Works in PLoS Computational Biology, 2019, Vol 15, Issue 2

Results: 58

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.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006800

By:

Plourde, Shayne M.;
Amom, Prativa;
Tan, Michelle;
Dawes, Adriana T.;
Dobritsa, Anna A.

Publication type:

Article

Modeling and MEG evidence of early consonance processing in auditory cortex.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006820

By:

Tabas, Alejandro;
Andermann, Martin;
Schuberth, Valeria;
Riedel, Helmut;
Balaguer-Ballester, Emili;
Rupp, André

Publication type:

Article

Learning the payoffs and costs of actions.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006285

By:

Möller, Moritz;
Bogacz, Rafal

Publication type:

Article

Predictability in process-based ensemble forecast of influenza.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006783

By:

Pei, Sen;
Cane, Mark A.;
Shaman, Jeffrey

Publication type:

Article

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006830

By:

Hoffmann, Moritz;
Fröhner, Christoph;
Noé, Frank

Publication type:

Article

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006733

By:

Damiani, Chiara;
Maspero, Davide;
Di Filippo, Marzia;
Colombo, Riccardo;
Pescini, Dario;
Graudenzi, Alex;
Westerhoff, Hans Victor;
Alberghina, Lilia;
Vanoni, Marco;
Mauri, Giancarlo

Publication type:

Article

Correction: Epistasis in genomic and survival data of cancer patients.

Published in:

2019

By:

Matlak, Dariusz;
Szczurek, Ewa

Publication type:

Correction Notice

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006678

By:

Ayati, Marzieh;
Wiredja, Danica;
Schlatzer, Daniela;
Maxwell, Sean;
Li, Ming;
Koyutürk, Mehmet;
Chance, Mark R.

Publication type:

Article

Script of scripts: A pragmatic workflow system for daily computational research.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006843

By:

Wang, Gao;
Peng, Bo

Publication type:

Article

PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You.

Published in:: PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006885
Publication type:: Article

Maximum entropy and population heterogeneity in continuous cell cultures.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006823

By:

Fernandez-de-Cossio-Diaz, Jorge;
Mulet, Roberto

Publication type:

Article

Development and validation of influenza forecasting for 64 temperate and tropical countries.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006742

By:

Kramer, Sarah C.;
Shaman, Jeffrey

Publication type:

Article

Phylogenies from dynamic networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006761

By:

Metzig, Cornelia;
Ratmann, Oliver;
Bezemer, Daniela;
Colijn, Caroline

Publication type:

Article

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006721

By:

Woloszynek, Stephen;
Zhao, Zhengqiao;
Chen, Jian;
Rosen, Gail L.

Publication type:

Article

Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006440

By:

Pham, Tuan;
Haas, Julie S.

Publication type:

Article

A computational model of epithelial solute and water transport along a human nephron.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006108

By:

Layton, Anita T.;
Layton, Harold E.

Publication type:

Article

Structure and variability of delay activity in premotor cortex.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006808

By:

Even-Chen, Nir;
Sheffer, Blue;
Vyas, Saurabh;
Ryu, Stephen I.;
Shenoy, Krishna V.

Publication type:

Article

Controlling seizure propagation in large-scale brain networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006805

By:

Olmi, Simona;
Petkoski, Spase;
Guye, Maxime;
Bartolomei, Fabrice;
Jirsa, Viktor

Publication type:

Article

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006799

By:

Funnell, Tyler;
Zhang, Allen W.;
Grewal, Diljot;
McKinney, Steven;
Bashashati, Ali;
Wang, Yi Kan;
Shah, Sohrab P.

Publication type:

Article

Independent working memory resources for egocentric and allocentric spatial information.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006563

By:

Aagten-Murphy, David;
Bays, Paul M.

Publication type:

Article

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006826

By:

van IJzendoorn, David G. P.;
Szuhai, Karoly;
Briaire-de Bruijn, Inge H.;
Kostine, Marie;
Kuijjer, Marieke L.;
Bovée, Judith V. M. G.

Publication type:

Article

Identifying individual risk rare variants using protein structure guided local tests (POINT).

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006722

By:

Marceau West, Rachel;
Lu, Wenbin;
Rotroff, Daniel M.;
Kuenemann, Melaine A.;
Chang, Sheng-Mao;
Wu, Michael C.;
Wagner, Michael J.;
Buse, John B.;
Motsinger-Reif, Alison A.;
Fourches, Denis;
Tzeng, Jung-Ying

Publication type:

Article

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006731

By:

Grytten, Ivar;
Rand, Knut D.;
Nederbragt, Alexander J.;
Storvik, Geir O.;
Glad, Ingrid K.;
Sandve, Geir K.

Publication type:

Article

Multi-modality in gene regulatory networks with slow promoter kinetics.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006784

By:

Ali Al-Radhawi, Muhammad;
Del Vecchio, Domitilla;
Sontag, Eduardo D.

Publication type:

Article

Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006819

By:

Rüdiger, Daniel;
Kupke, Sascha Young;
Laske, Tanja;
Zmora, Pawel;
Reichl, Udo

Publication type:

Article

Efficient neural decoding of self-location with a deep recurrent network.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006822

By:

Tampuu, Ardi;
Matiisen, Tambet;
Ólafsdóttir, H. Freyja;
Barry, Caswell;
Vicente, Raul

Publication type:

Article

A numerical approach for a discrete Markov model for progressing drug resistance of cancer.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006770

By:

Maeda, Masayuki;
Yamashita, Hideaki

Publication type:

Article

A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006787

By:

Uriu, Koichiro;
Tei, Hajime

Publication type:

Article

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006801

By:

Zhou, Hongyu;
Dong, Zheng;
Verkhivker, Gennady;
Zoltowski, Brian D.;
Tao, Peng

Publication type:

Article

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006772

By:

Peng, He;
Zeng, Xiangxiang;
Zhou, Yadi;
Zhang, Defu;
Nussinov, Ruth;
Cheng, Feixiong

Publication type:

Article

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006493

By:

Franz, Nico M.;
Musher, Lukas J.;
Brown, Joseph W.;
Yu, Shizhuo;
Ludäscher, Bertram

Publication type:

Article

Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006473

By:

Velez Rueda, Ana Julia;
Benítez, Guillermo I.;
Marchetti, Julia;
Hasenahuer, Marcia Anahí;
Fornasari, María Silvina;
Palopoli, Nicolas;
Parisi, Gustavo

Publication type:

Article

Identifying the mechanism for superdiffusivity in mouse fibroblast motility.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006732

By:

Passucci, Giuseppe;
Brasch, Megan E.;
Henderson, James H.;
Zaburdaev, Vasily;
Manning, M. Lisa

Publication type:

Article

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006792

By:

Monier, Brandon;
McDermaid, Adam;
Wang, Cankun;
Zhao, Jing;
Miller, Allison;
Fennell, Anne;
Ma, Qin

Publication type:

Article

Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006803

By:

Shahar, Nitzan;
Hauser, Tobias U.;
Moutoussis, Michael;
Moran, Rani;
Keramati, Mehdi;
null, null;
Dolan, Raymond J.

Publication type:

Article

Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006762

By:

Chen, Yangchun Frank;
Xia, Yu

Publication type:

Article

Maps of variability in cell lineage trees.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006745

By:

Hicks, Damien G.;
Speed, Terence P.;
Yassin, Mohammed;
Russell, Sarah M.

Publication type:

Article

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006785

By:

Funk, Sebastian;
Camacho, Anton;
Kucharski, Adam J.;
Lowe, Rachel;
Eggo, Rosalind M.;
Edmunds, W. John

Publication type:

Article

Network-guided prediction of aromatase inhibitor response in breast cancer.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006730

By:

Ruffalo, Matthew;
Thomas, Roby;
Chen, Jian;
Lee, Adrian V.;
Oesterreich, Steffi;
Bar-Joseph, Ziv

Publication type:

Article

How good are pathogenicity predictors in detecting benign variants?

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006481

By:

Niroula, Abhishek;
Vihinen, Mauno

Publication type:

Article

Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006771

By:

Julien, Moukhtar;
Trubuil, Alain;
Belcram, Katia;
Legland, David;
Khadir, Zhor;
Urbain, Aurélie;
Palauqui, Jean-Christophe;
Andrey, Philippe

Publication type:

Article

Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006769

By:

Rogers, Nicholas;
Hermiz, John;
Ganji, Mehran;
Kaestner, Erik;
Kılıç, Kıvılcım;
Hossain, Lorraine;
Thunemann, Martin;
Cleary, Daniel R.;
Carter, Bob S.;
Barba, David;
Devor, Anna;
Halgren, Eric;
Dayeh, Shadi A.;
Gilja, Vikash

Publication type:

Article

A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006766

By:

Zhang, Qingtian;
Hu, Xiaolin;
Hong, Bo;
Zhang, Bo

Publication type:

Article

BioJava 5: A community driven open-source bioinformatics library.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006791

By:

Lafita, Aleix;
Bliven, Spencer;
Prlić, Andreas;
Guzenko, Dmytro;
Rose, Peter W.;
Bradley, Anthony;
Pavan, Paolo;
Myers-Turnbull, Douglas;
Valasatava, Yana;
Heuer, Michael;
Larson, Matt;
Burley, Stephen K.;
Duarte, Jose M.

Publication type:

Article

A local measure of symmetry and orientation for individual spikes of grid cells.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006804

By:

Weber, Simon N.;
Sprekeler, Henning

Publication type:

Article

Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006782

By:

Tiroshi, Lior;
Goldberg, Joshua A.

Publication type:

Article

Information integration in large brain networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006807

By:

Toker, Daniel;
Sommer, Friedrich T.

Publication type:

Article

Apollo: Democratizing genome annotation.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006790

By:

Dunn, Nathan A.;
Unni, Deepak R.;
Diesh, Colin;
Munoz-Torres, Monica;
Harris, Nomi L.;
Yao, Eric;
Rasche, Helena;
Holmes, Ian H.;
Elsik, Christine G.;
Lewis, Suzanna E.

Publication type:

Article

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006693

By:

Metwally, Ahmed A.;
Yu, Philip S.;
Reiman, Derek;
Dai, Yang;
Finn, Patricia W.;
Perkins, David L.

Publication type:

Article

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006657

By:

Allahyar, Amin;
Ubels, Joske;
de Ridder, Jeroen

Publication type:

Article