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ORCIDPLoS Computational Biology, Volume 10
Volume 10, Number 1, January 2014
- Weixiong Zhang
:
Ten Simple Rules for Writing Research Papers.
- Ruth Nussinov:
The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead.
- Kavisha Ramdayal, Miranda D. Stobbe, Tarun Mishra, Magali Michaut:
Building the Future of Bioinformatics through Student-Facilitated Conferencing. - Reeta Rani Singhania, Dhatri Madduru, Pranathi Pappu, Sameera Panchangam, Renuka Suravajhala, Mohanalatha Chandrasekharan:
The Making of the Women in Biology Forum (WiB) at Bioclues.
- Isabel Marques, Paulo Almeida, Renato J. Alves, Maria João Dias, Ana Godinho, José B. Pereira-Leal:
Bioinformatics Projects Supporting Life-Sciences Learning in High Schools.
- Marc-Oliver Gewaltig, Robert C. Cannon:
Current Practice in Software Development for Computational Neuroscience and How to Improve It.
- Bin Hu, Hua-Xin Liao, S. Munir Alam, Byron Goldstein:
Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion. - Jonathan D. Drover:
Timing over Tuning: Overcoming the Shortcomings of a Line Attractor during a Working Memory Task. - Paul Verbruggen, Tim Heinemann, Erik M. M. Manders, Gesa von Bornstaedt, Roel van Driel, Thomas Höfer:
Robustness of DNA Repair through Collective Rate Control. - Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black:
De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function. - Omar Gutierrez-Arenas, Olivia Eriksson, Jeanette Hellgren Kotaleski:
Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants. - Devin L. O'Connor, Adam Runions, Aaron Sluis, Jennifer Bragg, John P. Vogel, Przemyslaw Prusinkiewicz, Sarah Hake:
A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses. - Geetu Tuteja, Karen Betancourt Moreira, Tisha Chung, Jenny Chen, Aaron M. Wenger, Gill Bejerano:
Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data. - Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés:
Global Patterns of Protein Domain Gain and Loss in Superkingdoms. - Claude Gérard, Didier Gonze, Frédéric Lemaigre, Béla Novák:
A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches. - Jayanthi Santhanam, Lars Råberg, Andrew F. Read, Nicholas Jon Savill:
Immune-Mediated Competition in Rodent Malaria Is Most Likely Caused by Induced Changes in Innate Immune Clearance of Merozoites. - Federico Comoglio, Renato Paro:
Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila. - Rosalyn J. Moran, Mkael Symmonds, Raymond J. Dolan, Karl J. Friston:
The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan. - Geoffrey L. Johnston, Peter W. Gething, Simon I. Hay, David L. Smith, David A. Fidock:
Modeling Within-Host Effects of Drugs on Plasmodium falciparum Transmission and Prospects for Malaria Elimination. - Biswa Sengupta, Simon Barry Laughlin, Jeremy Edward Niven:
Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency. - Jean Daunizeau, Vincent Adam, Lionel Rigoux:
VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data. - Zoltan Palmai, Christian Seifert, Frauke Gräter, Erika Balog:
An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis. - Zsuzsa Ákos, Róbert Beck, Máté Nagy, Tamás Vicsek, Enikö Kubinyi:
Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs. - Jia Chen, Haicen Yue, Qi Ouyang:
Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model. - Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson:
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. - Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider:
Machine Learning Estimates of Natural Product Conformational Energies. - Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter:
Fast Reconstruction of Compact Context-Specific Metabolic Network Models. - Aidan I. Brown, Peter K. Kim, Andrew D. Rutenberg:
PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes. - Moritz Helias, Tom Tetzlaff, Markus Diesmann:
The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics. - Yi-Fei Huang, Geoffrey Brian Golding:
Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures. - Kasper Jensen, Gianni Panagiotou, Irene Kouskoumvekaki:
Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level. - Jacob G. Scott, Anita B. Hjelmeland, Prakash Chinnaiyan, Alexander R. A. Anderson, David Basanta:
Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity. - John G. Koland:
Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation. - Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský:
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. - Ran Darshan, Arthur Leblois, David Hansel:
Interference and Shaping in Sensorimotor Adaptations with Rewards. - David J. Klinke II:
Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study. - Behruz Bozorg, Pawel Krupinski, Henrik Jönsson:
Stress and Strain Provide Positional and Directional Cues in Development. - W. Garrett Jenkinson, John K. Goutsias:
Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching. - Gesham Magombedze, Shigetoshi Eda, Vitaly V. Ganusov:
Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants. - Thomas A. Dunton, Joseph E. Goose, David J. Gavaghan, Mark S. P. Sansom, James M. Osborne:
The Free Energy Landscape of Dimerization of a Membrane Protein, NanC. - Sean T. Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso, Garrett B. Stanley:
The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity. - Bratislav Misic, Olaf Sporns, Anthony Randal McIntosh:
Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks. - Nicole Bohme Carnegie, Rui Wang, Vladimir A. Novitsky, Victor De Gruttola:
Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data. - Shelly Mahlab, Michal Linial:
Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective. - Axel von Kamp, Steffen Klamt:
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. - Michela Riz, Matthias Braun, Morten Gram Pedersen:
Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells. - Joshua Evan Auerbach, Josh C. Bongard:
Environmental Influence on the Evolution of Morphological Complexity in Machines. - Aaron C. Miller, Linnea A. Polgreen, Philip Polgreen:
Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting. - Gasper Tkacik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, Michael J. Berry II:
Searching for Collective Behavior in a Large Network of Sensory Neurons. - Roberta Santoro, Michelle Moerel, Federico De Martino, Rainer Goebel, Kâmil Ugurbil, Essa Yacoub, Elia Formisano:
Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex. - Mehdi Adibi, James Scott McDonald, Colin W. G. Clifford, Ehsan Arabzadeh:
Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses. - Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U. Muckenthaler, Stefan Legewie:
A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis. - Jacqueline M. Fulvio, C. Shawn Green, Paul R. Schrater:
Task-Specific Response Strategy Selection on the Basis of Recent Training Experience.
Volume 10, Number 2, February 2014
- Katrina Pavelin, Sangya Pundir, Jennifer A. Cham:
Ten Simple Rules for Running Interactive Workshops.
- Segun A. Fatumo, Sayane Shome, Geoff MacIntyre:
Workshops: A Great Way to Enhance and Supplement a Degree.
- Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen:
Combining Experiments and Simulations Using the Maximum Entropy Principle. - Tapesh Santra, Walter Kolch, Boris N. Kholodenko:
Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration. - Chung-Jung Tsai, Ruth Nussinov:
A Unified View of "How Allostery Works".
- Lingxue Zhang, Seyoung Kim:
Learning Gene Networks under SNP Perturbations Using eQTL Datasets. - Katherine C. H. Amrine, Wesley D. Swingley, David H. Ardell:
tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria. - Yu Hu, Joel Zylberberg, Eric Shea-Brown:
The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes. - Thomas Garcia, Leonardo Gregory Brunnet, Silvia De Monte:
Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups. - Cristina Savin, Peter Dayan, Máté Lengyel:
Optimal Recall from Bounded Metaplastic Synapses: Predicting Functional Adaptations in Hippocampal Area CA3. - Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino, Michele Caselle:
A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes. - Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel:
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses. - Pascal Carrivain, Maria Barbi, Jean-Marc Victor:
In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics. - James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux:
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. - Oliver W. Layton, N. Andrew Browning:
A Unified Model of Heading and Path Perception in Primate MSTd. - Kerstin Hünniger, Teresa Lehnert, Kristin Bieber, Ronny Martin, Marc Thilo Figge, Oliver Kurzai:
A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood. - Oscar Lao, Fan Liu, Andreas Wollstein, Manfred Kayser:
GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans. - Elad Noor, Arren Bar-Even, Avi I. Flamholz, Ed Reznik, Wolfram Liebermeister, Ron Milo:
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism. - Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas:
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design. - Alan E. Bilsland, Katrina Stevenson, Yu Liu, Stacey Hoare, Claire J. Cairney, Jon Roffey, W. Nicol Keith:
Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms. - Shyam Srinivasan, Jia Sheng Hu, D. Spencer Currle, Ernest S. Fung, Wayne B. Hayes, Arthur D. Lander, Edwin S. Monuki:
A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain. - Florian Lesaint, Olivier Sigaud, Shelly B. Flagel, Terry E. Robinson, Mehdi Khamassi:
Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations. - Saliha Ece Acuner Ozbabacan, Attila Gürsoy, Ruth Nussinov, Ozlem Keskin:
The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. - Zeina Shreif, Vipul Periwal:
A Network Characteristic That Correlates Environmental and Genetic Robustness. - Markku Nurhonen, Kari Auranen:
Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement. - Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker:
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. - Germán A. Enciso, Douglas R. Kellogg, Arturo Vargas:
Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint. - Peilin Jia, Zhongming Zhao:
VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data. - Chad Liu, Chuan-Yuan Li, Fan Yuan:
Mathematical Modeling of the Phoenix Rising Pathway. - Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson:
The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery. - Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas:
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. - Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard:
Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia.
Volume 10, Number 3, March 2014
- James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane:
Ten Simple Rules for Effective Computational Research.
- Sebastian J. Schultheiß, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, Magali Michaut:
Crossing Borders for Science. - Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider:
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.
- Jean Peccoud:
If You Can't Measure It, You Can't Manage It.
- Nico J. D. Nagelkerke, Paul Arora, Prabhat Jha, Brian Williams, Lyle McKinnon, Sake J. De Vlas:
The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling.
- Florian Klimm, Danielle S. Bassett, Jean M. Carlson, Peter J. Mucha:
Resolving Structural Variability in Network Models and the Brain. - Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. - Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford:
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. - Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger:
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. - Ewa Szczurek, Niko Beerenwinkel:
Modeling Mutual Exclusivity of Cancer Mutations. - Chase Cockrell, Scott Christley, Gary An:
Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT). - David Kappel, Bernhard Nessler, Wolfgang Maass:
STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning. - Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel:
Viral Quasispecies Assembly via Maximal Clique Enumeration. - Jian Zhou, Olga G. Troyanskaya:
Global Quantitative Modeling of Chromatin Factor Interactions. - Wondimu Teka, Toma M. Marinov, Fidel Santamaría:
Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model. - Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya:
A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects. - Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms:
Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach. - Alexandros Goulas, Matteo Bastiani, Gleb Bezgin, Harry B. M. Uylings, Alard Roebroeck, Peter Stiers:
Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain. - Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad:
Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems. - Noah C. Benson, Omar H. Butt, David H. Brainard, Geoffrey Karl Aguirre:
Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy. - Megan A. Cummins, Pavan J. Dalal, Marco Bugana, Stefano Severi, Eric A. Sobie:
Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence. - Colin J. Worby, Marc Lipsitch, William P. Hanage:
Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data. - Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yufang Jin:
Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map. - Hazem Toutounji, Gordon Pipa:
Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations. - Teresa Szczepinska, Jan Kutner, Michal Kopczynski, Krzysztof Pawlowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski, Maga Rowicka:
Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases. - Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq:
Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing. - Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne:
Computational Analyses of Synergism in Small Molecular Network Motifs. - Arnaud Messé, David Rudrauf, Habib Benali, Guillaume Marrelec:
Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities.