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Full-Text Articles in Genetics and Genomics
An Open Data Format For Visualization And Analysis Of Cross-Linked Mass Spectrometry Results., Michael R Hoopmann, Luis Mendoza, Eric W Deutsch, David Shteynberg, Robert L Moritz
An Open Data Format For Visualization And Analysis Of Cross-Linked Mass Spectrometry Results., Michael R Hoopmann, Luis Mendoza, Eric W Deutsch, David Shteynberg, Robert L Moritz
Articles, Abstracts, and Reports
Protein-protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topographical interactions. Protein cross-link data analysis is aided by dozens of algorithm choices, but hindered by a lack of a common format for representing results. Consequently, interoperability between algorithms and pipelines utilizing chemical cross-linking remains a challenge. pepXML is an open, widely-used format for representing spectral search algorithm results that has facilitated information exchange and pipeline development for typical shotgun mass spectrometry analyses. We describe an extension of this format …
Fastpop: A Rapid Principal Component Derived Method To Infer Intercontinental Ancestry Using Genetic Data, Yafang Li, Jinyoung Byun, Guoshuai Cai, Xiangjun Xiao, Younghun Han, Olivier Cornelis, James E. Dinulos, Joe Dennis, Douglas Easton, Ivan Gorlov, Michael F. Seldin, Christopher I. Amos
Fastpop: A Rapid Principal Component Derived Method To Infer Intercontinental Ancestry Using Genetic Data, Yafang Li, Jinyoung Byun, Guoshuai Cai, Xiangjun Xiao, Younghun Han, Olivier Cornelis, James E. Dinulos, Joe Dennis, Douglas Easton, Ivan Gorlov, Michael F. Seldin, Christopher I. Amos
Dartmouth Scholarship
Identifying subpopulations within a study and inferring intercontinental ancestry of the samples are important steps in genome wide association studies. Two software packages are widely used in analysis of substructure: Structure and Eigenstrat. Structure assigns each individual to a population by using a Bayesian method with multiple tuning parameters. It requires considerable computational time when dealing with thousands of samples and lacks the ability to create scores that could be used as covariates. Eigenstrat uses a principal component analysis method to model all sources of sampling variation. However, it does not readily provide information directly relevant to ancestral origin; the …
Climp: Clustering Motifs Via Maximal Cliques With Parallel Computing Design., Shaoqiang Zhang, Yong Chen
Climp: Clustering Motifs Via Maximal Cliques With Parallel Computing Design., Shaoqiang Zhang, Yong Chen
College of Science & Mathematics Departmental Research
A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif …