Search results | J. Murrey Atkins Library

Title: JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Author: Jacobs, Donald J., Avery, Chris
Date Created: 2021
Subjects--Topical: Biology, Proteins
Description: Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized soft...

Title: JED: a Java essential dynamics program for comparative analysis of protein trajectories
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
Date Created: 2017
Subjects--Topical: Biology, Proteins
Description: Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to dete...

Title: Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
Author: Loraine, Ann, Yao, Jianchao, Chang, Chunqi, Roux, Stanley J.
Date Created: 2008
Subjects--Topical: Genomics, Bioinformatics
Description: Background: Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlat...

Title: EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Author: Janies, Daniel, Witter, Zachary, Linchangco, Gregorio V., Jr.
Date Created: 2016
Subjects--Topical: Genomics, Biology
Description: Background: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echin...