July 2017

PCSF: An R-package for network-based interpretation of high-throughput data

Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee

PLOS Computational Biology: published July 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005694

Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits

John Palmer, Adam Keane, Pulin Gong

PLOS Computational Biology: published July 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005669

A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

Oliver J. Maclaren, Aimée Parker, Carmen Pin, Simon R. Carding, Alastair J. M. Watson, Alexander G. Fletcher, Helen M. Byrne, Philip K. Maini

PLOS Computational Biology: published July 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005688

Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment

Ethan F. Oblak, Jarrod A. Lewis-Peacock, James S. Sulzer

PLOS Computational Biology: published July 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005681

Dissociating error-based and reinforcement-based loss functions during sensorimotor learning

Joshua G. A. Cashaback, Heather R. McGregor, Ayman Mohatarem, Paul L. Gribble

PLOS Computational Biology: published July 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005623

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen

PLOS Computational Biology: published July 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005176

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Zixuan Cang, Guo-Wei Wei

PLOS Computational Biology: published July 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005690

Upregulation of an inward rectifying K⁺ channel can rescue slow Ca²⁺ oscillations in K(ATP) channel deficient pancreatic islets

Vehpi Yildirim, Suryakiran Vadrevu, Benjamin Thompson, Leslie S. Satin, Richard Bertram

PLOS Computational Biology: published July 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005686

Growth of bacteria in 3-d colonies

Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R. Levin, Ilya Nemenman

PLOS Computational Biology: published July 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005679

Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks

Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus

PLOS Computational Biology: published July 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005672

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales

Lukas Bartonek, Bojan Zagrovic

PLOS Computational Biology: published July 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005648

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande

PLOS Computational Biology: published July 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005659

Spatial dynamics and control of a crop pathogen with mixed-mode transmission

Christopher Finn McQuaid, Frank van den Bosch, Anna Szyniszewska, Titus Alicai, Anthony Pariyo, Patrick Chiza Chikoti, Christopher Aidan Gilligan

PLOS Computational Biology: published July 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005654

Adjudicating between face-coding models with individual-face fMRI responses

Johan D. Carlin, Nikolaus Kriegeskorte

PLOS Computational Biology: published July 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005604

A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing

Haruo Hosoya, Aapo Hyvärinen

PLOS Computational Biology: published July 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005667

Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference

Giorgos Minas, David A. Rand

PLOS Computational Biology: published July 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005676

Reconstructing the regulatory circuit of cell fate determination in yeast mating response

Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo

PLOS Computational Biology: published July 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005671

β-adrenergic signaling broadly contributes to LTP induction

Joanna Jȩdrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T Blackwell

PLOS Computational Biology: published July 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005657

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

Koon-Kiu Yan, Shaoke Lou, Mark Gerstein

PLOS Computational Biology: published July 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005647

A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation

Warren D. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli

PLOS Computational Biology: published July 21, 2017 | https://doi.org/10.1371/journal.pcbi.1005627

Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan

Carla Aimé, Jean-Baptiste André, Michel Raymond

PLOS Computational Biology: published July 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005631

Advances in using Internet searches to track dengue

Shihao Yang, Samuel C. Kou, Fred Lu, John S. Brownstein, Nicholas Brooke, Mauricio Santillana

PLOS Computational Biology: published July 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005607

Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective

James R. H. Cooke, Arjan C. ter Horst, Robert J. van Beers, W. Pieter Medendorp

PLOS Computational Biology: published July 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005554

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Meric Ataman, Vassily Hatzimanikatis

PLOS Computational Biology: published July 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005513

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Meric Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis

PLOS Computational Biology: published July 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005444

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Marti-Renom

PLOS Computational Biology: published July 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005665

CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets

Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha

PLOS Computational Biology: published July 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005653

Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes

Marta Lukačišinová, Sebastian Novak, Tiago Paixão

PLOS Computational Biology: published July 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005609

Atomistic fingerprint of hyaluronan–CD44 binding

Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara

PLOS Computational Biology: published July 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005663

Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models

Connor Sharp, James Bray, Nicholas G. Housden, Martin C. J. Maiden, Colin Kleanthous

PLOS Computational Biology: published July 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005652

A curated genome-scale metabolic model of Bordetella pertussis metabolism

Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn

PLOS Computational Biology: published July 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005639

Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach

András Szabó, Roeland M. H. Merks

PLOS Computational Biology: published July 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005635

Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models

Laurent Mackay, Hana Zemkova, Stanko S. Stojilkovic, Arthur Sherman, Anmar Khadra

PLOS Computational Biology: published July 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005643

A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis

Mathieu Bottier, Sylvain Blanchon, Gabriel Pelle, Emilie Bequignon, Daniel Isabey, André Coste, Estelle Escudier, James B. Grotberg, Jean-François Papon, Marcel Filoche, Bruno Louis

PLOS Computational Biology: published July 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005605

A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling

Mathieu Bottier, Marta Peña Fernández, Gabriel Pelle, Daniel Isabey, Bruno Louis, James B. Grotberg, Marcel Filoche

PLOS Computational Biology: published July 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005552

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

Aseel Shomar, Lukas Geyrhofer, Noam E. Ziv, Naama Brenner

PLOS Computational Biology: published July 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005668

Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model

Gamze Gürsoy, Yun Xu, Jie Liang

PLOS Computational Biology: published July 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005658

Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis

Sang-Woo Lee, Yoshihiro Morishita

PLOS Computational Biology: published July 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005651

Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance

Kamran Kaveh, Yutaka Takahashi, Michael A. Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Z. Leder, Susanta K. Hui

PLOS Computational Biology: published July 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005482

Cover

Interaction fingerprint of hyaluronan and its CD44 receptor

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