Works in PLoS Computational Biology, 2022, Vol 18, Issue 7

Results: 61

Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010343

By:

Tao, Jiaye;
Wang, Heping;
Wang, Wenjian;
Mi, Na;
Zhang, Wei;
Wen, Qiujia;
Ouyang, Jiajing;
Liang, Xinyun;
Chen, Min;
Guo, Wentao;
Li, Guoming;
Liu, Jun;
Zhao, Hanning;
Wang, Xin;
Li, Xuemeng;
Feng, Shengjun;
Liu, Xinguang;
He, Zhiwei;
Zhao, Zuguo

Publication type:

Article

Cheater suppression and stochastic clearance through quorum sensing.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010292

By:

Moffett, Alexander S.;
Thomas, Peter J.;
Hinczewski, Michael;
Eckford, Andrew W.

Publication type:

Article

Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010275

By:

Amin, Rafiul;
Faghih, Rose T.

Publication type:

Article

Inferring the nature of linguistic computations in the brain.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010269

By:

Ten Oever, Sanne;
Kaushik, Karthikeya;
Martin, Andrea E.

Publication type:

Article

The dopamine circuit as a reward-taxis navigation system.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010340

By:

Karin, Omer;
Alon, Uri

Publication type:

Article

Suprathreshold perceptual decisions constrain models of confidence.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010318

By:

Locke, Shannon M.;
Landy, Michael S.;
Mamassian, Pascal

Publication type:

Article

Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010291

By:

Christensen, Alexander Kier;
Piggott, Matthew D.;
van Sebille, Erik;
van Reeuwijk, Maarten;
Pawar, Samraat

Publication type:

Article

Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010329

By:

Chabas, Hélène;
Müller, Viktor;
Bonhoeffer, Sebastian;
Regoes, Roland R.

Publication type:

Article

Examining the impact of ICU population interaction structure on modeled colonization dynamics of Staphylococcus aureus.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010352

By:

Mietchen, Matthew S.;
Short, Christopher T.;
Samore, Matthew;
Lofgren, Eric T.

Publication type:

Article

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010220

By:

Bacon, Wendi;
Holinski, Alexandra;
Pujol, Marina;
Wilmott, Meredith;
Morgan, Sarah L

Publication type:

Article

The computational relationship between reinforcement learning, social inference, and paranoia.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010326

By:

Barnby, Joseph M.;
Mehta, Mitul A.;
Moutoussis, Michael

Publication type:

Article

Chemophoresis engine: A general mechanism of ATPase-driven cargo transport.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010324

By:

Sugawara, Takeshi;
Kaneko, Kunihiko

Publication type:

Article

A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010319

By:

Angelini, Erin;
Wang, Yue;
Zhou, Joseph Xu;
Qian, Hong;
Huang, Sui

Publication type:

Article

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010310

By:

Freeman, Tom C.;
Horsewell, Sebastian;
Patir, Anirudh;
Harling-Lee, Josh;
Regan, Tim;
Shih, Barbara B.;
Prendergast, James;
Hume, David A.;
Angus, Tim

Publication type:

Article

Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010314

By:

Cecilia, Hélène;
Vriens, Roosmarie;
Wichgers Schreur, Paul J.;
de Wit, Mariken M.;
Métras, Raphaëlle;
Ezanno, Pauline;
ten Bosch, Quirine A.

Publication type:

Article

Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010254

By:

Ruiz-Martinez, Alvaro;
Gong, Chang;
Wang, Hanwen;
Sov́e, Richard J.;
Mi, Haoyang;
Kimko, Holly;
Popel, Aleksander S.

Publication type:

Article

Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009996

By:

Yuhn, Changyoung;
Oshima, Marie;
Chen, Yan;
Hayakawa, Motoharu;
Yamada, Shigeki

Publication type:

Article

Haisu: Hierarchically supervised nonlinear dimensionality reduction.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010351

By:

VanHorn, Kevin Christopher;
Çobanoğlu, Murat Can

Publication type:

Article

Ten simple rules to host an inclusive conference.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010164

By:

Joo, Rocío;
Sánchez-Tapia, Andrea;
Mortara, Sara;
Bellini Saibene, Yanina;
Turner, Heather;
Hug Peter, Dorothea;
Morandeira, Natalia Soledad;
Bannert, Matt;
Almazrouq, Batool;
Hare, Elizabeth;
Ación, Laura;
Narváez-Gómez, Juan Pablo;
Alfaro Córdoba, Marcela;
Marini, Federico;
Giordano, Rita;
Canelón, Silvia;
Ebou, Anicet;
Upadhya, Adithi R.;
Chávez, Joselyn;
Ravi, Janani

Publication type:

Article

The spectrum of covariance matrices of randomly connected recurrent neuronal networks with linear dynamics.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010327

By:

Hu, Yu;
Sompolinsky, Haim

Publication type:

Article

Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010306

By:

Galbraith, Madeline;
Bocci, Federico;
Onuchic, José N.

Publication type:

Article

Modelling the modulation of cortical Up-Down state switching by astrocytes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010296

By:

Blum Moyse, Lisa;
Berry, Hugues

Publication type:

Article

Pooling strategies in V1 can account for the functional and structural diversity across species.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010270

By:

Boutin, Victor;
Franciosini, Angelo;
Chavane, Frédéric;
Perrinet, Laurent U.

Publication type:

Article

Asymmetric and adaptive reward coding via normalized reinforcement learning.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010350

By:

Louie, Kenway

Publication type:

Article

Helix 8 in chemotactic receptors of the complement system.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009994

By:

Wisniewski, Szymon;
Dragan, Paulina;
Makal, Anna;
Latek, Dorota

Publication type:

Article

Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010330

By:

Jimenez-Guardeño, Jose M.;
Ortega-Prieto, Ana Maria;
Menendez Moreno, Borja;
Maguire, Thomas J. A.;
Richardson, Adam;
Diaz-Hernandez, Juan Ignacio;
Diez Perez, Javier;
Zuckerman, Mark;
Mercadal Playa, Albert;
Cordero Deline, Carlos;
Malim, Michael H.;
Martinez-Nunez, Rocio Teresa

Publication type:

Article

Leveraging a physiologically-based quantitative translational modeling platform for designing B cell maturation antigen-targeting bispecific T cell engagers for treatment of multiple myeloma.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009715

By:

Yoneyama, Tomoki;
Kim, Mi-Sook;
Piatkov, Konstantin;
Wang, Haiqing;
Zhu, Andy Z. X.

Publication type:

Article

Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010328

By:

Liu, Long;
Meng, Qingyu;
Weng, Cherry;
Lu, Qing;
Wang, Tong;
Wen, Yalu

Publication type:

Article

Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010311

By:

Brennan, Jennifer;
Jain, Lalit;
Garman, Sofia;
Donnelly, Ann E.;
Wright, Erik Scott;
Jamieson, Kevin

Publication type:

Article

To what extent naringenin binding and membrane depolarization shape mitoBK channel gating—A machine learning approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010315

By:

Richter-Laskowska, Monika;
Trybek, Paulina;
Bednarczyk, Piotr;
Wawrzkiewicz-Jałowiecka, Agata

Publication type:

Article

Modeling scenarios for mitigating outbreaks in congregate settings.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010308

By:

Blumberg, Seth;
Lu, Phoebe;
Kwan, Ada T.;
Hoover, Christopher M.;
Lloyd-Smith, James O.;
Sears, David;
Bertozzi, Stefano M.;
Worden, Lee

Publication type:

Article

Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010323

By:

Eissa, Tahra L.;
Gold, Joshua I.;
Josić, Krešimir;
Kilpatrick, Zachary P.

Publication type:

Article

Modulation transfer functions for audiovisual speech.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010273

By:

Pedersen, Nicolai F.;
Dau, Torsten;
Hansen, Lars Kai;
Hjortkjær, Jens

Publication type:

Article

Network resonance can be generated independently at distinct levels of neuronal organization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010364

By:

Stark, Eran;
Levi, Amir;
Rotstein, Horacio G.

Publication type:

Article

Dimensionality reduction of longitudinal 'omics data using modern tensor factorizations.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010212

By:

Mor, Uria;
Cohen, Yotam;
Valdés-Mas, Rafael;
Kviatcovsky, Denise;
Elinav, Eran;
Avron, Haim

Publication type:

Article

If you don't let it in, you don't have to get it out: Thought preemption as a method to control unwanted thoughts.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010285

By:

Fradkin, Isaac;
Eldar, Eran

Publication type:

Article

Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010287

By:

Gupta, Chirag;
Xu, Jielin;
Jin, Ting;
Khullar, Saniya;
Liu, Xiaoyu;
Alatkar, Sayali;
Cheng, Feixiong;
Wang, Daifeng

Publication type:

Article

NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010265

By:

Huang, Yuanhao;
Wang, Bingjiang;
Liu, Jie

Publication type:

Article

Modelling livestock infectious disease control policy under differing social perspectives on vaccination behaviour.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010235

By:

Hill, Edward M.;
Prosser, Naomi S.;
Ferguson, Eamonn;
Kaler, Jasmeet;
Green, Martin J.;
Keeling, Matt J.;
Tildesley, Michael J.

Publication type:

Article

Ten simple rules for designing and running a computing minor for bio/chem students.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010202

By:

Reyes, Rochelle-Jan;
Hosmane, Nina;
Ihorn, Shasta;
Johnson, Milo;
Kulkarni, Anagha;
Nelson, Jennifer;
Savvides, Michael;
Ta, Duc;
Yoon, Ilmi;
Pennings, Pleuni S.

Publication type:

Article

Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010322

By:

Fröhlich, Fabian;
Sorger, Peter K.

Publication type:

Article

What are housekeeping genes?

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010295

By:

Joshi, Chintan J.;
Ke, Wenfan;
Drangowska-Way, Anna;
O'Rourke, Eyleen J.;
Lewis, Nathan E.

Publication type:

Article

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010184

By:

Wang, Yu;
Sun, Fengzhu;
Lin, Wei;
Zhang, Shuqin

Publication type:

Article

RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010293

By:

Ma, Hongli;
Wen, Han;
Xue, Zhiyuan;
Li, Guojun;
Zhang, Zhaolei

Publication type:

Article

Thalamic deep brain stimulation paradigm to reduce consciousness: Cortico-striatal dynamics implicated in mechanisms of consciousness.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010294

By:

Redinbaugh, Michelle J.;
Afrasiabi, Mohsen;
Phillips, Jessica M.;
Kambi, Niranjan A.;
Mohanta, Sounak;
Raz, Aeyal;
Saalmann, Yuri B.

Publication type:

Article

The accuracy of absolute differential abundance analysis from relative count data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010284

By:

Roche, Kimberly E.;
Mukherjee, Sayan

Publication type:

Article

Local and collective transitions in sparsely-interacting ecological communities.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010274

By:

Marcus, Stav;
Turner, Ari M.;
Bunin, Guy

Publication type:

Article

Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009834

By:

Paik, Hyojung;
Kim, Jimin;
Seo, Sangjae

Publication type:

Article

Non-zero mean alpha oscillations revealed with computational model and empirical data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010272

By:

Studenova, Alina A.;
Villringer, Arno;
Nikulin, Vadim V.

Publication type:

Article

Model-based translation of DNA damage signaling dynamics across cell types.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010264

By:

Heldring, Muriel M.;
Wijaya, Lukas S.;
Niemeijer, Marije;
Yang, Huan;
Lakhal, Talel;
Le Dévédec, Sylvia E.;
van de Water, Bob;
Beltman, Joost B.

Publication type:

Article