Works matching IS 1553734X AND DT 2022

Results: 903

DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009797

By:

O'Connor, Owen M.;
Alnahhas, Razan N.;
Lugagne, Jean-Baptiste;
Dunlop, Mary J.

Publication type:

Article

Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009778

By:

Lasso, Gorka;
Khan, Saad;
Allen, Stephanie A.;
Mariano, Margarette;
Florez, Catalina;
Orner, Erika P.;
Quiroz, Jose A.;
Quevedo, Gregory;
Massimi, Aldo;
Hegde, Aditi;
Wirchnianski, Ariel S.;
Bortz III, Robert H.;
Malonis, Ryan J.;
Georgiev, George I.;
Tong, Karen;
Herrera, Natalia G.;
Morano, Nicholas C.;
Garforth, Scott J.;
Malaviya, Avinash;
Khokhar, Ahmed

Publication type:

Article

Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants—An exemplar of how human disturbance impacts group-living species.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009792

By:

Wiśniewska, Maggie;
Puga-Gonzalez, Ivan;
Lee, Phyllis;
Moss, Cynthia;
Russell, Gareth;
Garnier, Simon;
Sueur, Cédric

Publication type:

Article

Ictal wavefront propagation in slices and simulations with conductance-based refractory density model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009782

By:

Chizhov, Anton V.;
Amakhin, Dmitry V.;
Smirnova, Elena Yu.;
Zaitsev, Aleksey V.

Publication type:

Article

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009781

By:

Bryer, Alexander J.;
Reddy, Tyler;
Lyman, Edward;
Perilla, Juan R.

Publication type:

Article

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009793

By:

Jia, Chen;
Singh, Abhyudai;
Grima, Ramon

Publication type:

Article

Ultrafast population coding and axo-somatic compartmentalization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009775

By:

Zhang, Chenfei;
Hofmann, David;
Neef, Andreas;
Wolf, Fred

Publication type:

Article

Controlling gene expression timing through gene regulatory architecture.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009745

By:

Ali, Md Zulfikar;
Brewster, Robert C.

Publication type:

Article

The evolutionary maintenance of Lévy flight foraging.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009490

By:

Campeau, Winston;
Simons, Andrew M.;
Stevens, Brett

Publication type:

Article

A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009733

By:

Mattern, Jann Paul;
Glauninger, Kristof;
Britten, Gregory L.;
Casey, John R.;
Hyun, Sangwon;
Wu, Zhen;
Armbrust, E. Virginia;
Harchaoui, Zaid;
Ribalet, François

Publication type:

Article

Identification of periodic attractors in Boolean networks using a priori information.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009702

By:

Münzner, Ulrike;
Mori, Tomoya;
Krantz, Marcus;
Klipp, Edda;
Akutsu, Tatsuya

Publication type:

Article

Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009758

By:

Miski, Marcell;
Keömley-Horváth, Bence Márk;
Rákóczi Megyeriné, Dorina;
Csikász-Nagy, Attila;
Gáspári, Zoltán

Publication type:

Article

Optimism and pessimism in optimised replay.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009634

By:

Antonov, Georgy;
Gagne, Christopher;
Eldar, Eran;
Dayan, Peter

Publication type:

Article

An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009738

By:

Turner, William;
Feuerriegel, Daniel;
Hester, Robert;
Bode, Stefan

Publication type:

Article

A deep generative model of 3D single-cell organization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009155

By:

Donovan-Maiye, Rory M.;
Brown, Jackson M.;
Chan, Caleb K.;
Ding, Liya;
Yan, Calysta;
Gaudreault, Nathalie;
Theriot, Julie A.;
Maleckar, Mary M.;
Knijnenburg, Theo A.;
Johnson, Gregory R.

Publication type:

Article

Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009779

By:

Handzlik, Joanna E.;
Manu

Publication type:

Article

Computable early Caenorhabditis elegans embryo with a phase field model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009755

By:

Kuang, Xiangyu;
Guan, Guoye;
Wong, Ming-Kin;
Chan, Lu-Yan;
Zhao, Zhongying;
Tang, Chao;
Zhang, Lei

Publication type:

Article

Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009780

By:

Nguyen, Le Khanh Ngan;
Megiddo, Itamar;
Howick, Susan

Publication type:

Article

The activity of human enhancers is modulated by the splicing of their associated lncRNAs.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009722

By:

Tan, Jennifer Yihong;
Marques, Ana Claudia

Publication type:

Article

Formation, collective motion, and merging of macroscopic bacterial aggregates.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009153

By:

Courcoubetis, George;
Gangan, Manasi S.;
Lim, Sean;
Guo, Xiaokan;
Haas, Stephan;
Boedicker, James Q.

Publication type:

Article

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009628

By:

Xu, Zhi Ming;
Rüeger, Sina;
Zwyer, Michaela;
Brites, Daniela;
Hiza, Hellen;
Reinhard, Miriam;
Rutaihwa, Liliana;
Borrell, Sonia;
Isihaka, Faima;
Temba, Hosiana;
Maroa, Thomas;
Naftari, Rastard;
Hella, Jerry;
Sasamalo, Mohamed;
Reither, Klaus;
Portevin, Damien;
Gagneux, Sebastien;
Fellay, Jacques

Publication type:

Article

Dominating lengthscales of zebrafish collective behaviour.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009394

By:

Yang, Yushi;
Turci, Francesco;
Kague, Erika;
Hammond, Chrissy L.;
Russo, John;
Royall, C. Patrick

Publication type:

Article

Asymmetries around the visual field: From retina to cortex to behavior.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009771

By:

Kupers, Eline R.;
Benson, Noah C.;
Carrasco, Marisa;
Winawer, Jonathan

Publication type:

Article

Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009610

By:

Strouwen, Arno;
Nicolaï, Bart M.;
Goos, Peter

Publication type:

Article

Self-organization of collective escape in pigeon flocks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009772

By:

Papadopoulou, Marina;
Hildenbrandt, Hanno;
Sankey, Daniel W. E.;
Portugal, Steven J.;
Hemelrijk, Charlotte K.

Publication type:

Article

Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models.

Published in:

2022

By:

Joshi, Chintan J.;
Schinn, Song-Min;
Richelle, Anne;
Shamie, Isaac;
O'Rourke, Eyleen J.;
Lewis, Nathan E.

Publication type:

Correction Notice

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009749

By:

Martin, Benjamin;
Dans, Pablo D.;
Wieczór, Milosz;
Villegas, Nuria;
Brun-Heath, Isabelle;
Battistini, Federica;
Terrazas, Montserrat;
Orozco, Modesto

Publication type:

Article

Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009762

By:

Wu, Yan;
Xue, Lingfeng;
Huang, Wen;
Deng, Minghua;
Lin, Yihan

Publication type:

Article

Interpretable machine learning for high-dimensional trajectories of aging health.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009746

By:

Farrell, Spencer;
Mitnitski, Arnold;
Rockwood, Kenneth;
Rutenberg, Andrew D.

Publication type:

Article

A lexical approach for identifying behavioural action sequences.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009672

By:

Reddy, Gautam;
Desban, Laura;
Tanaka, Hidenori;
Roussel, Julian;
Mirat, Olivier;
Wyart, Claire

Publication type:

Article

Increasing neural network robustness improves match to macaque V1 eigenspectrum, spatial frequency preference and predictivity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009739

By:

Kong, Nathan C. L.;
Margalit, Eshed;
Gardner, Justin L.;
Norcia, Anthony M.

Publication type:

Article

Ten simple rules for researchers who want to develop web apps.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009663

By:

Saia, Sheila M.;
Nelson, Natalie G.;
Young, Sierra N.;
Parham, Stanton;
Vandegrift, Micah

Publication type:

Article

Beyond advertising: New infrastructures for publishing integrated research objects.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009651

By:

DuPre, Elizabeth;
Holdgraf, Chris;
Karakuzu, Agah;
Tetrel, Loïc;
Bellec, Pierre;
Stikov, Nikola;
Poline, Jean-Baptiste

Publication type:

Article

Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data.

Published in:

2022

By:

Qi, Jing;
Zhou, Yang;
Zhao, Zicen;
Jin, Shuilin

Publication type:

Correction Notice

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009731

By:

Krishnakumar, Raga;
Ruffing, Anne M.

Publication type:

Article

Computational investigation of blood cell transport in retinal microaneurysms.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009728

By:

Li, He;
Deng, Yixiang;
Sampani, Konstantina;
Cai, Shengze;
Li, Zhen;
Sun, Jennifer K.;
Karniadakis, George E.

Publication type:

Article

Microsimulation based quantitative analysis of COVID-19 management strategies.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009693

By:

Reguly, István Z.;
Csercsik, Dávid;
Juhász, János;
Tornai, Kálmán;
Bujtár, Zsófia;
Horváth, Gergely;
Keömley-Horváth, Bence;
Kós, Tamás;
Cserey, György;
Iván, Kristóf;
Pongor, Sándor;
Szederkényi, Gábor;
Röst, Gergely;
Csikász-Nagy, Attila

Publication type:

Article

Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1009667

By:

Jiang, Xuexia;
Isogai, Tadamoto;
Chi, Joseph;
Danuser, Gaudenz

Publication type:

Article

A fast lasso-based method for inferring higher-order interactions.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010730

By:

Elmes, Kieran;
Heywood, Astra;
Huang, Zhiyi;
Gavryushkin, Alex

Publication type:

Article

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010384

By:

Ogane, Tomonori;
Noshiro, Daisuke;
Ando, Toshio;
Yamashita, Atsuko;
Sugita, Yuji;
Matsunaga, Yasuhiro

Publication type:

Article

Robust and brain-like working memory through short-term synaptic plasticity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010776

By:

Kozachkov, Leo;
Tauber, John;
Lundqvist, Mikael;
Brincat, Scott L.;
Slotine, Jean-Jacques;
Miller, Earl K.

Publication type:

Article

Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010765

By:

Embacher, Peter A.;
Germanova, Tsvetelina E.;
Roscioli, Emanuele;
McAinsh, Andrew D.;
Burroughs, Nigel J.

Publication type:

Article

Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010244

By:

Fridman, Yulia;
Wang, Zihan;
Maslov, Sergei;
Goyal, Akshit

Publication type:

Article

Dynamic causal modelling shows a prominent role of local inhibition in alpha power modulation in higher visual cortex.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1009988

By:

Van de Steen, Frederik;
Pinotsis, Dimitris;
Devos, Wouter;
Colenbier, Nigel;
Bassez, Iege;
Friston, Karl;
Marinazzo, Daniele

Publication type:

Article

Mesoscopic description of hippocampal replay and metastability in spiking neural networks with short-term plasticity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010809

By:

Pietras, Bastian;
Schmutz, Valentin;
Schwalger, Tilo

Publication type:

Article

Mechanistic model for human brain metabolism and its connection to the neurovascular coupling.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010798

By:

Sundqvist, Nicolas;
Sten, Sebastian;
Thompson, Peter;
Andersson, Benjamin Jan;
Engström, Maria;
Cedersund, Gunnar

Publication type:

Article

The effects of base rate neglect on sequential belief updating and real-world beliefs.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010796

By:

Ashinoff, Brandon K.;
Buck, Justin;
Woodford, Michael;
Horga, Guillermo

Publication type:

Article

Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010793

By:

Zhu, Yi-Heng;
Zhang, Chengxin;
Yu, Dong-Jun;
Zhang, Yang

Publication type:

Article

The catecholamine precursor Tyrosine reduces autonomic arousal and decreases decision thresholds in reinforcement learning and temporal discounting.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010785

By:

Mathar, David;
Erfanian Abdoust, Mani;
Marrenbach, Tobias;
Tuzsus, Deniz;
Peters, Jan

Publication type:

Article

An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010761

By:

Chen, Xueer;
Chen, Lujia;
Kürten, Cornelius H. L.;
Jabbari, Fattaneh;
Vujanovic, Lazar;
Ding, Ying;
Lu, Binfeng;
Lu, Kevin;
Kulkarni, Aditi;
Tabib, Tracy;
Lafyatis, Robert;
Cooper, Gregory F.;
Ferris, Robert;
Lu, Xinghua

Publication type:

Article