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August 2009, Volume 5, Issue 8
- 1-13 Detection of Functional Modes in Protein Dynamics
by Jochen S Hub & Bert L de Groot - 1-17 Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
by Leighton Pritchard & Hui Liu & Clare Booth & Emma Douglas & Patrice François & Jacques Schrenzel & Peter E Hedley & Paul R J Birch & Ian K Toth - 1-20 Evolutionary Triplet Models of Structured RNA
by Robert K Bradley & Ian Holmes - 1-24 Qualia: The Geometry of Integrated Information
by David Balduzzi & Giulio Tononi
July 2009, Volume 5, Issue 7
- 1-9 Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels
by Guido Gigante & Maurizio Mattia & Jochen Braun & Paolo Del Giudice - 1-10 Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation
by Daniel Geberth & Marc-Thorsten Hütt - 1-10 Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
by Andrew J Olaharski & Nina Gonzaludo & Hans Bitter & David Goldstein & Stephan Kirchner & Hirdesh Uppal & Kyle Kolaja - 1-10 Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
by Flávio Codeço Coelho & Claudia T Codeço - 1-12 Semantic Similarity in Biomedical Ontologies
by Catia Pesquita & Daniel Faria & André O Falcão & Phillip Lord & Francisco M Couto
June 2009, Volume 5, Issue 6
- 1-4 Ten Simple Rules for Choosing between Industry and Academia
by David B Searls - 1-9 Exploring the Free Energy Landscape: From Dynamics to Networks and Back
by Diego Prada-Gracia & Jesús Gómez-Gardeñes & Pablo Echenique & Fernando Falo - 1-11 A Probabilistic Model of RNA Conformational Space
by Jes Frellsen & Ida Moltke & Martin Thiim & Kanti V Mardia & Jesper Ferkinghoff-Borg & Thomas Hamelryck - 1-11 Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
by Nobuyoshi Nagamine & Takayuki Shirakawa & Yusuke Minato & Kentaro Torii & Hiroki Kobayashi & Masaya Imoto & Yasubumi Sakakibara - 1-12 The Effect of Ongoing Exposure Dynamics in Dose Response Relationships
by Josep M Pujol & Joseph E Eisenberg & Charles N Haas & James S Koopman - 1-14 Taking the Lag out of Jet Lag through Model-Based Schedule Design
by Dennis A Dean , II & Daniel B Forger & Elizabeth B Klerman - 1-14 Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
by Zhang Zhang & Jeffrey P Townsend
May 2009, Volume 5, Issue 5
- 1-11 SHRiMP: Accurate Mapping of Short Color-space Reads
by Stephen M Rumble & Phil Lacroute & Adrian V Dalca & Marc Fiume & Arend Sidow & Michael Brudno - 1-13 How to Get the Most out of Your Curation Effort
by Andrey Rzhetsky & Hagit Shatkay & W John Wilbur - 1-14 Functional Brain Networks Develop from a “Local to Distributed” Organization
by Damien A Fair & Alexander L Cohen & Jonathan D Power & Nico U F Dosenbach & Jessica A Church & Francis M Miezin & Bradley L Schlaggar & Steven E Petersen - 1-15 Fast Statistical Alignment
by Robert K Bradley & Adam Roberts & Michael Smoot & Sudeep Juvekar & Jaeyoung Do & Colin Dewey & Ian Holmes & Lior Pachter - 1-16 Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
by Quentin J M Huys & Liam Paninski - 1-16 A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
by Gregory D Friedland & Nils-Alexander Lakomek & Christian Griesinger & Jens Meiler & Tanja Kortemme - 1-18 Prediction of Protein Binding Regions in Disordered Proteins
by Bálint Mészáros & István Simon & Zsuzsanna Dosztányi - 1-18 Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
by Yasser Roudi & Sheila Nirenberg & Peter E Latham
April 2009, Volume 5, Issue 4
- 1-2 Ten Simple Rules To Combine Teaching and Research
by Quentin Vicens & Philip E Bourne - 1-4 Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology
by B J Morrison McKay & Clare Sansom - 1-6 Polymorphism Data Can Reveal the Origin of Species Abundance Statistics
by Yosef E Maruvka & Nadav M Shnerb - 1-11 Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
by James Robert White & Niranjan Nagarajan & Mihai Pop - 1-12 Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons
by Cheng Ly & Brent Doiron - 1-14 Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis
by Gitanjali Yadav & Rajesh S Gokhale & Debasisa Mohanty - 1-16 Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
by Jan Eichhorn & Fabian Sinz & Matthias Bethge - 1-21 Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
by Zheng Yang & Peter Májek & Ivet Bahar
March 2009, Volume 5, Issue 3
- 1-7 T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
by Aidan MacNamara & Ulrich Kadolsky & Charles R M Bangham & Becca Asquith - 1-9 Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
by Jeremy E Purvis & Ravi Radhakrishnan & Scott L Diamond - 1-10 Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
by Boian S Alexandrov & Vladimir Gelev & Sang Wook Yoo & Alan R Bishop & Kim Ø Rasmussen & Anny Usheva - 1-10 Accurate Prediction of Peptide Binding Sites on Protein Surfaces
by Evangelia Petsalaki & Alexander Stark & Eduardo García-Urdiales & Robert B Russell - 1-10 Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
by Barry J Grant & Alemayehu A Gorfe & J Andrew McCammon - 1-11 BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
by Allen W Bryan Jr. & Matthew Menke & Lenore J Cowen & Susan L Lindquist & Bonnie Berger - 1-12 A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
by Gabriel Krouk & Daniel Tranchina & Laurence Lejay & Alexis A Cruikshank & Dennis Shasha & Gloria M Coruzzi & Rodrigo A Gutiérrez - 1-12 Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
by Matthew A Hibbs & Chad L Myers & Curtis Huttenhower & David C Hess & Kai Li & Amy A Caudy & Olga G Troyanskaya - 1-13 Broadband Criticality of Human Brain Network Synchronization
by Manfred G Kitzbichler & Marie L Smith & Søren R Christensen & Ed Bullmore - 1-13 “I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing
by Matthias S Keil - 1-13 Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
by Oscar Westesson & Ian Holmes - 1-15 Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation
by Emili Balaguer-Ballester & Nicholas R Clark & Martin Coath & Katrin Krumbholz & Susan L Denham - 1-15 Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
by Arash Bahrami & Amir H Assadi & John L Markley & Hamid R Eghbalnia - 1-20 Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures
by Alberto Pascual-García & David Abia & Ángel R Ortiz & Ugo Bastolla - 1-24 Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
by Patrick Blomquist & Anna Devor & Ulf G Indahl & Istvan Ulbert & Gaute T Einevoll & Anders M Dale
February 2009, Volume 5, Issue 2
- 1-10 Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
by John M Higgins & David T Eddington & Sangeeta N Bhatia & L Mahadevan - 1-13 The Temporal Winner-Take-All Readout
by Maoz Shamir - 1-14 Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
by Michael D Daily & Jeffrey J Gray
April 2009, Volume 5, Issue 1
- 1-9 Estimating the Location and Spatial Extent of a Covert Anthrax Release
by Judith Legrand & Joseph R Egan & Ian M Hall & Simon Cauchemez & Steve Leach & Neil M Ferguson
January 2009, Volume 5, Issue 1
- 1-7 Action Potential Initiation in the Hodgkin-Huxley Model
by Lucy J Colwell & Michael P Brenner - 1-12 Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
by Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta - 1-12 Evolutionary Sequence Modeling for Discovery of Peptide Hormones
by Kemal Sonmez & Naunihal T Zaveri & Ilan A Kerman & Sharon Burke & Charles R Neal & Xinmin Xie & Stanley J Watson & Lawrence Toll - 1-15 Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
by Wenxu Tong & Ying Wei & Leonel F Murga & Mary Jo Ondrechen & Ronald J Williams - 1-20 Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
by Sinisa Pajevic & Dietmar Plenz
December 2008, Volume 4, Issue 12
- 1-3 I Am Not a Scientist, I Am a Number
by Philip E Bourne & J Lynn Fink - 1-7 Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation
by Antonio Scialdone & Mario Nicodemi - 1-7 The Morphological Identity of Insect Dendrites
by Hermann Cuntz & Friedrich Forstner & Juergen Haag & Alexander Borst - 1-7 Disordered Flanks Prevent Peptide Aggregation
by Sanne Abeln & Daan Frenkel - 1-12 Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
by Da-Wei Li & Sandipan Mohanty & Anders Irbäck & Shuanghong Huo - 1-14 Game Theory of Mind
by Wako Yoshida & Ray J Dolan & Karl J Friston - 1-14 Search Algorithms as a Framework for the Optimization of Drug Combinations
by Diego Calzolari & Stefania Bruschi & Laurence Coquin & Jennifer Schofield & Jacob D Feala & John C Reed & Andrew D McCulloch & Giovanni Paternostro
November 2008, Volume 4, Issue 11
- 1-7 A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
by Stefan Auer & Filip Meersman & Christopher M Dobson & Michele Vendruscolo - 1-12 Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration
by Nicolas Maubourguet & Annick Lesne & Jean-Pierre Changeux & Uwe Maskos & Philippe Faure - 1-14 Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks
by Sheila M Reynolds & Lukas Käll & Michael E Riffle & Jeff A Bilmes & William Stafford Noble - 1-21 A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
by Anshul Kundaje & Xiantong Xin & Changgui Lan & Steve Lianoglou & Mei Zhou & Li Zhang & Christina Leslie - 1-23 Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
by Jonathan M Carlson & Zabrina L Brumme & Christine M Rousseau & Chanson J Brumme & Philippa Matthews & Carl Kadie & James I Mullins & Bruce D Walker & P Richard Harrigan & Philip J R Goulder & David Heckerman - 1-24 Hierarchical Models in the Brain
by Karl Friston
October 2008, Volume 4, Issue 10
- 1-9 Aggregation Propensity of the Human Proteome
by Elodie Monsellier & Matteo Ramazzotti & Niccolò Taddei & Fabrizio Chiti - 1-10 Support Vector Machines and Kernels for Computational Biology
by Asa Ben-Hur & Cheng Soon Ong & Sören Sonnenburg & Bernhard Schölkopf & Gunnar Rätsch - 1-10 Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs
by Ran Elkon & Reuven Agami - 1-10 Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
by Piers J Ingram & Michael P H Stumpf & Jaroslav Stark - 1-12 Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
by Yang Shen & Ioannis Ch Paschalidis & Pirooz Vakili & Sandor Vajda - 1-12 Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire
by Anandamohan Ghosh & Y Rho & A R McIntosh & R Kötter & V K Jirsa - 1-13 Cell Groups Reveal Structure of Stimulus Space
by Carina Curto & Vladimir Itskov - 1-16 The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation
by David M Santucci & Sridhar Raghavachari
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 - 1-18 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 - 1-9 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 - 1-17 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
July 2008, Volume 4, Issue 7
- 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 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
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 - 1-20 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 - 1-9 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 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
- 1-10 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 - 1-12 Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution
by Ilya Nemenman & Geoffrey D Lewen & William Bialek & Rob R de Ruyter van Steveninck - 1-14 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
January 2008, Volume 4, Issue 1
- 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 - 1-11 Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
by Guo-Cheng Yuan & Jun S Liu
December 2007, Volume 3, Issue 12
- 1-5 Getting Started in Probabilistic Graphical Models
by Edoardo M Airoldi
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 - 1-7 Predicting Gene Expression from Sequence: A Reexamination
by Yuan Yuan & Lei Guo & Lei Shen & Jun S Liu - 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 - 1-12 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 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
- 1-5 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 - 1-16 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 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 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 - 1-18 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
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
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 - 1-10 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