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PLoS 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.