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ORCIDPLoS Computational Biology, Volume 9
Volume 9, Number 1, January 2013
- Jeroen de Ridder
, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg:
Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator.
- Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize Shirdel, Igor Jurisica:
Visual Data Mining of Biological Networks: One Size Does Not Fit All.
- Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz:
Approximate Bayesian Computation.
- Luca Ciandrini, Ian Stansfield, M. Carmen Romano:
Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation. - Gkikas Magiorkinis, Vana Sypsa, Emmanouil Magiorkinis, Dimitrios Paraskevis, Antigoni Katsoulidou, Robert Belshaw, Christophe Fraser, Oliver George Pybus, Angelos Hatzakis:
Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics. - Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf:
Maximizing the Information Content of Experiments in Systems Biology. - Fabian H. Sinz, Matthias Bethge:
Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images. - Hang Yu, Klaus Schulten:
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations. - Ming Hu, Ke Deng, Zhaohui S. Qin, Jesse R. Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu:
Bayesian Inference of Spatial Organizations of Chromosomes. - George Forrest Young, Luca Scardovi, Andrea Cavagna, Irene Giardina, Naomi Ehrich Leonard:
Starling Flock Networks Manage Uncertainty in Consensus at Low Cost. - Mathieu d'Acremont, Eleonora Fornari, Peter Bossaerts:
Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task. - Linan Xu, Naushaba Hasin, Manli Shen, Jianwei He, Youlin Xue, Xiaohong Zhou, Sarah Perrett, Youtao Song, Gary W. Jones:
Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation. - Vladislav Volman, Maxim Bazhenov, Terrence J. Sejnowski:
Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma. - Michael A. Buice, Carson C. Chow:
Dynamic Finite Size Effects in Spiking Neural Networks. - Holly E. Gerhard, Felix A. Wichmann, Matthias Bethge:
How Sensitive Is the Human Visual System to the Local Statistics of Natural Images? - Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains:
Significance Analysis of Prognostic Signatures. - Thomas Lemmin, Cinque S. Soto, Graham Clinthorne, William F. DeGrado, Matteo Dal Peraro:
Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations. - Stefan Wuchty, Dolores Arjona, Peter O. Bauer:
Important miRs of Pathways in Different Tumor Types. - Yohan Kim, Jonathan W. Yewdell, Alessandro Sette, Björn Peters:
Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation. - Karen E. Joyce, Satoru Hayasaka, Paul J. Laurienti:
The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack. - Corentin M. Barbu, Andrew Hong, Jennifer M. Manne, Dylan S. Small, Javier E. Quintanilla Calderón, Karthik Sethuraman, Víctor Quispe-Machaca, Jenny Ancca-Juárez, Juan G. Cornejo del Carpio, Fernando S. Málaga Chavez, César Náquira, Michael Z. Levy:
The Effects of City Streets on an Urban Disease Vector. - Yann Le Cunff, Annette Baudisch, Khashayar Pakdaman:
How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns. - Sebastian Funk, Hiroshi Nishiura, Hans Heesterbeek, W. John Edmunds, Francesco Checchi:
Identifying Transmission Cycles at the Human-Animal Interface: The Role of Animal Reservoirs in Maintaining Gambiense Human African Trypanosomiasis. - A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu:
ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information. - Cédric Debès, Minglei Wang, Gustavo Caetano-Anollés, Frauke Gräter:
Evolutionary Optimization of Protein Folding. - Giovanni Settanni, David Serquera, Piotr E. Marszalek, Emanuele Paci, Laura S. Itzhaki:
Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin. - Jeromos Vukov, Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco:
Reward from Punishment Does Not Emerge at All Costs. - Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xiaohan Dai, Jianfeng Wang, Hongen Li, Xin Wang, Wei Tan, Mingjing Luo, Xiaodi Niu, Xuming Deng:
Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore. - Giovanni Lo Iacono, Frank van den Bosch, Chris A. Gilligan:
Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty. - Niklas Wilming, Simon Harst, Nico M. Schmidt, Peter König:
Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy. - Ruian Ke, Piers J. Ingram, Ken Haynes:
An Integrative Model of Ion Regulation in Yeast. - Wyming Lee Pang, Amardeep Kaur, Alexander V. Ratushny, Aleksandar Cvetkovic, Sunil Kumar, Min Pan, Adam P. Arkin, John D. Aitchison, Michael W. W. Adams, Nitin S. Baliga:
Metallochaperones Regulate Intracellular Copper Levels. - Kristy Nowak-Lovato, Ludmil B. Alexandrov, Afsheen Banisadr, Amy L. Bauer, Alan R. Bishop, Anny Usheva, Fangping Mu, Elizabeth Hong-Geller, Kim Ø. Rasmussen, William S. Hlavacek, Boian S. Alexandrov:
Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. - Graham Rockwell, Nicholas J. Guido, George M. Church:
Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective. - Sandra V. Bennun, Kevin J. Yarema, Michael J. Betenbaugh, Frederick J. Krambeck:
Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures. - Cibele Vieira Falkenberg, Leslie M. Loew:
Computational Analysis of Rho GTPase Cycling. - Stefka Tyanova, Jürgen Cox, Jesper V. Olsen, Matthias Mann, Dmitrij Frishman:
Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins. - Nol Chindapol, Jaap A. Kaandorp, Carolina Cronemberger, Tali Mass, Amatzia Genin:
Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics. - Anatoly Rinberg, Adam L. Taylor, Eve Marder:
The Effects of Temperature on the Stability of a Neuronal Oscillator. - Satomi Matsuoka, Tatsuo Shibata, Masahiro Ueda:
Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions. - Omry Koren, Dan Knight, Antonio González, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley:
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. - Cornelis van de Kamp, Peter J. Gawthrop, Henrik Gollee, Ian D. Loram:
Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties? - Pengsheng Zheng, Christos Dimitrakakis, Jochen Triesch:
Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex. - Nives Skunca, Matko Bosnjak, Anita Krisko, Pance Panov, Saso Dzeroski, Tomislav Smuc, Fran Supek:
Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships. - Anne L. Wheeler, Cátia M. Teixeira, Afra H. Wang, Xuejian Xiong, Natasa Kovacevic, Jason P. Lerch, Anthony Randal McIntosh, John Parkinson, Paul W. Frankland:
Identification of a Functional Connectome for Long-Term Fear Memory in Mice. - Martin H. Schaefer, Tiago J. S. Lopes, Nancy Mah, Jason E. Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Caroline Louis-Jeune, Amie J. Eisfeld, Gabriele Neumann, Carol Perez-Iratxeta, Yoshihiro Kawaoka, Hiroaki Kitano, Miguel A. Andrade-Navarro:
Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. - Mario Pujato, Thomas MacCarthy, András Fiser, Aviv Bergman:
The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks.
Volume 9, Number 2, February 2013
- Philip E. Bourne:
Let's Make Those Book Chapters Open Too!
- Romain Daniel Cazé, Mark D. Humphries, Boris S. Gutkin:
Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions. - Andrea Censi, Andrew D. Straw, Rosalyn W. Sayaman, Richard M. Murray, Michael H. Dickinson:
Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila. - Carsten Magnus:
Virus Neutralisation: New Insights from Kinetic Neutralisation Curves. - Paul Michael Loriaux, Glenn Tesler, Alexander Hoffmann:
Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models. - Lizhe Zhu, Peter G. Bolhuis, Jocelyne Vreede:
The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions. - Michael Thomas, Dylan Jayatilaka, Ben Corry:
An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules. - Kolbjørn Tunstrøm, Yael Katz, Christos C. Ioannou, Cristián Huepe, Matthew J. Lutz, Iain D. Couzin:
Collective States, Multistability and Transitional Behavior in Schooling Fish. - Kieran Alden, Mark Read, Jonathan Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark C. Coles:
Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems. - David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin:
The Vast, Conserved Mammalian lincRNome. - David C. Sterratt, Daniel Lyngholm, David J. Willshaw, Ian D. Thompson:
Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package. - Andraz Stozer, Marko Gosak, Jurij Dolensek, Matjaz Perc, Marko Marhl, Marjan Slak Rupnik, Dean Korosak:
Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices. - Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov:
Enhancing Human Spermine Synthase Activity by Engineered Mutations. - Min-Cheol Kim, Devin M. Neal, Roger D. Kamm, H. Harry Asada:
Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries. - Shaiyan Keshvari, Ronald Van den Berg, Wei Ji Ma:
No Evidence for an Item Limit in Change Detection. - Cherrie H. T. Kong, Derek R. Laver, Mark B. Cannell:
Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach. - Paul Michael Loriaux, Alexander Hoffmann:
A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways. - Ying Li, Guang Li, Haifang Wang, Jiulin Du, Jun Yan:
Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish. - Tanya Gurieva, Martin C. J. Bootsma, Marc J. M. Bonten:
Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus. - Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. - Baktash Babadi, L. F. Abbott:
Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity. - Thomas Stockner, Therese R. Montgomery, Oliver Kudlacek, Rene Weissensteiner, Gerhard F. Ecker, Michael Freissmuth, Harald H. Sitte:
Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model. - Jimin Song, Mona Singh:
From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization. - Falk Lieder, Jean Daunizeau, Marta I. Garrido, Karl J. Friston, Klaas E. Stephan:
Modelling Trial-by-Trial Changes in the Mismatch Negativity. - Charlotte Prévost, Daniel C. McNamee, Ryan K. Jessup, Peter Bossaerts, John P. O'Doherty:
Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning. - Claudia Clopath, Nicolas Brunel:
Optimal Properties of Analog Perceptrons with Excitatory Weights. - Wei-Yi Cheng, Tai-Hsien Ou Yang, Dimitris Anastassiou:
Biomolecular Events in Cancer Revealed by Attractor Metagenes. - Alexander T. Dilthey, Stephen Leslie, Loukas Moutsianas, Judong Shen, Charles Cox, Matthew R. Nelson, Gil McVean:
Multi-Population Classical HLA Type Imputation. - Davide Reato, Fernando Gasca, Abhishek Datta, Marom Bikson, Lisa Marshall, Lucas C. Parra:
Transcranial Electrical Stimulation Accelerates Human Sleep Homeostasis. - Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada:
Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin. - Roberto Latorre, Rafael Levi, Pablo Varona:
Transformation of Context-dependent Sensory Dynamics into Motor Behavior. - Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva:
Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics. - Shao-Shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel:
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling. - Eduardo J. Izquierdo, Randall D. Beer:
Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis. - Robert R. Kerr, Anthony N. Burkitt, Doreen A. Thomas, Matthieu Gilson, David B. Grayden:
Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs. - Shanshan Cheng, Charles L. Brooks III:
Viral Capsid Proteins Are Segregated in Structural Fold Space. - Benjamin M. Althouse, Oscar Patterson-Lomba, Georg M. Goerg, Laurent Hébert-Dufresne:
The Timing and Targeting of Treatment in Influenza Pandemics Influences the Emergence of Resistance in Structured Populations.
Volume 9, Number 3, March 2013
- Thomas Lengauer, Ruth Nussinov:
New Methods Section in PLOS Computational Biology.
- Erik M. Volz, Katia Koelle, Trevor Bedford:
Viral Phylodynamics. - Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria:
Evolving Digital Ecological Networks.
- Simon Garnier, Maud Combe, Christian Jost, Guy Theraulaz:
Do Ants Need to Estimate the Geometrical Properties of Trail Bifurcations to Find an Efficient Route? A Swarm Robotics Test Bed. - Tina Toni, Bruce Tidor:
Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology. - Clive G. Bowsher, Margaritis Voliotis, Peter S. Swain:
The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks. - James B. Gilmore, Anthony D. Kelleher, David A. Cooper, John M. Murray:
Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action. - Brad Busse, Stephen J. Smith:
Automated Analysis of a Diverse Synapse Population. - Michael A. Carlin, Mounya Elhilali:
Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds. - Simon Garnier, Tucker Murphy, Matthew J. Lutz, Edward Hurme, Simon Leblanc, Iain D. Couzin:
Stability and Responsiveness in a Self-Organized Living Architecture. - Christoph Schmal, Peter Reimann, Dorothee Staiger:
A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana. - Christopher P. Said, David J. Heeger:
A Model of Binocular Rivalry and Cross-orientation Suppression. - Kirill S. Korolev:
The Fate of Cooperation during Range Expansions. - Marta I. Garrido, Maneesh Sahani, Raymond J. Dolan:
Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain. - Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd:
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq. - Himadri Mukhopadhyay, Shaun-Paul Cordoba, Philip K. Maini, P. Anton van der Merwe, Omer Dushek:
Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity. - Hermann B. Frieboes, Bryan R. Smith, Yao-Li Chuang, Ken Ito, Allison M. Roettgers, Sanjiv Sam Gambhir, Vittorio Cristini:
An Integrated Computational/Experimental Model of Lymphoma Growth. - Syed Abbas Bukhari, Gustavo Caetano-Anollés:
Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes. - Yuguo Yu, Thomas S. McTavish, Michael L. Hines, Gordon M. Shepherd, Cesare Valenti, Michele Migliore:
Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit. - Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti:
Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19. - Philip Stegmaier, Alexander E. Kel, Edgar Wingender, Jürgen Borlak:
A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs. - Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward:
Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection. - Laura Matrajt, M. Elizabeth Halloran, Ira M. Longini Jr.:
Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza. - Alane Izu, Ted Cohen, Victor DeGruttola:
Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases. - Luis E. C. Rocha, Vincent D. Blondel:
Bursts of Vertex Activation and Epidemics in Evolving Networks. - Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, Rui Kuang:
Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment. - Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser, Francisco S. Domingues:
Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage. - Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen:
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum.