Journal: PLoS Computational Biology

Volume 3, Issue 9

0 -- 0David Corney, R. Beau Lotto. What Are Lightness Illusions and Why Do We See Them?
0 -- 0Chakra Chennubhotla, Ivet Bahar. Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
0 -- 0Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Martí-Renom, Baldo Oliva. Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
0 -- 0Philip E. Bourne, Steven E. Brenner. Developing Computational Biology
0 -- 0Yasser Roudi, Peter E. Latham. A Balanced Memory Network
0 -- 0Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, Florentin Wörgötter. Correction: Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning
0 -- 0Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni. A Computational Approach to the Functional Screening of Genomes
0 -- 0Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler. Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
0 -- 0Mookyung Cheon, Iksoo Chang, Sandipan Mohanty, Leila M. Luheshi, Christopher M. Dobson, Michele Vendruscolo, Giorgio Favrin. Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
0 -- 0Liang Qiao, Robert B. Nachbar, Ioannis G. Kevrekidis, Stanislav Y. Shvartsman. Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling
0 -- 0Mukund Thattai, Yoram Burak, Boris I. Shraiman. The Origins of Specificity in Polyketide Synthase Protein Interactions
0 -- 0Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin. Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
0 -- 0Baltazar D. Aguda, Andrew B. Goryachev. From Pathways Databases to Network Models of Switching Behavior
0 -- 0Soundara Raghavan Pavithra, Ranjit Kumar, Utpal Tatu. Plasmodium falciparum
0 -- 0Eric Grosch. Reply to "Ten Simple Rules for Getting Published"
0 -- 0Rafael Palacios, Julio Collado-Vides. Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go
0 -- 0Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova. A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
0 -- 0Doron Betel, Kevin E. Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W. V. Hogue. Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
0 -- 0Elaine Angelino, Michael P. Brenner. Excitability Constraints on Voltage-Gated Sodium Channels

Volume 3, Issue 8

0 -- 0Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin, David Horn. Functional Representation of Enzymes by Specific Peptides
0 -- 0Meron Gurkiewicz, Alon Korngreen. A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm
0 -- 0Mathias Franzius, Henning Sprekeler, Laurenz Wiskott. Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells
0 -- 0Yihai Yu, Guanyu Wang, Rahul Simha, Weiqun Peng, Frank Turano, Chen Zeng. Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network
0 -- 0Robert S. Kuczenski, Kevin C. Hong, Jordi García-Ojalvo, Kelvin H. Lee. PERIOD-TIMELESS Interval Timer May Require an Additional Feedback Loop
0 -- 0Sergey Kryazhimskiy, Ulf Dieckmann, Simon A. Levin, Jonathan Dushoff. On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
0 -- 0Elisabeth L. Humphris, Tanja Kortemme. Design of Multi-Specificity in Protein Interfaces
0 -- 0Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones. Inferring Function Using Patterns of Native Disorder in Proteins
0 -- 0David Golomb, Karnit Donner, Liron Shacham, Dan Shlosberg, Yael Amitai, David Hansel. Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons
0 -- 0Cédric Notredame. Recent Evolutions of Multiple Sequence Alignment Algorithms
0 -- 0Burton W. Andrews, Pablo A. Iglesias. An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells
0 -- 0Roland Schäfer, Eleni Vasilaki, Walter Senn. Perceptual Learning via Modification of Cortical Top-Down Signals
0 -- 0James V. Stone. Distributed Representations Accelerate Evolution of Adaptive Behaviours
0 -- 0Chris J. Needham, James R. Bradford, Andrew J. Bulpitt, David R. Westhead. A Primer on Learning in Bayesian Networks for Computational Biology
0 -- 0Sylvain V. Costes, Artem L. Ponomarev, James L. Chen, David Nguyen, Francis A. Cucinotta, Mary Helen Barcellos-Hoff. Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
0 -- 0Aviv Bergman, Gil Atzmon, Kenny Ye, Thomas MacCarthy, Nir Barzilai. Buffering Mechanisms in Aging: A Systems Approach Toward Uncovering the Genetic Component of Aging
0 -- 0Irmtraud M. Meyer, István Miklós. SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
0 -- 0Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander. Automated Protein Subfamily Identification and Classification
0 -- 0Andrew E. Teschendorff, Michel Journée, Pierre-Antoine Absil, Rodolphe Sepulchre, Carlos Caldas. Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis
0 -- 0Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst Dieter Gilles, Steffen Klamt, Burkhart Schraven. A Logical Model Provides Insights into T Cell Receptor Signaling
0 -- 0Georg K. Gerber, Robin D. Dowell, Tommi Jaakkola, David K. Gifford. Automated Discovery of Functional Generality of Human Gene Expression Programs
0 -- 0Masako Ogura, J. Christian Perez, Peer R. E. Mittl, Hae-Kyung Lee, Geidrius Dailide, Shumin Tan, Yoshiyuki Ito, Ousman Secka, Daiva Dailidiene, Kalyani Putty, Douglas E. Berg, Awdhesh Kalia. Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Volume 3, Issue 7

0 -- 0Anton Zilman, Stefano Di Talia, Brian T. Chait, Michael P. Rout, Marcelo O. Magnasco. Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport
0 -- 0Reut Shalgi, Daniel Lieber, Moshe Oren, Yitzhak Pilpel. Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network
0 -- 0Konstantin B. Zeldovich, Peiqiu Chen, Boris E. Shakhnovich, Eugene I. Shakhnovich. A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
0 -- 0Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E. Warburton. Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation
0 -- 0Zhi Wang, Jianzhi Zhang. Correction: In Search of the Biological Significance of Modular Structures in Protein Networks
0 -- 0Andrew B. Goryachev, Alexandra V. Pokhilko. Correction: Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes
0 -- 0Bertrand C. W. Tanner, Thomas L. Daniel, Michael Regnier. Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle
0 -- 0Robert G. Endres, Joseph J. Falke, Ned S. Wingreen. Chemotaxis Receptor Complexes: From Signaling to Assembly
0 -- 0Michiel van Boven, Marion Koopmans, Mirna Du Ry van Beest Holle, Adam Meijer, Don Klinkenberg, Christl A. Donnelly, Hans Heesterbeek. Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households
0 -- 0Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, Florentin Wörgötter. Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning
0 -- 0Yanay Ofran, Burkhard Rost. Protein-Protein Interaction Hotspots Carved into Sequences
0 -- 0Jacques Colinge, Keiryn L. Bennett. Introduction to Computational Proteomics
0 -- 0Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp. Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
0 -- 0Martin Meier-Schellersheim, Xuehua Xu, Bastian Robert Angermann, Eric J. Kunkel, Tian Jin, Ronald N. Germain. Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method
0 -- 0Carol Shiels, Niall M. Adams, Suhail A. Islam, David A. Stephens, Paul S. Freemont. Quantitative Analysis of Cell Nucleus Organisation
0 -- 0Deyan Luan, Michael Zai, Jeffrey D. Varner. Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies
0 -- 0Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt. Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins
0 -- 0Alborz Mahdavi, Ryan E. Davey, Patrick Bhola, Ting Yin, Peter W. Zandstra. Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control
0 -- 0Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald R. Breaker, Martin Tompa, Walter L. Ruzzo. cis-Regulatory Noncoding RNA in Prokaryotes
0 -- 0Anastasia Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma. Drosophila melanogaster
0 -- 0Avner Schlessinger, Jinfeng Liu, Burkhard Rost. Natively Unstructured Loops Differ from Other Loops
0 -- 0Marcel E. Curlin, Shyamala Iyer, John E. Mittler. Optimal Timing and Duration of Induction Therapy for HIV-1 Infection
0 -- 0Patricia A. Ryan, Brian W. Kirk, Chad W. Euler, Raymond Schuch, Vincent A. Fischetti. Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
0 -- 0Barry G. Hall, Stephen J. Salipante. Retraction: Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees

Volume 3, Issue 6

0 -- 0Juilee Thakar, Mylisa Pilione, Girish Kirimanjeswara, Eric T. Harvill, Réka Albert. Modeling Systems-Level Regulation of Host Immune Responses
0 -- 0Mikiya Otsuji, Shuji Ishihara, Carl Co, Kozo Kaibuchi, Atsushi Mochizuki, Shinya Kuroda. A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity
0 -- 0Milan van Hoek, Paulien Hogeweg. Lac Operon: An Evolutionary Perspective
0 -- 0B. Silvano Zanutto, John E. R. Staddon. Correction: Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals
0 -- 0Henning Sprekeler, Christian Michaelis, Laurenz Wiskott. Slowness: An Objective for Spike-Timing-Dependent Plasticity?
0 -- 0Cécile Caretta-Cartozo, Paolo De Los Rios, Francesco Piazza, Pietro Liò. S. pombe
0 -- 0David B. Searls. A View from the Dark Side
0 -- 0Oscar M. Rueda, Ramón Díaz-Uriarte. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH
0 -- 0Sukhbinder Kumar, Klaas E. Stephan, Jason D. Warren, Karl J. Friston, Timothy D. Griffiths. Hierarchical Processing of Auditory Objects in Humans
0 -- 0Stephen Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. M. Jones. A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
0 -- 0Zengjian Hu, Donnell Bowen, William M. Southerland, Antonio del Sol, Yongping Pan, Ruth Nussinov, Buyong Ma. Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
0 -- 0Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer. CpG Island Mapping by Epigenome Prediction
0 -- 0Adi L. Tarca, Vincent J. Carey, Xue-wen Chen, Roberto Romero, Sorin Draghici. Machine Learning and Its Applications to Biology
0 -- 0Marcelo Camperi, Timothy C. Tricas, Brandon R. Brown. From Morphology to Neural Information: The Electric Sense of the Skate
0 -- 0Bruno Delord, Hugues Berry, Emmanuel Guigon, Stéphane Genet. A New Principle for Information Storage in an Enzymatic Pathway Model
0 -- 0Merry Maisel. ISCB Honors Temple F. Smith and Eran Segal
0 -- 0Zhi Wang, Jianzhi Zhang. In Search of the Biological Significance of Modular Structures in Protein Networks
0 -- 0Harish Shankaran, Haluk Resat, H. Steven Wiley. Cell Surface Receptors for Signal Transduction and Ligand Transport: A Design Principles Study
0 -- 0Lawrence Hunter, Russ B. Altman, Philip E. Bourne. The International Society for Computational Biology 10th Anniversary
0 -- 0Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble. Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes

Volume 3, Issue 5

0 -- 0Thomas C. Erren, Michael Erren. "Simple Rules for Editors"? Here is One Rule to Tackle Neglected Problems of Publishing
0 -- 0Thomas Lengauer, B. J. Morrison McKay, Burkhard Rost. ISMB/ECCB 2007: The Premier Conference on Computational Biology
0 -- 0A. Aldo Faisal, Simon B. Laughlin. Stochastic Simulations on the Reliability of Action Potential Propagation in Thin Axons
0 -- 0Omri Barak, Misha Tsodyks. Correction: Persistent Activity in Neural Networks with Dynamic Synapses
0 -- 0Thomas C. Erren, Philip E. Bourne. Ten Simple Rules for a Good Poster Presentation
0 -- 0Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer. HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation
0 -- 0Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko. A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes
0 -- 0Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich. Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
0 -- 0Mark Patterson, Barbara Cohen. "Simple Rules for Editors"? Here Is One Rule to Tackle Neglected Problems of Publishing: Response from PLoS
0 -- 0Tristan Ursell, Kerwyn Casey Huang, Eric L. Peterson, Rob Phillips. Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions
0 -- 0Scott Doniger, Justin C. Fay. Frequent Gain and Loss of Functional Transcription Factor Binding Sites
0 -- 0Fang Liu, Eivind Tøstesen, Jostein K. Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G. Thilly, Eivind Hovig. The Human Genomic Melting Map
0 -- 0Eli Koren, Galit Lev-Maor, Gil Ast. The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons
0 -- 0Raffaele Vardavas, Romulus Breban, Sally Blower. Can Influenza Epidemics Be Prevented by Voluntary Vaccination?
0 -- 0Robert P. Zinzen, Dmitri A. Papatsenko. Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development
0 -- 0Gabriel D. Puccini, Maria V. Sanchez-Vives, Albert Compte. Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits
0 -- 0Michal Brylinski, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochanczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman. Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
0 -- 0Adam M. Phillippy, Jacquline A. Mason, Kunmi Ayanbule, Daniel D. Sommer, Elisa Taviani, Anwar Huq, Rita R. Colwell, Ivor T. Knight, Steven L. Salzberg. Comprehensive DNA Signature Discovery and Validation
0 -- 0Jasmin Fisher, Nir Piterman, Alex Hajnal, Thomas A. Henzinger. C. elegans Vulval Development
0 -- 0B. Silvano Zanutto, John E. R. Staddon. Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals

Volume 3, Issue 4

0 -- 0Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein. The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
0 -- 0Mark Gerstein, Shawn M. Douglas. RNAi Development
0 -- 0David Dingli, Arne Traulsen, Franziska Michor. Correction: (A)Symmetric Stem Cell Replication and Cancer
0 -- 0Benjamin A. Shoemaker, Anna R. Panchenko. Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
0 -- 0Gerton Lunter. Dog as an Outgroup to Human and Mouse
0 -- 0Filipe Tostevin, Pieter Rein ten Wolde, Martin Howard. Fundamental Limits to Position Determination by Concentration Gradients
0 -- 0Samuel Bernard, Didier Gonze, Branka Cajavec, Hanspeter Herzel, Achim Kramer. Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus
0 -- 0Gert Jan Boender, Thomas J. Hagenaars, Annemarie Bouma, Gonnie Nodelijk, Armin R. W. Elbers, Mart C. M. de Jong, Michiel van Boven. Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry
0 -- 0Sebastian Maurer-Stroh, Manfred Koranda, Wolfgang Benetka, Georg Schneider 0001, Fernanda L. Sirota, Frank Eisenhaber. Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins
0 -- 0Jun Zhu, Matthew C. Wiener, Chunsheng Zhang, Arthur Fridman, Eric Minch, Pek Y. Lum, Jeffrey R. Sachs, Eric E. Schadt. Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations
0 -- 0Scott Christley, Mark S. Alber, Stuart A. Newman. Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model
0 -- 0Ji Lee, Zhihua Li, Rachel Brower-Sinning, Bino John. Regulatory Circuit of Human MicroRNA Biogenesis
0 -- 0Zhaoping Li, Keith A. May. Psychophysical Tests of the Hypothesis of a Bottom-Up Saliency Map in Primary Visual Cortex
0 -- 0David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins, Nebojsa Jojic. Coping with Viral Diversity in HIV Vaccine Design
0 -- 0Philip E. Bourne. Ten Simple Rules for Making Good Oral Presentations
0 -- 0Mary Qu Yang, Laura M. Koehly, Laura Elnitski. Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes
0 -- 0Yili Chen, Thomas W. Blackwell, Ji Chen, Jing Gao, Angel W. Lee, David J. States. MYC Recognition Site Binding and Function
0 -- 0Matteo Barberis, Edda Klipp, Marco Vanoni, Lilia Alberghina. 1/S Network
0 -- 0Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen. Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Volume 3, Issue 3

0 -- 0Pedro Beltrão, Luis Serrano. Correction: Specificity and Evolvability in Eukaryotic Protein Interaction Networks
0 -- 0Igor N. Berezovsky, Konstantin B. Zeldovich, Eugene I. Shakhnovich. Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins
0 -- 0Qiang Zhang, Melvin E. Andersen. Dose Response Relationship in Anti-Stress Gene Regulatory Networks
0 -- 0David Dingli, Arne Traulsen, Franziska Michor. (A)Symmetric Stem Cell Replication and Cancer
0 -- 0Kun Yang, Wenzhe Ma, Huanhuan Liang, Qi Ouyang, Chao Tang, Luhua Lai. Dynamic Simulations on the Arachidonic Acid Metabolic Network
0 -- 0Shaun Mahony, Philip E. Auron, Panayiotis V. Benos. DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
0 -- 0David Babineau, John E. Lewis, André Longtin. Spatial Acuity and Prey Detection in Weakly Electric Fish
0 -- 0David Talavera, Christine Vogel, Modesto Orozco, Sarah A. Teichmann, Xavier de la Cruz. The (In)dependence of Alternative Splicing and Gene Duplication
0 -- 0Xudong Dai, Angus T. De Souza, Hongyue Dai, David L. Lewis, Chang-Kyu Lee, Andy G. Spencer, Hans Herweijer, Jim E. Hagstrom, Peter S. Linsley, Douglas E. Bassett, Roger G. Ulrich, Yudong D. He. PPARα siRNA-Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy
0 -- 0Aleksejs Kontijevskis, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Henryk Jan Komorowski, Jarl E. S. Wikberg. A Look Inside HIV Resistance through Retroviral Protease Interaction Maps
0 -- 0Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang. Characterization and Identification of MicroRNA Core Promoters in Four Model Species
0 -- 0Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini. Discovering Motifs in Ranked Lists of DNA Sequences
0 -- 0Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J. Low, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer, Francisco S. Domingues. Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
0 -- 0Axel Bernal, Koby Crammer, Artemis G. Hatzigeorgiou, Fernando Pereira. Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
0 -- 0Quentin Vicens, Philip E. Bourne. Ten Simple Rules for a Successful Collaboration
0 -- 0Eric P. Nawrocki, Sean R. Eddy. Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
0 -- 0Andrea Ciliberto, Fabrizio Capuani, John J. Tyson. Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation
0 -- 0Benjamin A. Shoemaker, Anna R. Panchenko. Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases
0 -- 0Barry G. Hall, Stephen J. Salipante. Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
0 -- 0Matthew Onsum, Christopher V. Rao. A Mathematical Model for Neutrophil Gradient Sensing and Polarization
0 -- 0Pierre Nicolas, Kyoung-Mee Kim, Darryl Shibata, Simon Tavaré. The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns
0 -- 0Sandeep Krishna, Sergei Maslov, Kim Sneppen. Escherichia coli SOS Response: A Quantitative Model
0 -- 0Keun-Young Kim, Jin Wang. Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch
0 -- 0Regina Brockmann, Andreas Beyer, Jürgen J. Heinisch, Thomas Wilhelm. Posttranscriptional Expression Regulation: What Determines Translation Rates?

Volume 3, Issue 2

0 -- 0Gunnar Rätsch, Sören Sonnenburg, Jagan Srinivasan, Hanh Witte, Klaus-Robert Müller, Ralf J. Sommer, Bernhard Schölkopf. Caenorhabditis elegans Genome Annotation Using Machine Learning
0 -- 0David L. Bostick, Charles L. Brooks III. Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel
0 -- 0Haibo Yu, Liang Ma, Yang Yang, Qiang Cui. Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues
0 -- 0Sophie Achard, Ed Bullmore. Efficiency and Cost of Economical Brain Functional Networks
0 -- 0Pedro Beltrão, Luis Serrano. Specificity and Evolvability in Eukaryotic Protein Interaction Networks
0 -- 0Haibo Yu, Liang Ma, Yang Yang, Qiang Cui. Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations
0 -- 0Timothée Masquelier, Simon J. Thorpe. Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity
0 -- 0Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A. Garraway, Edward A. Fox, Ephraim P. Hochberg, Ingo K. Mellinghoff, Matthias D. Hofer, Aurelien Descazeaud, Mark A. Rubin, Matthew Meyerson, Wing Hung Wong, William R. Sellers, Cheng Li. Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
0 -- 0Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra. From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
0 -- 0Carl Zimmer. Correction: The Genome: An Outsider's View
0 -- 0Stefano Ciliberti, Olivier C. Martin, Andreas Wagner. Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology
0 -- 0Andreas Handel, Roland R. Regoes, Rustom Antia. Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance
0 -- 0Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut. Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics
0 -- 0Lawrence C. Lee, Florence Horn, Fred E. Cohen. Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association
0 -- 0Perttu S. Niemelä, Samuli Ollila, Marja T. Hyvönen, Mikko Karttunen, Ilpo Vattulainen. Assessing the Nature of Lipid Raft Membranes
0 -- 0Omri Barak, Misha Tsodyks. Persistent Activity in Neural Networks with Dynamic Synapses
0 -- 0Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali. Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
0 -- 0Olivier Cinquin. Repressor Dimerization in the Zebrafish Somitogenesis Clock

Volume 3, Issue 12

0 -- 0Tamir Tuller, Martin Kupiec, Eytan Ruppin. S. cerevisiae
0 -- 0Saurabh Asthana, Mikhail A. Roytberg, John A. Stamatoyannopoulos, Shamil R. Sunyaev. Analysis of Sequence Conservation at Nucleotide Resolution
0 -- 0John W. Pepper, Kathleen Sprouffske, Carlo C. Maley. Animal Cell Differentiation Patterns Suppress Somatic Evolution
0 -- 0A. Katharina Wilkins, Paul I. Barton, Bruce Tidor. The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism
0 -- 0Robert M. Seymour, C. Patrick Doncaster. Density Dependence Triggers Runaway Selection of Reduced Senescence
0 -- 0Edoardo M. Airoldi. Getting Started in Probabilistic Graphical Models
0 -- 0Thomas C. Erren. The Long and Thorny Road to Publication in Quality Journals
0 -- 0Yael Katz, William L. Kath, Nelson Spruston, Michael E. Hasselmo. Coincidence Detection of Place and Temporal Context in a Network Model of Spiking Hippocampal Neurons
0 -- 0Andrea P. Weber, Richard H. R. Hahnloser. Spike Correlations in a Songbird Agree with a Simple Markov Population Model
0 -- 0Andreas Handel, Ira M. Longini Jr., Rustom Antia. Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread
0 -- 0João A. N. Filipe, Eleanor M. Riley, Christopher J. Drakeley, Colin J. Sutherland, Azra C. Ghani. Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model
0 -- 0Sebastian Bassi, Virginia González, Gustavo Parisi. Computational Biology in Argentina
0 -- 0Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber. Social Interactions in Myxobacterial Swarming
0 -- 0Jingchun Zhu, J. Zachary Sanborn, Mark Diekhans, Craig B. Lowe, Tom H. Pringle, David Haussler. Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage
0 -- 0Kanika Bajaj, Mallur S. Madhusudhan, Bharat V. Adkar, Purbani Chakrabarti, C. Ramakrishnan, Andrej Sali, Raghavan Varadarajan. Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability
0 -- 0Carlos Gomez-Uribe, George C. Verghese, Leonid A. Mirny. Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering
0 -- 0Antonio del Sol, Pablo Carbonell. The Modular Organization of Domain Structures: Insights into Protein-Protein Binding

Volume 3, Issue 11

0 -- 0Marco Loh, Edmund T. Rolls, Gustavo Deco. A Dynamical Systems Hypothesis of Schizophrenia
0 -- 0Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf. P. falciparum
0 -- 0Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu. Predicting Gene Expression from Sequence: A Reexamination
0 -- 0Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost. An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
0 -- 0Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink. A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast
0 -- 0Naoki Masuda, Brent Doiron. Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination
0 -- 0Kaoru Sugimura, Kohei Shimono, Tadashi Uemura, Atsushi Mochizuki. Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites
0 -- 0Lei Xie, Jian Wang, Philip E. Bourne. In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
0 -- 0Xiaohong Li, Steven G. Self, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid. Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection
0 -- 0Sven Zenker, Jonathan Rubin, Gilles Clermont. From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses
0 -- 0Max A. Alekseyev, Pavel A. Pevzner. Are There Rearrangement Hotspots in the Human Genome?
0 -- 0Toni Gabaldón, Martijn A. Huynen. From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism
0 -- 0Hailiang Huang, Bruno Jedynak, Joel S. Bader. Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
0 -- 0Saurabh Sinha, Xin He. cis-Regulatory Modules
0 -- 0Doron Betel, Robert P. Sheridan, Debora S. Marks, Chris Sander. Computational Analysis of Mouse piRNA Sequence and Biogenesis
0 -- 0Martin Willensdorfer, Reinhard Bürger, Martin A. Nowak. Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast
0 -- 0Ariel Fernández. Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network
0 -- 0Mario Nicodemi, Antonella Prisco. Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation
0 -- 0Morten Lindow, Anders Jacobsen, Sanne Nygaard, Yuan Mang, Anders Krogh. Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants
0 -- 0Shai Kaplan, Shalev Itzkovitz, Ehud Y. Shapiro. A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases
0 -- 0Erel Levine, Peter McHale, Herbert Levine. Small Regulatory RNAs May Sharpen Spatial Expression Patterns
0 -- 0Sebastian Bassi. A Primer on Python for Life Science Researchers
0 -- 0Keith B. Godfrey, Nicholas V. Swindale. Retinal Wave Behavior through Activity-Dependent Refractory Periods
0 -- 0Juan A. G. Ranea, Corin Yeats, Alastair Grant, Christine A. Orengo. Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
0 -- 0Oliver Redfern, Andrew P. Harrison, Timothy Dallman, Frances M. G. Pearl, Christine A. Orengo. CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
0 -- 0Tirso Pons, Luis A. Montero, Juan P. Febles. Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country
0 -- 0Michael Graupner, Nicolas Brunel. STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways
0 -- 0Peter M. Kasson, Vijay S. Pande. Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
0 -- 0Chen-Hsiang Yeang, David Haussler. Detecting Coevolution in and among Protein Domains
0 -- 0Jongrae Kim, Pat Heslop-Harrison, Ian Postlethwaite, Declan G. Bates. Dictyostelium Aggregation Make cAMP Oscillations Robust
0 -- 0Kevin P. Keegan, Suraj Pradhan, Ji-Ping Wang, Ravi Allada. Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
0 -- 0Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W. Kinzler, Victor E. Velculescu, Bert Vogelstein, Martin A. Nowak. Genetic Progression and the Waiting Time to Cancer
0 -- 0Jenny Gu, Philip E. Bourne. Ten Simple Rules for Graduate Students

Volume 3, Issue 10

0 -- 0Chakra Chennubhotla, Ivet Bahar. Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
0 -- 0Olga G. Troyanskaya. "Getting Started In...": A Series Not to Miss
0 -- 0X. Shirley Liu. Getting Started in Tiling Microarray Analysis
0 -- 0José Rino, Teresa Carvalho, José Braga, Joana M. P. Desterro, Reinhard Lührmann, Maria Carmo-Fonseca. A Stochastic View of Spliceosome Assembly and Recycling in the Nucleus
0 -- 0E. Penelope Holland, James N. Aegerter, Calvin Dytham, Graham C. Smith. Landscape as a Model: The Importance of Geometry
0 -- 0Gajendra W. Suryavanshi, Narendra M. Dixit. Emergence of Recombinant Forms of HIV: Dynamics and Scaling
0 -- 0Benjamin de Bivort, Sui Huang, Yaneer Bar-Yam. Empirical Multiscale Networks of Cellular Regulation
0 -- 0Siebe B. van Albada, Pieter Rein ten Wolde. Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways
0 -- 0John Porrill, Paul Dean. Cerebellar Motor Learning: When Is Cortical Plasticity Not Enough?
0 -- 0Simeone Marino, Dhruv Sud, Hillarie Plessner, Philana Ling Lin, John Chan, JoAnne L. Flynn, Denise E. Kirschner. Differences in Reactivation of Tuberculosis Induced from Anti-TNF Treatments Are Based on Bioavailability in Granulomatous Tissue
0 -- 0Tom C. Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J. Grocock, Shiri Freilich, Janet Thornton, Anton J. Enright. Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
0 -- 0Ovidiu Lipan, Jean-Marc Navenot, Zixuan Wang, Lei Huang, Stephen C. Peiper. Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
0 -- 0Gene W. Yeo, Xiangdong Xu, Tiffany Y. Liang, Alysson R. Muotri, Christian T. Carson, Nicole G. Coufal, Fred H. Gage. Alternative Splicing Events Identified in Human Embryonic Stem Cells and Neural Progenitors
0 -- 0Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson. Rhizobium etli
0 -- 0Jennifer Listgarten, Nicole Frahm, Carl Myers Kadie, Christian Brander, David Heckerman. A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
0 -- 0Ryan N. Gutenkunst, Joshua J. Waterfall, Fergal P. Casey, Kevin S. Brown, Christopher R. Myers, James P. Sethna. Universally Sloppy Parameter Sensitivities in Systems Biology Models
0 -- 0Goran Neshich. Computational Biology in Brazil
0 -- 0Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin. Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
0 -- 0Thomas C. Erren, Paul Cullen, Michael Erren, Philip E. Bourne. Ten Simple Rules for Doing Your Best Research, According to Hamming
0 -- 0Jonathan J. Ward, Janet M. Thornton. Saccharomyces Transcription Factor Network
0 -- 0Tony Vladusich, Marcel P. Lucassen, Frans W. Cornelissen. Brightness and Darkness as Perceptual Dimensions

Volume 3, Issue 1

0 -- 0Ying Wei, Dagmar Ringe, Mark A. Wilson, Mary Jo Ondrechen. Identification of Functional Subclasses in the DJ-1 Superfamily Proteins
0 -- 0Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost. Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope
0 -- 0Fran Lewitter. Moving Education Forward
0 -- 0John E. Wertz, Karen F. McGregor, Debra E. Bessen. Detecting Key Structural Features within Highly Recombined Genes
0 -- 0Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard. Drosophila melanogaster
0 -- 0Gina Cannarozzi, Adrian Schneider, Gaston H. Gonnet. A Phylogenomic Study of Human, Dog, and Mouse
0 -- 0Neil Kumar, Alejandro Wolf-Yadlin, Forest M. White, Douglas A. Lauffenburger. Modeling HER2 Effects on Cell Behavior from Mass Spectrometry Phosphotyrosine Data
0 -- 0Wolfgang Maass, Prashant Joshi, Eduardo D. Sontag. Computational Aspects of Feedback in Neural Circuits
0 -- 0Thomas Höfer. In Remembrance: Reinhart Heinrich 1946-2006
0 -- 0Sanne Abeln, Carlo Teubner, Charlotte M. Deane. Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
0 -- 0Tamara Kinzer-Ursem, Jennifer J. Linderman. Both Ligand- and Cell-Specific Parameters Control Ligand Agonism in a Kinetic Model of G Protein-Coupled Receptor Signaling
0 -- 0Hideaki Ogasawara, Tomokazu Doi, Kenji Doya, Mitsuo Kawato. Nitric Oxide Regulates Input Specificity of Long-Term Depression and Context Dependence of Cerebellar Learning
0 -- 0Sol Efroni, David Harel, Irun R. Cohen. Emergent Dynamics of Thymocyte Development and Lineage Determination
0 -- 0Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Shakhnovich. Protein and DNA Sequence Determinants of Thermophilic Adaptation
0 -- 0Peter Schattner. Automated Querying of Genome Databases