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ORCIDPLoS Computational Biology, Volume 3
Volume 3, Number 1, January 2007
- Fran Lewitter:
Moving Education Forward.
- Peter Schattner:
Automated Querying of Genome Databases.
- Thomas Höfer
:
In Remembrance: Reinhart Heinrich 1946-2006.
- 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
- 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.
- 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.
- 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
- Quentin Vicens, Philip E. Bourne:
Ten Simple Rules for a Successful Collaboration.
- Benjamin A. Shoemaker, Anna R. Panchenko:
Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases.
- 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. - Barry G. Hall, Stephen J. Salipante:
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.
- Pedro Beltrão, Luis Serrano:
Correction: Specificity and Evolvability in Eukaryotic Protein Interaction Networks.
Volume 3, Number 4, April 2007
- Philip E. Bourne:
Ten Simple Rules for Making Good Oral Presentations.
- Benjamin A. Shoemaker, Anna R. Panchenko:
Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners.
- 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.
- Gerton Lunter:
Dog as an Outgroup to Human and Mouse. - Mark Gerstein, Shawn M. Douglas:
RNAi Development.
- David Dingli, Arne Traulsen, Franziska Michor:
Correction: (A)Symmetric Stem Cell Replication and Cancer.
Volume 3, Number 5, May 2007
- Thomas C. Erren, Philip E. Bourne:
Ten Simple Rules for a Good Poster Presentation.
- Thomas Lengauer, B. J. Morrison McKay, Burkhard Rost:
ISMB/ECCB 2007: The Premier Conference on Computational Biology.
- 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?
- 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.
- Omri Barak, Misha Tsodyks:
Correction: Persistent Activity in Neural Networks with Dynamic Synapses.
Volume 3, Number 6, June 2007
- 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.
- Adi L. Tarca, Vincent J. Carey, Xue-wen Chen, Roberto Romero, Sorin Draghici:
Machine Learning and Its Applications to Biology.
- David B. Searls:
A View from the Dark Side.
- 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.
- 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
- Jacques Colinge, Keiryn L. Bennett:
Introduction to Computational Proteomics.
- Carol Shiels, Niall M. Adams, Suhail A. Islam, David A. Stephens, Paul S. Freemont:
Quantitative Analysis of Cell Nucleus Organisation.
- 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.