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PLOS Computational Biology

2005 - 2020

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Volume 16, issue 2, 2020

Inferring TF activation order in time series scRNA-Seq studies pp. 1-19 Downloads
Chieh Lin, Jun Ding and Ziv Bar-Joseph
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network pp. 1-19 Downloads
Andrei Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M Frahm and Dima L Shepelyansky
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein pp. 1-24 Downloads
Joël R Pradines, Victor Farutin, Nicholas A Cilfone, Abouzar Ghavami, Elma Kurtagic, Jamey Guess, Anthony M Manning and Ishan Capila
Ten Simple Rules to becoming a principal investigator pp. 1-13 Downloads
John S Tregoning and Jason E McDermott
Navigable maps of structural brain networks across species pp. 1-20 Downloads
Antoine Allard and M Ángeles Serrano
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice pp. 1-20 Downloads
Aleksandr Kovaltsuk, Matthew I J Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück and Charlotte M Deane
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method pp. 1-17 Downloads
Kosuke Hamazaki and Hiroyoshi Iwata
Multi-state design of flexible proteins predicts sequences optimal for conformational change pp. 1-29 Downloads
Marion F Sauer, Alexander M Sevy, James E Crowe and Jens Meiler
Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies pp. 1-18 Downloads
Shuang Song, Wei Jiang, Lin Hou and Hongyu Zhao
Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells pp. 1-18 Downloads
Toshinori Namba and Shuji Ishihara
A generative growth model for thalamocortical axonal branching in primary visual cortex pp. 1-23 Downloads
Pegah Kassraian-Fard, Michael Pfeiffer and Roman Bauer
Predicting colorectal cancer risk from adenoma detection via a two-type branching process model pp. 1-23 Downloads
Brian M Lang, Jack Kuipers, Benjamin Misselwitz and Niko Beerenwinkel
Early prediction of antigenic transitions for influenza A/H3N2 pp. 1-23 Downloads
Lauren A Castro, Trevor Bedford and Lauren Ancel Meyers
Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials pp. 1-27 Downloads
Daniel B Reeves, Yunda Huang, Elizabeth R Duke, Bryan T Mayer, E Fabian Cardozo-Ojeda, Florencia A Boshier, David A Swan, Morgane Rolland, Merlin L Robb, John R Mascola, Myron S Cohen, Lawrence Corey, Peter B Gilbert and Joshua T Schiffer
Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit pp. 1-27 Downloads
Florian Ott, Dimitrije Marković, Alexander Strobel and Stefan J Kiebel
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic pp. 1-16 Downloads
Susanne Reimering, Sebastian Muñoz and Alice C McHardy
SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases pp. 1-12 Downloads
Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein and Tim Jeske
Bayesian inference and comparison of stochastic transcription elongation models pp. 1-21 Downloads
Jordan Douglas, Richard Kingston and Alexei J Drummond
Surprise response as a probe for compressed memory states pp. 1-21 Downloads
Hadar Levi-Aharoni, Oren Shriki and Naftali Tishby
Changes-of-mind in the absence of new post-decision evidence pp. 1-21 Downloads
Nadim A A Atiya, Arkady Zgonnikov, Denis O’Hora, Martin Schoemann, Stefan Scherbaum and KongFatt Wong-Lin
Ten simple rules for getting started on Twitter as a scientist pp. 1-9 Downloads
Veronika Cheplygina, Felienne Hermans, Casper Albers, Natalia Bielczyk and Ionica Smeets

Volume 16, issue 1, 2020

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples pp. 1-22 Downloads
Edward W Huang, Ameya Bhope, Jing Lim, Saurabh Sinha and Amin Emad
Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism pp. 1-17 Downloads
Melanie Gerken, Sergej Kakorin, Kamel Chibani and Karl-Josef Dietz
Interpreting neural decoding models using grouped model reliance pp. 1-17 Downloads
Simon Valentin, Maximilian Harkotte and Tzvetan Popov
Learning from animals: How to Navigate Complex Terrains pp. 1-17 Downloads
Henghui Zhu, Hao Liu, Armin Ataei, Yonatan Munk, Thomas Daniel and Ioannis Ch Paschalidis
VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning pp. 1-17 Downloads
Jiwoong Kim, David E Greenberg, Reed Pifer, Shuang Jiang, Guanghua Xiao, Samuel A Shelburne, Andrew Koh, Yang Xie and Xiaowei Zhan
Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs pp. 1-20 Downloads
Benjamin Allen, Christine Sample, Robert Jencks, James Withers, Patricia Steinhagen, Lori Brizuela, Joshua Kolodny, Darren Parke, Gabor Lippner and Yulia A Dementieva
Limits on amplifiers of natural selection under death-Birth updating pp. 1-13 Downloads
Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee and Martin A Nowak
BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis pp. 1-12 Downloads
Manoj Kumar, Cameron T Ellis, Qihong Lu, Hejia Zhang, Mihai Capotă, Theodore L Willke, Peter J Ramadge, Nicholas B Turk-Browne and Kenneth A Norman
The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations pp. 1-16 Downloads
Christie A Bahlai and Elise F Zipkin
Computational optimization of associative learning experiments pp. 1-23 Downloads
Filip Melinscak and Dominik R Bach
Emergence of social inequality in the spatial harvesting of renewable public goods pp. 1-25 Downloads
Jaideep Joshi, Åke Brännström and Ulf Dieckmann
Notch signaling and taxis mechanims regulate early stage angiogenesis: A mathematical and computational model pp. 1-31 Downloads
Rocío Vega, Manuel Carretero, Rui D M Travasso and Luis L Bonilla
Increasing growth rate slows adaptation when genotypes compete for diffusing resources pp. 1-14 Downloads
Jeremy M Chacón, Allison K Shaw and William R Harcombe
Collaboration leads to cooperation on sparse networks pp. 1-11 Downloads
Simon D Angus and Jonathan Newton
A new method for inferring timetrees from temporally sampled molecular sequences pp. 1-24 Downloads
Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L Kosakovsky Pond, Jessica Priest, Jiamin Deng and Sudhir Kumar
A system for tracking whisker kinematics and whisker shape in three dimensions pp. 1-24 Downloads
Rasmus S Petersen, Andrea Colins Rodriguez, Mathew H Evans, Dario Campagner and Michaela S E Loft
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power pp. 1-19 Downloads
Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam and Thomas Simonson
Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming pp. 1-21 Downloads
Jake P Taylor-King, Asbjørn N Riseth, Will Macnair and Manfred Claassen
A single reaction-diffusion equation for the multifarious eruptions of urticaria pp. 1-18 Downloads
Sungrim Seirin-Lee, Yuhki Yanase, Shunsuke Takahagi and Michihiro Hide
Emergence and suppression of cooperation by action visibility in transparent games pp. 1-32 Downloads
Anton M Unakafov, Thomas Schultze, Alexander Gail, Sebastian Moeller, Igor Kagan, Stephan Eule and Fred Wolf

Volume 15, issue 12, 2019

Statistics of correlated percolation in a bacterial community pp. 1-19 Downloads
Xiaoling Zhai, Joseph W Larkin, Kaito Kikuchi, Samuel E Redford, Ushasi Roy, Gürol M Süel and Andrew Mugler
Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication pp. 1-19 Downloads
Razie Yousefi and Maga Rowicka
Benchmarking network algorithms for contextualizing genes of interest pp. 1-14 Downloads
Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy Jenkins and Melody K Morris
Autistic traits influence the strategic diversity of information sampling: Insights from two-stage decision models pp. 1-29 Downloads
Haoyang Lu, Li Yi and Hang Zhang
CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data pp. 1-18 Downloads
Kai Kang, Qian Meng, Igor Shats, David M Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li and Leping Li
Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15 pp. 1-18 Downloads
Akira Endo, Mitsuo Uchida, Adam J Kucharski and Sebastian Funk
ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest pp. 1-30 Downloads
Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B Freimer and Jae Hoon Sul
Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models pp. 1-21 Downloads
Colette Mair, Sema Nickbakhsh, Richard Reeve, Jim McMenamin, Arlene Reynolds, Rory N Gunson, Pablo R Murcia and Louise Matthews
Protons in small spaces: Discrete simulations of vesicle acidification pp. 1-21 Downloads
Apeksha Singh, Frank V Marcoline, Salome Veshaguri, Aimee W Kao, Marcel Bruchez, Joseph A Mindell, Dimitrios Stamou and Michael Grabe
Overlap matrix completion for predicting drug-associated indications pp. 1-21 Downloads
Mengyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu and Jianxin Wang
The effect of inhibition on rate code efficiency indicators pp. 1-21 Downloads
Tomas Barta and Lubomir Kostal
Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model pp. 1-28 Downloads
John E Mittler, James T Murphy, Sarah E Stansfield, Kathryn Peebles, Geoffrey S Gottlieb, Neil F Abernethy, Molly C Reid, Steven M Goodreau and Joshua T Herbeck
Nine quick tips for analyzing network data pp. 1-10 Downloads
Vincent Miele, Catherine Matias, Stéphane Robin and Stéphane Dray
A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation pp. 1-26 Downloads
Matthew C Pharris, Neal M Patel, Tyler G VanDyk, Thomas M Bartol, Terrence J Sejnowski, Mary B Kennedy, Melanie I Stefan and Tamara L Kinzer-Ursem
Chemotaxis in external fields: Simulations for active magnetic biological matter pp. 1-26 Downloads
Agnese Codutti, Klaas Bente, Damien Faivre and Stefan Klumpp
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters pp. 1-20 Downloads
Christine Jandrasits, Stefan Kröger, Walter Haas and Bernhard Y Renard
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs pp. 1-20 Downloads
Yongcui Wang, Shilong Chen, Luonan Chen and Yong Wang
Neuronal population model of globular bushy cells covering unit-to-unit variability pp. 1-38 Downloads
Go Ashida, Helen T Heinermann and Jutta Kretzberg
Incomplete information about the partner affects the development of collaborative strategies in joint action pp. 1-23 Downloads
Vinil T Chackochan and Vittorio Sanguineti
NUFEB: A massively parallel simulator for individual-based modelling of microbial communities pp. 1-23 Downloads
Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P Curtis and Paolo Zuliani
Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling pp. 1-23 Downloads
Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini and Alessandro Paiardini
From energy to cellular forces in the Cellular Potts Model: An algorithmic approach pp. 1-23 Downloads
Elisabeth G Rens and Leah Edelstein-Keshet
Probing neural networks for dynamic switches of communication pathways pp. 1-23 Downloads
Holger Finger, Richard Gast, Christian Gerloff, Andreas K Engel and Peter König
The dynamics of motor learning through the formation of internal models pp. 1-25 Downloads
Camilla Pierella, Maura Casadio, Ferdinando A Mussa-Ivaldi and Sara A Solla
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory pp. 1-25 Downloads
Shu Wang, Jia-Ren Lin, Eduardo D Sontag and Peter K Sorger
Stability of spontaneous, correlated activity in mouse auditory cortex pp. 1-25 Downloads
Richard F Betzel, Katherine C Wood, Christopher Angeloni, Maria Neimark Geffen and Danielle S Bassett
Molecular sampling at logarithmic rates for next-generation sequencing pp. 1-12 Downloads
Caroline Horn and Julia Salzman
Motion prediction enables simulated MR-imaging of freely moving model organisms pp. 1-16 Downloads
Markus Reischl, Mazin Jouda, Neil MacKinnon, Erwin Fuhrer, Natalia Bakhtina, Andreas Bartschat, Ralf Mikut and Jan G Korvink
Statistical inference in ensemble modeling of cellular metabolism pp. 1-16 Downloads
Tuure Hameri, Marc-Olivier Boldi and Vassily Hatzimanikatis

Volume 15, issue 11, 2019

Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture pp. 1-35 Downloads
Jilin W J L Wang, Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet and Plamen Ch Ivanov
Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance pp. 1-28 Downloads
Charlotte Le Mouel and Romain Brette
A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology pp. 1-28 Downloads
Chen Zhao, Adam C Mirando, Richard J Sové, Thalyta X Medeiros, Brian H Annex and Aleksander S Popel
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets pp. 1-29 Downloads
M S Vijayabaskar, Debbie K Goode, Nadine Obier, Monika Lichtinger, Amber M L Emmett, Fatin N Zainul Abidin, Nisar Shar, Rebecca Hannah, Salam A Assi, Michael Lie-A-Ling, Berthold Gottgens, Georges Lacaud, Valerie Kouskoff, Constanze Bonifer and David R Westhead
A model of how depth facilitates scene-relative object motion perception pp. 1-29 Downloads
Oliver W Layton and D C Niehorster
Neural field models for latent state inference: Application to large-scale neuronal recordings pp. 1-23 Downloads
Michael E Rule, David Schnoerr, Matthias H Hennig and Guido Sanguinetti
No substantial change in the balance between model-free and model-based control via training on the two-step task pp. 1-23 Downloads
Elmar D Grosskurth, Dominik R Bach, Marcos Economides, Quentin J M Huys and Lisa Holper
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences pp. 1-27 Downloads
Ilya Plyusnin, Liisa Holm and Petri Törönen
Predicting neuronal dynamics with a delayed gain control model pp. 1-27 Downloads
Jingyang Zhou, Noah C Benson, Kendrick Kay and Jonathan Winawer
Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer pp. 1-27 Downloads
Miranda D Stobbe, Gian A Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P Whalley, Emanuele Raineri and Ivo G Gut
A novel network control model for identifying personalized driver genes in cancer pp. 1-27 Downloads
Wei-Feng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao and Luonan Chen
Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps pp. 1-32 Downloads
Yichen Zheng and Thomas Wiehe
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process pp. 1-17 Downloads
Jifan Shi, Tiejun Li, Luonan Chen and Kazuyuki Aihara
Tonic exploration governs both flexibility and lapses pp. 1-37 Downloads
R Becket Ebitz, Brianna J Sleezer, Hank P Jedema, Charles W Bradberry and Benjamin Y Hayden
Large-scale cortical travelling waves predict localized future cortical signals pp. 1-34 Downloads
David M Alexander, Tonio Ball, Andreas Schulze-Bonhage and Cees van Leeuwen
Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex pp. 1-19 Downloads
Marilia Menezes de Oliveira, James C Pang, Peter A Robinson, Xiaochen Liu and Mark M Schira
Uncovering the subtype-specific temporal order of cancer pathway dysregulation pp. 1-19 Downloads
Sahand Khakabimamaghani, Dujian Ding, Oliver Snow and Martin Ester
Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S pp. 1-19 Downloads
Nicholas G Reich, Craig J McGowan, Teresa K Yamana, Abhinav Tushar, Evan L Ray, Dave Osthus, Sasikiran Kandula, Logan C Brooks, Willow Crawford-Crudell, Graham Casey Gibson, Evan Moore, Rebecca Silva, Matthew Biggerstaff, Michael A Johansson, Roni Rosenfeld and Jeffrey Shaman
Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data pp. 1-24 Downloads
Prashant Rangarajan, Sandeep K Mody and Madhav Marathe

Volume 15, issue 10, 2019

Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort pp. 1-18 Downloads
Gabriel Balaban, Brian P Halliday, Wenjia Bai, Bradley Porter, Carlotta Malvuccio, Pablo Lamata, Christopher A Rinaldi, Gernot Plank, Daniel Rueckert, Sanjay K Prasad and Martin J Bishop
The folded X-pattern is not necessarily a statistical signature of decision confidence pp. 1-18 Downloads
Manuel Rausch and Michael Zehetleitner
Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations pp. 1-29 Downloads
Bogdan Barz, Jennifer Loschwitz and Birgit Strodel
Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers pp. 1-29 Downloads
David J Wooten, Sarah M Groves, Darren R Tyson, Qi Liu, Jing S Lim, Réka Albert, Carlos F Lopez, Julien Sage and Vito Quaranta
Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein pp. 1-29 Downloads
Ruchi Lohia, Reza Salari and Grace Brannigan
Evaluation of linear and non-linear activation dynamics models for insect muscle pp. 1-30 Downloads
Nalin Harischandra, Anthony J Clare, Jure Zakotnik, Laura M L Blackburn, Tom Matheson and Volker Dürr
Categorical encoding of decision variables in orbitofrontal cortex pp. 1-27 Downloads
Arno Onken, Jue Xie, Stefano Panzeri and Camillo Padoa-Schioppa
Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations pp. 1-27 Downloads
Carmichael F Ong, Thomas Geijtenbeek, Jennifer L Hicks and Scott L Delp
Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation pp. 1-27 Downloads
Alireza Kazemi, Bruno Louis, Daniel Isabey, Gary F Nieman, Louis A Gatto, Joshua Satalin, Sarah Baker, James B Grotberg and Marcel Filoche
Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity pp. 1-27 Downloads
Siva Venkadesh, Alexander O Komendantov, Diek W Wheeler, David J Hamilton and Giorgio A Ascoli
Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach pp. 1-32 Downloads
Iran R Roman, Auriel Washburn, Edward W Large, Chris Chafe and Takako Fujioka
Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals pp. 1-32 Downloads
Neil J Bruce, Daniele Narzi, Daniel Trpevski, Siri C van Keulen, Anu G Nair, Ursula Röthlisberger, Rebecca C Wade, Paolo Carloni and Jeanette Hellgren Kotaleski
SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways pp. 1-28 Downloads
Elisa Salviato, Vera Djordjilović, Monica Chiogna and Chiara Romualdi
Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling pp. 1-28 Downloads
Parul Maheshwari, Hao Du, Jen Sheen, Sarah M Assmann and Reka Albert
A computational account of threat-related attentional bias pp. 1-21 Downloads
Toby Wise, Jochen Michely, Peter Dayan and Raymond J Dolan
Phylogenetic correlations can suffice to infer protein partners from sequences pp. 1-24 Downloads
Guillaume Marmier, Martin Weigt and Anne-Florence Bitbol
Estimating influenza incidence using search query deceptiveness and generalized ridge regression pp. 1-23 Downloads
Reid Priedhorsky, Ashlynn R Daughton, Martha Barnard, Fiona O’Connell and Dave Osthus
Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism pp. 1-1 Downloads
The PLOS Computational Biology Staff
Correction: Generation of Binary Tree-Child phylogenetic networks pp. 1-1 Downloads
Gabriel Cardona, Joan Carles Pons and Celine Scornavacca
Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer pp. 1-1 Downloads
Margaret P Chapman, Tyler Risom, Anil J Aswani, Ellen M Langer, Rosalie C Sears and Claire J Tomlin
Correction: Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer pp. 1-1 Downloads
Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello and Erik de Schutter
Correction: Bayesian hypothesis testing and experimental design for two-photon imaging data pp. 1-1 Downloads
Luke E Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler and Philipp Berens
Color improves edge classification in human vision pp. 1-15 Downloads
Camille Breuil, Ben J Jennings, Simon Barthelmé, Nathalie Guyader and Frederick A A Kingdom
Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice pp. 1-31 Downloads
Mehran Spitmaan, Oihane Horno, Emily Chu and Alireza Soltani
Bayesian inference of neuronal assemblies pp. 1-31 Downloads
Giovanni Diana, Thomas T J Sainsbury and Martin P Meyer
A simulation of the random and directed motion of dendritic cells in chemokine fields pp. 1-16 Downloads
Avery Parr, Nicholas R Anderson and Daniel A Hammer
Uncovering and characterizing splice variants associated with survival in lung cancer patients pp. 1-16 Downloads
Sean West, Sushil Kumar, Surinder K Batra, Hesham Ali and Dario Ghersi
Ten simple rules for providing optimal administrative support to research teams pp. 1-9 Downloads
Romina Garrido, Casandra A Trowbridge and Nana Tamura
TAPES: A tool for assessment and prioritisation in exome studies pp. 1-9 Downloads
Alexandre Xavier, Rodney J Scott and Bente A Talseth-Palmer
Ten simple rules to aid in achieving a vision pp. 1-5 Downloads
Philip E Bourne
Hypergraph-based connectivity measures for signaling pathway topologies pp. 1-26 Downloads
Nicholas Franzese, Adam Groce, T M Murali and Anna Ritz
Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature pp. 1-22 Downloads
Qiao Liu, Di He and Lei Xie
A Kuramoto model of self-other integration across interpersonal synchronization strategies pp. 1-17 Downloads
Ole Adrian Heggli, Joana Cabral, Ivana Konvalinka, Peter Vuust and Morten L Kringelbach
Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi pp. 1-20 Downloads
Guillermo Vidal-Diez de Ulzurrun, Tsung-Yu Huang, Ching-Wen Chang, Hung-Che Lin and Yen-Ping Hsueh

Volume 15, issue 9, 2019

Cost-benefit trade-offs in decision-making and learning pp. 1-28 Downloads
Nura Sidarus, Stefano Palminteri and Valérian Chambon
Executable pathway analysis using ensemble discrete-state modeling for large-scale data pp. 1-21 Downloads
Rohith Palli, Mukta G Palshikar and Juilee Thakar
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data pp. 1-21 Downloads
Allison L Hicks, Nicole Wheeler, Leonor Sánchez-Busó, Jennifer L Rakeman, Simon R Harris and Yonatan H Grad
Deconvolving multiplexed protease signatures with substrate reduction and activity clustering pp. 1-18 Downloads
Qinwei Zhuang, Brandon Alexander Holt, Gabriel A Kwong and Peng Qiu
Generation of Binary Tree-Child phylogenetic networks pp. 1-29 Downloads
Gabriel Cardona, Joan Carles Pons and Celine Scornavacca
LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes pp. 1-27 Downloads
Olivier Collier, Véronique Stoven and Jean-Philippe Vert
Estimating information in time-varying signals pp. 1-33 Downloads
Sarah Anhala Cepeda-Humerez, Jakob Ruess and Gašper Tkačik
Perspective: Dimensions of the scientific method pp. 1-14 Downloads
Eberhard O Voit
Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination pp. 1-14 Downloads
Alexander D Becker, Amy Wesolowski, Ottar N Bjørnstad and Bryan T Grenfell
Invariant neural responses for sensory categories revealed by the time-varying information for communication calls pp. 1-43 Downloads
Julie E Elie and Frédéric E Theunissen
Network trade-offs and homeostasis in Arabidopsis shoot architectures pp. 1-19 Downloads
Adam Conn, Arjun Chandrasekhar, Martin van Rongen, Ottoline Leyser, Joanne Chory and Saket Navlakha
Benchmarking network propagation methods for disease gene identification pp. 1-24 Downloads
Sergio Picart-Armada, Steven J Barrett, David R Willé, Alexandre Perera-Lluna, Alex Gutteridge and Benoit H Dessailly
Loop analysis of blood pressure/volume homeostasis pp. 1-24 Downloads
Bruno Burlando, Franco Blanchini and Giulia Giordano
On measuring selection in cancer from subclonal mutation frequencies pp. 1-15 Downloads
Ivana Bozic, Chay Paterson and Bartlomiej Waclaw
A flexible and generalizable model of online latent-state learning pp. 1-31 Downloads
Amy L Cochran and Josh M Cisler
Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space pp. 1-22 Downloads
Michaëlle N Mayalu, Min-Cheol Kim and H Harry Asada
Fast and near-optimal monitoring for healthcare acquired infection outbreaks pp. 1-22 Downloads
Bijaya Adhikari, Bryan Lewis, Anil Vullikanti, José Mauricio Jiménez and B Aditya Prakash
Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making pp. 1-22 Downloads
Amir Dezfouli and Bernard W Balleine
Time scales and wave formation in non-linear spatial public goods games pp. 1-22 Downloads
Gregory J Kimmel, Philip Gerlee and Philipp M Altrock
Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform pp. 1-22 Downloads
Anna Matveeva, Michael Fichtner, Katherine McAllister, Christopher McCann, Marc Sturrock, Daniel B Longley and Jochen H M Prehn
The FACTS model of speech motor control: Fusing state estimation and task-based control pp. 1-26 Downloads
Benjamin Parrell, Vikram Ramanarayanan, Srikantan Nagarajan and John Houde
Prepaid parameter estimation without likelihoods pp. 1-42 Downloads
Merijn Mestdagh, Stijn Verdonck, Kristof Meers, Tim Loossens and Francis Tuerlinckx
Ten simple rules for helping newcomers become contributors to open projects pp. 1-10 Downloads
Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye and Greg Wilson
Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity pp. 1-38 Downloads
Kaiser Niknam, Amir Akbarian, Kelsey Clark, Yasin Zamani, Behrad Noudoost and Neda Nategh
Close spatial arrangement of mutants favors and disfavors fixation pp. 1-20 Downloads
Yunming Xiao and Bin Wu
Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints pp. 1-17 Downloads
Srinivasan Venkatramanan, Jiangzhuo Chen, Arindam Fadikar, Sandeep Gupta, Dave Higdon, Bryan Lewis, Madhav Marathe, Henning Mortveit and Anil Vullikanti
Designing combination therapies with modeling chaperoned machine learning pp. 1-17 Downloads
Yin Zhang, Julie M Huynh, Guan-Sheng Liu, Richard Ballweg, Kayenat S Aryeh, Andrew L Paek and Tongli Zhang
MHC binding affects the dynamics of different T-cell receptors in different ways pp. 1-17 Downloads
Bernhard Knapp, P Anton van der Merwe, Omer Dushek and Charlotte M Deane
Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons pp. 1-34 Downloads
Timothy Rumbell and James Kozloski
EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology pp. 1-13 Downloads
Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée and Pauline Ezanno

Volume 15, issue 8, 2019

Bayesian hypothesis testing and experimental design for two-photon imaging data pp. 1-27 Downloads
Luke E Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler and Philipp Berens
A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes pp. 1-30 Downloads
Jung Min Han and Vipul Periwal
Predicting kinase inhibitors using bioactivity matrix derived informer sets pp. 1-29 Downloads
Huikun Zhang, Spencer S Ericksen, Ching-pei Lee, Gene E Ananiev, Nathan Wlodarchak, Peng Yu, Julie C Mitchell, Anthony Gitter, Stephen J Wright, F Michael Hoffmann, Scott A Wildman and Michael A Newton
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties pp. 1-29 Downloads
Ljubisa Miskovic, Jonas Béal, Michael Moret and Vassily Hatzimanikatis
Every which way? On predicting tumor evolution using cancer progression models pp. 1-29 Downloads
Ramon Diaz-Uriarte and Claudia Vasallo
Predicting the effects of deep brain stimulation using a reduced coupled oscillator model pp. 1-28 Downloads
Gihan Weerasinghe, Benoit Duchet, Hayriye Cagnan, Peter Brown, Christian Bick and Rafal Bogacz
A computational model for gonadotropin releasing cells in the teleost fish medaka pp. 1-28 Downloads
Geir Halnes, Simen Tennøe, Trude M Haug, Gaute T Einevoll, Finn-Arne Weltzien and Kjetil Hodne
Transient crosslinking kinetics optimize gene cluster interactions pp. 1-28 Downloads
Benjamin Walker, Dane Taylor, Josh Lawrimore, Caitlin Hult, David Adalsteinsson, Kerry Bloom and M Gregory Forest
Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer pp. 1-19 Downloads
Morgan Craig, Kamran Kaveh, Alec Woosley, Andrew S Brown, David Goldman, Elliot Eton, Ravindra M Mehta, Andrew Dhawan, Kazuya Arai, M Mamunur Rahman, Sidi Chen, Martin A Nowak and Aaron Goldman
Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity pp. 1-33 Downloads
Audrey Denizot, Misa Arizono, U Valentin Nägerl, Hédi Soula and Hugues Berry
Directed migration shapes cooperation in spatial ecological public goods games pp. 1-14 Downloads
Felix Funk and Christoph Hauert
Twelve quick tips for designing sound dynamical models for bioprocesses pp. 1-8 Downloads
Francis Mairet and Olivier Bernard
Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma pp. 1-25 Downloads
Pieter Verbeke and Tom Verguts
The formation of preference in risky choice pp. 1-25 Downloads
Moshe Glickman, Orian Sharoni, Dino J Levy, Ernst Niebur, Veit Stuphorn and Marius Usher
Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease pp. 1-25 Downloads
Song Cui, Qiang Wu, James West and Jiangping Bai
Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability pp. 1-25 Downloads
Vladimir A Fedorov, Philipp S Orekhov, Ekaterina G Kholina, Artem A Zhmurov, Fazoil I Ataullakhanov, Ilya B Kovalenko and Nikita B Gudimchuk
FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics pp. 1-23 Downloads
Michael Gabel, Tobias Hohl, Andrea Imle, Oliver T Fackler and Frederik Graw
Variation in plastic responses to light results from selection in different competitive environments—A game theoretical approach using virtual plants pp. 1-23 Downloads
Franca J Bongers, Jacob C Douma, Yoh Iwasa, Ronald Pierik, Jochem B Evers and Niels P R Anten
Reappraising the utility of Google Flu Trends pp. 1-16 Downloads
Sasikiran Kandula and Jeffrey Shaman
A generative learning model for saccade adaptation pp. 1-35 Downloads
Carlos R Cassanello, Florian Ostendorf and Martin Rolfs
Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI pp. 1-35 Downloads
Georgia Koppe, Hazem Toutounji, Peter Kirsch, Stefanie Lis and Daniel Durstewitz
Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions pp. 1-35 Downloads
Joel A Paulson, Marc Martin-Casas and Ali Mesbah
PanoView: An iterative clustering method for single-cell RNA sequencing data pp. 1-17 Downloads
Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J Zack, Seth Blackshaw and Jiang Qian
Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study pp. 1-17 Downloads
Laura W Pomeroy, Hyeyoung Kim, Ningchuan Xiao, Mark Moritz and Rebecca Garabed
Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation pp. 1-34 Downloads
Michael A Colman
On the optimal design of metabolic RNA labeling experiments pp. 1-22 Downloads
Alexey Uvarovskii, Isabel S Naarmann- de Vries and Christoph Dieterich
Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models pp. 1-26 Downloads
Thi Mui Pham, Mirjam Kretzschmar, Xavier Bertrand, Martin Bootsma and on behalf of COMBACTE-MAGNET Consortium

Volume 15, issue 7, 2019

Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks pp. 1-4 Downloads
Christian L Vestergaard and Mathieu Génois
With an eye on uncertainty: Modelling pupillary responses to environmental volatility pp. 1-22 Downloads
Peter Vincent, Thomas Parr, David Benrimoh and Karl J Friston
Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned pp. 1-22 Downloads
David Zwicker
Depressive symptoms are associated with blunted reward learning in social contexts pp. 1-22 Downloads
Lou Safra, Coralie Chevallier and Stefano Palminteri
Human online adaptation to changes in prior probability pp. 1-26 Downloads
Elyse H Norton, Luigi Acerbi, Wei Ji Ma and Michael S Landy
Identifying determinants of persistent MRSA bacteremia using mathematical modeling pp. 1-26 Downloads
Tsuyoshi Mikkaichi, Michael R Yeaman, Alexander Hoffmann and Systems Immunobiology Group Mrsa
Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers pp. 1-26 Downloads
Jessica M Conway, Alan S Perelson and Jonathan Z Li
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data pp. 1-26 Downloads
Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J Williams, Weini Huang, Giulio Caravagna, Trevor A Graham and Andrea Sottoriva
Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas pp. 1-17 Downloads
Víctor M Pérez-García, Luis E Ayala-Hernández, Juan Belmonte-Beitia, Philippe Schucht, Michael Murek, Andreas Raabe and Juan Sepúlveda
Think: Theory for Africa pp. 1-5 Downloads
Christopher B Currin, Phumlani N Khoza, Alexander D Antrobus, Peter E Latham, Tim P Vogels and Joseph V Raimondo
Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications pp. 1-23 Downloads
Joseph A Lewnard, Benjamin A Lopman, Umesh D Parashar, Aisleen Bennett, Naor Bar-Zeev, Nigel A Cunliffe, Prasanna Samuel, M Lourdes Guerrero, Guillermo Ruiz-Palacios, Gagandeep Kang and Virginia E Pitzer
Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks pp. 1-23 Downloads
Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf and Thomas Dandekar
Information-theoretic analysis of multivariate single-cell signaling responses pp. 1-23 Downloads
Tomasz Jetka, Karol Nienałtowski, Tomasz Winarski, Sławomir Błoński and Michał Komorowski
Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources pp. 1-1 Downloads
Yoram Zarai and Tamir Tuller
Foraging as an evidence accumulation process pp. 1-25 Downloads
Jacob D Davidson and Ahmed El Hady
Disease gene prediction for molecularly uncharacterized diseases pp. 1-14 Downloads
Juan J Cáceres and Alberto Paccanaro
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks pp. 1-8 Downloads
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H Nguyen, Sara Brin Rosenthal, Fernando Pérez and Peter W Rose
Ten simple rules for giving an effective academic job talk pp. 1-8 Downloads
Shayna A Sura, Lauren L Smith, Monique R Ambrose, C Eduardo Guerra Amorim, Annabel C Beichman, Ana C R Gomez, Mark Juhn, Gaurav S Kandlikar, Julie S Miller, Jazlyn Mooney, Riley O Mummah, Kirk E Lohmueller and James O Lloyd-Smith
Machine and deep learning meet genome-scale metabolic modeling pp. 1-24 Downloads
Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske and Claudio Angione
A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth pp. 1-28 Downloads
Shiva Rudraraju, Derek E Moulton, Régis Chirat, Alain Goriely and Krishna Garikipati
Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction pp. 1-21 Downloads
Maarten H G Heusinkveld, Wouter Huberts, Joost Lumens, Theo Arts, Tammo Delhaas and Koen D Reesink
Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential pp. 1-21 Downloads
Aleksandra Karolak, Sharan Poonja and Katarzyna A Rejniak
Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity pp. 1-29 Downloads
Stefano Recanatesi, Gabriel Koch Ocker, Michael A Buice and Eric Shea-Brown
Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference pp. 1-29 Downloads
Chunhui Cai, Gregory F Cooper, Kevin N Lu, Xiaojun Ma, Shuping Xu, Zhenlong Zhao, Xueer Chen, Yifan Xue, Adrian V Lee, Nathan Clark, Vicky Chen, Songjian Lu, Lujia Chen, Liyue Yu, Harry S Hochheiser, Xia Jiang, Q Jane Wang and Xinghua Lu
Modeling human intuitions about liquid flow with particle-based simulation pp. 1-29 Downloads
Christopher J Bates, Ilker Yildirim, Joshua B Tenenbaum and Peter Battaglia
DART-ID increases single-cell proteome coverage pp. 1-30 Downloads
Albert Tian Chen, Alexander Franks and Nikolai Slavov
Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation pp. 1-32 Downloads
Nicolas Cazin, Martin Llofriu Alonso, Pablo Scleidorovich Chiodi, Tatiana Pelc, Bruce Harland, Alfredo Weitzenfeld, Jean-Marc Fellous and Peter Ford Dominey
Robustness of respiratory rhythm generation across dynamic regimes pp. 1-27 Downloads
Jonathan E Rubin and Jeffrey C Smith

Volume 15, issue 6, 2019

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame pp. 1-22 Downloads
Rohan V Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Participants and Rhiju Das
Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells pp. 1-26 Downloads
Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay and Marek Kimmel
Ten simple rules for successfully hosting an intern at a scientific software company pp. 1-4 Downloads
Kristine Briedis, Yi-Shiou Chen and Scott Markel
Learning to use past evidence in a sophisticated world model pp. 1-20 Downloads
Sanjeevan Ahilan, Rebecca B Solomon, Yannick-André Breton, Kent Conover, Ritwik K Niyogi, Peter Shizgal and Peter Dayan
Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies pp. 1-34 Downloads
Payam Piray, Amir Dezfouli, Tom Heskes, Michael J Frank and Nathaniel D Daw
Telling ecological networks apart by their structure: A computational challenge pp. 1-13 Downloads
Matthew J Michalska-Smith and Stefano Allesina
Charting pathways to climate change mitigation in a coupled socio-climate model pp. 1-16 Downloads
Thomas M Bury, Chris T Bauch and Madhur Anand
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training pp. 1-12 Downloads
Annette McGrath, Katherine Champ, Catherine A Shang, Ellen van Dam, Cath Brooksbank and Sarah L Morgan
How single neuron properties shape chaotic dynamics and signal transmission in random neural networks pp. 1-35 Downloads
Samuel P Muscinelli, Wulfram Gerstner and Tilo Schwalger
Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria pp. 1-1 Downloads
The PLOS Computational Biology Staff
Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses pp. 1-1 Downloads
Sven Zenker, Jonathan Rubin and Gilles Clermont
Evolution of interface binding strengths in simplified model of protein quaternary structure pp. 1-15 Downloads
Alexander S Leonard and Sebastian E Ahnert
Evidence accumulation is biased by motivation: A computational account pp. 1-15 Downloads
Filip Gesiarz, Donal Cahill and Tali Sharot
Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes pp. 1-15 Downloads
Atsushi Kamimura, Yoshiya J Matsubara, Kunihiko Kaneko and Nobuto Takeuchi
Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales pp. 1-25 Downloads
Joshua M Mueller, Primoz Ravbar, Julie H Simpson and Jean M Carlson
A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model pp. 1-31 Downloads
Erlend Hodneland, Erik Hanson, Ove Sævareid, Geir Nævdal, Arvid Lundervold, Veronika Šoltészová, Antonella Z Munthe-Kaas, Andreas Deistung, Jürgen R Reichenbach and Jan M Nordbotten
Models that learn how humans learn: The case of decision-making and its disorders pp. 1-33 Downloads
Amir Dezfouli, Kristi Griffiths, Fabio Ramos, Peter Dayan and Bernard W Balleine
Ten quick tips for effective dimensionality reduction pp. 1-19 Downloads
Lan Huong Nguyen and Susan Holmes
A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test pp. 1-24 Downloads
David Hasler, Pinelopi Anagnostopoulou, Sylvia Nyilas, Philipp Latzin, Johannes Schittny and Dominik Obrist
Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model pp. 1-36 Downloads
Mahua Roy and Stacey D Finley
Modeling the temporal dynamics of the gut microbial community in adults and infants pp. 1-21 Downloads
Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D Silverman, Itzhak Mizrahi and Eran Halperin
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome pp. 1-21 Downloads
Kymberleigh A Pagel, Danny Antaki, AoJie Lian, Matthew Mort, David N Cooper, Jonathan Sebat, Lilia M Iakoucheva, Sean D Mooney and Predrag Radivojac
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH) pp. 1-21 Downloads
Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis and Dani Or
Open collaborative writing with Manubot pp. 1-21 Downloads
Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene and Anthony Gitter
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences pp. 1-21 Downloads
Ingoo Lee, Jongsoo Keum and Hojung Nam
Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants pp. 1-18 Downloads
Romain Ligneul
Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations pp. 1-27 Downloads
Hanne Hoitzing, Payam A Gammage, Lindsey Van Haute, Michal Minczuk, Iain G Johnston and Nick S Jones
Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis pp. 1-27 Downloads
Takaaki Yonekura, Akitoshi Iwamoto, Hironori Fujita and Munetaka Sugiyama
Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons pp. 1-27 Downloads
Sharmila Venugopal, Soju Seki, David H Terman, Antonios Pantazis, Riccardo Olcese, Martina Wiedau-Pazos and Scott H Chandler

Volume 15, issue 5, 2019

Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares pp. 1-21 Downloads
Yuning Hao, Ming Yan, Blake R Heath, Yu L Lei and Yuying Xie
Beyond Bouma's window: How to explain global aspects of crowding? pp. 1-28 Downloads
Adrien Doerig, Alban Bornet, Ruth Rosenholtz, Gregory Francis, Aaron M Clarke and Michael H Herzog
Human representation of multimodal distributions as clusters of samples pp. 1-29 Downloads
Jingwei Sun, Jian Li and Hang Zhang
Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features pp. 1-18 Downloads
David A Knowles, Gina Bouchard and Sylvia Plevritis
Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes pp. 1-18 Downloads
Anupama Sharma, Shakti N Menon, V Sasidevan and Sitabhra Sinha
Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias pp. 1-30 Downloads
Ming Bo Cai, Nicolas W Schuck, Jonathan W Pillow and Yael Niv
Parameter estimation and identifiability in a neural population model for electro-cortical activity pp. 1-27 Downloads
Agus Hartoyo, Peter J Cadusch, David T J Liley and Damien G Hicks
Ten quick tips for using a Raspberry Pi pp. 1-11 Downloads
Anthony C Fletcher and Cameron Mura
The statistics of epidemic transitions pp. 1-14 Downloads
John M Drake, Tobias S Brett, Shiyang Chen, Bogdan I Epureanu, Matthew J Ferrari, Éric Marty, Paige B Miller, Eamon B O’Dea, Suzanne M O’Regan, Andrew W Park and Pejman Rohani
State-aware detection of sensory stimuli in the cortex of the awake mouse pp. 1-24 Downloads
Audrey J Sederberg, Aurélie Pala, He J V Zheng, Biyu J He and Garrett B Stanley
Efficient algorithms to discover alterations with complementary functional association in cancer pp. 1-24 Downloads
Rebecca Sarto Basso, Dorit S Hochbaum and Fabio Vandin
Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal pp. 1-19 Downloads
Jakob Lund Dideriksen and Dario Farina
Modeling enamel matrix secretion in mammalian teeth pp. 1-12 Downloads
Teemu J Häkkinen, S Susanna Sova, Ian J Corfe, Leo Tjäderhane, Antti Hannukainen and Jukka Jernvall
Comprehensively benchmarking applications for detecting copy number variation pp. 1-12 Downloads
Le Zhang, Wanyu Bai, Na Yuan and Zhenglin Du
Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis pp. 1-16 Downloads
Yaser Saffar Talori, Jing-Shan Zhao, Yun-Fei Liu, Wen-Xiu Lu, Zhi-Heng Li and Jingmai Kathleen O'Connor
Interacting cells driving the evolution of multicellular life cycles pp. 1-16 Downloads
Yuanxiao Gao, Arne Traulsen and Yuriy Pichugin
Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions pp. 1-16 Downloads
Matti Javanainen, Giray Enkavi, Ramon Guixà-Gonzaléz, Waldemar Kulig, Hector Martinez-Seara, Ilya Levental and Ilpo Vattulainen
A quick guide for using Microsoft OneNote as an electronic laboratory notebook pp. 1-9 Downloads
Santiago Guerrero, Andrés López-Cortés, Jennyfer M García-Cárdenas, Pablo Saa, Alberto Indacochea, Isaac Armendáriz-Castillo, Ana Karina Zambrano, Verónica Yumiceba, Andy Pérez-Villa, Patricia Guevara-Ramírez, Oswaldo Moscoso-Zea, Joel Paredes, Paola E Leone and César Paz-y-Miño
Perturbing low dimensional activity manifolds in spiking neuronal networks pp. 1-23 Downloads
Emil Wärnberg and Arvind Kumar
Notice of Republication: Ten simple rules for organizing a webinar series pp. 1-1 Downloads
The PLOS Computational Biology Staff
An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis pp. 1-25 Downloads
Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias and Christoforos Nikolaou
Differential sustained and transient temporal processing across visual streams pp. 1-26 Downloads
Anthony Stigliani, Brianna Jeska and Kalanit Grill-Spector
Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG pp. 1-22 Downloads
Natalie Schaworonkow and Vadim V Nikulin
Noise-precision tradeoff in predicting combinations of mutations and drugs pp. 1-17 Downloads
Avichai Tendler, Anat Zimmer, Avi Mayo and Uri Alon
Uncovering functional signature in neural systems via random matrix theory pp. 1-20 Downloads
Assaf Almog, M Renate Buijink, Ori Roethler, Stephan Michel, Johanna H Meijer, Jos H T Rohling and Diego Garlaschelli
Forecasting national and regional influenza-like illness for the USA pp. 1-20 Downloads
Michal Ben-Nun, Pete Riley, James Turtle, David P Bacon and Steven Riley
Ten quick tips for biocuration pp. 1-7 Downloads
Y Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C Munoz-Torres, Drashtti V Vasant, Eleanor Williams and Melissa Haendel
Ten simple rules for carrying out and writing meta-analyses pp. 1-7 Downloads
Diego A Forero, Sandra Lopez-Leon, Yeimy González-Giraldo and Pantelis G Bagos
Correction: How pupil responses track value-based decision-making during and after reinforcement learning pp. 1-2 Downloads
Joanne C Van Slooten, Sara Jahfari, Tomas Knapen and Jan Theeuwes
Wisdom of crowds in computational biology pp. 1-2 Downloads
Jason A Papin and Feilim Mac Gabhann

Volume 15, issue 4, 2019

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis pp. 1-28 Downloads
Remco Bouckaert, Timothy G Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K Mendes, Nicola F Müller, Huw A Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler and Alexei J Drummond
TASmania: A bacterial Toxin-Antitoxin Systems database pp. 1-28 Downloads
Hatice Akarsu, Patricia Bordes, Moise Mansour, Donna-Joe Bigot, Pierre Genevaux and Laurent Falquet
Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms pp. 1-21 Downloads
Kyriaki Kalimeri, Matteo Delfino, Ciro Cattuto, Daniela Perrotta, Vittoria Colizza, Caroline Guerrisi, Clement Turbelin, Jim Duggan, John Edmunds, Chinelo Obi, Richard Pebody, Ana O Franco, Yamir Moreno, Sandro Meloni, Carl Koppeschaar, Charlotte Kjelsø, Ricardo Mexia and Daniela Paolotti
Chemical features mining provides new descriptive structure-odor relationships pp. 1-21 Downloads
Carmen C Licon, Guillaume Bosc, Mohammed Sabri, Marylou Mantel, Arnaud Fournel, Caroline Bushdid, Jerome Golebiowski, Celine Robardet, Marc Plantevit, Mehdi Kaytoue and Moustafa Bensafi
Approximate Bayesian estimation of coevolutionary arms races pp. 1-21 Downloads
Scott L Nuismer and Bob Week
Neural crest streaming as an emergent property of tissue interactions during morphogenesis pp. 1-21 Downloads
András Szabó, Eric Theveneau, Melissa Turan and Roberto Mayor
SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species pp. 1-30 Downloads
Đorđe Miladinović, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian Baumann, Antoine Adamantidis, Steven A Brown and Joachim M Buhmann
Imperfect Bayesian inference in visual perception pp. 1-27 Downloads
Elina Stengård and Ronald van den Berg
A multiscale model of epigenetic heterogeneity-driven cell fate decision-making pp. 1-27 Downloads
Núria Folguera-Blasco, Rubén Pérez-Carrasco, Elisabet Cuyàs, Javier A Menendez and Tomás Alarcón
Contextual influence on confidence judgments in human reinforcement learning pp. 1-27 Downloads
Maël Lebreton, Karin Bacily, Stefano Palminteri and Jan Engelmann
Learning and forgetting using reinforced Bayesian change detection pp. 1-41 Downloads
Vincent Moens and Alexandre Zénon
Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs pp. 1-18 Downloads
Cheng Liang, Shengpeng Yu and Jiawei Luo
A Bayesian framework for the analysis of systems biology models of the brain pp. 1-29 Downloads
Joshua Russell-Buckland, Christopher P Barnes and Ilias Tachtsidis
A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism pp. 1-29 Downloads
Oveis Jamialahmadi, Sameereh Hashemi-Najafabadi, Ehsan Motamedian, Stefano Romeo and Fatemeh Bagheri
Ten simple rules towards healthier research labs pp. 1-8 Downloads
Fernando T Maestre
Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size pp. 1-24 Downloads
Daniel I S Rosenbloom, Peter Bacchetti, Mars Stone, Xutao Deng, Ronald J Bosch, Douglas D Richman, Janet D Siliciano, John W Mellors, Steven G Deeks, Roger G Ptak, Rebecca Hoh, Sheila M Keating, Melanie Dimapasoc, Marta Massanella, Jun Lai, Michele D Sobolewski, Deanna A Kulpa, Michael P Busch and for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group
Confidence resets reveal hierarchical adaptive learning in humans pp. 1-24 Downloads
Micha Heilbron and Florent Meyniel
Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions pp. 1-19 Downloads
Anne Richelle, Austin W T Chiang, Chih-Chung Kuo and Nathan E Lewis
Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features pp. 1-35 Downloads
Craig A Magaret, David C Benkeser, Brian D Williamson, Bhavesh R Borate, Lindsay N Carpp, Ivelin S Georgiev, Ian Setliff, Adam S Dingens, Noah Simon, Marco Carone, Christopher Simpkins, David Montefiori, Galit Alter, Wen-Han Yu, Michal Juraska, Paul T Edlefsen, Shelly Karuna, Nyaradzo M Mgodi, Srilatha Edugupanti and Peter B Gilbert
Revealing evolutionary constraints on proteins through sequence analysis pp. 1-16 Downloads
Shou-Wen Wang, Anne-Florence Bitbol and Ned S Wingreen
Isolating and quantifying the role of developmental noise in generating phenotypic variation pp. 1-31 Downloads
Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble and Ylenia Chiari
I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment pp. 1-23 Downloads
Stelios Pavlidis, Calixte Monast, Matthew J Loza, Patrick Branigan, Kiang F Chung, Ian M Adcock, Yike Guo, Anthony Rowe and Frédéric Baribaud
A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation pp. 1-25 Downloads
Marko Järvenpää, Mohamad R Abdul Sater, Georgia K Lagoudas, Paul C Blainey, Loren G Miller, James A McKinnell, Susan S Huang, Yonatan H Grad and Pekka Marttinen
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks pp. 1-25 Downloads
Graeme Benstead-Hume, Xiangrong Chen, Suzanna R Hopkins, Karen A Lane, Jessica A Downs and Frances M G Pearl
Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder pp. 1-25 Downloads
Abrar E Al-Shaer, George R Flentke, Mark E Berres, Ana Garic and Susan M Smith
GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity pp. 1-25 Downloads
Lex E Flagel, Benjamin K Blackman, Lila Fishman, Patrick J Monnahan, Andrea Sweigart and John K Kelly
Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits pp. 1-34 Downloads
Yifan Gu, Yang Qi and Pulin Gong
Bet-hedging strategies in expanding populations pp. 1-17 Downloads
Paula Villa Martín, Miguel A Muñoz and Simone Pigolotti
Model diagnostics and refinement for phylodynamic models pp. 1-17 Downloads
Max S Y Lau, Bryan T Grenfell, Colin J Worby and Gavin J Gibson
Ten simple rules for organizing a webinar series pp. 1-7 Downloads
Faisal M Fadlelmola, Sumir Panji, Azza E Ahmed, Amel Ghouila, Wisdom A Akurugu, Jean-Baka Domelevo Entfellner, Oussema Souiai, Nicola Mulder and H3ABioNet Research working group as members of the H3Africa Consortium
Network motifs and their origins pp. 1-7 Downloads
Lewi Stone, Daniel Simberloff and Yael Artzy-Randrup
Ten simple rules for providing a meaningful research experience to high school students pp. 1-7 Downloads
Emily A Lescak, Kate M O’Neill, Giovanna M Collu and Subhamoy Das
Physical constraints on accuracy and persistence during breast cancer cell chemotaxis pp. 1-20 Downloads
Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler and Bumsoo Han
Inferring neural circuit structure from datasets of heterogeneous tuning curves pp. 1-38 Downloads
Takafumi Arakaki, G Barello and Yashar Ahmadian
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) pp. 1-10 Downloads
Hailong Meng, Gur Yaari, Christopher R Bolen, Stefan Avey and Steven H Kleinstein
Evolutionary multiplayer games on graphs with edge diversity pp. 1-22 Downloads
Qi Su, Lei Zhou and Long Wang

Volume 15, issue 3, 2019

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows pp. 1-19 Downloads
Pei-Chi Yang, Shweta Purawat, Pek U Ieong, Mao-Tsuen Jeng, Kevin R DeMarco, Igor Vorobyov, Andrew D McCulloch, Ilkay Altintas, Rommie E Amaro and Colleen E Clancy
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations pp. 1-19 Downloads
Ramu Anandakrishnan, Robin T Varghese, Nicholas A Kinney and Harold R Garner
A spectrum of routing strategies for brain networks pp. 1-24 Downloads
Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P van den Heuvel, Patric Hagmann and Olaf Sporns
Myopic control of neural dynamics pp. 1-24 Downloads
David Hocker and Il Memming Park
A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus pp. 1-24 Downloads
Sifat A Moon, Lee W Cohnstaedt, D Scott McVey and Caterina M Scoglio
Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks pp. 1-33 Downloads
Manuel Beiran and Srdjan Ostojic
In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics pp. 1-18 Downloads
David R Berg, Chetan P Offord, Iris Kemler, Matthew K Ennis, Lawrence Chang, George Paulik, Zeljko Bajzer, Claudia Neuhauser and David Dingli
LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities pp. 1-18 Downloads
Lei Wang, Zhu-Hong You, Xing Chen, Yang-Ming Li, Ya-Nan Dong, Li-Ping Li and Kai Zheng
Scalable nonlinear programming framework for parameter estimation in dynamic biological system models pp. 1-29 Downloads
Sungho Shin, Ophelia S Venturelli and Victor M Zavala
Computational geometry for modeling neural populations: From visualization to simulation pp. 1-41 Downloads
Marc de Kamps, Mikkel Lepperød and Yi Ming Lai
Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition pp. 1-27 Downloads
Marieke Rohde, Kenichi Narioka, Jochen J Steil, Lina K Klein and Marc O Ernst
The gradient of the reinforcement landscape influences sensorimotor learning pp. 1-27 Downloads
Joshua G A Cashaback, Christopher K Lao, Dimitrios J Palidis, Susan K Coltman, Heather R McGregor and Paul L Gribble
Rapid interpretation of small-angle X-ray scattering data pp. 1-27 Downloads
Marie Weiel, Ines Reinartz and Alexander Schug
An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections pp. 1-32 Downloads
T Alex Perkins, Robert C Reiner, Guido España, Quirine A ten Bosch, Amit Verma, Kelly A Liebman, Valerie A Paz-Soldan, John P Elder, Amy C Morrison, Steven T Stoddard, Uriel Kitron, Gonzalo M Vazquez-Prokopec, Thomas W Scott and David L Smith
ChIPulate: A comprehensive ChIP-seq simulation pipeline pp. 1-32 Downloads
Vishaka Datta, Sridhar Hannenhalli and Rahul Siddharthan
Humans use multi-objective control to regulate lateral foot placement when walking pp. 1-28 Downloads
Jonathan B Dingwell and Joseph P Cusumano
Determination of effective synaptic conductances using somatic voltage clamp pp. 1-28 Downloads
Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou and David Cai
Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence pp. 1-21 Downloads
Manh Cuong Ngô, Mads Peter Heide-Jørgensen and Susanne Ditlevsen
A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations pp. 1-21 Downloads
Weiling Li, Lin Lin, Raunaq Malhotra, Lei Yang, Raj Acharya and Mary Poss
Optimizing the depth and the direction of prospective planning using information values pp. 1-21 Downloads
Can Eren Sezener, Amir Dezfouli and Mehdi Keramati
Latent goal models for dynamic strategic interaction pp. 1-21 Downloads
Shariq N Iqbal, Lun Yin, Caroline B Drucker, Qian Kuang, Jean-François Gariépy, Michael L Platt and John M Pearson
Building a mechanistic mathematical model of hepatitis C virus entry pp. 1-26 Downloads
Mphatso Kalemera, Dilyana Mincheva, Joe Grove and Christopher J R Illingworth
A dynamic power-law sexual network model of gonorrhoea outbreaks pp. 1-20 Downloads
Lilith K Whittles, Peter J White and Xavier Didelot
Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data pp. 1-20 Downloads
Finlay Campbell, Anne Cori, Neil Ferguson and Thibaut Jombart
Evolutionary model for the unequal segregation of high copy plasmids pp. 1-17 Downloads
Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn and Johannes Müller
Bacterial surface colonization, preferential attachment and fitness under periodic stress pp. 1-17 Downloads
Maor Grinberg, Tomer Orevi and Nadav Kashtan
Bayes-optimal estimation of overlap between populations of fixed size pp. 1-17 Downloads
Daniel B Larremore
Soma-axon coupling configurations that enhance neuronal coincidence detection pp. 1-34 Downloads
Joshua H Goldwyn, Michiel W H Remme and John Rinzel
Ten principles for machine-actionable data management plans pp. 1-15 Downloads
Tomasz Miksa, Stephanie Simms, Daniel Mietchen and Sarah Jones
Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability pp. 1-1 Downloads
Vasileios Vavourakis, Triantafyllos Stylianopoulos and Peter A Wijeratne
Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines pp. 1-40 Downloads
Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Kevin Alessandri, Pierre Nassoy and Dirk Drasdo
Methods for computing the maximum performance of computational models of fMRI responses pp. 1-25 Downloads
Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano and Federico De Martino
A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell pp. 1-25 Downloads
Robert John Holash and Brian R MacIntosh
Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas pp. 1-25 Downloads
Lawrence W Sheppard, Emma J Defriez, Philip C Reid and Daniel C Reuman
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling pp. 1-25 Downloads
Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D Price, Chenguang Liu and Zhuo Wang
Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits pp. 1-23 Downloads
Florian Eberhardt, Andreas V M Herz and Stefan Häusler
Agent-based modeling of morphogenetic systems: Advantages and challenges pp. 1-31 Downloads
Chad M Glen, Melissa L Kemp and Eberhard O Voit
Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome pp. 1-31 Downloads
Bernardo P de Almeida, André F Vieira, Joana Paredes, Mónica Bettencourt-Dias and Nuno L Barbosa-Morais
Spatial clustering and common regulatory elements correlate with coordinated gene expression pp. 1-16 Downloads
Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A Taft, Guang Yao, Fan Bai and Jianhua Xing

Volume 15, issue 2, 2019

Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited pp. 1-19 Downloads
Dave Osthus, Ashlynn R Daughton and Reid Priedhorsky
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis pp. 1-19 Downloads
Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk and Mark R Chance
Predictability in process-based ensemble forecast of influenza pp. 1-19 Downloads
Sen Pei, Mark A Cane and Jeffrey Shaman
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas pp. 1-19 Downloads
David G P van IJzendoorn, Karoly Szuhai, Inge H Briaire- de Bruijn, Marie Kostine, Marieke L Kuijjer and Judith V M G Bovée
Identifying individual risk rare variants using protein structure guided local tests (POINT) pp. 1-24 Downloads
Rachel Marceau West, Wenbin Lu, Daniel M Rotroff, Melaine A Kuenemann, Sheng-Mao Chang, Michael C Wu, Michael J Wagner, John B Buse, Alison A Motsinger-Reif, Denis Fourches and Jung-Ying Tzeng
A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks pp. 1-24 Downloads
Koichiro Uriu and Hajime Tei
Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors pp. 1-29 Downloads
Lior Tiroshi and Joshua A Goldberg
Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos pp. 1-27 Downloads
Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui and Philippe Andrey
Learning the payoffs and costs of actions pp. 1-32 Downloads
Moritz Möller and Rafal Bogacz
Maps of variability in cell lineage trees pp. 1-32 Downloads
Damien G Hicks, Terence P Speed, Mohammed Yassin and Sarah M Russell
Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion pp. 1-36 Downloads
Nico M Franz, Lukas J Musher, Joseph W Brown, Shizhuo Yu and Bertram Ludäscher
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction pp. 1-21 Downloads
Amin Allahyar, Joske Ubels and Jeroen de Ridder
Phylogenies from dynamic networks pp. 1-21 Downloads
Cornelia Metzig, Oliver Ratmann, Daniela Bezemer and Caroline Colijn
Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components pp. 1-21 Downloads
Nicholas Rogers, John Hermiz, Mehran Ganji, Erik Kaestner, Kıvılcım Kılıç, Lorraine Hossain, Martin Thunemann, Daniel R Cleary, Bob S Carter, David Barba, Anna Devor, Eric Halgren, Shadi A Dayeh and Vikash Gilja
A local measure of symmetry and orientation for individual spikes of grid cells pp. 1-21 Downloads
Simon N Weber and Henning Sprekeler
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis pp. 1-28 Downloads
Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D Zoltowski and Peng Tao
Social evolution under demographic stochasticity pp. 1-13 Downloads
David V McLeod and Troy Day
Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions pp. 1-22 Downloads
Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora and Udo Reichl
Efficient neural decoding of self-location with a deep recurrent network pp. 1-22 Downloads
Ardi Tampuu, Tambet Matiisen, H Freyja Ólafsdóttir, Caswell Barry and Raul Vicente
Information integration in large brain networks pp. 1-26 Downloads
Daniel Toker and Friedrich T Sommer
ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics pp. 1-26 Downloads
Moritz Hoffmann, Christoph Fröhner and Frank Noé
Independent working memory resources for egocentric and allocentric spatial information pp. 1-20 Downloads
David Aagten-Murphy and Paul M Bays
Development and validation of influenza forecasting for 64 temperate and tropical countries pp. 1-20 Downloads
Sarah C Kramer and Jeffrey Shaman
How good are pathogenicity predictors in detecting benign variants? pp. 1-17 Downloads
Abhishek Niroula and Mauno Vihinen
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications pp. 1-17 Downloads
He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov and Feixiong Cheng
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15 pp. 1-17 Downloads
Sebastian Funk, Anton Camacho, Adam J Kucharski, Rachel Lowe, Rosalind M Eggo and W John Edmunds
Structure and variability of delay activity in premotor cortex pp. 1-17 Downloads
Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I Ryu and Krishna V Shenoy
Identifying the mechanism for superdiffusivity in mouse fibroblast motility pp. 1-15 Downloads
Giuseppe Passucci, Megan E Brasch, James H Henderson, Vasily Zaburdaev and M Lisa Manning
A numerical approach for a discrete Markov model for progressing drug resistance of cancer pp. 1-15 Downloads
Masayuki Maeda and Hideaki Yamashita
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis pp. 1-15 Downloads
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell and Qin Ma
Correction: Epistasis in genomic and survival data of cancer patients pp. 1-1 Downloads
Dariusz Matlak and Ewa Szczurek
Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana pp. 1-25 Downloads
Shayne M Plourde, Prativa Amom, Michelle Tan, Adriana T Dawes and Anna A Dobritsa
Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling pp. 1-25 Downloads
Nitzan Shahar, Tobias U Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, Consortium Nspn and Raymond J Dolan
Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks pp. 1-16 Downloads
Ahmed A Metwally, Philip S Yu, Derek Reiman, Yang Dai, Patricia W Finn and David L Perkins

Volume 15, issue 1, 2019

The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments pp. 1-23 Downloads
Zachary R Fox and Brian Munsky
Deep image reconstruction from human brain activity pp. 1-23 Downloads
Guohua Shen, Tomoyasu Horikawa, Kei Majima and Yukiyasu Kamitani
On identifying collective displacements in apo-proteins that reveal eventual binding pathways pp. 1-18 Downloads
Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal and Surajit Sengupta
OpenCASA: A new open-source and scalable tool for sperm quality analysis pp. 1-18 Downloads
Carlos Alquézar-Baeta, Silvia Gimeno-Martos, Sara Miguel-Jiménez, Pilar Santolaria, Jesús Yániz, Inmaculada Palacín, Adriana Casao, José Álvaro Cebrián-Pérez, Teresa Muiño-Blanco and Rosaura Pérez-Pé
Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects pp. 1-1 Downloads
The PLOS Computational Biology Staff
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor pp. 1-29 Downloads
Keesha E Erickson, Oleksii S Rukhlenko, Md Shahinuzzaman, Kalina P Slavkova, Yen Ting Lin, Ryan Suderman, Edward C Stites, Marian Anghel, Richard G Posner, Dipak Barua, Boris N Kholodenko and William S Hlavacek
Prediction of ultra-high-order antibiotic combinations based on pairwise interactions pp. 1-15 Downloads
Itay Katzir, Murat Cokol, Bree B Aldridge and Uri Alon
Predicting change: Approximate inference under explicit representation of temporal structure in changing environments pp. 1-31 Downloads
Dimitrije Marković, Andrea M F Reiter and Stefan J Kiebel
Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model pp. 1-24 Downloads
Anna C Sales, Karl J Friston, Matthew W Jones, Anthony E Pickering and Rosalyn J Moran
Sour grapes and sweet victories: How actions shape preferences pp. 1-24 Downloads
Fabien Vinckier, Lionel Rigoux, Irma T Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau and Mathias Pessiglione
Computational translation of genomic responses from experimental model systems to humans pp. 1-19 Downloads
Douglas K Brubaker, Elizabeth A Proctor, Kevin M Haigis and Douglas A Lauffenburger
Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis pp. 1-19 Downloads
Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W Pasternak and Marta Filizola
Calcium phosphate precipitation inhibits mitochondrial energy metabolism pp. 1-19 Downloads
Sathyavani Malyala, Yizhu Zhang, Jasiel O Strubbe and Jason N Bazil
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems pp. 1-4 Downloads
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel and Anders Wallqvist
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli pp. 1-26 Downloads
David Hodgson, Andrew D Rowan, Francesco Falciani and Carole J Proctor
PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data pp. 1-26 Downloads
Yu-Han H Hsu, Claire Churchhouse, Tune H Pers, Josep M Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K Morgen, Clicerio Gonzalez, Maria E Gonzalez, Tonu Esko and Joel N Hirschhorn
Spatial synchronization codes from coupled rate-phase neurons pp. 1-42 Downloads
Joseph D Monaco, Rose M De Guzman, Hugh T Blair and Kechen Zhang
Protein—protein binding supersites pp. 1-17 Downloads
Raji Viswanathan, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller and Andras Fiser
A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex pp. 1-20 Downloads
Margot C Bjoring and C Daniel Meliza
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