All Papers in PLOS Computational Biology, April 2015

58 papers found.

• Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
  Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
  Topics: optimisation (31) hydrogen bond (12) active site (7) free energy (5) water molecules (5)
• A Bayesian Model of Category-Specific Emotional Brain Responses
  Tor D. Wager, Jian Kang, Timothy D. Johnson, Thomas E. Nichols, Ajay B. Satpute, Lisa Feldman Barrett
  Topics: basal ganglia (17) Bayesian model (8) posterior distribution (7) brain regions (6) generative models (6)
• Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery
  Sébastien Giguère, François Laviolette, Mario Marchand, Denise Tremblay, Sylvain Moineau, Xinxia Liang, Éric Biron, Jacques Corbeil
  Topics: peptides (110) amino acids (28) machine learning (17) training set (9) correlation coefficient (7)
• NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
  Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel
  Topics: KEGG (15) signaling pathway (10) single cell (10) cell population (8) simulation study (7)
• Embodied Choice: How Action Influences Perceptual Decision Making
  Nathan F. Lepora, Giovanni Pezzulo
  Topics: decision making (40) Experimental Data (8) decision-making (6) feedback loop (5) choice task (3)
• Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies
  Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields
  Topics: regression model (6) Wilcoxon (6) synergistic effects (4) experimental conditions (3) kinase (3)
• A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
  Susan Dina Ghiassian, Jörg Menche, Albert-László Barabási
  Topics: p-value (10) true positives (9) connected component (4) Fisher’s exact (3) Fisher’s exact test (3)
• Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis
  Rodrigo Cilla, Vinodh Mechery, Beatriz Hernandez de Madrid, Steven Del Signore, Ivan Dotu, Victor Hatini
  Topics: Differential Equation (4) molecular dynamics (3)
• Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data
  Peter Klimek, Alexandra Kautzky-Willer, Anna Chmiel, Irmgard Schiller-Frühwirth, Stefan Thurner
  Topics: age group (10) p-value (7) discovery rate (5) false discovery rate (5) confidence intervals (3)
• Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills
  Kai Olav Ellefsen, Jean-Baptiste Mouret, Jeff Clune
  Topics: neural networks (38) Hebbian (8) learning algorithms (8) “null model” (7) reinforcement learning (7)
• Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
  Juan Palacios-Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael Comb, Mark L. Grimes
  Topics: phosphorylation (104) kinase (44) cell lines (39) signaling pathways (28) peptides (11)
• Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
  Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel Rozowsky, William Meyerson, Mark B. Gerstein
  Topics: gene expression (39) regulatory network (17) expression data (12) genome-wide (11) protein-protein interactions (8)
• Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
  Fabio Pardi, Celine Scornavacca
  Topics: phylogenetic (36) maximum likelihood (4)
• Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae
  Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana
  Topics: mRNA (16) gene expression (9) transcriptional (8) cell cycle (6) statistical significance (6)
• A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States
  Manoj Gambhir, Thomas A. Clark, Simon Cauchemez, Sara Y. Tartof, David L. Swerdlow, Neil M. Ferguson
  Topics: age group (5) epidemiological models (5) mathematical model (5) model parameter (5) Parameter estimates (3)
• The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
  Ross S. Williamson, Maneesh Sahani, Jonathan W. Pillow
  Topics: log-likelihood (30) basis functions (20) mutual information (14) maximum likelihood (12) Poisson model (11)
• Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks
  Adam J. Kucharski, W. John Edmunds
  Topics: age group (39) R0 (30) maximum likelihood (14) branching process (11) confidence interval (5)
• The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient
  Michael D. O’Connell, Gregory T. Reeves
  Topics: gene expression (42) parameter sets (10) Sensitivity analysis (6) experimental data (5) Hill coefficient (3)
• Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation
  Ethan S. Sokol, Sandhya Sanduja, Dexter X. Jin, Daniel H. Miller, Robert A. Mathis, Piyush B. Gupta
  Topics: stem cells (40) ICA (10) gene expression (7) transcription factors (6) experimental conditions (4)
• Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation
  Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan
  Topics: base pairs (22) hydrogen bond (17) RMSD (8) MD simulation (4) Molecular dynamics (4)
• Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
  Timo R. Maarleveld, Meike T. Wortel, Brett G. Olivier, Bas Teusink, Frank J. Bruggeman
  Topics: growth conditions (15) E. coli (10) input-output (8) input-output relationship (5) steady-state (4)
• Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control
  Simon Sponberg, Thomas L. Daniel, Adrienne L. Fairhall
  Topics: linear combination (6) cross-validated (3) predictive power (3) principal component (3)
• Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth
  Ka Wai Lin, Angela Liao, Amina A. Qutub
  Topics: rate constants (22) signaling pathway (20) cell line (17) sensitivity analysis (9) initial conditions (8)
• The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease
  Stefan Flasche, Olivier Le Polain de Waroux, Katherine L. O’Brien, W. John Edmunds
  Topics: meta-analysis (5) age groups (3) Sensitivity analysis (3) simple model (3)
• Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
  Paul Egan, Jeffrey Moore, Christian Schunn, Jonathan Cagan, Philip LeDuc
  Topics: binding site (6) biological systems (4) simulation results (3)
• Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection
  Changwang Zhang, Shi Zhou, Elisabetta Groppelli, Pierre Pellegrino, Ian Williams, Persephone Borrow, Benjamin M. Chain, Clare Jolly
  Topics: T cell (66) cell-to-cell (46) immune response (11) cell density (8) mathematical model (8)
• Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study
  Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid
  Topics: peptides (23) E. coli (11) hydrogen bonds (9) molecular dynamics (6) water molecules (5)
• Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks
  Daniel K. Wells, Yishan Chuang, Louis M. Knapp, Dirk Brockmann, William L. Kath, Joshua N. Leonard
  Topics: immune cells (9) sensitivity analysis (8) tumor growth (8) cancer cells (5) immune response (5)
• Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
  Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg
  Topics: cytokine (16) principal components (16) machine learning (13) standard deviation (11) AUC (8)
• A Bayesian Ensemble Approach for Epidemiological Projections
  Tom Lindström, Michael Tildesley, Colleen Webb
  Topics: Bayesian model (10) probability distributions (7) epidemiological models (5) sensitivity analysis (4) normal distribution (3)
• Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations
  Fernando R. Fernandez, Paola Malerba, John A. White
  Topics: input-output (58) firing rate (23) ANOVA (9) power-law (9) steady-state (5)
• Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency
  Nancy K. Drew, Mackenzie A. Eagleson, Danny B. Baldo Jr., Kevin Kit Parker, Anna Grosberg
  Topics: sample size (12) standard deviation (9) cytoskeleton (7) experimental data (6) substrates (6)
• Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling
  Lorenza A. D’Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller
  Topics: phosphorylation (52) signaling pathways (32) MAPK (29) experimental data (20) feedback loops (20)
• Cell Fate Reprogramming by Control of Intracellular Network Dynamics
  Jorge G. T. Zañudo, Réka Albert
  Topics: T cell (26) network model (20) initial conditions (18) cell fate (9) standard deviation (9)
• Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans
  Mei Zhan, Matthew M. Crane, Eugeni V. Entchev, Antonio Caballero, Diana Andrea Fernandes de Abreu, QueeLim Ch’ng, Hang Lu
  Topics: training set (13) SVM (12) computational time (5) false positives (4) MATLAB (4)
• A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions
  Pedro Saa, Lars K. Nielsen
  Topics: rate constants (19) parameter sets (18) substrates (15) kinetic parameters (6) experimental data (5)
• The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
  Daniel Bendor
  Topics: simulated neurons (29) computational model (20) excitatory input (16) excitation and inhibition (14) statistically significant (11)
• Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent
  Andy Phaiboun, Yiming Zhang, Boryung Park, Minsu Kim
  Topics: cell density (35) cell growth (18) wild type (15) E. coli (14) mathematical modeling (7)
• Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment
  Hannah R. Meredith, Allison J. Lopatkin, Deverick J. Anderson, Lingchong You
  Topics: lysis (37) predictive power (24) subpopulations (14) Time course (11) Hill coefficient (5)
• A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors
  Tae J. Lee, Jeffrey Wong, Sena Bae, Anna Jisu Lee, Allison Lopatkin, Fan Yuan, Lingchong You
  Topics: power-law (42) E. coli (20) HeLa cells (16) cell lines (10) cytometry (10)
• Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program
  Noa Slater, Yoram Louzoun, Loren Gragert, Martin Maiers, Ansu Chatterjee, Mark Albrecht
  Topics: haplotypes (127) sample size (24) power law (13) power-law (10) EM algorithm (7)
• Three-Dimensional Gradients of Cytokine Signaling between T Cells
  Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer
  Topics: cytokine (143) T cells (36) cell-to-cell (12) upregulate (10) cell population (8)
• Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
  Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich
  Topics: Monte Carlo (14) point mutations (14) destabilizing (11) RMSD (9) wild type (8)
• Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty
  Nik J. Cunniffe, Richard O. J. H. Stutt, R. Erik DeSimone, Tim R. Gottwald, Christopher A. Gilligan
  Topics: optimal control (16) optimised (12) epidemiological model (5) decision makers (4) case study (3)
• The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
  Xiliang Zheng, Jin Wang
  Topics: free energy (57) ligands (39) power law (17) small molecules (14) Gaussian distributed (10)
• Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations
  Albertas Janulevicius, Mark van Loosdrecht, Cristian Picioreanu
  Topics: long-range (19)
• Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
  Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple , the FANTOM Consortium
  Topics: time course (23) time series (19) transcription factors (15) mRNA (12) transcriptional (10)
• MAGMA: Generalized Gene-Set Analysis of GWAS Data
  Christiaan A. de Leeuw, Joris M. Mooij, Tom Heskes, Danielle Posthuma
  Topics: SNP (21) gene sets (20) regression model (20) p-value (17) linear regression (7)
• Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer
  Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp
  Topics: growth rate (46) cell cycle (35) budding yeast (16) parameter estimation (11) cell growth (9)
• General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
  Joon-Young Moon, UnCheol Lee, Stefanie Blain-Moraes, George A. Mashour
  Topics: coupling strength (22) simulation results (7) analytical results (6) network model (6) standard deviation (6)
• Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits
  Naoki Hiratani, Tomoki Fukai
  Topics: synaptic weight (44) feedforward (14) ICA (13) membrane potential (13) firing rate (12)
• ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
  Gabriel R. A. Margarido, David Heckerman
  Topics: SNP (23) de novo (9) estimation accuracy (8) haplotypes (7) allele frequency (6)
• Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum
  Jyotika Bahuguna, Ad Aertsen, Arvind Kumar
  Topics: firing rates (89) basal ganglia (21) feedforward (15) subpopulations (13) spike train (10)
• Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism
  Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff
  Topics: transcriptional (21) eukaryotic (19) mRNA (18) rate constant (14) population level (10)
• Cell-Specific Cardiac Electrophysiology Models
  Willemijn Groenendaal, Francis A. Ortega, Armen R. Kherlopian, Andrew C. Zygmunt, Trine Krogh-Madsen, David J. Christini
  Topics: action potential (38) experimental data (21) parameter estimation (19) ICaL (10) cell-to-cell (6)
• Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations
  Debabani Ganguly, Jianhan Chen
  Topics: long-range (21) wild-type (16) phosphorylation (10) force field (9) de novo (5)
• Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease
  William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy
  Topics: mutual information (18) sequencing data (17) amino acid (15) phylogenetic (7) true positives (6)
• Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
  Ayala Matzner, Izhar Bar-Gad
  Topics: spike train (54) firing rate (49) Poisson process (14) experimental data (7) Poisson model (6)