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ORCIDPLoS Computational Biology, Volume 12
Volume 12, Number 1, January 2016
- Andrew Lonsdale
, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow:
Ten Simple Rules for a Bioinformatics Journal Club.
- John D. Blischak, Emily R. Davenport, Greg Wilson:
A Quick Introduction to Version Control with Git and GitHub.
- Ezio Bartocci, Pietro Liò:
Computational Modeling, Formal Analysis, and Tools for Systems Biology.
- Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts:
Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity. - Iman Farasat, Howard M. Salis:
A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. - Gabriel A. Al-Ghalith, Emmanuel Montassier, Henry N. Ward, Dan Knight:
NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. - Kai J. Miller, Gerwin Schalk, Dora Hermes, Jeffrey G. Ojemann, Rajesh P. N. Rao:
Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change. - Troy Day, Andrew F. Read:
Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance? - Matthew A. Oberhardt, Raphy Zarecki, Leah Reshef, Fangfang Xia, Miquel Duran-Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben-Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin:
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. - Olga Kononova, Joost Snijder, Yaroslav Kholodov, Kenneth A. Marx, Gijs J. L. Wuite, Wouter H. Roos, Valeri Barsegov:
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles. - Isaure Chauvot de Beauchêne, Sjoerd Jacob de Vries, Martin Zacharias:
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. - Susanne Gerber, Martina Fröhlich, Hella Lichtenberg-Fraté, Sergey Shabala, Lana Shabala, Edda Klipp:
A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. - Araks Martirosyan, Matteo Figliuzzi, Enzo Marinari, Andrea De Martino:
Probing the Limits to MicroRNA-Mediated Control of Gene Expression. - Andrew R. Gallimore, A. Radu Aricescu, Michisuke Yuzaki, Radu Calinescu:
A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression. - Alexandre Ismail, Vincent Leroux, Myriam Smadja, Lucie Gonzalez, Murielle Lombard, Fabien Pierrel, Caroline Mellot-Draznieks, Marc Fontecave:
Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6. - Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco:
Social Norms of Cooperation in Small-Scale Societies. - C. Brandon Ogbunugafor, C. Scott Wylie, Ibrahim Diakite, Daniel M. Weinreich, Daniel L. Hartl:
Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance. - David Lamparter, Daniel Marbach, Rico Rueedi, Zoltán Kutalik, Sven Bergmann:
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. - Jacob G. Scott, Alexander G. Fletcher, Alexander R. A. Anderson, Philip K. Maini:
Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model. - Masafumi Oizumi, Shun-ichi Amari, Toru Yanagawa, Naotaka Fujii, Naotsugu Tsuchiya:
Measuring Integrated Information from the Decoding Perspective. - Laura Fumanelli, Marco Ajelli, Stefano Merler, Neil M. Ferguson, Simon Cauchemez:
Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics. - Juan P. Bustamante, Leandro G. Radusky, Leonardo Boechi, Dario A. Estrin, Arjen ten Have, Marcelo A. Marti:
Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. - Keng Boon Wee, Raphael Tze Chuen Lee, Jing Lin, Zacharias Aloysius Dwi Pramono, Sebastian Maurer-Stroh:
Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance. - Srivas Chennu, Stuart O'Connor, Ram Adapa, David K. Menon, Tristan A. Bekinschtein:
Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness. - Jaline Gerardin, Caitlin A. Bever, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger:
Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission. - Lin Chao, Camilla Ulla Rang, Audrey Menegaz Proenca, Jasper Ubirajara Chao:
Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation. - Duncan K. Ralph, Frederick A. Matsen IV:
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation. - Akram Méndez, Luis Mendoza:
A Network Model to Describe the Terminal Differentiation of B Cells. - Samira Yazdi, Matthias Stein, Fredrik Elinder, Magnus Andersson, Erik Lindahl:
The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. - Jennifer A. Hobbs, Regan Blythe Towal, Mitra J. Z. Hartmann:
Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad. - Marco Agostino Deriu, Gianvito Grasso, Jack A. Tuszynski, Diego Gallo, Umberto Morbiducci, Andrea Danani:
Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates. - Daniel D. Seaton, Jawahar Krishnan:
Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments. - Jayna Raghwani, Samir Bhatt, Oliver G. Pybus:
Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection. - Andrea N. Kravats, Sam Tonddast-Navaei, George Stan:
Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines. - Jessica M. Conway, Alan S. Perelson:
Residual Viremia in Treated HIV+ Individuals. - Junaid Hassan, Zhi Qu, Linda L. Bergaust, Lars R. Bakken:
Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes. - Zhen Song, Alain Karma, James N. Weiss, Zhilin Qu:
Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network. - In Jun Park, Andrew M. Hein, Yuriy V. Bobkov, Matthew A. Reidenbach, Barry W. Ache, José C. Príncipe:
Neurally Encoding Time for Olfactory Navigation. - Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger:
Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling. - Van Ngo, Yibo Wang, Stephan Haas, Sergei Yu Noskov, Robert A. Farley:
K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Nav Channels. - Almudena Pino-Ángeles, John M. Leveritt III, Themis Lazaridis:
Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family. - Maria E. Tomasso, Micheal J. Tarver, Deepa Devarajan, Steven T. Whitten:
Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities.
Volume 12, Number 2, February 2016
- PLOS Computational Biology 2015 Reviewer Thank You.
- James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen E. Parkinson, Catherine Brooksbank:
Ten Simple Rules for Selecting a Bio-ontology.
- Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher J. Fields, Karsten Hokamp, Monica C. Munoz-Torres:
The 2015 Bioinformatics Open Source Conference (BOSC 2015).
- Jessica Hedge, Daniel J. Wilson:
Practical Approaches for Detecting Selection in Microbial Genomes.
- Nicola J. Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S. Pillay, Jacky L. Snoep, Özlem Tastan Bishop, Nicki Tiffin:
The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. - Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren:
Computational Cancer Biology: An Evolutionary Perspective.
- William M. Jacobs, Tuomas P. J. Knowles, Daan Frenkel:
Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function. - Yasin Senbabaoglu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander:
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. - Swami Iyer, Timothy Killingback:
Evolution of Cooperation in Social Dilemmas on Complex Networks. - Beata Hat, Marek Kochanczyk, Marta N. Bogdal, Tomasz Lipniacki:
Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System. - H. Francis Song, Guangyu R. Yang, Xiao-Jing Wang:
Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks: A Simple and Flexible Framework. - Bertrand H. Lemasson, Colby J. Tanner, Eric Dimperio:
A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator's Visual Confusion. - Caroline A. Lea-Carnall, Marcelo A. Montemurro, Nelson J. Trujillo-Barreto, Laura M. Parkes, Wael El-Deredy:
Cortical Resonance Frequencies Emerge from Network Size and Connectivity. - David Angulo-Garcia, Joshua D. Berke, Alessandro Torcini:
Cell Assembly Dynamics of Sparsely-Connected Inhibitory Networks: A Simple Model for the Collective Activity of Striatal Projection Neurons. - Skander Mensi, Olivier Hagens, Wulfram Gerstner, Christian Pozzorini:
Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons. - Andrew Chay, Ilaria Zamparo, Andreas Koschinski, Manuela Zaccolo, Kim T. Blackwell:
Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons. - Joao A. Ascensao, Pratik Datta, Baris Hancioglu, Eduardo D. Sontag, Maria L. Gennaro, Oleg A. Igoshin:
Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis. - Tiziano Dallavilla, Laurence Abrami, Patrick A. Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis, F. Gisou van der Goot:
Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin. - Vahid Rahmati, Knut Kirmse, Dimitrije Markovic, Knut Holthoff, Stefan J. Kiebel:
Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference. - Jordi van Gestel, Martin A. Nowak:
Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles. - Juntao Liu, Guojun Li, Zheng Chang, Ting Yu, Bingqiang Liu, Rick McMullen, Pengyin Chen, Xiuzhen Huang:
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. - Megan A. Greischar, Nicole Mideo, Andrew F. Read, Ottar N. Bjørnstad:
Quantifying Transmission Investment in Malaria Parasites. - Thomas Miconi, Rufin VanRullen:
A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure. - Oren Shriki, Dovi Yellin:
Optimal Information Representation and Criticality in an Adaptive Sensory Recurrent Neuronal Network. - Jingtao Lu, Michael-Rock Goldsmith, Christopher M. Grulke, Daniel T. Chang, Raina D. Brooks, Jeremy A. Leonard, Martin B. Phillips, Ethan D. Hypes, Matthew J. Fair, Rogelio Tornero-Velez, Jeffre Johnson, Curtis C. Dary, Yu-Mei Tan:
Developing a Physiologically-Based Pharmacokinetic Model Knowledgebase in Support of Provisional Model Construction. - Benjamin Boucher, Anna Y. Lee, Michael T. Hallett, Sarah Jenna:
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways. - Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen:
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks. - Yong Liu, Min Wu, Chunyan Miao, Peilin Zhao, Xiaoli Li:
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. - Nick Jagiella, Benedikt Müller, Margareta Müller, Irene E. Vignon-Clementel, Dirk Drasdo:
Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data. - Zohar Z. Bronfman, Noam Brezis, Marius Usher:
Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism. - Paul Ardin, Fei Peng, Michael Mangan, Konstantinos Lagogiannis, Barbara Webb:
Using an Insect Mushroom Body Circuit to Encode Route Memory in Complex Natural Environments. - Travis E. Gibson, Amir Bashan, Hong-Tai Cao, Scott T. Weiss, Yang-Yu Liu:
On the Origins and Control of Community Types in the Human Microbiome. - Viljami R. Salmela, Linda Henriksson, Simo Vanni:
Radial Frequency Analysis of Contour Shapes in the Visual Cortex. - Joshua M. Inouye, Francisco J. Valero Cuevas:
Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption. - Daniel Miner, Jochen Triesch:
Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring. - Emily P. Harvey, Alona Ben-Tal:
Robust Unidirectional Airflow through Avian Lungs: New Insights from a Piecewise Linear Mathematical Model. - Artémis Llamosi, Andrés M. González-Vargas, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen, Grégory Batt:
What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. - Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. - Benjamin D. Dalziel, Ottar N. Bjørnstad, Willem G. van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell:
Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns. - Hiromasa Takemura, Cesar F. Caiafa, Brian A. Wandell, Franco Pestilli:
Ensemble Tractography. - Harendra Guturu, Sandeep Chinchali, Shoa L. Clarke, Gill Bejerano:
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. - Davi R. Ortega, Igor B. Zhulin:
Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex. - Steven W. Paugh, David R. Coss, Ju Bao, Lucas T. Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael R. Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching-Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik J. Bonten, William E. Evans:
MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression. - Mathieu Schiess, Robert Urbanczik, Walter Senn:
Somato-dendritic Synaptic Plasticity and Error-backpropagation in Active Dendrites. - Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger, Holger Gohlke:
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. - Leonid Chindelevitch, Caroline Colijn, Prashini Moodley, Douglas Wilson, Ted Cohen:
ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. - Javier Macía, Romilde Manzoni, Núria Conde-Pueyo, Arturo Urrios, Eulàlia de Nadal, Ricard V. Solé, Francesc Posas:
Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia. - Ioannis Vlachos, Taskin Deniz, Ad Aertsen, Arvind Kumar:
Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control. - Victor Garcia, Marcus W. Feldman, Roland R. Regoes:
Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection. - Yohan J. John, Basilis Zikopoulos, Daniel Bullock, Helen Barbas:
The Emotional Gatekeeper: A Computational Model of Attentional Selection and Suppression through the Pathway from the Amygdala to the Inhibitory Thalamic Reticular Nucleus. - Jan O. Haerter, Namiko Mitarai, Kim Sneppen:
Food Web Assembly Rules for Generalized Lotka-Volterra Equations. - Ivana Bozic, Jeffrey M. Gerold, Martin A. Nowak:
Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution. - Jon Lund Steffensen, Keith Dufault-Thompson, Ying Zhang:
PSAMM: A Portable System for the Analysis of Metabolic Models. - Mathias Foo, David E. Somers, Pan-Jun Kim:
Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System.
Volume 12, Number 3, March 2016
- Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.
- Yoo-Ah Kim, Dong-Yeon Cho, Teresa M. Przytycka:
Understanding Genotype-Phenotype Effects in Cancer via Network Approaches. - Christine Vogel:
Systems Approaches to the Eukaryotic Stress Response.
- Sarina Grutsch, Sven Brüschweiler, Martin Tollinger:
NMR Methods to Study Dynamic Allostery.
- Vaclav Cvicek, William A. Goddard III, Ravinder Abrol:
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. - Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James L. Stevens:
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. - Sara Sheehan, Yun S. Song:
Deep Learning for Population Genetic Inference. - Sandhya P. Tiwari, Nathalie Reuter:
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. - Maryna Kapustina, Denis Tsygankov, Jia Zhao, Timothy Wessler, Xiaofeng Yang, Alex Chen, Nathan Roach, Timothy C. Elston, Qi Wang, Ken Jacobson, M. Gregory Forest:
Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions. - Mikhail Shubin, Artem Lebedev, Outi Lyytikäinen, Kari Auranen:
Revealing the True Incidence of Pandemic A(H1N1)pdm09 Influenza in Finland during the First Two Seasons - An Analysis Based on a Dynamic Transmission Model. - Takeshi Nishimura, Futoshi Mori, Sho Hanida, Kiyoshi Kumahata, Shigeru Ishikawa, Kaouthar Samarat, Takako Miyabe-Nishiwaki, Misato Hayashi, Masaki Tomonaga, Juri Suzuki, Tetsuro Matsuzawa, Teruo Matsuzawa:
Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo. - J. Christian J. Ray, Michelle L. Wickersheim, Ameya P. Jalihal, Yusuf O. Adeshina, Tim F. Cooper, Gábor Balázsi:
Cellular Growth Arrest and Persistence from Enzyme Saturation. - Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, Amy H. Andreotti:
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.