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Full-Text Articles in Life Sciences

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 …


Supporting Biomedical Research In The Era Of Omics And Precision Medicine, Rolando Garcia-Milian, Denise Hersey, Nathan Rupp Aug 2016

Supporting Biomedical Research In The Era Of Omics And Precision Medicine, Rolando Garcia-Milian, Denise Hersey, Nathan Rupp

Rolando Garcia-Milian


This annual report (2015-2016) provides a continuing view on the position of the Cushing/Whitney Medical Library End-user Bioinformatics Program. Besides the report on the three main areas of training, resources and tools, and consultations, it contains the results of the recent assessment “Information and Needs Assessment for Biomedical Research in the Omics Era” During this period, 741 Yale affiliates attended (out of 1240 registered) the end-user bioinformatics training and presentations organized by the Medical Library.  This year, the number of Ingenuity Pathway Analysis and MetaCore accounts continued to grow. Consequently, the number and length of research support consultations (130 researchers …


Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover May 2016

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and visualize information; …


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 …


Library Support For Biomedical Research In The Omics Era: 2014- 2015 Report, Rolando Garcia-Milian May 2015

Library Support For Biomedical Research In The Omics Era: 2014- 2015 Report, Rolando Garcia-Milian

Rolando Garcia-Milian

The decreased cost of high-throughput technologies has enabled its use as the main research methods to study biological processes and disorders. In order to understand the relevance of the data generated by these methods, the researcher needs mining and integrating the enormous amount of biomedical information and knowledge contained in the text of the scientific literature and biomedical databases. Accordingly, the ability to access and examine molecular data should not be restricted to bioinformaticians or those with exceptional computer skills. In May 2014, the Cushing/Whitney Medical Library began to provide end-user bioinformatics support to the biomedical researchers of the Yale …


Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian May 2014

Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian

Rolando Garcia-Milian

The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools (e.g. KNALIJ, Quertle, NextBio, iHOP, SemMed, GoPubMed, etc) may be of help when sorting through this abundance of literature, as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions.


Introduction To Genome Browsers, Rolando Garcia-Milian Dec 2013

Introduction To Genome Browsers, Rolando Garcia-Milian

Rolando Garcia-Milian

In this workshop we will learn how to navigate the genome browsers from NCBI's Genome Workbench, UCSC Genome Browser, and Ensembl. These browsers are valuable tools when identifying, localizing genes, and looking at their information in the genomic context. By using concrete examples, it will be shown how to locate a human gene, download a gene sequence and its upstream sequence, locate Single Nucleotide Polymorphisms (SNPs) and conserved regions, and use the browsers to download results in a batch.