Search Results - "PLoS computational biology"

Covasim: An agent-based model of COVID-19 dynamics and interventions by Kerr, Cliff C, Stuart, Robyn M, Mistry, Dina, Abeysuriya, Romesh G, Rosenfeld, Katherine, Hart, Gregory R, Núñez, Rafael C, Cohen, Jamie A, Selvaraj, Prashanth, Hagedorn, Brittany, George, Lauren, Jastrzebski, Michal, Izzo, Amanda S, Fowler, Greer, Palmer, Anna, Delport, Dominic, Scott, Nick, Kelly, Sherrie L, Bennette, Caroline S, Wagner, Bradley G, Chang, Stewart T, Oron, Assaf P, Wenger, Edward A, Panovska-Griffiths, Jasmina, Famulare, Michael, Klein, Daniel J

“…The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here…”
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RESCRIPt: Reproducible sequence taxonomy reference database management by Robeson, 2nd, Michael S, O'Rourke, Devon R, Kaehler, Benjamin D, Ziemski, Michal, Dillon, Matthew R, Foster, Jeffrey T, Bokulich, Nicholas A

“…Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for…”
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads by Wick, Ryan R, Judd, Louise M, Gorrie, Claire L, Holt, Kathryn E

“…The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific…”
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MUMmer4: A fast and versatile genome alignment system by Marçais, Guillaume, Delcher, Arthur L, Phillippy, Adam M, Coston, Rachel, Salzberg, Steven L, Zimin, Aleksey

“…The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major…”
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly by Ghurye, Jay, Rhie, Arang, Walenz, Brian P, Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M, Koren, Sergey

“…Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In…”
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MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data by Huson, Daniel H, Beier, Sina, Flade, Isabell, Górska, Anna, El-Hadidi, Mohamed, Mitra, Suparna, Ruscheweyh, Hans-Joachim, Tappu, Rewati

“…There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve…”
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Transcriptomics technologies by Lowe, Rohan, Shirley, Neil, Bleackley, Mark, Dolan, Stephen, Shafee, Thomas

“…Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an…”
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DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences by Lee, Ingoo, Keum, Jongsoo, Nam, Hojung

“…Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo…”
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Deep convolutional networks do not classify based on global object shape by Baker, Nicholas, Lu, Hongjing, Erlikhman, Gennady, Kellman, Philip J

“…Deep convolutional networks (DCNNs) are achieving previously unseen performance in object classification, raising questions about whether DCNNs operate…”
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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx by Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena

“…The advent of Next-Generation Sequencing (NGS) technologies has opened new perspectives in deciphering the genetic mechanisms underlying complex diseases…”
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Sequence determinants of protein phase behavior from a coarse-grained model by Dignon, Gregory L, Zheng, Wenwei, Kim, Young C, Best, Robert B, Mittal, Jeetain

“…Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid…”
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Systems biology informed deep learning for inferring parameters and hidden dynamics by Yazdani, Alireza, Lu, Lu, Raissi, Maziar, Karniadakis, George Em

“…Mathematical models of biological reactions at the system-level lead to a set of ordinary differential equations with many unknown parameters that need to be…”
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MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction by Chen, Xing, Yin, Jun, Qu, Jia, Huang, Li

“…Recently, a growing number of biological research and scientific experiments have demonstrated that microRNA (miRNA) affects the development of human complex…”
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PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems by Ghaffarizadeh, Ahmadreza, Heiland, Randy, Friedman, Samuel H, Mumenthaler, Shannon M, Macklin, Paul

“…Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from…”
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Metacoder: An R package for visualization and manipulation of community taxonomic diversity data by Foster, Zachary S L, Sharpton, Thomas J, Grünwald, Niklaus J

“…Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color…”
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LASSI: A lattice model for simulating phase transitions of multivalent proteins by Choi, Jeong-Mo, Dar, Furqan, Pappu, Rohit V

“…Many biomolecular condensates form via spontaneous phase transitions that are driven by multivalent proteins. These molecules are biological instantiations of…”
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Waste not, want not: why rarefying microbiome data is inadmissible by McMurdie, Paul J, Holmes, Susan

“…Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach…”
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ProMod3-A versatile homology modelling toolbox by Studer, Gabriel, Tauriello, Gerardo, Bienert, Stefan, Biasini, Marco, Johner, Niklaus, Schwede, Torsten

“…Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad…”
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Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments by Van Valen, David A, Kudo, Takamasa, Lane, Keara M, Macklin, Derek N, Quach, Nicolas T, DeFelice, Mialy M, Maayan, Inbal, Tanouchi, Yu, Ashley, Euan A, Covert, Markus W

“…Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this…”
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OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing by Hinch, Robert, Probert, William J M, Nurtay, Anel, Kendall, Michelle, Wymant, Chris, Hall, Matthew, Lythgoe, Katrina, Bulas Cruz, Ana, Zhao, Lele, Stewart, Andrea, Ferretti, Luca, Montero, Daniel, Warren, James, Mather, Nicole, Abueg, Matthew, Wu, Neo, Legat, Olivier, Bentley, Katie, Mead, Thomas, Van-Vuuren, Kelvin, Feldner-Busztin, Dylan, Ristori, Tommaso, Finkelstein, Anthony, Bonsall, David G, Abeler-Dörner, Lucie, Fraser, Christophe

“…SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how…”
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