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Bioinformatics

Selected Works

Selected Works

Genomics

Articles 1 - 6 of 6

Full-Text Articles in Life Sciences

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu Sep 2019

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu

Yong Chen

BACKGROUND: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem.

METHODS: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand the …

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Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke Dec 2018

Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke

Ray Enke Ph.D.

This in class activity introduces basic bioinformatics analysis using the Saccharomyces Genome Database (SGD) and the UniProt Database. The yeast URA3 gene is studied in this activity, however, any other yeast gene can be substituted. This activity is designed for novice instructors and students for implementation into core biology lecture or lab courses.

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De-Identified Interviews For The Study: Data Challenges Of Biomedical Researchers In The Age Of Omics, Rolando Garcia-Milian, Denise Hersey, Milica Vukmirovic Jan 2018

De-Identified Interviews For The Study: Data Challenges Of Biomedical Researchers In The Age Of Omics, Rolando Garcia-Milian, Denise Hersey, Milica Vukmirovic

Rolando Garcia-Milian


Background: High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor.
Methods: A multimodal needs assessment analysis, combined an online survey of 860 Yale-affiliated researchers and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10® software according to the thematic analysis approach.
Results: The survey response rate was …

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Statistical Contributions To Bioinformatics: Design, Modeling, Structure Learning, And Integration, Jeffrey S. Morris, Veera Baladandayuthapani Dec 2016

Statistical Contributions To Bioinformatics: Design, Modeling, Structure Learning, And Integration, Jeffrey S. Morris, Veera Baladandayuthapani

Jeffrey S. Morris

The advent of high-throughput multi-platform genomics technologies providing whole-genome molecular summaries of biological samples has revolutionalized biomedical research. These technologies yield highly structured big data, whose analysis poses significant quantitative challenges. The field of Bioinformatics has emerged to deal with these challenges, and is comprised of many quantitative and biological scientists working together to eectively process these data and extract the treasure trove of information they contain. Statisticians, with their deep understanding of variability and uncertainty quantification, play a key role in these efforts. In this article, we attempt to summarize some of the key contributions of statisticians to bioinformatics, …

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Making Sense Of Genomic Variation: Part 1 Snp Annotation, Rolando Garcia-Milian Mar 2016

Making Sense Of Genomic Variation: Part 1 Snp Annotation, Rolando Garcia-Milian

Rolando Garcia-Milian

The  specific combination of genetic variation in an individual defines not  only the external appearance but also susceptibility to diseases,  cancer, genetic disorders, drug response, etc. This explains the great  interest in discovering and cataloging these variations and using them  for disease association and functional studies, among others. In this  session we will review the most popular databases and tools to annotate,  analyze and visualize genetic variations. Some of the databases and  tools that will be discussed are:
-dbSNP
- Online Mendelian Inheritance in Man a comprehensive, authoritative compendium of human genes and genetic phenotypes.
- GWAS Catalog
-  EBI's …

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Bayesian Methods For Expression-Based Integration, Elizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju C. Manyam, Veera Baladandayuthapani Dec 2012

Bayesian Methods For Expression-Based Integration, Elizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju C. Manyam, Veera Baladandayuthapani

Jeffrey S. Morris

We propose methods to integrate data across several genomic platforms using a hierarchical Bayesian analysis framework that incorporates the biological relationships among the platforms to identify genes whose expression is related to clinical outcomes in cancer. This integrated approach combines information across all platforms, leading to increased statistical power in finding these predictive genes, and further provides mechanistic information about the manner in which the gene affects the outcome. We demonstrate the advantages of the shrinkage estimation used by this approach through a simulation, and finally, we apply our method to a Glioblastoma Multiforme dataset and identify several genes potentially …

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