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PLoS 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.