Computational Tools for the Multiscale Analysis of Hi-C Data in Bacterial Chromosomes.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1390-0_10
Abstract: Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework aiming at capturing and quantifying… read more here.
Keywords: bacterial chromosomes; analysis; tools multiscale; computational tools ... See more keywords
Web-Based Computational Tools for the Prediction and Analysis of Posttranslational Modifications of Proteins.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9055-9_1
Abstract: The increase in the number of Web-based resources on posttranslational modification sites (PTMSs) in proteins is accelerating. This chapter presents a set of computational protocols describing how to work with the Internet resources when dealing… read more here.
Keywords: web based; prediction analysis; computational tools; based computational ... See more keywords
Computational Tools for Quantifying Concordance in Single-Cell Fate.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9224-9_6
Abstract: Cells are dynamic biological systems that interact with each other and their surrounding environment. Understanding how cell extrinsic and intrinsic factors control cell fate is fundamental to many biological experiments. However, due to transcriptional heterogeneity… read more here.
Keywords: single cell; concordance; computational tools; cell fate ... See more keywords
Joint refinement of FRET measurements using spectroscopic and computational tools.
Sign Up to like & getrecommendations! Published in 2017 at "Analytical biochemistry"
DOI: 10.1016/j.ab.2017.01.011
Abstract: The variability of the orientation factor is a long-standing challenge in converting FRET efficiency measurements into donor-acceptor distances. We propose the use of molecular dynamics (MD) simulations to characterize orientation distributions and thus improve the… read more here.
Keywords: orientation; fret; computational tools; donor acceptor ... See more keywords
Making fundamental scientific discoveries by combining information from literature, databases, and computational tools – An example
Sign Up to like & getrecommendations! Published in 2021 at "Computational and Structural Biotechnology Journal"
DOI: 10.1016/j.csbj.2021.04.052
Abstract: In recent years, the amount of available literature, data and computational tools has increased exponentially, providing opportunities and challenges to make use of this vast amount of material. Here, we describe how we utilized publicly… read more here.
Keywords: literature; information; making fundamental; example ... See more keywords
Computational Tools to Expedite the Identification of Potential PXR Modulators in Complex Natural Product Mixtures: A Case Study with Five Closely Related Licorice Species
Sign Up to like & getrecommendations! Published in 2022 at "ACS Omega"
DOI: 10.1021/acsomega.2c03240
Abstract: The genus Glycyrrhiza, comprising approximately 36 spp., possesses complex structural diversity and is documented to possess a wide spectrum of biological activities. Understanding and finding the mechanisms of efficacy or safety for a plant-based therapy… read more here.
Keywords: licorice; modulators complex; pxr; computational tools ... See more keywords
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Functional Genomics"
DOI: 10.1093/bfgp/elac019
Abstract: Cell-cell interactions (CCIs) are essential for multicellular organisms to coordinate biological processes and functions. Many molecules and signaling processes can mediate CCIs. One classical type of CCI mediator is the interaction between secreted ligands and… read more here.
Keywords: interaction; cell; ligand receptor; computational tools ... See more keywords
Design and Development of Computational Tools for Analyzing Elements of Hindi Poetry
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Access"
DOI: 10.1109/access.2022.3204388
Abstract: Poetry writing is a qualitative subject and so is its analysis. Mapping of these poetic elements onto a scale of real numbers is a lacking necessity. Albeit, Hindi literary heritage, being so huge and glorified,… read more here.
Keywords: design development; tools analyzing; language; poetry ... See more keywords
The doors of precision: Reenergizing psychiatric drug development with psychedelics and open access computational tools.
Sign Up to like & getrecommendations! Published in 2022 at "Science advances"
DOI: 10.1126/sciadv.abp8283
Abstract: Psychedelics paired with new applications of computational tools might help bypass the imprecision of psychiatric diagnosis and connect measures of behavior to specific physiologic targets. read more here.
Keywords: psychiatric drug; reenergizing psychiatric; precision reenergizing; computational tools ... See more keywords
Assessment, improvement, and comparison of different computational tools used for the simulation of heat transport in nanostructures
Sign Up to like & getrecommendations! Published in 2021 at "Simulation"
DOI: 10.1177/00375497211009611
Abstract: In this work we compare different implementations of two interatomic potential models, one the empirical Tersoff–Brenner and the other the semi-empirical tight-binding, to be used in the thermal tr... read more here.
Keywords: improvement comparison; assessment improvement; computational tools; comparison different ... See more keywords
Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance
Sign Up to like & getrecommendations! Published in 2019 at "PLoS ONE"
DOI: 10.1371/journal.pone.0221235
Abstract: Mutational signatures refer to patterns in the occurrence of somatic mutations that might be uniquely ascribed to particular mutational process. Tumour mutation catalogues can reveal mutational signatures but are often consistent with the mutation spectra… read more here.
Keywords: computational tools; comparison performance; tools detect; performance ... See more keywords