Journal: PLoS Computational Biology

Volume 16, Issue 6

0 -- 0Joseph C. Ayoob, Joshua D. Kangas. 10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats
0 -- 0Víctor A. López-Agudelo, Tom A. Mendum, Emma Laing, HuiHai Wu, Andres Baena, Luis F. Barrera, Dany J. V. Beste, Rigoberto Rios-Estepa. A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
0 -- 0David V. Conesa, Blas Echebarria, Angelina Peñaranda, Inmaculada R. Cantalapiedra, Yohannes Shiferaw, Enrique Alvarez-Lacalle. Two-variable nullcline analysis of ionic general equilibrium predicts calcium homeostasis in ventricular myocytes
0 -- 0Florent Meyniel. Brain dynamics for confidence-weighted learning
0 -- 0Sandra Mayr, Fabian Hauser, Sujitha Puthukodan, Markus Axmann, Janett Göhring, Jaroslaw Jacak. Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model
0 -- 0Guosheng Yi, Warren M. Grill. Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block
0 -- 0Jonathan Carruthers, Grant Lythe, Martín López-García, Joseph Gillard, Thomas R. Laws, Roman Lukaszewski, Carmen Molina-París. Stochastic dynamics of Francisella tularensis infection and replication
0 -- 0Lindsay Rutter, Dianne Cook. bigPint: A Bioconductor visualization package that makes big data pint-sized
0 -- 0Philip Kleinert, Beth Martin, Martin Kircher. HemoMIPs - Automated analysis and result reporting pipeline for targeted sequencing data
0 -- 0Atte S. A. Eskelinen, Petri Tanska, Cristina Florea, Gustavo A. Orozco, Petro Julkunen, Alan J. Grodzinsky, Rami K. Korhonen. Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus
0 -- 0Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke Ojewole, Bruce Randall Donald. Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface
0 -- 0Lauren A. White, Sue VandeWoude, Meggan E. Craft. A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence
0 -- 0Garikoitz Lerma-Usabiaga, Noah C. Benson, Jonathan Winawer, Brian A. Wandell. A validation framework for neuroimaging software: The case of population receptive fields
0 -- 0Giulio Ruffini, Ricardo Salvador, Ehsan Tadayon, Roser Sanchez-Todo, Alvaro Pascual-Leone, Emiliano Santarnecchi. Realistic modeling of mesoscopic ephaptic coupling in the human brain
0 -- 0Emili Balaguer-Ballester, Ramon Nogueira, Juan M. Abofalia, Rubén Moreno-Bote, Maria V. Sanchez-Vives. Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions
0 -- 0Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel J. Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E. Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook. A crowdsourced set of curated structural variants for the human genome
0 -- 0Damiano Piovesan, András Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon, Silvio C. E. Tosatto. Assessing predictors for new post translational modification sites: A case study on hydroxylation
0 -- 0Niklas Korsbo, Henrik Jönsson. It's about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
0 -- 0Rebecca H. Chisholm, Nikki Sonenberg, Jake A. Lacey, Malcolm I. McDonald, Manisha Pandey, Mark R. Davies, Steven Y. C. Tong, Jodie McVernon, Nicholas Geard. Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection
0 -- 0Mikkel Herholdt Jensen, Eliza J. Morris, Hai Tran, Michael A. Nash, Cheemeng Tan. Stochastic ordering of complexoform protein assembly by genetic circuits
0 -- 0Will Xiao, Gabriel Kreiman. XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
0 -- 0Ethan D. Evans, Chengzhen Dai, Siavash Isazadeh, Shinkyu Park, Carlo Ratti, Eric J. Alm. Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites
0 -- 0Nimrod Sherf, Maoz Shamir. Multiplexing rhythmic information by spike timing dependent plasticity
0 -- 0Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin. G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
0 -- 0Satoshi Ii, Hiroki Kitade, Shunichi Ishida, Yohsuke Imai, Yoshiyuki Watanabe, Shigeo Wada. Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm
0 -- 0Shintaro Nagata, Macoto Kikuchi. Emergence of cooperative bistability and robustness of gene regulatory networks
0 -- 0A. Armean Wright, Ghassan N. Fayad, James F. Selgrade, Mette S. Olufsen. Mechanistic model of hormonal contraception
0 -- 0Jens Karschau, André Scholich, Jonathan Wise, Hernán Morales-Navarrete, Yannis Kalaidzidis, Marino Zerial, Benjamin M. Friedrich. Resilience of three-dimensional sinusoidal networks in liver tissue
0 -- 0Hoe-Han Goh, Philip E. Bourne. Ten simple rules for researchers while in isolation from a pandemic
0 -- 0Aleksey V. Zimin, Steven L. Salzberg. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
0 -- 0Jan J. Domanski, Mark S. P. Sansom, Phillip J. Stansfeld, Robert B. Best. Atomistic mechanism of transmembrane helix association
0 -- 0Bartlomiej Tomiczek, Wojciech Delewski, Lukasz Nierzwicki, Milena Stolarska, Igor Grochowina, Brenda Schilke, Rafal Dutkiewicz, Marta A. Uzarska, Szymon J. Ciesielski, Jacek Czub, Elizabeth A. Craig, Jaroslaw Marszalek. Two-step mechanism of J-domain action in driving Hsp70 function
0 -- 0Abolfazl Ramezanpour, Alireza Mashaghi. Disease evolution in reaction networks: Implications for a diagnostic problem
0 -- 0Bruno Miranda, W. M. Nishantha Malalasekera, Timothy Edward John Behrens, Peter Dayan, Steven W. Kennerley. Combined model-free and model-sensitive reinforcement learning in non-human primates
0 -- 0Jakob Rosenbauer, Chengting Zhang, Benjamin Mattes, Ines Reinartz, Kyle Wedgwood, Simone Schindler, Claude Sinner, Steffen Scholpp, Alexander Schug. Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis
0 -- 0Hanxin Zhang, Torsten Dahlén, Atif Khan, Gustaf Edgren, Andrey Rzhetsky. Measurable health effects associated with the daylight saving time shift
0 -- 0David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T. Grant Belgard, Alice Zhang, Victor Hanson-Smith. A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
0 -- 0Mario J. C. Ayala, Daniel A. M. Villela. Early transmission of sensitive strain slows down emergence of drug resistance in Plasmodium vivax
0 -- 0Fabian Konrath, Anna Mittermeier, Elena Cristiano, Jana Wolf, Alexander Loewer. A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics
0 -- 0Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P. Trzeciakowski, Andreea Trache, Yi Jiang. Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry
0 -- 0Stefanie Duvigneau, Robert Dürr, Tanja Laske, Mandy Bachmann, Melanie Dostert, Achim Kienle. Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing - Application to influenza vaccine production
0 -- 0Yuxiu Shao, Jiwei Zhang, Louis Tao. Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure
0 -- 0Matthijs Pals, Terrence C. Stewart, Elkan G. Akyürek, Jelmer P. Borst. A functional spiking-neuron model of activity-silent working memory in humans based on calcium-mediated short-term synaptic plasticity
0 -- 0Wan Yang, Eric H. Y. Lau, Benjamin J. Cowling. Dynamic interactions of influenza viruses in Hong Kong during 1998-2018
0 -- 0Nima Nouri, Steven H. Kleinstein. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
0 -- 0Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein. Epigenome-based splicing prediction using a recurrent neural network
0 -- 0Dirke Imig, Nadine Pollak, Frank Allgöwer, Markus Rehm. Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis
0 -- 0Hui Yu, Shilin Zhao, Scott Ness, Huining Kang, Quanhu Sheng, David C. Samuels, Olufunmilola Oyebamiji, Ying-Yong Zhao, Yan Guo. Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats
0 -- 0Hadi Rahmaninejad, Tom Pace, Shashank Bhatt, Bin Sun, Peter M. Kekenes-Huskey. Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions
0 -- 0A. Ivanenko, P. Watkins, Marcel A. J. van Gerven, K. Hammerschmidt, Bernhard Englitz. Classifying sex and strain from mouse ultrasonic vocalizations using deep learning
0 -- 0Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell. Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
0 -- 0Fatemeh Khatami, Monty A. Escabí. Spiking network optimized for word recognition in noise predicts auditory system hierarchy
0 -- 0Miguel Capllonch-Juan, Francisco Sepulveda. Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves
0 -- 0Samuel R. Bray, Bo Wang. Forecasting unprecedented ecological fluctuations
0 -- 0Yu Hu, Kai Wang, Mingyao Li. Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
0 -- 0Andrew K. Smith, Glen E. P. Ropella, Mitchell R. McGill, Preethi Krishnan, Lopamudra Dutta, Ryan C. Kennedy, Hartmut Jaeschke, C. Anthony Hunt. Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms
0 -- 0Zhenxing Wu, Kai Zhao. Taste of time: A porous-medium model for human tongue surface with implications for early taste perception
0 -- 0Hélène Ruffieux, Jérôme Carayol, Radu Popescu, Mary-Ellen Harper, Robert Dent, Wim H. M. Saris, Arne Astrup, Jörg Hager, Anthony C. Davison, Armand Valsesia. A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma
0 -- 0Seha Kim, Johannes Burge. Natural scene statistics predict how humans pool information across space in surface tilt estimation
0 -- 0Alexey Savelyev, Gary Gorbet, Amy Henrickson, Borries Demeler. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment
0 -- 0Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse. Circuits with broken fibration symmetries perform core logic computations in biological networks
0 -- 0Federico Sevlever, Juan Pablo Di-Bella, Alejandra C. Ventura. Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves