M Jedynak & Joel S Bader
October 2007, Volume 3, Issue 10
- 1-8 Universally Sloppy Parameter Sensitivities in Systems Biology Models
by Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna - 1-8 A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
by Jennifer Listgarten & Nicole Frahm & Carl Kadie & Christian Brander & David Heckerman - 1-10 Brightness and Darkness as Perceptual Dimensions
by Tony Vladusich & Marcel P Lucassen & Frans W Cornelissen - 1-11 Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
by Tom C Freeman & Leon Goldovsky & Markus Brosch & Stijn van Dongen & Pierre Mazière & Russell J Grocock & Shiri Freilich & Janet Thornton & Anton J Enright - 1-12 Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
by Ovidiu Lipan & Jean-Marc Navenot & Zixuan Wang & Lei Huang & Stephen C Peiper - 1-14 Landscape as a Model: The Importance of Geometry
by E Penelope Holland & James N Aegerter & Calvin Dytham & Graham C Smith
September 2007, Volume 3, Issue 9
- 1-2 Reply to “Ten Simple Rules for Getting Published”
by Eric Grosch - 1-5 From Pathways Databases to Network Models of Switching Behavior
by Baltazar D Aguda & Andrew B Goryachev - 1-7 Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
by Doron Betel & Kevin E Breitkreuz & Ruth Isserlin & Danielle Dewar-Darch & Mike Tyers & Christopher W V Hogue - 1-8 Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling
by Liang Qiao & Robert B Nachbar & Ioannis G Kevrekidis & Stanislav Y Shvartsman - 1-11 Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
by Chakra Chennubhotla & Ivet Bahar - 1-12 Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
by Mookyung Cheon & Iksoo Chang & Sandipan Mohanty & Leila M Luheshi & Christopher M Dobson & Michele Vendruscolo & Giorgio Favrin
August 2007, Volume 3, Issue 8
- 1-1 On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
by Sergey Kryazhimskiy & Ulf Dieckmann & Simon A Levin & Jonathan Dushoff - 1-4 Recent Evolutions of Multiple Sequence Alignment Algorithms
by Cédric Notredame - 1-8 A Primer on Learning in Bayesian Networks for Computational Biology
by Chris J Needham & James R Bradford & Andrew J Bulpitt & David R Westhead - 1-9 An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells
by Burton W Andrews & Pablo A Iglesias - 1-9 PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop
by Robert S Kuczenski & Kevin C Hong & Jordi García-Ojalvo & Kelvin H Lee - 1-10 Functional Representation of Enzymes by Specific Peptides
by Vered Kunik & Yasmine Meroz & Zach Solan & Ben Sandbank & Uri Weingart & Eytan Ruppin & David Horn - 1-12 Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
by Sylvain V Costes & Artem Ponomarev & James L Chen & David Nguyen & Francis A Cucinotta & Mary Helen Barcellos-Hoff - 1-13 Automated Protein Subfamily Identification and Classification
by Duncan P Brown & Nandini Krishnamurthy & Kimmen Sjölander - 1-14 Design of Multi-Specificity in Protein Interfaces
by Elisabeth L Humphris & Tanja Kortemme - 1-15 Automated Discovery of Functional Generality of Human Gene Expression Programs
by Georg K Gerber & Robin D Dowell & Tommi S Jaakkola & David K Gifford - 1-15 A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm
by Meron Gurkiewicz & Alon Korngreen - 1-15 Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons
by David Golomb & Karnit Donner & Liron Shacham & Dan Shlosberg & Yael Amitai & David Hansel - 1-16 Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis
by Andrew E Teschendorff & Michel Journée & Pierre A Absil & Rodolphe Sepulchre & Carlos Caldas - 1-18 Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells
by Mathias Franzius & Henning Sprekeler & Laurenz Wiskott
July 2007, Volume 3, Issue 7
- 1-8 Quantitative Analysis of Cell Nucleus Organisation
by Carol Shiels & Niall M Adams & Suhail A Islam & David A Stephens & Paul S Freemont - 1-8 Protein–Protein Interaction Hotspots Carved into Sequences
by Yanay Ofran & Burkhard Rost - 1-9 Chemotaxis Receptor Complexes: From Signaling to Assembly
by Robert G Endres & Joseph J Falke & Ned S Wingreen - 1-10 Introduction to Computational Proteomics
by Jacques Colinge & Keiryn L Bennett - 1-12 Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
by Fereydoun Hormozdiari & Petra Berenbrink & Nataša Pržulj & S Cenk Sahinalp - 1-12 Natively Unstructured Loops Differ from Other Loops
by Avner Schlessinger & Jinfeng Liu & Burkhard Rost - 1-13 Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
by Anastasia A Samsonova & Mahesan Niranjan & Steven Russell & Alvis Brazma - 1-13 Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies
by Deyan Luan & Michael Zai & Jeffrey D Varner - 1-17 Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle
by Bertrand C W Tanner & Thomas L Daniel & Michael Regnier - 1-18 Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
by Patricia A Ryan & Brian W Kirk & Chad W Euler & Raymond Schuch & Vincent A Fischetti - 1-18 Optimal Timing and Duration of Induction Therapy for HIV-1 Infection
by Marcel E Curlin & Shyamala Iyer & John E Mittler
June 2007, Volume 3, Issue 6
- 1-3 The International Society for Computational Biology 10th Anniversary
by Lawrence Hunter & Russ B Altman & Philip E Bourne - 1-4 A View from the Dark Side
by David B Searls - 1-7 Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes
by Andrey A Ptitsyn & Sanjin Zvonic & Jeffrey M Gimble - 1-8 Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH
by Oscar M Rueda & Ramón Díaz-Uriarte - 1-9 Hierarchical Processing of Auditory Objects in Humans
by Sukhbinder Kumar & Klaas E Stephan & Jason D Warren & Karl J Friston & Timothy D Griffiths - 1-11 Machine Learning and Its Applications to Biology
by Adi L Tarca & Vincent J Carey & Xue-wen Chen & Roberto Romero & Sorin Drăghici - 1-13 Slowness: An Objective for Spike-Timing–Dependent Plasticity?
by Henning Sprekeler & Christian Michaelis & Laurenz Wiskott - 1-15 A Mass Conserved Reaction–Diffusion System Captures Properties of Cell Polarity
by Mikiya Otsuji & Shuji Ishihara & Carl Co & Kozo Kaibuchi & Atsushi Mochizuki & Shinya Kuroda
May 2007, Volume 3, Issue 5
- 1-1 “Simple Rules for Editors”? Here is One Rule to Tackle Neglected Problems of Publishing
by Thomas C Erren & Michael Erren - 1-2 Ten Simple Rules for a Good Poster Presentation
by Thomas C Erren & Philip E Bourne - 1-4 ISMB/ECCB 2007: The Premier Conference on Computational Biology
by Thomas Lengauer & B J Morrison McKay & Burkhard Rost - 1-10 Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions
by Tristan Ursell & Kerwyn Casey Huang & Eric Peterson & Rob Phillips - 1-11 Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
by Timothy E Reddy & Charles DeLisi & Boris E Shakhnovich - 1-12 Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development
by Jasmin Fisher & Nir Piterman & Alex Hajnal & Thomas A Henzinger - 1-13 Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits
by Gabriel D Puccini & Maria V Sanchez-Vives & Albert Compte - 1-13 The Human Genomic Melting Map
by Fang Liu & Eivind Tøstesen & Jostein K Sundet & Tor-Kristian Jenssen & Christoph Bock & Geir Ivar Jerstad & William G Thilly & Eivind Hovig
April 2007, Volume 3, Issue 4
- 1-2 Ten Simple Rules for Making Good Oral Presentations
by Philip E Bourne - 1-7 Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
by Benjamin A Shoemaker & Anna R Panchenko - 1-11 Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model
by Scott Christley & Mark S Alber & Stuart A Newman - 1-18 Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network
by Matteo Barberis & Edda Klipp & Marco Vanoni & Lilia Alberghina
March 2007, Volume 3, Issue 3
- 1-2 Ten Simple Rules for a Successful Collaboration
by Quentin Vicens & Philip E Bourne - 1-9 Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
by Barry G Hall & Stephen J Salipante - 1-10 Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
by Axel Bernal & Koby Crammer & Artemis Hatzigeorgiou & Fernando Pereira - 1-10 Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
by Oliver Sander & Tobias Sing & Ingolf Sommer & Andrew J Low & Peter K Cheung & P Richard Harrigan & Thomas Lengauer & Francisco S Domingues - 1-13 Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch
by Keun-Young Kim & Jin Wang - 1-14 DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
by Shaun Mahony & Philip E Auron & Panayiotis V Benos - 1-15 Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
by Eric P Nawrocki & Sean R Eddy - 1-19 Dose Response Relationship in Anti-Stress Gene Regulatory Networks
by Qiang Zhang & Melvin E Andersen
February 2007, Volume 3, Issue 2
- 1-10 Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology
by Stefano Ciliberti & Olivier C Martin & Andreas Wagner - 1-11 Repressor Dimerization in the Zebrafish Somitogenesis Clock
by Olivier Cinquin - 1-11 From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
by Jomol P Mathew & Barry S Taylor & Gary D Bader & Saiju Pyarajan & Marco Antoniotti & Arul M Chinnaiyan & Chris Sander & Steven J Burakoff & Bud Mishra - 1-14 Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
by Rachel Karchin & Alvaro N A Monteiro & Sean V Tavtigian & Marcelo A Carvalho & Andrej Sali
January 2007, Volume 3, Issue 1
- 1-1 In Remembrance: Reinhart Heinrich 1946–2006
by Thomas Höfer - 1-2 Moving Education Forward
by Fran Lewitter - 1-13 Nitric Oxide Regulates Input Specificity of Long-Term Depression and Context Dependence of Cerebellar Learning
by Hideaki Ogasawara & Tomokazu Doi & Kenji Doya & Mitsuo Kawato - 1-20 Computational Aspects of Feedback in Neural Circuits
by Wolfgang Maass & Prashant Joshi & Eduardo D Sontag
December 2006, Volume 2, Issue 12
- 1-6 On Side-Chain Conformational Entropy of Proteins
by Jinfeng Zhang & Jun S Liu - 1-7 Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity
by Alon Kaufman & Gideon Dror & Isaac Meilijson & Eytan Ruppin - 1-8 Cooperation is Fleeting in the World of Transposable Elements
by Andreas Wagner - 1-9 Transcriptional Regulation by Competing Transcription Factor Modules
by Rutger Hermsen & Sander Tans & Pieter Rein ten Wolde - 1-13 Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens
by Jeroen de Ridder & Anthony Uren & Jaap Kool & Marcel Reinders & Lodewyk Wessels - 1-15 DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals
by Éric Fernandez & Renaud Schiappa & Jean-Antoine Girault & Nicolas Le Novère
November 2006, Volume 2, Issue 11
- 1-2 Ten Simple Rules for Selecting a Postdoctoral Position
by Philip E Bourne & Iddo Friedberg - 1-7 Robustness and Fragility in Immunosenescence
by Sean P Stromberg & Jean Carlson