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ORCIDPLoS Computational Biology, Volume 6
Volume 6, Number 1, January 2010
- Kimmen Sjölander:
Getting Started in Structural Phylogenomics.
- Allyson L. Lister
, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider:
Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009.
- Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider:
Live Coverage of Scientific Conferences Using Web Technologies.
- Mark M. Schira, Christopher W. Tyler, Branka Spehar, Michael Breakspear:
Modeling Magnification and Anisotropy in the Primate Foveal Confluence. - Jaebum Kim, Ryan Cunningham, Brian James, Stefan Wyder, Joshua D. Gibson, Oliver Niehuis, Evgeny M. Zdobnov, Hugh M. Robertson, Gene E. Robinson, John H. Werren, Saurabh Sinha:
Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances. - Ingo Bojak, David T. J. Liley:
Axonal Velocity Distributions in Neural Field Equations. - Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam:
Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. - Dennis L. Chao, M. Elizabeth Halloran, Valerie J. Obenchain, Ira M. Longini Jr.:
FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model. - Lufang Zhou, Miguel Antonio Aon, Tabish Almas, Sonia Cortassa, Raimond L. Winslow, Brian O'Rourke:
A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network. - Pei-Chi Yang, Junko Kurokawa, Tetsushi Furukawa, Colleen E. Clancy:
Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study. - Stefan Pinkert, Jörg Schultz, Jörg Reichardt:
Protein Interaction Networks - More Than Mere Modules. - Richard A. Neher, Thomas Leitner:
Recombination Rate and Selection Strength in HIV Intra-patient Evolution. - Volker Egelhofer, Ida Schomburg, Dietmar Schomburg:
Automatic Assignment of EC Numbers. - Yossi Ben Zion, Gur Yaari, Nadav M. Shnerb:
Optimizing Metapopulation Sustainability through a Checkerboard Strategy. - Aroop Sircar, Jeffrey J. Gray:
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models. - Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith:
Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. - Ronald Van den Berg, Jos B. T. M. Roerdink, Frans W. Cornelissen:
A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding. - Sharat J. Vayttaden, Jacqueline Friedman, Tuan M. Tran, Thomas C. Rich, Carmen W. Dessauer, Richard B. Clark:
Quantitative Modeling of GRK-Mediated β2AR Regulation. - Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon:
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. - Wee Siong Goh, Yuriy L. Orlov, Jingmei Li, Neil D. Clarke:
Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local. - Nicolas Tabareau, Jean-Jacques E. Slotine, Quang-Cuong Pham:
How Synchronization Protects from Noise. - Anna Dvorkin, Henry Szechtman, Ilan Golani:
Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration. - Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance:
An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer. - Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan:
Associating Genes and Protein Complexes with Disease via Network Propagation. - Wei Zhang, Jun Zhu, Eric E. Schadt, Jun S. Liu:
A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules. - Daniel Seeliger, Bert L. de Groot:
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations. - Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan:
Network-Free Inference of Knockout Effects in Yeast. - Marc Röttig, Christian Rausch, Oliver Kohlbacher:
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families. - Christiaan Klijn, Jan Bot, David J. Adams, Marcel J. T. Reinders, Lodewyk F. A. Wessels, Jos Jonkers:
Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach. - Jason N. Bazil, Gregery T. Buzzard, Ann E. Rundell:
Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics. - Lukas Burger, Erik van Nimwegen:
Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments.
Volume 6, Number 2, February 2010
- Nelson N. Gichora, Segun A. Fatumo, Mtakai V. Ngara, Noura Chelbat, Kavisha Ramdayal, Kenneth B. Opap, Geoffrey H. Siwo, Marion O. Adebiyi, Amina El Gonnouni, Denis Zofou, Amal A. M. Maurady, Ezekiel F. Adebiyi, Etienne P. de Villiers, Daniel K. Masiga, Jeffrey W. Bizzaro, Prashanth Suravajhala, Sheila C. Ommeh, Winston Hide:
Ten Simple Rules for Organizing a Virtual Conference - Anywhere. - Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne:
A Review of 2009 for PLoS Computational Biology.
- Florian Markowetz:
How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens.
- Philip E. Bourne, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Roland L. Dunbrack Jr., Andreas Prlic, Greg B. Quinn, Peter W. Rose, Raship Shah, Wendy Tao, Brian D. Weitzner, Benjamin T. Yukich:
Will Widgets and Semantic Tagging Change Computational Biology?
- John C. Wooley, Adam Godzik, Iddo Friedberg:
A Primer on Metagenomics.
- Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin:
Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture. - Liqi Han, Jim Hanan, Peter M. Gresshoff:
Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation. - Antony B. Holmes, Sara Kalvala, David E. Whitworth:
Spatial Simulations of Myxobacterial Development. - Murat Cirit, Matej Krajcovic, Colin K. Choi, Erik S. Welf, Alan F. Horwitz, Jason M. Haugh:
Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells. - Neema L. Salimi, Bosco K. Ho, David A. Agard:
Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease. - Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin:
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. - Myungsook Kim, Ted Huang, Ted Abel, Kim T. Blackwell:
Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation. - Rahul C. Deo, Luke Hunter, Gregory D. Lewis, Guillaume Pare, Ramachandran S. Vasan, Daniel Chasman, Thomas J. Wang, Robert E. Gerszten, Frederick P. Roth:
Interpreting Metabolomic Profiles using Unbiased Pathway Models. - Sashi Marella, Bard Ermentrout:
Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks. - Kalpana Dokka, Robert V. Kenyon, Emily A. Keshner, Konrad P. Körding:
Self versus Environment Motion in Postural Control. - Jonathan Tang, C. Anthony Hunt:
Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion. - Florence Thuderoz, Maria-Ana Simonet, Olivier Hansen, Nicolas Pasqual, Aurélie Dariz, Thierry-Pascal Baum, Vivien Hierle, Jacques Demongeot, Patrice-Noël Marche, Evelyne Jouvin-Marche:
Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus. - Patrick G. T. Walker, Simon Cauchemez, Raphaëlle Métras, Do Huu Dung, Dirk Pfeiffer, Azra C. Ghani:
A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam. - Takashi Nakano, Tomokazu Doi, Junichiro Yoshimoto, Kenji Doya:
A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity. - Jun Zhu, Yanqing Chen, Amy S. Leonardson, Kai Wang, John R. Lamb, Valur Emilsson, Eric E. Schadt:
Characterizing Dynamic Changes in the Human Blood Transcriptional Network. - Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka:
Conditions for the Evolution of Gene Clusters in Bacterial Genomes. - Ester Vilaprinyó, Rui Alves, Albert Sorribas:
Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes. - Shirley Pepke, Tamara Kinzer-Ursem, Stefan Mihalas, Mary B. Kennedy:
A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II. - J. Christian J. Ray, Oleg A. Igoshin:
Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems. - Patrick Garrigan, Charles P. Ratliff, Jennifer M. Klein, Peter Sterling, David H. Brainard, Vijay Balasubramanian:
Design of a Trichromatic Cone Array. - Ivan Junier, Olivier C. Martin, François Képès:
Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization. - Silpa Suthram, Joel Dudley, Annie P. Chiang, Rong Chen, Trevor Hastie, Atul J. Butte:
Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. - Jinghui Luo, Jean-Didier Maréchal, Sebastian Wärmländer, Astrid Gräslund, Alex Perálvarez-Marín:
In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network. - Wanjun Gu, Tong Zhou, Claus O. Wilke:
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes. - Sohyoung Kim, Mirit I. Aladjem, Geoffrey B. McFadden, Kurt W. Kohn:
Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage. - Vitaly V. Ganusov, José A. M. Borghans, Rob J. De Boer:
Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations. - Fred P. Davis, Andrej Sali:
The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures. - Tong Yang, Zheng Wang, Fang Wu, Jingwei Tan, Yijun Shen, Erguang Li, Jingzhi Dai, Ronghai Shen, Gang Li, Jinsong Wu, Luochun Wang, Haibo Wang, Yanjun Liu:
A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis.
Volume 6, Number 3, March 2010
- Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein:
Getting Started in Gene Orthology and Functional Analysis.
- Bernie J. Daigle Jr., Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald Reaven, Philip S. Tsao, Russ B. Altman:
Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance. - Carlos Espinosa-Soto, Andreas Wagner:
Specialization Can Drive the Evolution of Modularity. - Max von Kleist, Stephan Menz, Wilhelm Huisinga:
Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. - Thomas A. House, Matt J. Keeling:
The Impact of Contact Tracing in Clustered Populations. - James O. Wrabl, Vincent J. Hilser:
Investigating Homology between Proteins using Energetic Profiles. - Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov:
Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. - Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu, Liping Wei:
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions. - Samuel Bernard, Branka Cajavec Bernard, Francis Lévi, Hanspeter Herzel:
Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules. - Carsten Magnus, Roland R. Regoes:
Estimating the Stoichiometry of HIV Neutralization. - Timothy Nugent, David T. Jones:
Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. - Tjibbe Donker, Jacco Wallinga, Hajo Grundmann:
Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks. - Carey D. Nadell, Kevin R. Foster, João B. Xavier:
Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation. - Nikita Vladimirov, Dirk Lebiedz, Victor Sourjik:
Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria. - Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt:
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function. - Sergi Bermúdez i Badia, Ulysses Bernardet, Paul F. M. J. Verschure:
Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector. - Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro:
Effects of Transcriptional Pausing on Gene Expression Dynamics. - Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin:
Detailed Simulations of Cell Biology with Smoldyn 2.1. - Christina Vasalou, Michael A. Henson:
A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus. - Jun Cai, Dan Xie, Zhewen Fan, Hiram Chipperfield, John Marden, Wing H. Wong, Sheng Zhong:
Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells. - Michael Sherback, Francisco J. Valero Cuevas, Raffaello D'Andrea:
Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly. - Will D. Penny, Klaas E. Stephan, Jean Daunizeau, Maria J. Rosa, Karl J. Friston, Thomas M. Schofield, Alexander P. Leff:
Comparing Families of Dynamic Causal Models. - Muyoung Heo, Eugene I. Shakhnovich:
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response. - Julian M. L. Budd, Krisztina Kovács, Alex S. Ferecskó, Péter Buzás, Ulf T. Eysel, Zoltán F. Kisvárday:
Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation. - Chun Wu, Michael T. Bowers, Joan-Emma Shea:
Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils. - Sean R. McGuffee, Adrian H. Elcock:
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm. - Christelle Reynès, Hélène Host, Anne-Claude Camproux, Guillaume Laconde, Florence Leroux, Anne Mazars, Benoit Deprez, Robin Fahraeus, Bruno O. Villoutreix, Olivier Sperandio:
Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods. - Gabriele Lillacci, Mustafa Khammash:
Parameter Estimation and Model Selection in Computational Biology. - Peter W. Battaglia, Massimiliano Di Luca, Marc O. Ernst, Paul R. Schrater, Tonja Machulla, Daniel J. Kersten:
Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception. - Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya:
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species. - Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins:
Estimating the Stochastic Bifurcation Structure of Cellular Networks. - Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev:
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.
Volume 6, Number 4, April 2010
- Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne:
PLoS Computational Biology Conference Postcards from PSB 2010.
- Dirk Helbing, Attila Szolnoki, Matjaz Perc, György Szabó:
Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions. - Erika Cerasti, Alessandro Treves:
How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus? - Akihiko Nakajima, Takako Isshiki, Kunihiko Kaneko, Shuji Ishihara:
Robustness under Functional Constraint: The Genetic Network for Temporal Expression in Drosophila Neurogenesis. - Xuejing Li, Casandra Panea, Chris H. Wiggins, Valerie Reinke, Christina S. Leslie:
Learning "graph-mer" Motifs that Predict Gene Expression Trajectories in Development. - Jussi Aittoniemi, Heidi de Wet, Frances M. Ashcroft, Mark S. P. Sansom:
Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study. - Daniel Ting, Guoli Wang, Maxim V. Shapovalov, Rajib Mitra, Michael I. Jordan, Roland L. Dunbrack Jr.:
Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model. - Liming Wang, Jack Xin, Qing Nie:
A Critical Quantity for Noise Attenuation in Feedback Systems. - Ariel Zylberberg, Diego Fernández Slezak, Pieter R. Roelfsema, Stanislas Dehaene, Mariano Sigman:
The Brain's Router: A Cortical Network Model of Serial Processing in the Primate Brain. - Timothy E. Schlub, Redmond P. Smyth, Andrew J. Grimm, Johnson Mak, Miles P. Davenport:
Accurately Measuring Recombination between Closely Related HIV-1 Genomes. - Elena Phoka, Hermann Cuntz, Arnd Roth, Michael Häusser:
A New Approach for Determining Phase Response Curves Reveals that Purkinje Cells Can Act as Perfect Integrators. - Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan:
Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences. - Kenzie D. MacIsaac, Kinyui A. Lo, William Gordon, Shmulik Motola, Tali Mazor, Ernest Fraenkel:
A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression. - Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck:
Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex.