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ORCIDPLoS Computational Biology, Volume 13
Volume 13, Number 1, January 2017
- Ruth Nussinov
, Jason A. Papin, Ilya A. Vakser:
Computing the Dynamic Supramolecular Structural Proteome.
- Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti:
Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing. - Markus List, Peter Ebert, Felipe Albrecht:
Ten Simple Rules for Developing Usable Software in Computational Biology.
- Luca Cardelli, Rosa D. Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikász-Nagy:
Efficient Switches in Biology and Computer Science.
- Abby Tabor, Michael A. Thacker, G. Lorimer Moseley, Konrad P. Körding:
Pain: A Statistical Account.
- Stuart P. Wilson:
Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling. - Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H. E. Tiesinga, Morten Mørup, Marcel A. J. van Gerven:
The missing link: Predicting connectomes from noisy and partially observed tract tracing data. - Te Wu, Long Wang, Feng Fu:
Coevolutionary dynamics of phenotypic diversity and contingent cooperation. - Cox Lwaka Tamba, Yuan-Li Ni, Yuan-Ming Zhang:
Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies. - Richard John Wheeler:
Use of chiral cell shape to ensure highly directional swimming in trypanosomes. - Hoyon Hwang, Jiou Wang:
Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans. - Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das, Ranjith Padinhateeri:
Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure. - Nikolay Chenkov, Henning Sprekeler, Richard Kempter:
Memory replay in balanced recurrent networks. - Weikang Wang, Kuan Tao, Jing Wang, Gen Yang, Qi Ouyang, Yugang Wang, Lei Zhang, Feng Liu:
Exploring the inhibitory effect of membrane tension on cell polarization. - Shenshen Wang:
Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction. - Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas Schilling, Qing Nie:
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains. - Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem:
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. - Austin W. T. Chiang, Walt Y. L. Wu, Ting Wang, Ming-Jing Hwang:
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. - Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel:
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. - Hsiao-Han Chang, Colin J. Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R. Kamya, Sarah G. Staedke, Grant Dorsey, Maxwell Murphy, Daniel E. Neafsey, Anna E. Jeffreys, Christina Hubbart, Kirk A. Rockett, Roberto Amato, Dominic Kwiatkowski, Caroline O. Buckee, Bryan Greenhouse:
THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. - Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Luca Zarenghi, Matteo Ricchi, Luca Bolzoni:
The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks. - Marie Amalric, Liping Wang, Pierre Pica, Santiago Figueira, Mariano Sigman, Stanislas Dehaene:
The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers. - Vasileios Vavourakis, Peter A. Wijeratne, Rebecca Shipley, Marilena Loizidou, Triantafyllos Stylianopoulos, David J. Hawkes:
A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth. - Mina A. Khoei, Guillaume S. Masson, Laurent U. Perrinet:
The Flash-Lag Effect as a Motion-Based Predictive Shift. - Stewart Heitmann, Michael Rule, Wilson Truccolo, Bard Ermentrout:
Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation. - David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann, Zoltán Kutalik:
Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. - Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann:
Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes. - Veronika Koren, Sophie Denève:
Computational Account of Spontaneous Activity as a Signature of Predictive Coding. - Antonella Paladino, Monica Civera, Laura Belvisi, Giorgio Colombo:
High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design. - Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer:
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. - Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta, Holger Stark:
Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients. - William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie:
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. - Tamara Carla Bidone, Wonyeong Jung, Daniel Maruri, Carlos Borau, Roger D. Kamm, Taeyoon Kim:
Morphological Transformation and Force Generation of Active Cytoskeletal Networks. - Tanmay A. Gokhale, Jong M. Kim, Robert D. Kirkton, Nenad Bursac, Craig S. Henriquez:
Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies. - Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer, Katharina Schmack:
Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning. - Ignacio A. Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz:
Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses. - Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng:
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. - Edward S. Lee, Paul G. Thomas, Jeff E. Mold, Andrew J. Yates:
Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing. - Iris Reuveni, Sourav Ghosh, Edi Barkai:
Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons. - Hilje M. Doekes, Christophe Fraser, Katrina A. Lythgoe:
Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels. - Oded Barzelay, Miriam Furst, Omri Barak:
A New Approach to Model Pitch Perception Using Sparse Coding. - Bethany Levick, Andy South, Ian M. Hastings:
A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies. - Aysima Hacisuleyman, Burak Erman:
Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin. - Christian Donner, Klaus Obermayer, Hideaki Shimazaki:
Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations. - Gabrielle Stetz, Gennady M. Verkhivker:
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. - Alireza Yazdani, He Li, Jay D. Humphrey, George E. Karniadakis:
A General Shear-Dependent Model for Thrombus Formation. - Christoph Zimmer, Reza Yaesoubi, Ted Cohen:
A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. - Yaroslav Pollak, Sarah Goldberg, Roee Amit:
A Looping-Based Model for Quenching Repression. - Federica Giardina, Ethan O. Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner:
Inference of Transmission Network Structure from HIV Phylogenetic Trees. - Christopher M. Siwy, Christopher Lockhart, Dmitri K. Klimov:
Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent? - Kaitlyn M. Gayvert, Omar Aly, James Platt, Marcus W. Bosenberg, David F. Stern, Olivier Elemento:
A Computational Approach for Identifying Synergistic Drug Combinations. - Eric Jonas, Konrad Paul Körding:
Could a Neuroscientist Understand a Microprocessor? - Luc E. Coffeng, Cornelus Hermsen, Robert W. Sauerwein, Sake J. De Vlas:
The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection. - James M. Kunert, Joshua L. Proctor, Steven L. Brunton, J. Nathan Kutz:
Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion. - Andrea Insabato, Mario Pannunzi, Gustavo Deco:
Multiple Choice Neurodynamical Model of the Uncertain Option Task. - Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez:
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. - Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes G. Bode, Martina U. Muckenthaler, Stefan Legewie:
Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms. - Martina Michalikova, Michiel W. H. Remme, Richard Kempter:
Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma. - Pia Abel zur Wiesch, Fabrizio Clarelli, Ted Cohen:
Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies. - Nicholas A. Rossi, Mary J. Dunlop:
Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA. - Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu:
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. - Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher:
FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. - James M. Kunert, Pedro D. Maia, J. Nathan Kutz:
Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage. - Hualou Liang, Hongbin Wang:
Structure-Function Network Mapping and Its Assessment via Persistent Homology. - Elyse H. Norton, Stephen M. Fleming, Nathaniel D. Daw, Michael S. Landy:
Suboptimal Criterion Learning in Static and Dynamic Environments. - Chen Zhao, Jeffrey S. Isenberg, Aleksander S. Popel:
Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model.
Volume 13, Number 2, February 2017
- Julia V. Ponomarenko, Romina Garrido, Roderic Guigó:
Ten Simple Rules on How to Organize a Scientific Retreat. - Dyoni M. de Oliveira, Marcos Silveira Buckeridge, Wanderley Dantas dos Santos:
Ten Simple Rules for Developing a Successful Research Proposal in Brazil.
- Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M. Osborne, David J. Gavaghan, Helen M. Byrne:
The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt. - Miguel A. Fortuna, Luis Zaman, Charles Ofria, Andreas Wagner:
The genotype-phenotype map of an evolving digital organism. - Yihao Zhang, Krithika Abiraman, He Li, David M. Pierce, Anastasios V. Tzingounis, George Lykotrafitis:
Modeling of the axon membrane skeleton structure and implications for its mechanical properties. - Qian Qin, Jianxing Feng:
Imputation for transcription factor binding predictions based on deep learning. - Felipe Gerhard, Moritz Deger, Wilson Truccolo:
On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs. - Arno Klein, Satrajit S. Ghosh, Forrest Sheng Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan:
Mindboggling morphometry of human brains. - Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert Podolsky, Gregory Dyson, Robert P. Hausinger, Gerardo Andrés Cisneros:
ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding. - Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald:
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. - Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm:
Two dynamic regimes in the human gut microbiome. - Dongjun Chung, Hang J. Kim, Hongyu Zhao:
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. - Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta:
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. - Vinal V. Lakhani, Timothy C. Elston:
Testing the limits of gradient sensing. - Naomi V. Bradbury, William J. M. Probert, Katriona Shea, Michael C. Runge, Christopher Fonnesbeck, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley:
Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns. - John F. Magnotti, Michael S. Beauchamp:
A Causal Inference Model Explains Perception of the McGurk Effect and Other Incongruent Audiovisual Speech. - Jung-Min Han, Akihiko Tanimura, Vivien Kirk, James Sneyd:
A mathematical model of calcium dynamics in HSY cells. - Franca Schmid, Philbert S. Tsai, David Kleinfeld, Patrick Jenny, Bruno Weber:
Depth-dependent flow and pressure characteristics in cortical microvascular networks. - Mark P. Little, Jolyon H. Hendry:
Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer. - Alexander Miguel Monzon, Diego J. Zea, María Silvina Fornasari, Tadeo E. Saldaño, Sebastian Fernandez Alberti, Silvio C. E. Tosatto, Gustavo D. Parisi:
Conformational diversity analysis reveals three functional mechanisms in proteins. - James M. Osborne, Alexander G. Fletcher, Joe Pitt-Francis, Philip K. Maini, David J. Gavaghan:
Comparing individual-based approaches to modelling the self-organization of multicellular tissues. - Dong-Ping Yang, Hai-Jun Zhou, Changsong Zhou:
Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity. - Didac Santesmasses, Marco Mariotti, Roderic Guigó:
Computational identification of the selenocysteine tRNA (tRNASec) in genomes. - Franziska Oschmann, Konstantin Mergenthaler, Evelyn Jungnickel, Klaus Obermayer:
Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes. - Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina:
Elucidation of molecular kinetic schemes from macroscopic traces using system identification. - Pierre Millard, Kieran Smallbone, Pedro Mendes:
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. - Vivek Charu, Scott Zeger, Julia R. Gog, Ottar N. Bjørnstad, Stephen Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud:
Human mobility and the spatial transmission of influenza in the United States. - Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow:
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. - István Bartha, Paul J. McLaren, Chanson J. Brumme, P. Richard Harrigan, Amalio Telenti, Jacques Fellay:
Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control. - Tracey M. Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor:
Representing high throughput expression profiles via perturbation barcodes reveals compound targets. - Jarred R. Mondoñedo, Béla Suki:
Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema. - Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang:
A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons. - Hojjat Bazzazi, Aleksander S. Popel:
Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells. - Johannes Burge, Priyank Jaini:
Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise. - Daniel Magee, Marc A. Suchard, Matthew Scotch:
Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction. - William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard:
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. - David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga:
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. - Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. Lopez, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard C. Laubenbacher:
Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. - Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti:
Unifying view of mechanical and functional hotspots across class A GPCRs. - Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg, Jon Timmis:
ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour. - Mark Roper, Chrisantha Fernando, Lars Chittka:
Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees. - Miguel Won, Manuel Marques-Pita, Carlota Louro, Joana Gonçalves-Sá:
Early and Real-Time Detection of Seasonal Influenza Onset. - Berta Verd, Anton Crombach, Johannes Jaeger:
Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression. - Olga K. Kamneva:
Genome composition and phylogeny of microbes predict their co-occurrence in the environment. - Jerome M. Karp, Samuel Sparks, David Cowburn:
Effects of FGFR2 kinase activation loop dynamics on catalytic activity. - Guillaume Lajoie, Nedialko I. Krouchev, John F. Kalaska, Adrienne L. Fairhall, Eberhard E. Fetz:
Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface. - Christoph Thiel, Henrik Cordes, Lorenzo Fabbri, Hélène Eloise Aschmann, Vanessa Baier, Ines Smit, Francis Atkinson, Lars Mathias Blank, Lars Kuepfer:
A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations. - Jannis Schuecker, Maximilian Schmidt, Sacha J. van Albada, Markus Diesmann, Moritz Helias:
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.
Volume 13, Number 3, March 2017
- Matthew Zook, Solon Barocas, danah boyd, Kate Crawford, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara König, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale:
Ten simple rules for responsible big data research. - Christopher J. Lortie:
Ten simple rules for short and swift presentations.