June 2020

Cooperativity has an important role in regulating signaling responses. One of its forms, negative cooperativity, cannot be distinguished from two independent and different binding events based on equilibrium measurements only. Sevlever et al reports a computational work on the discrimination between these two scenarios. The methodology uses both steady-state and kinetic information, and both local and global information, global because it uses data form the complete dose-response curve. This study is not exclusive to ligand-receptor binding, it holds whenever two or more molecules undergo two successive binding events and the proposed method helps unveiling the microscopic details behind the data.

Image Credit: Axel Hernán Mazzeo and Federico Sevlever

Editorials

10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats

Joseph C. Ayoob, Joshua D. Kangas

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007911

Ten simple rules for researchers while in isolation from a pandemic

Hoe-Han Goh, Philip E. Bourne

PLOS Computational Biology: published June 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007946

Education

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007863

Research Articles

Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves

Miguel Capllonch-Juan, Francisco Sepulveda

PLOS Computational Biology: published June 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007826

Stochastic dynamics of Francisella tularensis infection and replication

Jonathan Carruthers, Grant Lythe, Martín López-García, Joseph Gillard, Thomas R. Laws, Roman Lukaszewski, Carmen Molina-París

PLOS Computational Biology: published June 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007752

Realistic modeling of mesoscopic ephaptic coupling in the human brain

Giulio Ruffini, Ricardo Salvador, Ehsan Tadayon, Roser Sanchez-Todo, Alvaro Pascual-Leone, Emiliano Santarnecchi

PLOS Computational Biology: published June 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007923

Two-step mechanism of J-domain action in driving Hsp70 function

Bartlomiej 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

PLOS Computational Biology: published June 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007913

Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms

Andrew K. Smith, Glen E. P. Ropella, Mitchell R. McGill, Preethi Krishnan, Lopamudra Dutta, Ryan C. Kennedy, Hartmut Jaeschke, C. Anthony Hunt

PLOS Computational Biology: published June 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007622

Brain dynamics for confidence-weighted learning

Florent Meyniel

PLOS Computational Biology: published June 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007935

A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma

Hélène Ruffieux, Jérôme Carayol, Radu Popescu, Mary-Ellen Harper, Robert Dent, Wim H. M. Saris, Arne Astrup, Jörg Hager, Anthony C. Davison, Armand Valsesia

PLOS Computational Biology: published June 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007882

Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis

Dirke Imig, Nadine Pollak, Frank Allgöwer, Markus Rehm

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007812

Taste of time: A porous-medium model for human tongue surface with implications for early taste perception

Zhenxing Wu, Kai Zhao

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007888

Disease evolution in reaction networks: Implications for a diagnostic problem

Abolfazl Ramezanpour, Alireza Mashaghi

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007889

Atomistic mechanism of transmembrane helix association

Jan Domański, Mark S. P. Sansom, Phillip J. Stansfeld, Robert B. Best

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007919

Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves

Federico Sevlever, Juan Pablo Di Bella, Alejandra C. Ventura

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007929

HemoMIPs—Automated analysis and result reporting pipeline for targeted sequencing data

Philip Kleinert, Beth Martin, Martin Kircher

PLOS Computational Biology: published June 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007956

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers

Yu Hu, Kai Wang, Mingyao Li

PLOS Computational Biology: published June 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007925

Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection

Rebecca H. Chisholm, Nikki Sonenberg, Jake A. Lacey, Malcolm I. McDonald, Manisha Pandey, Mark R. Davies, Steven Y. C. Tong, Jodie McVernon, Nicholas Geard

PLOS Computational Biology: published June 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007182

Two-variable nullcline analysis of ionic general equilibrium predicts calcium homeostasis in ventricular myocytes

David Conesa, Blas Echebarria, Angelina Peñaranda, Inmaculada R. Cantalapiedra, Yohannes Shiferaw, Enrique Alvarez-Lacalle

PLOS Computational Biology: published June 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007572

Measurable health effects associated with the daylight saving time shift

Hanxin Zhang, Torsten Dahlén, Atif Khan, Gustaf Edgren, Andrey Rzhetsky

PLOS Computational Biology: published June 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007927

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

Hui Yu, Shilin Zhao, Scott Ness, Huining Kang, Quanhu Sheng, David C. Samuels, Olufunmilola Oyebamiji, Ying-yong Zhao, Yan Guo

PLOS Computational Biology: published June 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007968

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

Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke A. Ojewole, Bruce R. Donald

PLOS Computational Biology: published June 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007447

A functional spiking-neuron model of activity-silent working memory in humans based on calcium-mediated short-term synaptic plasticity

Matthijs Pals, Terrence C. Stewart, Elkan G. Akyürek, Jelmer P. Borst

PLOS Computational Biology: published June 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007936

A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data

David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T. Grant Belgard, Alice Zhang, Victor Hanson-Smith

PLOS Computational Biology: published June 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007770

Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure

Yuxiu Shao, Jiwei Zhang, Louis Tao

PLOS Computational Biology: published June 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007265

Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry

Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P. Trzeciakowski, Andreea Trache, Yi Jiang

PLOS Computational Biology: published June 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007693

A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence

Lauren A. White, Sue VandeWoude, Meggan E. Craft

PLOS Computational Biology: published June 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007457

A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks

Víctor A. López-Agudelo, Tom A. Mendum, Emma Laing, HuiHai Wu, Andres Baena, Luis F. Barrera, Dany J. V. Beste, Rigoberto Rios-Estepa

PLOS Computational Biology: published June 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007533

Kilohertz waveforms optimized to produce closed-state Na⁺ channel inactivation eliminate onset response in nerve conduction block

Guosheng Yi, Warren M. Grill

PLOS Computational Biology: published June 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007766

bigPint: A Bioconductor visualization package that makes big data pint-sized

Lindsay Rutter, Dianne Cook

PLOS Computational Biology: published June 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007912

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization

Will Xiao, Gabriel Kreiman

PLOS Computational Biology: published June 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007973

Dynamic interactions of influenza viruses in Hong Kong during 1998-2018

Wan Yang, Eric H. Y. Lau, Benjamin J. Cowling

PLOS Computational Biology: published June 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007989

Circuits with broken fibration symmetries perform core logic computations in biological networks

Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse

PLOS Computational Biology: published June 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007776

Early transmission of sensitive strain slows down emergence of drug resistance in Plasmodium vivax

Mario J. C. Ayala, Daniel A. M. Villela

PLOS Computational Biology: published June 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007945

Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment

Alexey Savelyev, Gary E. Gorbet, Amy Henrickson, Borries Demeler

PLOS Computational Biology: published June 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007942

Spiking network optimized for word recognition in noise predicts auditory system hierarchy

Fatemeh Khatami, Monty A. Escabí

PLOS Computational Biology: published June 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007558

A crowdsourced set of curated structural variants for the human genome

Lesley 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 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

PLOS Computational Biology: published June 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007933

Combined model-free and model-sensitive reinforcement learning in non-human primates

Bruno Miranda, W. M. Nishantha Malalasekera, Timothy E. Behrens, Peter Dayan, Steven W. Kennerley

PLOS Computational Biology: published June 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007944

Assessing predictors for new post translational modification sites: A case study on hydroxylation

Damiano Piovesan, Andras Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon, Silvio C. E. Tosatto

PLOS Computational Biology: published June 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007967

Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm

Satoshi Ii, Hiroki Kitade, Shunichi Ishida, Yohsuke Imai, Yoshiyuki Watanabe, Shigeo Wada

PLOS Computational Biology: published June 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007943

Classifying sex and strain from mouse ultrasonic vocalizations using deep learning

A. Ivanenko, P. Watkins, M. A. J. van Gerven, K. Hammerschmidt, B. Englitz

PLOS Computational Biology: published June 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007918

Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

Nima Nouri, Steven H. Kleinstein

PLOS Computational Biology: published June 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007977

Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions

Emili Balaguer-Ballester, Ramon Nogueira, Juan M. Abofalia, Ruben Moreno-Bote, Maria V. Sanchez-Vives

PLOS Computational Biology: published June 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007862

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis

Jakob Rosenbauer, Chengting Zhang, Benjamin Mattes, Ines Reinartz, Kyle Wedgwood, Simone Schindler, Claude Sinner, Steffen Scholpp, Alexander Schug

PLOS Computational Biology: published June 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007417

Natural scene statistics predict how humans pool information across space in surface tilt estimation

Seha Kim, Johannes Burge

PLOS Computational Biology: published June 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007947

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans

Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell

PLOS Computational Biology: published June 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007892

Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions

Hadi Rahmaninejad, Tom Pace, Shashank Bhatt, Bin Sun, Peter Kekenes-Huskey

PLOS Computational Biology: published June 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007903

Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus

Atte S. A. Eskelinen, Petri Tanska, Cristina Florea, Gustavo A. Orozco, Petro Julkunen, Alan J. Grodzinsky, Rami K. Korhonen

PLOS Computational Biology: published June 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007998

Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing—Application to influenza vaccine production

Stefanie Duvigneau, Robert Dürr, Tanja Laske, Mandy Bachmann, Melanie Dostert, Achim Kienle

PLOS Computational Biology: published June 29, 2020 | https://doi.org/10.1371/journal.pcbi.1007810

Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model

Sandra Mayr, Fabian Hauser, Sujitha Puthukodan, Markus Axmann, Janett Göhring, Jaroslaw Jacak

PLOS Computational Biology: published June 30, 2020 | https://doi.org/10.1371/journal.pcbi.1007902

Cover

Negative cooperativity identified by global measurements and kinetic discrimination

Editorials

Education

Research Articles

Related Articles

Related Articles

Related Articles