PLoS Computational Biology, Volume 3

Volume 3, Number 1, January 2007

Editorial

• 
  Fran Lewitter:
  Moving Education Forward.

Education

• 
  Peter Schattner:
  Automated Querying of Genome Databases.

Obituary

• 
  Thomas Höfer:
  In Remembrance: Reinhart Heinrich 1946-2006.

Research Articles

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

Volume 3, Number 2, February 2007

Perspective

• 
  Jomol 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.

Research Articles

• 
  Gunnar Rätsch, Sören Sonnenburg, Jagan Srinivasan, Hanh Witte, Klaus-Robert Müller, Ralf J. Sommer, Bernhard Schölkopf:
  Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning.
• 
  Perttu S. Niemelä, Samuli Ollila, Marja T. Hyvönen, Mikko Karttunen, Ilpo Vattulainen:
  Assessing the Nature of Lipid Raft Membranes.
• 
  Omri Barak, Misha Tsodyks:
  Persistent Activity in Neural Networks with Dynamic Synapses.
• 
  Haibo Yu, Liang Ma, Yang Yang, Qiang Cui:
  Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues.
• 
  Pedro Beltrão, Luis Serrano:
  Specificity and Evolvability in Eukaryotic Protein Interaction Networks.
• 
  Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali:
  Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning.
• 
  Philippe 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.
• 
  Timothée Masquelier, Simon J. Thorpe:
  Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity.
• 
  Olivier Cinquin:
  Repressor Dimerization in the Zebrafish Somitogenesis Clock.
• 
  Haibo Yu, Liang Ma, Yang Yang, Qiang Cui:
  Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations.
• 
  David L. Bostick, Charles L. Brooks III:
  Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel.
• 
  Stefano Ciliberti, Olivier C. Martin, Andreas Wagner:
  Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology.
• 
  Lawrence C. Lee, Florence Horn, Fred E. Cohen:
  Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association.
• 
  Sophie Achard, Ed Bullmore:
  Efficiency and Cost of Economical Brain Functional Networks.

Corrections

• 
  Rameen 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.
• 
  Andreas Handel, Roland R. Regoes, Rustom Antia:
  Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance.
• 
  Carl Zimmer:
  Correction: The Genome: An Outsider's View.

Volume 3, Number 3, March 2007

Editorial

• 
  Quentin Vicens, Philip E. Bourne:
  Ten Simple Rules for a Successful Collaboration.

Education

• 
  Benjamin A. Shoemaker, Anna R. Panchenko:
  Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases.

Research Articles

• 
  Eric P. Nawrocki, Sean R. Eddy:
  Query-Dependent Banding (QDB) for Faster RNA Similarity Searches.
• 
  Oliver 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.
• 
  Keun-Young Kim, Jin Wang:
  Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch.
• 
  Shaun Mahony, Philip E. Auron, Panayiotis V. Benos:
  DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies.
• 
  Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini:
  Discovering Motifs in Ranked Lists of DNA Sequences.
• 
  Igor N. Berezovsky, Konstantin B. Zeldovich, Eugene I. Shakhnovich:
  Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins.
• 
  Kun Yang, Wenzhe Ma, Huanhuan Liang, Qi Ouyang, Chao Tang, Luhua Lai:
  Dynamic Simulations on the Arachidonic Acid Metabolic Network.
• 
  Regina Brockmann, Andreas Beyer, Jürgen J. Heinisch, Thomas Wilhelm:
  Posttranscriptional Expression Regulation: What Determines Translation Rates?
• 
  Matthew Onsum, Christopher V. Rao:
  A Mathematical Model for Neutrophil Gradient Sensing and Polarization.
• 
  Sandeep Krishna, Sergei Maslov, Kim Sneppen:
  UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model.
• 
  Andrea Ciliberto, Fabrizio Capuani, John J. Tyson:
  Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation.
• 
  (Withdrawn) Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees.
• 
  David Dingli, Arne Traulsen, Franziska Michor:
  (A)Symmetric Stem Cell Replication and Cancer.
• 
  Axel Bernal, Koby Crammer, Artemis G. Hatzigeorgiou, Fernando Pereira:
  Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction.
• 
  Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang:
  Characterization and Identification of MicroRNA Core Promoters in Four Model Species.
• 
  Aleksejs 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.
• 
  Qiang Zhang, Melvin E. Andersen:
  Dose Response Relationship in Anti-Stress Gene Regulatory Networks.
• 
  Pierre Nicolas, Kyoung-Mee Kim, Darryl Shibata, Simon Tavaré:
  The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns.
• 
  Xudong 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.
• 
  David Talavera, Christine Vogel, Modesto Orozco, Sarah A. Teichmann, Xavier de la Cruz:
  The (In)dependence of Alternative Splicing and Gene Duplication.
• 
  David Babineau, John E. Lewis, André Longtin:
  Spatial Acuity and Prey Detection in Weakly Electric Fish.

Correction

• 
  Pedro Beltrão, Luis Serrano:
  Correction: Specificity and Evolvability in Eukaryotic Protein Interaction Networks.

Volume 3, Number 4, April 2007

Editorial

• 
  Philip E. Bourne:
  Ten Simple Rules for Making Good Oral Presentations.

Education

• 
  Benjamin A. Shoemaker, Anna R. Panchenko:
  Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners.

Research Articles

• 
  David 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.
• 
  Scott Christley, Mark S. Alber, Stuart A. Newman:
  Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model.
• 
  Filipe Tostevin, Pieter Rein ten Wolde, Martin Howard:
  Fundamental Limits to Position Determination by Concentration Gradients.
• 
  Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein:
  The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics.
• 
  Ji Lee, Zhihua Li, Rachel A. Brower-Sinning, Bino John:
  Regulatory Circuit of Human MicroRNA Biogenesis.
• 
  Gert 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.
• 
  Mary Qu Yang, Laura M. Koehly, Laura Elnitski:
  Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes.
• 
  Matteo Barberis, Edda Klipp, Marco Vanoni, Lilia Alberghina:
  Cell Size at S Phase Initiation: An Emergent Property of the G₁/S Network.
• 
  Sebastian 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.
• 
  Samuel Bernard, Didier Gonze, Branka Cajavec, Hanspeter Herzel, Achim Kramer:
  Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus.
• 
  Jun 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.
• 
  Zhaoping Li, Keith A. May:
  Psychophysical Tests of the Hypothesis of a Bottom-Up Saliency Map in Primary Visual Cortex.
• 
  Yili Chen, Thomas W. Blackwell, Ji Chen, Jing Gao, Angel W. Lee, David J. States:
  Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function.
• 
  Sebastian Maurer-Stroh, Manfred Koranda, Wolfgang Benetka, Georg Schneider, Fernanda L. Sirota, Frank Eisenhaber:
  Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins.

Correspondence

• 
  Gerton Lunter:
  Dog as an Outgroup to Human and Mouse.
• 
  Mark Gerstein, Shawn M. Douglas:
  RNAi Development.

Correction

• 
  David Dingli, Arne Traulsen, Franziska Michor:
  Correction: (A)Symmetric Stem Cell Replication and Cancer.

Volume 3, Number 5, May 2007

Editorial

• 
  Thomas C. Erren, Philip E. Bourne:
  Ten Simple Rules for a Good Poster Presentation.

Message from ISCB

• 
  Thomas Lengauer, B. J. Morrison McKay, Burkhard Rost:
  ISMB/ECCB 2007: The Premier Conference on Computational Biology.

Research Articles

• 
  Michal Brylinski, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochanczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman:
  Prediction of Functional Sites Based on the Fuzzy Oil Drop Model.
• 
  Eli Koren, Galit Lev-Maor, Gil Ast:
  The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons.
• 
  B. Silvano Zanutto, John E. R. Staddon:
  Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals.
• 
  Scott Doniger, Justin C. Fay:
  Frequent Gain and Loss of Functional Transcription Factor Binding Sites.
• 
  Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko:
  A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes.
• 
  Jasmin Fisher, Nir Piterman, Alex Hajnal, Thomas A. Henzinger:
  Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development.
• 
  Fang Liu, Eivind Tøstesen, Jostein K. Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G. Thilly, Eivind Hovig:
  The Human Genomic Melting Map.
• 
  Adam 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.
• 
  Gabriel D. Puccini, Maria V. Sanchez-Vives, Albert Compte:
  Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits.
• 
  Robert P. Zinzen, Dmitri A. Papatsenko:
  Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development.
• 
  Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer:
  HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation.
• 
  Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich:
  Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites.
• 
  A. Aldo Faisal, Simon B. Laughlin:
  Stochastic Simulations on the Reliability of Action Potential Propagation in Thin Axons.
• 
  Tristan Ursell, Kerwyn Casey Huang, Eric L. Peterson, Rob Phillips:
  Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions.
• 
  Raffaele Vardavas, Romulus Breban, Sally Blower:
  Can Influenza Epidemics Be Prevented by Voluntary Vaccination?

Correspondence

• 
  Thomas C. Erren, Michael Erren:
  "Simple Rules for Editors"? Here is One Rule to Tackle Neglected Problems of Publishing.
• 
  Mark Patterson, Barbara Cohen:
  "Simple Rules for Editors"? Here Is One Rule to Tackle Neglected Problems of Publishing: Response from PLoS.

Correction

• 
  Omri Barak, Misha Tsodyks:
  Correction: Persistent Activity in Neural Networks with Dynamic Synapses.

Volume 3, Number 6, June 2007

Messages from ISCB

• 
  Merry Maisel:
  ISCB Honors Temple F. Smith and Eran Segal.
• 
  Lawrence Hunter, Russ B. Altman, Philip E. Bourne:
  The International Society for Computational Biology 10th Anniversary.

Education

• 
  Adi L. Tarca, Vincent J. Carey, Xue-wen Chen, Roberto Romero, Sorin Draghici:
  Machine Learning and Its Applications to Biology.

Perspective

• 
  David B. Searls:
  A View from the Dark Side.

Research Articles

• 
  Henning Sprekeler, Christian Michaelis, Laurenz Wiskott:
  Slowness: An Objective for Spike-Timing-Dependent Plasticity?
• 
  Milan van Hoek, Paulien Hogeweg:
  The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective.
• 
  Oscar M. Rueda, Ramón Díaz-Uriarte:
  Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH.
• 
  Bruno Delord, Hugues Berry, Emmanuel Guigon, Stéphane Genet:
  A New Principle for Information Storage in an Enzymatic Pathway Model.
• 
  Marcelo Camperi, Timothy C. Tricas, Brandon R. Brown:
  From Morphology to Neural Information: The Electric Sense of the Skate.
• 
  Zengjian 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.
• 
  Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble:
  Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes.
• 
  Stephen B. 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.
• 
  Mikiya Otsuji, Shuji Ishihara, Carl Co, Kozo Kaibuchi, Atsushi Mochizuki, Shinya Kuroda:
  A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity.
• 
  Juilee Thakar, Mylisa Pilione, Girish Kirimanjeswara, Eric T. Harvill, Réka Albert:
  Modeling Systems-Level Regulation of Host Immune Responses.
• 
  Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer:
  CpG Island Mapping by Epigenome Prediction.
• 
  Sukhbinder Kumar, Klaas E. Stephan, Jason D. Warren, Karl J. Friston, Timothy D. Griffiths:
  Hierarchical Processing of Auditory Objects in Humans.
• 
  Harish Shankaran, Haluk Resat, H. Steven Wiley:
  Cell Surface Receptors for Signal Transduction and Ligand Transport: A Design Principles Study.
• 
  Cécile Caretta-Cartozo, Paolo De Los Rios, Francesco Piazza, Pietro Liò:
  Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe.
• 
  Zhi Wang, Jianzhi Zhang:
  In Search of the Biological Significance of Modular Structures in Protein Networks.

Correction

• 
  B. Silvano Zanutto, John E. R. Staddon:
  Correction: Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals.

Volume 3, Number 7, July 2007

Education

• 
  Jacques Colinge, Keiryn L. Bennett:
  Introduction to Computational Proteomics.

Review

• 
  Carol Shiels, Niall M. Adams, Suhail A. Islam, David A. Stephens, Paul S. Freemont:
  Quantitative Analysis of Cell Nucleus Organisation.

Research Articles

• 
  Michiel 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.
• 
  Robert G. Endres, Joseph J. Falke, Ned S. Wingreen:
  Chemotaxis Receptor Complexes: From Signaling to Assembly.
• 
  Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt:
  Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins.
• 
  Avner Schlessinger, Jinfeng Liu, Burkhard Rost:
  Natively Unstructured Loops Differ from Other Loops.
• 
  Deyan Luan, Michael Zai, Jeffrey D. Varner:
  Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies.
• 
  Anastasia Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma:
  Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster.
• 
  Bertrand C. W. Tanner, Thomas L. Daniel, Michael Regnier:
  Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle.
• 
  Yanay Ofran, Burkhard Rost:
  Protein-Protein Interaction Hotspots Carved into Sequences.
• 
  Anton Zilman, Stefano Di Talia, Brian T. Chait, Michael P. Rout, Marcelo O. Magnasco:
  Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport.
• 
  Reut Shalgi, Daniel Lieber, Moshe Oren, Yitzhak Pilpel:
  Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network.
• 
  Marcel E. Curlin, Shyamala Iyer, John E. Mittler:
  Optimal Timing and Duration of Induction Therapy for HIV-1 Infection.
• 
  Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, Florentin Wörgötter:
  Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning.
• 
  Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E. Warburton:
  Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation.
• 
  Konstantin 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.
• 
  Fereydoun 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.
• 
  Zizhen Yao, Jeffrey E. Barrick, Zasha Weinberg, Shane J. Neph, Ronald R. Breaker, Martin Tompa, Walter L. Ruzzo:
  A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes.
• 
  Alborz 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.
• 
  Patricia A. Ryan, Brian W. Kirk, Chad W. Euler, Raymond Schuch, Vincent A. Fischetti:
  Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes.
• 
  Martin 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.

Corrections

• 
  Andrew B. Goryachev, Alexandra V. Pokhilko:
  Correction: Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes.
• 
  Zhi Wang, Jianzhi Zhang:
  Correction: In Search of the Biological Significance of Modular Structures in Protein Networks.
• 
  (Withdrawn) Retraction: Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees.

Volume 3, Number 8, August 2007

Education Articles

• 
  Cédric Notredame:
  Recent Evolutions of Multiple Sequence Alignment Algorithms.
• 
  Chris J. Needham, James R. Bradford, Andrew J. Bulpitt, David R. Westhead:
  A Primer on Learning in Bayesian Networks for Computational Biology.

Research Articles

• 
  Mathias Franzius, Henning Sprekeler, Laurenz Wiskott:
  Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells.
• 
  Meron Gurkiewicz, Alon Korngreen:
  A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm.
• 
  Aviv Bergman, Gil Atzmon, Kenny Ye, Thomas MacCarthy, Nir Barzilai:
  Buffering Mechanisms in Aging: A Systems Approach Toward Uncovering the Genetic Component of Aging.
• 
  Yihai Yu, Guanyu Wang, Rahul Simha, Weiqun Peng, Frank Turano, Chen Zeng:
  Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network.
• 
  Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones:
  Inferring Function Using Patterns of Native Disorder in Proteins.
• 
  Julio 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.
• 
  Elisabeth L. Humphris, Tanja Kortemme:
  Design of Multi-Specificity in Protein Interfaces.
• 
  Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin, David Horn:
  Functional Representation of Enzymes by Specific Peptides.
• 
  Sergey 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.
• 
  Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander:
  Automated Protein Subfamily Identification and Classification.
• 
  Andrew E. Teschendorff, Michel Journée, Pierre-Antoine Absil, Rodolphe Sepulchre, Carlos Caldas:
  Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis.
• 
  Roland Schäfer, Eleni Vasilaki, Walter Senn:
  Perceptual Learning via Modification of Cortical Top-Down Signals.
• 
  Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford:
  Automated Discovery of Functional Generality of Human Gene Expression Programs.
• 
  Irmtraud M. Meyer, István Miklós:
  SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework.
• 
  Masako 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.
• 
  David Golomb, Karnit Donner, Liron Shacham, Dan Shlosberg, Yael Amitai, David Hansel:
  Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons.
• 
  James V. Stone:
  Distributed Representations Accelerate Evolution of Adaptive Behaviours.
• 
  Burton W. Andrews, Pablo A. Iglesias:
  An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells.
• 
  Robert S. Kuczenski, Kevin C. Hong, Jordi García-Ojalvo, Kelvin H. Lee:
  PERIOD-TIMELESS Interval Timer May Require an Additional Feedback Loop.
• 
  Sylvain 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.

Volume 3, Number 9, September 2007

Editorial

• 
  Philip E. Bourne, Steven E. Brenner:
  Developing Computational Biology.

Education

• 
  Baltazar D. Aguda, Andrew B. Goryachev:
  From Pathways Databases to Network Models of Switching Behavior.

Perspective

• 
  Rafael Palacios, Julio Collado-Vides:
  Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go.

Research Articles

• 
  Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni:
  A Computational Approach to the Functional Screening of Genomes.
• 
  David Corney, R. Beau Lotto:
  What Are Lightness Illusions and Why Do We See Them?
• 
  Can 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.
• 
  Liang Qiao, Robert B. Nachbar, Ioannis G. Kevrekidis, Stanislav Y. Shvartsman:
  Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling.
• 
  Mukund Thattai, Yoram Burak, Boris I. Shraiman:
  The Origins of Specificity in Polyketide Synthase Protein Interactions.
• 
  Chakra Chennubhotla, Ivet Bahar:
  Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.
• 
  Elaine Angelino, Michael P. Brenner:
  Excitability Constraints on Voltage-Gated Sodium Channels.
• 
  Doron 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.
• 
  Soundara Raghavan Pavithra, Ranjit Kumar, Utpal Tatu:
  Systems Analysis of Chaperone Networks in the Malarial Parasite Plasmodium falciparum.
• 
  Mookyung 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.
• 
  Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova:
  A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms.
• 
  Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Martí-Renom, Baldo Oliva:
  Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions.
• 
  Yasser Roudi, Peter E. Latham:
  A Balanced Memory Network.
• 
  Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin:
  Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes.

Correspondence

• 
  Eric Grosch:
  Reply to "Ten Simple Rules for Getting Published".

Correction

• 
  Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, Florentin Wörgötter:
  Correction: Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning.

Volume 3, Number 10, October 2007

Editorial

• 
  Thomas C. Erren, Paul Cullen, Michael Erren, Philip E. Bourne:
  Ten Simple Rules for Doing Your Best Research, According to Hamming.

Messages from ISCB

• 
  Xiaole Shirley Liu:
  Getting Started in Tiling Microarray Analysis.
• 
  Olga G. Troyanskaya:
  "Getting Started In...": A Series Not to Miss.

Perspective

• 
  Goran Neshich:
  Computational Biology in Brazil.

Research Articles

• 
  Gene 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.
• 
  John Porrill, Paul Dean:
  Cerebellar Motor Learning: When Is Cortical Plasticity Not Enough?
• 
  Jonathan J. Ward, Janet M. Thornton:
  Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network.
• 
  E. Penelope Holland, James N. Aegerter, Calvin Dytham, Graham C. Smith:
  Landscape as a Model: The Importance of Geometry.
• 
  José 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.
• 
  Gajendra W. Suryavanshi, Narendra M. Dixit:
  Emergence of Recombinant Forms of HIV: Dynamics and Scaling.
• 
  Tom C. Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J. Grocock, Shiri Freilich, Janet M. Thornton, Anton J. Enright:
  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data.
• 
  Tony Vladusich, Marcel P. Lucassen, Frans W. Cornelissen:
  Brightness and Darkness as Perceptual Dimensions.
• 
  Simeone 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.
• 
  Benjamin L. de Bivort, Sui Huang, Yaneer Bar-Yam:
  Empirical Multiscale Networks of Cellular Regulation.
• 
  Jennifer Listgarten, Nicole Frahm, Carl Myers Kadie, Christian Brander, David Heckerman:
  A Statistical Framework for Modeling HLA-Dependent T Cell Response Data.
• 
  Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin:
  Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix.
• 
  Siebe B. van Albada, Pieter Rein ten Wolde:
  Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways.
• 
  Ovidiu 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.
• 
  Ryan 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.
• 
  Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson:
  Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli.

Correction

• 
  Chakra Chennubhotla, Ivet Bahar:
  Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.

Volume 3, Number 11, November 2007

Editorial

• 
  Jenny Gu, Philip E. Bourne:
  Ten Simple Rules for Graduate Students.

Education

• 
  Sebastian Bassi:
  A Primer on Python for Life Science Researchers.

Perspective

• 
  Tirso Pons, Luis A. Montero, Juan P. Febles:
  Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country.

Research Articles

• 
  Lei Xie, Jian Wang, Philip E. Bourne:
  In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators.
• 
  Michael Graupner, Nicolas Brunel:
  STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways.
• 
  Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf:
  Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum.
• 
  Oliver 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.
• 
  Erel Levine, Peter T. McHale, Herbert Levine:
  Small Regulatory RNAs May Sharpen Spatial Expression Patterns.
• 
  Naoki Masuda, Brent Doiron:
  Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination.
• 
  Juan 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.
• 
  Morten Lindow, Anders Jacobsen Skanderup, Sanne Nygaard, Yuan Mang, Anders Krogh:
  Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants.
• 
  Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu:
  Predicting Gene Expression from Sequence: A Reexamination.
• 
  Xiaohong Li, Steven G. Self, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid:
  Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection.
• 
  Keith B. Godfrey, Nicholas V. Swindale:
  Retinal Wave Behavior through Activity-Dependent Refractory Periods.
• 
  Martin Willensdorfer, Reinhard Bürger, Martin A. Nowak:
  Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast.
• 
  Hailiang Huang, Bruno Jedynak, Joel S. Bader:
  Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps.
• 
  Art 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.
• 
  Shai Kaplan, Shalev Itzkovitz, Ehud Shapiro:
  A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases.
• 
  Kaoru Sugimura, Kohei Shimono, Tadashi Uemura, Atsushi Mochizuki:
  Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites.
• 
  Peter M. Kasson, Vijay S. Pande:
  Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.
• 
  Sven Zenker, Jonathan E. Rubin, Gilles Clermont:
  From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses.
• 
  Max A. Alekseyev, Pavel A. Pevzner:
  Are There Rearrangement Hotspots in the Human Genome?
• 
  Mario Nicodemi, Antonella Prisco:
  Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation.
• 
  Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink:
  A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast.
• 
  Saurabh Sinha, Xin He:
  MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules.
• 
  Jongrae Kim, Pat Heslop-Harrison, Ian Postlethwaite, Declan G. Bates:
  Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust.
• 
  Doron Betel, Robert P. Sheridan, Debora S. Marks, Chris Sander:
  Computational Analysis of Mouse piRNA Sequence and Biogenesis.
• 
  Niko 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.
• 
  Ariel Fernández:
  Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network.
• 
  Marco Loh, Edmund T. Rolls, Gustavo Deco:
  A Dynamical Systems Hypothesis of Schizophrenia.
• 
  Kevin P. Keegan, Suraj Pradhan, Ji-Ping Wang, Ravi Allada:
  Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes.
• 
  Chen-Hsiang Yeang, David Haussler:
  Detecting Coevolution in and among Protein Domains.
• 
  Toni Gabaldón, Martijn A. Huynen:
  From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism.

Volume 3, Number 12, December 2007

Message from ISCB

• 
  Edoardo M. Airoldi:
  Getting Started in Probabilistic Graphical Models.

Perspective

• 
  Sebastian Bassi, Virginia González, Gustavo D. Parisi:
  Computational Biology in Argentina.

Research Articles

• 
  Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber:
  Social Interactions in Myxobacterial Swarming.
• 
  Saurabh Asthana, Mikhail A. Roytberg, John A. Stamatoyannopoulos, Shamil R. Sunyaev:
  Analysis of Sequence Conservation at Nucleotide Resolution.
• 
  João 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.
• 
  Robert M. Seymour, C. Patrick Doncaster:
  Density Dependence Triggers Runaway Selection of Reduced Senescence.
• 
  Carlos Gomez-Uribe, George C. Verghese, Leonid A. Mirny:
  Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering.
• 
  Tamir Tuller, Martin Kupiec, Eytan Ruppin:
  Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae.
• 
  Andrea P. Weber, Richard H. R. Hahnloser:
  Spike Correlations in a Songbird Agree with a Simple Markov Population Model.
• 
  Yael Katz, William L. Kath, Nelson Spruston, Michael E. Hasselmo:
  Coincidence Detection of Place and Temporal Context in a Network Model of Spiking Hippocampal Neurons.
• 
  A. Katharina Wilkins, Paul I. Barton, Bruce Tidor:
  The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism.
• 
  Jingchun 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.
• 
  John W. Pepper, Kathleen Sprouffske, Carlo C. Maley:
  Animal Cell Differentiation Patterns Suppress Somatic Evolution.
• 
  Antonio del Sol, Pablo Carbonell:
  The Modular Organization of Domain Structures: Insights into Protein-Protein Binding.
• 
  Andreas Handel, Ira M. Longini Jr., Rustom Antia:
  Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread.
• 
  Kanika 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.

Correspondence

• 
  Thomas C. Erren:
  The Long and Thorny Road to Publication in Quality Journals.