Journal: PLoS Computational Biology

Volume 4, Issue 9

0 -- 0Phineus R. Markwick, Therese E. Malliavin, Michael Nilges. Structural Biology by NMR: Structure, Dynamics, and Interactions
0 -- 0Raja Mazumder, Sona Vasudevan. Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
0 -- 0Roeland Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier. Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
0 -- 0Neema Jamshidi, Bernhard Ø. Palsson. Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
0 -- 0Jeff Clune, Dusan Misevic, Charles Ofria, Richard E. Lenski, Santiago F. Elena, Rafael Sanjuán. Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
0 -- 0Van M. Savage, Eric J. Deeds, Walter Fontana. Sizing Up Allometric Scaling Theory
0 -- 0Mark Müller-Linow, Claus C. Hilgetag, Marc-Thorsten Hütt. Organization of Excitable Dynamics in Hierarchical Biological Networks
0 -- 0Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya. A Genomewide Functional Network for the Laboratory Mouse
0 -- 0Wallace F. Marshall. Modeling Recursive RNA Interference
0 -- 0Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
0 -- 0Robert Riley, Matteo Pellegrini, David Eisenberg. Mycobacterium tuberculosis
0 -- 0R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara. Insights into Protein-DNA Interactions through Structure Network Analysis
0 -- 0Francisco J. P. Lopes, Fernando M. C. Vieira, David M. Holloway, Paulo Mascarello Bisch, Alexander V. Spirov. Drosophila Embryo
0 -- 0Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom. Saccharomyces cerevisiae
0 -- 0Elena Rivas, Sean R. Eddy. Probabilistic Phylogenetic Inference with Insertions and Deletions
0 -- 0Mark A. Kramer, Anita K. Roopun, Lucy M. Carracedo, Roger D. Traub, Miles A. Whittington, Nancy Kopell. Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex
0 -- 0Klaus Wimmer, K. Jannis Hildebrandt, R. Matthias Hennig, Klaus Obermayer. Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2
0 -- 0Shrihari Sonavane, Pinak Chakrabarti. Cavities and Atomic Packing in Protein Structures and Interfaces
0 -- 0Xosé M. Fernández-Suarez, Ewan Birney. Advanced Genomic Data Mining
0 -- 0Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala. Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
0 -- 0Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin. A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction
0 -- 0John Archer, John W. Pinney, Jun Fan, Etienne Simon-Loriere, Eric J. Arts, Matteo Negroni, David L. Robertson. Identifying the Important HIV-1 Recombination Breakpoints

Volume 4, Issue 8

0 -- 0Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, James P. Basilion. Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers
0 -- 0Karl J. Friston. Mean-Fields and Neural Masses
0 -- 0Philip G. McQueen, F. Ellis McKenzie. Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics
0 -- 0M. Cecchini, A. Houdusse, Martin Karplus. Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements
0 -- 0Shobhit Gupta, Jonathan Dennis, Robert E. Thurman, Robert Kingston, John A. Stamatoyannopoulos, William Stafford Noble. Predicting Human Nucleosome Occupancy from Primary Sequence
0 -- 0Angelo Rosa, Ralf Everaers. Structure and Dynamics of Interphase Chromosomes
0 -- 0Zhengdong D. Zhang, Joel S. Rozowsky, Michael Snyder, Joseph T. Chang, Mark Gerstein. Modeling ChIP Sequencing In Silico with Applications
0 -- 0Elena Zotenko, Julián Mestre, Dianne P. O'Leary, Teresa M. Przytycka. Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
0 -- 0Shula Shazman, Yael Mandel-Gutfreund. Classifying RNA-Binding Proteins Based on Electrostatic Properties
0 -- 0Miler T. Lee, Junhyong Kim. Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs
0 -- 0Dominique Martinez, Noelia Montejo. A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe
0 -- 0Cheol E. Han, Michael A. Arbib, Nicolas Schweighofer. Stroke Rehabilitation Reaches a Threshold
0 -- 0Jana L. Gevertz, Salvatore Torquato. A Novel Three-Phase Model of Brain Tissue Microstructure
0 -- 0Austin Huang, Collin M. Stultz. The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau
0 -- 0Steve Horvath, Jun Dong. Geometric Interpretation of Gene Coexpression Network Analysis
0 -- 0Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt. Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
0 -- 0Marc Turcotte, Wei Tang, Elliott M. Ross. Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP
0 -- 0Michael Capalbo, Eric Postma, Rainer Goebel. Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System
0 -- 0James V. Stone, Peter E. Jupp. Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory
0 -- 0Sangjo Han, Dongsup Kim. Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways
0 -- 0Eilon Sharon, Shai Lubliner, Eran Segal. A Feature-Based Approach to Modeling Protein-DNA Interactions
0 -- 0Mark V. Albert, Adam Schnabel, David J. Field. Innate Visual Learning through Spontaneous Activity Patterns
0 -- 0Steven H. Kleinstein. Getting Started in Computational Immunology
0 -- 0Albert Kern, C. Heid, Willi-Hans Steeb, Norbert Stoop, Ruedi Stoop. Biophysical Parameters Modification Could Overcome Essential Hearing Gaps
0 -- 0Ronald C. Taylor, George K. Acquaah-Mensah, Mudita Singhal, Deepti Malhotra, Shyam Biswal. Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress
0 -- 0Rahul Siddharthan. PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
0 -- 0Turkan Haliloglu, Nir Ben-Tal. Cooperative Transition between Open and Closed Conformations in Potassium Channels
0 -- 0Yu Tanouchi, Dennis Tu, Jungsang Kim, Lingchong You. Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif
0 -- 0Lorenzo Farina, Alberto De Santis, Samanta Salvucci, Giorgio Morelli, Ida Ruberti. Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data
0 -- 0Alessandro Ambrosi, Claudia Cattoglio, Clelia Di Serio. Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach
0 -- 0Sorin Tanase-Nicola, Pieter Rein ten Wolde. Regulatory Control and the Costs and Benefits of Biochemical Noise
0 -- 0V. V. Krishnan, Edmond Y. Lau, Justin Yamada, Daniel P. Denning, Samir S. Patel, Michael E. Colvin, Michael F. Rexach. Intramolecular Cohesion of Coils Mediated by Phenylalanine-Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin
0 -- 0Tyler McMillen, T. Williams, P. Holmes. Nonlinear Muscles, Passive Viscoelasticity and Body Taper Conspire To Create Neuromechanical Phase Lags in Anguilliform Swimmers
0 -- 0Mark A. Ragan, Tim Littlejohn, Bruce Ross. Genome-Scale Computational Biology and Bioinformatics in Australia
0 -- 0Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote. Efficient Algorithms for Probing the RNA Mutation Landscape
0 -- 0Giancarlo La Camera, Barry J. Richmond. Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules
0 -- 0Michael Sammeth, Sylvain Foissac, Roderic Guigó. A General Definition and Nomenclature for Alternative Splicing Events
0 -- 0Gustavo Deco, Viktor K. Jirsa, Peter A. Robinson, Michael Breakspear, Karl J. Friston. The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields

Volume 4, Issue 7

0 -- 0Sungho Hong, Brian Nils Lundstrom, Adrienne L. Fairhall. Intrinsic Gain Modulation and Adaptive Neural Coding
0 -- 0Shaoying Lu, Mingxing Ouyang, Jihye Seong, Jin Zhang, Shu Chien, Yingxiao Wang. The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging
0 -- 0Christian L. Althaus, Rob J. De Boer. Dynamics of Immune Escape during HIV/SIV Infection
0 -- 0Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell. Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms
0 -- 0Ivan V. Surovtsev, Jeffrey J. Morgan, Paul A. Lindahl. Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis
0 -- 0Naren Ramakrishnan, Upinder S. Bhalla. Memory Switches in Chemical Reaction Space
0 -- 0Anton Crombach, Paulien Hogeweg. Evolution of Evolvability in Gene Regulatory Networks
0 -- 0Karthik Devarajan. Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology
0 -- 0Clare Sansom, B. J. Morrison McKay. ISCB Honors David Haussler and Aviv Regev
0 -- 0Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert. Predicting and Validating Protein Interactions Using Network Structure
0 -- 0Joseph Ivanic, Anders Wallqvist, Jaques Reifman. Probing the Extent of Randomness in Protein Interaction Networks
0 -- 0Dmitry A. Dmitriev, Roman A. Rakitov. Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
0 -- 0Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder. Unraveling Protein Networks with Power Graph Analysis
0 -- 0Stella Veretnik, J. Lynn Fink, Philip E. Bourne. Computational Biology Resources Lack Persistence and Usability
0 -- 0Guy A. Hoelzer, Rich Drewes, Jeffrey Meier, René Doursat. Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences
0 -- 0Neda Bagheri, Jörg Stelling, Francis J. Doyle III. Circadian Phase Resetting via Single and Multiple Control Targets
0 -- 0Wannipha Tongsima, Sissades Tongsima, Prasit Palittapongarnpim. Outlook on Thailand's Genomics and Computational Biology Research and Development
0 -- 0Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund. Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
0 -- 0Matthew C. Cowperthwaite, Evan P. Economo, William R. Harcombe, Eric L. Miller, Lauren Ancel Meyers. The Ascent of the Abundant: How Mutational Networks Constrain Evolution
0 -- 0Teunis J. P. van Dam, Berend Snel. Protein Complex Evolution Does Not Involve Extensive Network Rewiring
0 -- 0Todd E. Hudson, Laurence T. Maloney, Michael S. Landy. Optimal Compensation for Temporal Uncertainty in Movement Planning
0 -- 0Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, Ingolf Sommer. Local Function Conservation in Sequence and Structure Space
0 -- 0Anthony Randal McIntosh, Natasa Kovacevic, Roxane J. Itier. Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development
0 -- 0Adam A. Smith, Aaron L. Vollrath, Christopher A. Bradfield, Mark Craven. Similarity Queries for Temporal Toxicogenomic Expression Profiles
0 -- 0Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen. The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
0 -- 0Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo. Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions
0 -- 0Enrico Rossoni, Jianfeng Feng, Brunello Tirozzi, David Brown, Gareth Leng, Françoise Moos. Emergent Synchronous Bursting of Oxytocin Neuronal Network
0 -- 0Leehod Baruch, Shalev Itzkovitz, Michal Golan-Mashiach, Ehud Y. Shapiro, Eran Segal. Caenorhabditis elegans Neurons To Identify Genes That Mediate Synaptic Connectivity

Volume 4, Issue 6

0 -- 0Peter S. Kim, Peter P. Lee, Doron Levy. Dynamics and Potential Impact of the Immune Response to Chronic Myelogenous Leukemia
0 -- 0Joseph Schlecht, Matthew E. Kaplan, Kobus Barnard, Tatiana Karafet, Michael F. Hammer, Nirav C. Merchant. Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data
0 -- 0Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P. Xing. CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
0 -- 0Jason W. Locasale, Arup K. Chakraborty. Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins
0 -- 0David Balduzzi, Giulio Tononi. Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework
0 -- 0Kaustubh Supekar, Vinod Menon, Daniel L. Rubin, Mark A. Musen, Michael D. Greicius. Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease
0 -- 0Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga, Philip E. Bourne. Ten Simple Rules for Organizing a Scientific Meeting
0 -- 0Barbara Bryant. How To Advance Open International Scientific Exchange
0 -- 0Michal Linial, Jill P. Mesirov, B. J. Morrison McKay, Burkhard Rost. ISMB 2008 Toronto
0 -- 0Gunnar Cedersund, Jacob Roll, Erik Ulfhielm, Anna Danielsson, Henrik Tidefelt, Peter Strålfors. Model-Based Hypothesis Testing of Key Mechanisms in Initial Phase of Insulin Signaling
0 -- 0Upinder S. Bhalla. How To Record a Million Synaptic Weights in a Hippocampal Slice
0 -- 0Duncan E. Donohue, Giorgio A. Ascoli. A Comparative Computer Simulation of Dendritic Morphology

Volume 4, Issue 5

0 -- 0Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A. Komives, Peter G. Wolynes. The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures
0 -- 0Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel. Viral Population Estimation Using Pyrosequencing
0 -- 0Jong Min Lee 0002, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin. Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks
0 -- 0Sean R. Eddy. A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
0 -- 0Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luis Serrano, Frederic Rousseau, Joost Schymkowitz. Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
0 -- 0Erik De Schutter. Why Are Computational Neuroscience and Systems Biology So Separate?
0 -- 0Tatyana K. Korendyaseva, Denis N. Kuvatov, Vladimir A. Volkov, Michael V. Martinov, Victor M. Vitvitsky, Ruma Banerjee, Fazoil I. Ataullakhanov. An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism
0 -- 0Arbel D. Tadmor, Tsvi Tlusty. E. coli and Its Application to Perturbation of the rRNA Operon Copy Number
0 -- 0Mikhail I. Rabinovich, Ramón Huerta, Pablo Varona, Valentin S. Afraimovich. Transient Cognitive Dynamics, Metastability, and Decision Making
0 -- 0Suhita Nadkarni, Peter Jung, Herbert Levine. Astrocytes Optimize the Synaptic Transmission of Information
0 -- 0Scott A. Becker, Bernhard O. Palsson. Context-Specific Metabolic Networks Are Consistent with Experiments
0 -- 0Richard A. Goldstein, Orkun S. Soyer. Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics
0 -- 0Yasuko Sugase-Miyamoto, Zheng Liu, Matthew C. Wiener, Lance M. Optican, Barry J. Richmond. Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex
0 -- 0Kiyoko F. Aoki-Kinoshita. An Introduction to Bioinformatics for Glycomics Research
0 -- 0Shuixia Guo, Jianhua Wu, Mingzhou Ding, Jianfeng Feng. Uncovering Interactions in the Frequency Domain
0 -- 0Sean M. Cory, Theodore J. Perkins. Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation
0 -- 0Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter. Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma
0 -- 0Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey. Discovering Sequence Motifs with Arbitrary Insertions and Deletions
0 -- 0Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, Charles E. Lawrence. Measuring Global Credibility with Application to Local Sequence Alignment
0 -- 0Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Y. Shapiro. Estimating Cell Depth from Somatic Mutations
0 -- 0Edgardo Moreno, José María Gutiérrez. Ten Simple Rules for Aspiring Scientists in a Low-Income Country
0 -- 0Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand. Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
0 -- 0John Porrill, Paul Dean. Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing

Volume 4, Issue 4

0 -- 0Liping Wei, Jun Yu. Bioinformatics in China: A Personal Perspective
0 -- 0Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh. Biosynthetic Potentials of Metabolites and Their Hierarchical Organization
0 -- 0Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck. cis-Regulated Cyclic Nucleotide Binding Domains
0 -- 0Jian Qiu, William Stafford Noble. Predicting Co-Complexed Protein Pairs from Heterogeneous Data
0 -- 0Maria F. Laguna, Steffen Bohn, Eduardo A. Jagla. The Role of Elastic Stresses on Leaf Venation Morphogenesis
0 -- 0Yoram Vodovotz, Marie Csete, John Bartels, Steven Chang, Gary An. Translational Systems Biology of Inflammation
0 -- 0Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J. Raphael. Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer
0 -- 0Manuel João Costa, Eduardo Galembeck, Guilherme A. Marson, Bayardo B. Torres. A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics
0 -- 0Lubomir Kostal, Petr Lánský, Jean-Pierre Rospars. Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth
0 -- 0Ignacio E. Sánchez, Pedro Beltrão, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano. Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm
0 -- 0Alexej Abyzov, Alper Uzun, Phyllis R. Strauss, Valentin A. Ilyin. An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
0 -- 0Adrian Gustavo Turjanski, J. Silvio Gutkind, Robert B. Best, Gerhard Hummer. Binding-Induced Folding of a Natively Unstructured Transcription Factor
0 -- 0Greg J. Stephens, Bethany Johnson-Kerner, William Bialek, William S. Ryu. C. elegans
0 -- 0Raoul Huys, Breanna E. Studenka, Nicole L. Rheaume, Howard N. Zelaznik, Viktor K. Jirsa. Distinct Timing Mechanisms Produce Discrete and Continuous Movements
0 -- 0Sourav Bandyopadhyay, Ryan M. Kelley, Nevan J. Krogan, Trey Ideker. Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
0 -- 0Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman. Escherichia coli
0 -- 0Luca A. Finelli, Seth Haney, Maxim Bazhenov, Mark Stopfer, Terrence J. Sejnowski. Synaptic Learning Rules and Sparse Coding in a Model Sensory System
0 -- 0Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis. Drosophila Genomes
0 -- 0Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Björn Peters. A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach
0 -- 0Bruno B. Averbeck, Moonsang Seo. The Statistical Neuroanatomy of Frontal Networks in the Macaque
0 -- 0Jon Bohlin, Eystein Skjerve, David Ussery. Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes

Volume 4, Issue 3

0 -- 0William Ritchie, Samuel Granjeaud, Denis Puthier, Daniel Gautheret. Entropy Measures Quantify Global Splicing Disorders in Cancer
0 -- 0Carson C. Chow, Kevin D. Hall. The Dynamics of Human Body Weight Change
0 -- 0Feng-Jie Sun, Gustavo Caetano-Anollés. Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
0 -- 0Ilya Nemenman, Geoffrey D. Lewen, William Bialek, Robert R. de Ruyter van Steveninck. Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution
0 -- 0Alejandra C. Ventura, Jacques-A. Sepulchre, Sofía D. Merajver. A Hidden Feedback in Signaling Cascades Is Revealed
0 -- 0Hédi Hegyi, Peter Tompa. Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo
0 -- 0David Basanta, Mark A. Miodownik, Buzz Baum. The Evolution of Robust Development and Homeostasis in Artificial Organisms
0 -- 0Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li. Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation
0 -- 0Zenas Chao, Douglas J. Bakkum, Steve M. Potter. Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior
0 -- 0Edgardo Moreno, Bruno Lomonte, José María Gutiérrez. Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics
0 -- 0Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph. Escherichia coli
0 -- 0Sichun Yang, Benoît Roux. Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
0 -- 0Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich. Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics
0 -- 0Yossi Yovel, Matthias O. Franz, Peter Stilz, Hans-Ulrich Schnitzler. Plant Classification from Bat-Like Echolocation Signals
0 -- 0Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, Helmut Grubmüller. Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595
0 -- 0Isaac Shemer, Björn Brinne, Jesper Tegnér, Sten Grillner. Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus
0 -- 0Philip E. Bourne, J. Lynn Fink, Mark Gerstein. Open Access: Taking Full Advantage of the Content
0 -- 0Thomas Manke, Helge G. Roider, Martin Vingron. Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
0 -- 0Yasser Roudi, Alessandro Treves. What Information in a Model of a Cortical Patch
0 -- 0Yonatan Loewenstein. Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity
0 -- 0Alex Roxin, Anders Ledberg. Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation
0 -- 0Siu Kang, Katsunori Kitano, Tomoki Fukai. Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model
0 -- 0Ugo Ala, Rosario Michael Piro, Elena Grassi, Christian Damasco, Lorenzo Silengo, Martin Oti, Paolo Provero, Ferdinando Di Cunto. Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
0 -- 0Q. Tri Ho, Pieter Verboven, Bert E. Verlinden, Jeroen Lammertyn, Stefan Vandewalle, Bart M. Nicolaï. A Continuum Model for Metabolic Gas Exchange in Pear Fruit

Volume 4, Issue 2

0 -- 0Vesa P. Hytönen, Viola Vogel. How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism
0 -- 0Joshua F. Apgar, Jared E. Toettcher, Drew Endy, Forest M. White, Bruce Tidor. Stimulus Design for Model Selection and Validation in Cell Signaling
0 -- 0Lihua Zou, Sira Sriswasdi, Brian C. Ross, Patrycja Vasilyev Missiuro, Jun S. Liu, Hui Ge. C. elegans Early Embryogenesis
0 -- 0Douglas L. Theobald, Deborah S. Wuttke. Accurate Structural Correlations from Maximum Likelihood Superpositions
0 -- 0Ivan Coluzza, Alfonso De Simone, Franca Fraternali, Daan Frenkel. Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes
0 -- 0Michal J. Okoniewski, Crispin J. Miller. Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
0 -- 0Daniel Segura, Radhakrishnan Mahadevan, Katy Juarez, Derek R. Lovley. Geobacter sulfurreducens
0 -- 0Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan. Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding
0 -- 0Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau. Drosophila Pumilio
0 -- 0Sean Carver, Eatai Roth, Noah J. Cowan, Eric S. Fortune. Synaptic Plasticity Can Produce and Enhance Direction Selectivity
0 -- 0Rafi Haddad, Liran Carmel, Noam Sobel, David Harel. Predicting the Receptive Range of Olfactory Receptors
0 -- 0Dennis Kostka, Rainer Spang. Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
0 -- 0Fred Henrik Hamker, Marc Zirnsak, Dirk Calow, Markus Lappe. The Peri-Saccadic Perception of Objects and Space
0 -- 0Naomi Habib, Tommy Kaplan, Hanah Margalit, Nir Friedman. A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
0 -- 0Anna Dvorkin, Yoav Benjamini, Ilan Golani. Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction
0 -- 0Arend Hintze, Christoph Adami. Evolution of Complex Modular Biological Networks
0 -- 0Avner Wallach, Danny Eytan, Shimon Marom, Ron Meir. Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment
0 -- 0Héctor Marlosti Montiel Molina, César Millán-Pacheco, Nina Pastor, Gabriel del Rio. Computer-Based Screening of Functional Conformers of Proteins
0 -- 0Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram. The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks
0 -- 0Hai Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine. Control of Cation Permeation through the Nicotinic Receptor Channel
0 -- 0Leo C. McHugh, Jonathan W. Arthur. Computational Methods for Protein Identification from Mass Spectrometry Data
0 -- 0Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik. How Protein Stability and New Functions Trade Off
0 -- 0Elena J. Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G. Febbo, Sayan Mukherjee. Modeling Cancer Progression via Pathway Dependencies
0 -- 0Julius B. Lucks, David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin. Genome Landscapes and Bacteriophage Codon Usage
0 -- 0Zhaoping Li, Jingling Li. Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences
0 -- 0Tae Lee, Guang Yao, Joseph Nevins, Lingchong You. Sensing and Integration of Erk and PI3K Signals by Myc
0 -- 0Ganesh A. Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C. Sealfon. Getting Started in Biological Pathway Construction and Analysis
0 -- 0Navin Elango, Seong-Ho Kim, Eric Vigoda, Soojin V. Yi. Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation
0 -- 0Jennifer Listgarten, Zabrina L. Brumme, Carl Myers Kadie, Gao Xiaojiang, Bruce D. Walker, Mary Carrington, Philip J. R. Goulder, David Heckerman. Statistical Resolution of Ambiguous HLA Typing Data
0 -- 0Morgan C. Giddings. On the Process of Becoming a Great Scientist
0 -- 0Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja. Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability
0 -- 0Eric R. Paquet, Guillaume Rey, Felix Naef. Cis-Element
0 -- 0Peter Dayan, Quentin J. M. Huys. Serotonin, Inhibition, and Negative Mood

Volume 4, Issue 12

0 -- 0Da-wei Li, Sandipan Mohanty, Anders Irbäck, Shuanghong Huo. Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
0 -- 0Niamh C. Nowlan, Patrick J. Prendergast, Paula Murphy. Identification of Mechanosensitive Genes during Embryonic Bone Formation
0 -- 0Wako Yoshida, Raymond J. Dolan, Karl J. Friston. Game Theory of Mind
0 -- 0Ágnes Tóth-Petróczy, Christopher J. Oldfield, István Simon, Yuichiro Takagi, A. Keith Dunker, Vladimir N. Uversky, Mónika Fuxreiter. Malleable Machines in Transcription Regulation: The Mediator Complex
0 -- 0Christina Kiel, Dorothee Aydin, Luis Serrano. Association Rate Constants of Ras-Effector Interactions Are Evolutionarily Conserved
0 -- 0Sanne Abeln, Daan Frenkel. Disordered Flanks Prevent Peptide Aggregation
0 -- 0Claudia Clopath, Lorric Ziegler, Eleni Vasilaki, Lars Büsing, Wulfram Gerstner. Tag-Trigger-Consolidation: A Model of Early and Late Long-Term-Potentiation and Depression
0 -- 0Ha Youn Lee, Alan S. Perelson, Su-Chan Park, Thomas Leitner. Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
0 -- 0Antonio Scialdone, Mario Nicodemi. Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation
0 -- 0Nora C. Toussaint, Pierre Dönnes, Oliver Kohlbacher. A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines
0 -- 0Alberto Mazzoni, Stefano Panzeri, Nikos K. Logothetis, Nicolas Brunel. Encoding of Naturalistic Stimuli by Local Field Potential Spectra in Networks of Excitatory and Inhibitory Neurons
0 -- 0Hermann Cuntz, Friedrich Forstner, Jürgen Haag, Alexander Borst. The Morphological Identity of Insect Dendrites
0 -- 0Nikita Vladimirov, Linda Løvdok, Dirk Lebiedz, Victor Sourjik. Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate
0 -- 0Feng Liu, Xiao-Jing Wang. A Common Cortical Circuit Mechanism for Perceptual Categorical Discrimination and Veridical Judgment
0 -- 0Diego Calzolari, Stefania Bruschi, Laurence Coquin, Jennifer Schofield, Jacob D. Feala, John C. Reed, Andrew D. McCulloch, Giovanni Paternostro. Search Algorithms as a Framework for the Optimization of Drug Combinations
0 -- 0Philip E. Bourne, J. Lynn Fink. I Am Not a Scientist, I Am a Number
0 -- 0Takashi Nishikawa, Natali Gulbahce, Adilson E. Motter. Spontaneous Reaction Silencing in Metabolic Optimization

Volume 4, Issue 11

0 -- 0Sheila M. Reynolds, Lukas Käll, Michael Riffle, Jeff A. Bilmes, William Stafford Noble. Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks
0 -- 0Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko. Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes
0 -- 0Carlos J. Camacho, Yasuhiro Katsumata, Dana P. Ascherman. Structural and Thermodynamic Approach to Peptide Immunogenicity
0 -- 0Merav Parter, Nadav Kashtan, Uri Alon. Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
0 -- 0Murad Banaji, Alfred Mallet, Clare E. Elwell, Peter Nicholls, Chris E. Cooper. A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges
0 -- 0Stefan Auer, Filip Meersman, Christopher M. Dobson, Michele Vendruscolo. A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
0 -- 0Yuki Tsukada, Kazuhiro Aoki, Takeshi Nakamura, Yuichi Sakumura, Michiyuki Matsuda, Shin Ishii. Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking
0 -- 0Wan Kyu Kim, Edward M. Marcotte. Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
0 -- 0Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal. Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
0 -- 0Yuichi Yamashita, Jun Tani. Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment
0 -- 0Joern Toedling, Wolfgang Huber. Analyzing ChIP-chip Data Using Bioconductor
0 -- 0Shubhada R. Hegde, Palanisamy Manimaran, Shekhar C. Mande. Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
0 -- 0Goded Shahaf, Danny Eytan, Asaf Gal, Einat Kermany, Vladimir Lyakhov, Christoph Zrenner, Shimon Marom. Order-Based Representation in Random Networks of Cortical Neurons
0 -- 0Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Myers Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman. Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
0 -- 0Cedric Chauve, Eric Tannier. A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes
0 -- 0Roxana A. Stefanescu, Viktor K. Jirsa. A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons
0 -- 0Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina S. Leslie. A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
0 -- 0Eunjung Lee, Han-Yu Chuang, Jong-Won Kim 0001, Trey Ideker, Doheon Lee. Inferring Pathway Activity toward Precise Disease Classification
0 -- 0Adam B. Barrett, Mark C. W. van Rossum. Optimal Learning Rules for Discrete Synapses
0 -- 0Raúl Guantes, Juan F. Poyatos. Multistable Decision Switches for Flexible Control of Epigenetic Differentiation
0 -- 0Jonathan M. Guberman, Allison Fay, Jonathan Dworkin, Ned S. Wingreen, Zemer Gitai. PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
0 -- 0Nicolas Maubourguet, Annick Lesne, Jean-Pierre Changeux, Uwe Maskos, Philippe Faure. Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration
0 -- 0Andreea Munteanu, Ricard V. Solé. Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition
0 -- 0Karl J. Friston. Hierarchical Models in the Brain
0 -- 0Martin C. Stumpe, Helmut Grubmüller. Polar or Apolar - The Role of Polarity for Urea-Induced Protein Denaturation
0 -- 0Stefan J. Kiebel, Jean Daunizeau, Karl J. Friston. A Hierarchy of Time-Scales and the Brain
0 -- 0Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, Martin G. Reese. Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins
0 -- 0Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, John S. Mattick. Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

Volume 4, Issue 10

0 -- 0Duncan Hull, Steve Pettifer, Douglas B. Kell. Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
0 -- 0Steven A. Prescott, Yves De Koninck, Terrence J. Sejnowski. Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation
0 -- 0Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda. Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
0 -- 0Alexei Vazquez, Marcio A. de Menezes, Albert-László Barabási, Zoltán N. Oltvai. S. cerevisiae Glycolysis
0 -- 0David M. Santucci, Sridhar Raghavachari. The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation
0 -- 0Carina Curto, Vladimir Itskov. Cell Groups Reveal Structure of Stimulus Space
0 -- 0Anandamohan Ghosh, Y. Rho, Anthony Randal McIntosh, Rolf Kötter, Viktor K. Jirsa. Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire
0 -- 0Bastien Berret, Christian Darlot, Frédéric Jean, Thierry Pozzo, Charalambos Papaxanthis, Jean-Paul Gauthier. The Inactivation Principle: Mathematical Solutions Minimizing the Absolute Work and Biological Implications for the Planning of Arm Movements
0 -- 0Jacek Puchalka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos. Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology
0 -- 0Pascal Durrens, Macha Nikolski, David James Sherman. Fusion and Fission of Genes Define a Metric between Fungal Genomes
0 -- 0Gary Hon, Bing Ren, Wei Wang. ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
0 -- 0Szymon Stoma, Mikael Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas, Christophe Godin. Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development
0 -- 0Sungsam Gong, Tom L. Blundell. Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures
0 -- 0Elhanan Borenstein, David C. Krakauer. An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
0 -- 0Piers J. Ingram, Michael P. H. Stumpf, Jaroslav Stark. Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
0 -- 0Ran Elkon, Reuven Agami. Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs
0 -- 0Asa Ben-Hur, Cheng Soon Ong, Sören Sonnenburg, Bernhard Schölkopf, Gunnar Rätsch. Support Vector Machines and Kernels for Computational Biology
0 -- 0Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao. Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm
0 -- 0Elodie Monsellier, Matteo Ramazzotti, Niccolò Taddei, Fabrizio Chiti. Aggregation Propensity of the Human Proteome
0 -- 0Robert A. Legenstein, Dejan Pecevski, Wolfgang Maass. A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback
0 -- 0Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh. Organization of Physical Interactomes as Uncovered by Network Schemas
0 -- 0Marcelo Behar, Nan Hao, Henrik G. Dohlman, Timothy C. Elston. Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks
0 -- 0Marco Punta, Yanay Ofran. The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

Volume 4, Issue 1

0 -- 0Guo-Cheng Yuan, Jun S. Liu. Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
0 -- 0Will Fischer, H. X. Liao, Barton F. Haynes, Norman L. Letvin, Bette T. Korber. Coping with Viral Diversity in HIV Vaccine Design: A Response to Nickle et al
0 -- 0David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins. Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al
0 -- 0K. Bretonnel Cohen, Lawrence Hunter. Getting Started in Text Mining
0 -- 0Chuan-Yun Li, Xizeng Mao, Liping Wei. Genes and (Common) Pathways Underlying Drug Addiction
0 -- 0Daniela Raijman, Ron Shamir, Amos Tanay. Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
0 -- 0Dirk Holste, Uwe Ohler. Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events
0 -- 0Gil Hornung, Naama Barkai. Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
0 -- 0Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang, Francisco J. Barrantes. Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor
0 -- 0Malin C. Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg. In Silico Detection of Sequence Variations Modifying Transcriptional Regulation
0 -- 0Christina M. Weaver, Susan L. Wearne. Neuronal Firing Sensitivity to Morphologic and Active Membrane Parameters
0 -- 0Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson. Caulobacter crescentus Stalked Cells
0 -- 0Huiquan Wang, Craig J. Benham. Superhelical Destabilization in Regulatory Regions of Stress Response Genes
0 -- 0Clinton H. Hansen, Robert G. Endres, Ned S. Wingreen. Escherichia coli: A Molecular Model for Robust Precise Adaptation
0 -- 0Richard A. Notebaart, Bas Teusink, Roland J. Siezen, Balázs Papp. Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance
0 -- 0Chikara Furusawa, Kunihiko Kaneko. A Generic Mechanism for Adaptive Growth Rate Regulation
0 -- 0Nicolas Pinto, David D. Cox, James J. DiCarlo. Why is Real-World Visual Object Recognition Hard?
0 -- 0Matthew Menke, Bonnie Berger, Lenore Cowen. Matt: Local Flexibility Aids Protein Multiple Structure Alignment