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ORCIDPLoS Computational Biology, Volume 4
Volume 4, Number 1, January 2008
- K. Bretonnel Cohen, Lawrence Hunter
:
Getting Started in Text Mining.
- Dirk Holste, Uwe Ohler:
Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events.
- Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson:
A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells. - Guo-Cheng Yuan, Jun S. Liu:
Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion. - Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang, Francisco J. Barrantes:
Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor. - Richard A. Notebaart, Bas Teusink, Roland J. Siezen, Balázs Papp:
Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance. - Nicolas Pinto, David D. Cox, James J. DiCarlo:
Why is Real-World Visual Object Recognition Hard? - Malin C. Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg:
In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. - Christina M. Weaver, Susan L. Wearne:
Neuronal Firing Sensitivity to Morphologic and Active Membrane Parameters. - Huiquan Wang, Craig J. Benham:
Superhelical Destabilization in Regulatory Regions of Stress Response Genes. - Chikara Furusawa, Kunihiko Kaneko:
A Generic Mechanism for Adaptive Growth Rate Regulation. - Daniela Raijman, Ron Shamir, Amos Tanay:
Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites. - Matthew Menke, Bonnie Berger, Lenore Cowen:
Matt: Local Flexibility Aids Protein Multiple Structure Alignment. - Clinton H. Hansen, Robert G. Endres, Ned S. Wingreen:
Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation. - Chuan-Yun Li, Xizeng Mao, Liping Wei:
Genes and (Common) Pathways Underlying Drug Addiction. - Gil Hornung, Naama Barkai:
Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback.
- Will Fischer, H. X. Liao, Barton F. Haynes, Norman L. Letvin, Bette T. Korber:
Coping with Viral Diversity in HIV Vaccine Design: A Response to Nickle et al. - David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins:
Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.
Volume 4, Number 2, February 2008
- Ganesh A. Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C. Sealfon:
Getting Started in Biological Pathway Construction and Analysis.
- Michal J. Okoniewski, Crispin J. Miller:
Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor.
- Leo C. McHugh, Jonathan W. Arthur:
Computational Methods for Protein Identification from Mass Spectrometry Data.
- Julius B. Lucks, David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin:
Genome Landscapes and Bacteriophage Codon Usage. - Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik:
How Protein Stability and New Functions Trade Off. - Lihua Zou, Sira Sriswasdi, Brian C. Ross, Patrycja Vasilyev Missiuro, Jun S. Liu, Hui Ge:
Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis. - Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja:
Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability. - Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram:
The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks. - Ivan Coluzza, Alfonso De Simone, Franca Fraternali, Daan Frenkel:
Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes. - Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan:
Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding. - Héctor Marlosti Montiel Molina, César Millán-Pacheco, Nina Pastor, Gabriel del Rio:
Computer-Based Screening of Functional Conformers of Proteins. - Naomi Habib, Tommy Kaplan, Hanah Margalit, Nir Friedman:
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval. - Tae J. Lee, Guang Yao, Joseph Nevins, Lingchong You:
Sensing and Integration of Erk and PI3K Signals by Myc. - Navin Elango, Seong-Ho Kim, Eric Vigoda, Soojin V. Yi:
Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation. - Jennifer Listgarten, Zabrina L. Brumme, Carl Myers Kadie, Gao Xiaojiang, Bruce D. Walker, Mary Carrington, Philip J. R. Goulder, David Heckerman:
Statistical Resolution of Ambiguous HLA Typing Data. - Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau:
Identification of Synaptic Targets of Drosophila Pumilio. - Anna Dvorkin, Yoav Benjamini, Ilan Golani:
Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction. - Zhaoping Li, Jingling Li:
Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences. - Dennis Kostka, Rainer Spang:
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures. - Vesa P. Hytönen, Viola Vogel:
How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism. - Elena J. Edelman, Justin Guinney, Jen-Tsan A. Chi, Phillip G. Febbo, Sayan Mukherjee:
Modeling Cancer Progression via Pathway Dependencies. - Avner Wallach, Danny Eytan, Shimon Marom, Ron Meir:
Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment. - Joshua F. Apgar, Jared E. Toettcher, Drew Endy, Forest M. White, Bruce Tidor:
Stimulus Design for Model Selection and Validation in Cell Signaling. - Fred H. Hamker, Marc Zirnsak, Dirk Calow, Markus Lappe:
The Peri-Saccadic Perception of Objects and Space. - Sean Carver, Eatai Roth, Noah J. Cowan, Eric S. Fortune:
Synaptic Plasticity Can Produce and Enhance Direction Selectivity. - Eric R. Paquet, Guillaume Rey, Felix Naef:
Modeling an Evolutionary Conserved Circadian Cis-Element. - Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine:
Control of Cation Permeation through the Nicotinic Receptor Channel. - Douglas L. Theobald, Deborah S. Wuttke:
Accurate Structural Correlations from Maximum Likelihood Superpositions. - Arend Hintze, Christoph Adami:
Evolution of Complex Modular Biological Networks. - Daniel Segura, Radhakrishnan Mahadevan, Katy Juarez, Derek R. Lovley:
Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens. - Peter Dayan, Quentin J. M. Huys:
Serotonin, Inhibition, and Negative Mood. - Rafi Haddad, Liran Carmel, Noam Sobel, David Harel:
Predicting the Receptive Range of Olfactory Receptors.
- Morgan C. Giddings:
On the Process of Becoming a Great Scientist.
Volume 4, Number 3, March 2008
- Philip E. Bourne, J. Lynn Fink, Mark Gerstein:
Open Access: Taking Full Advantage of the Content.
- Edgardo Moreno, Bruno Lomonte, José María Gutiérrez:
Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics.
- Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li:
Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation. - David Basanta, Mark A. Miodownik, Buzz Baum:
The Evolution of Robust Development and Homeostasis in Artificial Organisms. - Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, Helmut Grubmüller:
Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. - Isaac Shemer, Björn Brinne, Jesper Tegnér, Sten Grillner:
Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus. - Zenas C. Chao, Douglas J. Bakkum, Steve M. Potter:
Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior. - Ugo Ala, Rosario Michael Piro, Elena Grassi, Christian Damasco, Lorenzo Silengo, Martin Oti, Paolo Provero, Ferdinando Di Cunto:
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis. - Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph:
A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. - Carson C. Chow, Kevin D. Hall:
The Dynamics of Human Body Weight Change. - Alex Roxin, Anders Ledberg:
Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation. - Sichun Yang, Benoît Roux:
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms. - Yasser Roudi, Alessandro Treves:
Representing Where along with What Information in a Model of a Cortical Patch. - Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich:
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. - Yossi Yovel, Matthias O. Franz, Peter Stilz, Hans-Ulrich Schnitzler:
Plant Classification from Bat-Like Echolocation Signals. - Thomas Manke, Helge G. Roider, Martin Vingron:
Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions. - Alejandra C. Ventura, Jacques-A. Sepulchre, Sofía D. Merajver:
A Hidden Feedback in Signaling Cascades Is Revealed. - William Ritchie, Samuel Granjeaud, Denis Puthier, Daniel Gautheret:
Entropy Measures Quantify Global Splicing Disorders in Cancer. - Yonatan Loewenstein:
Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity. - Hédi Hegyi, Peter Tompa:
Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo. - Feng-Jie Sun, Gustavo Caetano-Anollés:
Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses. - Siu Kang, Katsunori Kitano, Tomoki Fukai:
Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model. - Q. Tri Ho, Pieter Verboven, Bert E. Verlinden, Jeroen Lammertyn, Stefan Vandewalle, Bart M. Nicolaï:
A Continuum Model for Metabolic Gas Exchange in Pear Fruit. - Ilya Nemenman, Geoffrey D. Lewen, William Bialek, Robert R. de Ruyter van Steveninck:
Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution.
Volume 4, Number 4, April 2008
- Manuel João Costa, Eduardo Galembeck, Guilherme A. Marson, Bayardo B. Torres:
A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics.
- Liping Wei, Jun Yu:
Bioinformatics in China: A Personal Perspective.
- Yoram Vodovotz, Márie Csete, John Bartels, Steven Chang, Gary An:
Translational Systems Biology of Inflammation.
- Greg J. Stephens, Bethany Johnson-Kerner, William Bialek, William S. Ryu:
Dimensionality and Dynamics in the Behavior of C. elegans. - Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael:
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. - Lubomir Kostal, Petr Lánský, Jean-Pierre Rospars:
Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth. - Raoul Huys, Breanna E. Studenka, Nicole L. Rheaume, Howard N. Zelaznik, Viktor K. Jirsa:
Distinct Timing Mechanisms Produce Discrete and Continuous Movements. - Alexej Abyzov, Alper Uzun, Phyllis R. Strauss, Valentin A. Ilyin:
An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. - Jian Qiu, William Stafford Noble:
Predicting Co-Complexed Protein Pairs from Heterogeneous Data. - Jon Bohlin, Eystein Skjerve, David Ussery:
Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes. - Luca A. Finelli, Seth Haney, Maxim Bazhenov, Mark Stopfer, Terrence J. Sejnowski:
Synaptic Learning Rules and Sparse Coding in a Model Sensory System. - Sourav Bandyopadhyay, Ryan M. Kelley, Nevan J. Krogan, Trey Ideker:
Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. - Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis:
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes. - María Fabiana Laguna, Steffen Bohn, Eduardo A. Jagla:
The Role of Elastic Stresses on Leaf Venation Morphogenesis. - Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck:
A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains. - Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman:
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli. - Adrian Gustavo Turjanski, J. Silvio Gutkind, Robert B. Best, Gerhard Hummer:
Binding-Induced Folding of a Natively Unstructured Transcription Factor. - Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Björn Peters:
A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach. - Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh:
Biosynthetic Potentials of Metabolites and Their Hierarchical Organization. - Bruno B. Averbeck, Moonsang Seo:
The Statistical Neuroanatomy of Frontal Networks in the Macaque. - Ignacio E. Sánchez, Pedro Beltrão, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano:
Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm.
Volume 4, Number 5, May 2008
- Edgardo Moreno, José María Gutiérrez:
Ten Simple Rules for Aspiring Scientists in a Low-Income Country.
- Kiyoko F. Aoki-Kinoshita:
An Introduction to Bioinformatics for Glycomics Research.
- Erik De Schutter:
Why Are Computational Neuroscience and Systems Biology So Separate?
- Sean R. Eddy:
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation. - Shuixia Guo, Jianhua Wu, Mingzhou Ding, Jianfeng Feng:
Uncovering Interactions in the Frequency Domain. - Suhita Nadkarni, Peter Jung, Herbert Levine:
Astrocytes Optimize the Synaptic Transmission of Information. - Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter:
Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma. - Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luis Serrano, Frederic Rousseau, Joost Schymkowitz:
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments. - Richard A. Goldstein, Orkun S. Soyer:
Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics. - John Porrill, Paul Dean:
Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing. - Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin:
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks. - Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand:
Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins. - Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A. Komives, Peter G. Wolynes:
The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures. - Yasuko Sugase-Miyamoto, Zheng Liu, Matthew C. Wiener, Lance M. Optican, Barry J. Richmond:
Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex. - Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, Charles E. Lawrence:
Measuring Global Credibility with Application to Local Sequence Alignment. - Scott A. Becker, Bernhard O. Palsson:
Context-Specific Metabolic Networks Are Consistent with Experiments. - Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro:
Estimating Cell Depth from Somatic Mutations. - Sean M. Cory, Theodore J. Perkins:
Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation. - Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey:
Discovering Sequence Motifs with Arbitrary Insertions and Deletions. - Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel:
Viral Population Estimation Using Pyrosequencing. - Arbel D. Tadmor, Tsvi Tlusty:
A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number.