PLoS Computational Biology, Volume 2

Volume 2, Number 1, January 2006

Education

• 
  Fran Lewitter:
  Welcome to PLoS Computational Biology "Education".

Research Articles

• 
  Tingjun Hou, Ken Chen, William A. McLaughlin, Benzhuo Lu, Wei Wang:
  Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain.
• 
  Jose M. G. Vilar, Ronald Jansen, Chris Sander:
  Signal Processing in the TGF-β Superfamily Ligand-Receptor Network.
• 
  Charles W. Sugnet, Karpagam Srinivasan, Tyson Clark, Georgeann O'Brien, Melissa S. Cline, Hui Wang, Alan Williams, David Kulp, John Blume, David Haussler, Manuel Ares:
  Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays.
• 
  Timothy E. Allen, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson:
  Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization.
• 
  Gerton Lunter, Chris P. Ponting, Jotun Hein:
  Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model.

Correction

• 
  Daniel A. Beard:
  Correction: A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation.

Volume 2, Number 2, February 2006

Editorial

• 
  Philip E. Bourne, Leo M. Chalupa:
  Ten Simple Rules for Getting Grants.

Message from ISCB

• 
  Goran Neshich, Philip E. Bourne, Søren Brunak:
  ISMB 2006.

Research Articles

• 
  Qian Peng, Pavel A. Pevzner, Glenn Tesler:
  The Fragile Breakage versus Random Breakage Models of Chromosome Evolution.
• 
  Kay Hamacher, Joanna Trylska, James Andrew McCammon:
  Dependency Map of Proteins in the Small Ribosomal Subunit.
• 
  Yang Zhang, Mark E. DeVries, Jeffrey Skolnick:
  Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
• 
  Kai Puolamäki, Mikael Fortelius, Heikki Mannila:
  Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods.
• 
  Sander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend:
  Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors.

Correction

• 
  Nicola Cannata, Emanuela Merelli, Russ B. Altman:
  Correction: Time to Organize the Bioinformatics Resourceome.

Volume 2, Number 3, March 2006

Research Articles

• 
  Igor V. Tetko, Georg Haberer, Stephen Rudd, Blake C. Meyers, Hans-Werner Mewes, Klaus F. X. Mayer:
  Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana.
• 
  Vitaly V. Ganusov, Rob J. De Boer:
  Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection.
• 
  Raúl Guantes, Juan F. Poyatos:
  Dynamical Principles of Two-Component Genetic Oscillators.
• 
  Claus C. Hilgetag, Helen Barbas:
  Role of Mechanical Factors in the Morphology of the Primate Cerebral Cortex.
• 
  David Holcman, Misha Tsodyks:
  The Emergence of Up and Down States in Cortical Networks.
• 
  Gustavo Glusman, Shizhen Qin, M. Raafat El-Gewely, Andrew F. Siegel, Jared C. Roach, Leroy E. Hood, Arian F. A. Smit:
  A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions.
• 
  Andrey A. Ptitsyn, Sanjin Zvonic, Steven A. Conrad, L. Keith Scott, Randall L. Mynatt, Jeffrey M. Gimble:
  Circadian Clocks Are Resounding in Peripheral Tissues.
• 
  Mark Yandell, Chris Mungall, Chris Smith, Simon Prochnik, Joshua S. Kaminker, George Hartzell, Suzanna Lewis, Gerald M. Rubin:
  Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes.

Correspondence

• 
  Peter D. Keightley, Martin J. Lercher, Adam Eyre-Walker:
  Understanding the Degradation of Hominid Gene Control.
• 
  Eliot C. Bush, Bruce T. Lahn:
  Authors' Reply.

Corrections

• 
  Yang Zhang, Mark E. DeVries, Jeffrey Skolnick:
  Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
• 
  Hung D. Nguyen, Maki Yoshihama, Naoya Kenmochi:
  Correction: New Maximum Likelihood Estimators for Eukaryotic Intron Evolution.

Volume 2, Number 4, April 2006

Education

• 
  Kenzie D. MacIsaac, Ernest Fraenkel:
  Practical Strategies for Discovering Regulatory DNA Sequence Motifs.

Research Articles

• 
  Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Öjvind Johansson, Wyeth W. Wasserman, Elizabeth M. Simpson:
  SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions.
• 
  Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo:
  Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome.
• 
  Karen Lipkow:
  Changing Cellular Location of CheZ Predicted by Molecular Simulations.
• 
  Chung-Jung Tsai, Jie Zheng, Ruth Nussinov:
  Designing a Nanotube Using Naturally Occurring Protein Building Blocks.
• 
  Eli S. Groban, Arjun Narayanan, Matthew P. Jacobson:
  Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation.
• 
  Jakob Skou Pedersen, Gill Bejerano, Adam C. Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler:
  Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.
• 
  Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola:
  Codon Usage Domains over Bacterial Chromosomes.
• 
  Bosco K. Ho, Ken A. Dill:
  Folding Very Short Peptides Using Molecular Dynamics.
• 
  Thomas Gisiger, Michel Kerszberg:
  A Model for Integrating Elementary Neural Functions into Delayed-Response Behavior.

Correspondence

• 
  David Sankoff:
  The Signal in the Genomes.

Volume 2, Number 5, May 2006

Research Articles

• 
  Christine Vogel, Cyrus Chothia:
  Protein Family Expansions and Biological Complexity.
• 
  Enrique Blanco, Xavier Messeguer, Temple F. Smith, Roderic Guigó:
  Transcription Factor Map Alignment of Promoter Regions.
• 
  Anthony A. Philippakis, Brian W. Busser, Stephen S. Gisselbrecht, Fangxue Sherry He, Beatriz Estrada, Alan M. Michelson, Martha L. Bulyk:
  Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells.
• 
  Frank J. Poelwijk, Daniel J. Kiviet, Sander J. Tans:
  Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data.
• 
  Rhonald C. Lua, Alexander Y. Grosberg:
  Statistics of Knots, Geometry of Conformations, and Evolution of Proteins.
• 
  Theodore J. Perkins, Johannes Jaeger, John Reinitz, Leon Glass:
  Reverse Engineering the Gap Gene Network of Drosophila melanogaster.
• 
  Christian L. Barrett, Bernhard O. Palsson:
  Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach.
• 
  J. Starmer, Anne-Marie Stomp, Mladen A. Vouk, Donald L. Bitzer:
  Predicting Shine-Dalgarno Sequence Locations Exposes Genome Annotation Errors.
• 
  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:
  Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays.
• 
  Matthieu Legendre, William Ritchie, Fabrice Lopez, Daniel Gautheret:
  Differential Repression of Alternative Transcripts: A Screen for miRNA Targets.
• 
  Nizar N. Batada, Larry A. Shepp, David O. Siegmund, Michael Levitt:
  Spatial Regulation and the Rate of Signal Transduction Activation.
• 
  Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, Baochen Shi, Yong Zhang, Jie Wang, Tao Wu, Runsheng Chen:
  Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors.
• 
  Philip Wong, Dmitrij Frishman:
  Fold Designability, Distribution, and Disease.
• 
  Örjan Svensson, Lars Arvestad, Jens Lagergren:
  Genome-Wide Survey for Biologically Functional Pseudogenes.

Correction

• 
  Bosco K. Ho, Ken A. Dill:
  Correction: Folding Very Short Peptides Using Molecular Dynamics.

Volume 2, Number 6, June 2006

Education

• 
  Duncan P. Brown, Kimmen Sjölander:
  Functional Classification Using Phylogenomic Inference.

Review

• 
  Bette T. Korber, Montiago LaBute, Karina Yusim:
  Immunoinformatics Comes of Age.

Research Articles

• 
  Mikita Suyama, Eoghan D. Harrington, Peer Bork, David Torrents:
  Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes.
• 
  David Fange, Johan Elf:
  Noise-Induced Min Phenotypes in E. coli.
• 
  Sergei L. Kosakovsky Pond, Simon D. W. Frost, Zehava Grossman, Michael B. Gravenor, Douglas D. Richman, Andrew J. Leigh Brown:
  Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses.
• 
  Paul D. Williams, David D. Pollock, Benjamin P. Blackburne, Richard A. Goldstein:
  Assessing the Accuracy of Ancestral Protein Reconstruction Methods.
• 
  Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter:
  Parametric Alignment of Drosophila Genomes.
• 
  Gevorg Grigoryan, Fei Zhou, Steve R. Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating:
  Ultra-Fast Evaluation of Protein Energies Directly from Sequence.
• 
  W. David Wick, Peter B. Gilbert, Steven G. Self:
  On Modeling HIV and T Cells In Vivo: Assessing Causal Estimators in Vaccine Trials.
• 
  Vinay Varadan, Dimitris Anastassiou:
  Inference of Disease-Related Molecular Logic from Systems-Based Microarray Analysis.
• 
  Andreas Beyer, Christopher T. Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker:
  Integrated Assessment and Prediction of Transcription Factor Binding.
• 
  Vitaly V. Ganusov, Sergei S. Pilyugin, Rafi Ahmed, Rustom Antia:
  How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?
• 
  Jos Käfer, Paulien Hogeweg, Athanasius F. M. Marée:
  Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences.
• 
  Samiul Hasan, Sabine Daugelat, P. S. Srinivasa Rao, Mark Schreiber:
  Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis.
• 
  Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S. Wilson, John Sidney, Ole Lund, Søren Buus, Alessandro Sette:
  A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules.
• 
  Malin C. Lagerström, Anders R. Hellström, David E. Gloriam, Thomas P. Larsson, Helgi B. Schiöth, Robert Fredriksson:
  The G Protein-Coupled Receptor Subset of the Chicken Genome.

Correction

• 
  Igor V. Tetko, Georg Haberer, Stephen Rudd, Blake C. Meyers, Hans-Werner Mewes, Klaus F. X. Mayer:
  Correction: Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana.

Volume 2, Number 7, July 2006

Review

• 
  Ulisses M. Braga-Neto, Ernesto T. A. Marques Jr.:
  From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards.

Research Articles

• 
  Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C. Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash:
  Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System.
• 
  Arun Mehra, Christian I. Hong, Mi Shi, Jennifer J. Loros, Jay C. Dunlap, Peter Ruoff:
  Circadian Rhythmicity by Autocatalysis.
• 
  Adrian H. Elcock:
  Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome.
• 
  Sven Mika, Burkhard Rost:
  Protein-Protein Interactions More Conserved within Species than across Species.
• 
  Brynn H. Voy, Jon A. Scharff, Andy D. Perkins, Arnold M. Saxton, Bhavesh Borate, Elissa J. Chesler, Lisa K. Branstetter, Michael A. Langston:
  Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms.
• 
  Patrick D. Schloss, Jo Handelsman:
  Toward a Census of Bacteria in Soil.
• 
  Pablo Achard, Erik De Schutter:
  Complex Parameter Landscape for a Complex Neuron Model.
• 
  Marcus Kaiser, Claus C. Hilgetag:
  Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems.
• 
  Jennifer L. Kabat, Sergio Barberan-Soler, Paul McKenna, Hiram Clawson, Tracy Farrer, Alan M. Zahler:
  Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes.
• 
  Nizar N. Batada, Laurence D. Hurst, Mike Tyers:
  Evolutionary and Physiological Importance of Hub Proteins.
• 
  Jenny Gu, Michael Gribskov, Philip E. Bourne:
  Wiggle - Predicting Functionally Flexible Regions from Primary Sequence.
• 
  Markus J. Herrgård, Stephen S. Fong, Bernhard Ø. Palsson:
  Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles.
• 
  Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li:
  Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance.
• 
  Jin Wang, Qiang Lu, H. Peter Lu:
  Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition.
• 
  Feng Ding, Nikolay V. Dokholyan:
  Emergence of Protein Fold Families through Rational Design.

Correspondence

• 
  Hung D. Nguyen, Maki Yoshihama, Naoya Kenmochi:
  Authors' Reply.
• 
  Miklós Csürös:
  On the Estimation of Intron Evolution.

Correction

• 
  Vitaly V. Ganusov, Sergei S. Pilyugin, Rafi Ahmed, Rustom Antia:
  Correction: How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?

Volume 2, Number 8, August 2006

Editorial

• 
  Philip E. Bourne:
  One Year of PLoS Computational Biology.

Message from ISCB

• 
  Merry Maisel:
  ISCB Honors Michael S. Waterman and Mathieu Blanchette.

Review

• 
  Robert C. Cannon, Giampaolo D'Alessandro:
  The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics.

Research Articles

• 
  Carene Rizzon, Loïc Ponger, Brandon S. Gaut:
  Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice.
• 
  Åsa K. Björklund, Diana Ekman, Arne Elofsson:
  Expansion of Protein Domain Repeats.
• 
  Yonatan Bilu, Tomer Shlomi, Naama Barkai, Eytan Ruppin:
  Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States.
• 
  Sabrina L. Spencer, Ryan A. Gerety, Kenneth J. Pienta, Stephanie Forrest:
  Modeling Somatic Evolution in Tumorigenesis.
• 
  Almut Scherer, Marcel Salathé, Sebastian Bonhoeffer:
  High Epitope Expression Levels Increase Competition between T Cells.
• 
  Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson:
  Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
• 
  Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, Yixue Li:
  Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families.
• 
  Firas Swidan, Eduardo P. C. Rocha, Michael Shmoish, Ron Y. Pinter:
  An Integrative Method for Accurate Comparative Genome Mapping.
• 
  Chad Haynes, Christopher J. Oldfield, Fei Ji, Niels Klitgord, Michael E. Cusick, Predrag Radivojac, Vladimir N. Uversky, Marc Vidal, Lilia M. Iakoucheva:
  Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes.
• 
  Chunguang Li, Luonan Chen, Kazuyuki Aihara:
  Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples.

Correction

• 
  Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li:
  Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance.

Volume 2, Number 9, September 2006

Editorial

• 
  Philip E. Bourne, Alon Korngreen:
  Ten Simple Rules for Reviewers.

Perspective

• 
  Susan M. Baxter, Steven W. Day, Jacquelyn S. Fetrow, Stephanie J. Reisinger:
  Scientific Software Development Is Not an Oxymoron.

Research Articles

• 
  Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder:
  The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry.
• 
  Christian Mulder, Marja Wouterse, Markus Raubuch, Willem Roelofs, Michiel Rutgers:
  Can Transgenic Maize Affect Soil Microbial Communities?
• 
  Leo Goodstadt, Chris P. Ponting:
  Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human.
• 
  Xiaolin Cheng, Hai-Long Wang, Barry J. Grant, Steven M. Sine, James Andrew McCammon:
  Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors.
• 
  Feilim Mac Gabhann, James W. Ji, Aleksander S. Popel:
  Computational Model of Vascular Endothelial Growth Factor Spatial Distribution in Muscle and Pro-Angiogenic Cell Therapy.
• 
  Thomas Hamelryck, John T. Kent, Anders Krogh:
  Sampling Realistic Protein Conformations Using Local Structural Bias.
• 
  Daniel A. Beard:
  Modeling of Oxygen Transport and Cellular Energetics Explains Observations on In Vivo Cardiac Energy Metabolism.
• 
  Stefan Legewie, Nils Blüthgen, Hanspeter Herzel:
  Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability.
• 
  Peter Virnau, Leonid A. Mirny, Mehran Kardar:
  Intricate Knots in Proteins: Function and Evolution.
• 
  Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson:
  Transcriptional Dynamics of the Embryonic Stem Cell Switch.
• 
  Manuel Barrio, Kevin Burrage, André Leier, Tianhai Tian:
  Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation.
• 
  Raul Rodriguez-Esteban, Ivan Iossifov, Andrey Rzhetsky:
  Imitating Manual Curation of Text-Mined Facts in Biomedicine.
•