Bioinformatics at the Medical Library
Jan 6, 2016
Many genetic variants are novel or rare which makes difficult their clinical interpretation. The DECIPHER Consortium was initiated in 2004 as a community of academic centers of Clinical Genetics who submit consented, anonymized genotype and phenotype data from patients with rare genomic disorders for sharing with other clinicians and researchers. The identification of patients sharing variants in a given locus with common phenotypic... Read More
Nov 24, 2015
Last night, while preparing an RNAseq dataset for functional analysis. I found this problem again. When opening high-throughput data results into Excel be aware that this software will convert (by default) some gene symbols into a date format- see examples in the table below. These conversions are not reversible so the original name cannot be recovered. Zeeberg et al. reported this problem back in 2004. If you are not aware of this and proceed with the functional analysis, those genes (... Read More
Oct 15, 2015
The Yale Medical Library is providing to all Yale affiliates free access to two of the most powerful commercial bioinformatics tools for the analysis of omics data: MetaCore and Ingenuity Pathway Analysis. This is part of a pilot project conducted by the medical library in order to find sustainable and long term access to these tools. Please register for these upcoming trainings if you are interested in learning how to use these tools or if you need a refresher.
For questions on how to register... Read More
Sep 25, 2015
Due to product updates, IPA will be unavailable from 8PM EST on Friday, September 25th thru 3PM EST on Sunday, September 27th, 2015.
Aug 21, 2015
The National Center for Biotechnology Information is developing a new type of BLAST called SmartBLAST. It process the user query in such a way that presents the three best matches from the non-redundant protein sequence database along with the two best protein matches from well-studied reference species. In addition, it provides results that match the query from the Conserved Domain Database (CDD)
SmartBLAST accepts only one query at a time- either as FASTA sequence or protein accession number/... Read More
Jul 27, 2015
Yale University undergraduates, graduate students, post-doctoral researchers, faculty, and staff are invited to submit posters for the 2015 Yale Day of Data, which will be held on September 18, 2015. Any researcher who uses data for research can submit a poster!
The Day of Data is a university-wide event that will feature speakers from a number of disciplines discussing how they use data in their work. The presentations and posters from the 2013 & 2014 Day of Data events are available... Read More
Jul 8, 2015
Introduction to Ingenuity Pathway Analysis
Description: What is IPA and what questions can it address?
Overview of key features in IPA
Ingenuity Knowledge Base
Search & Pathway Building - Gene/ Chemical, Functions, Drug Targets
Advanced Search: Limiting results to a molecule type, family or disease-association.
Building pathways: Creating a pathway, pathway navigating, Using Build and Overlay tools
Bioprofiler
Dataset Analysis: Interpretation of Gene, Transcript,... Read More
Jun 9, 2015
QUIAGEN has announced the launching of its new tool Clinical Insight® (QCI) for interpreting and reporting on genomic variant resulting from next-generation sequencing. According to this company, the new tool can classify variant, identify treatment options, and perform geographical clinical trial matching. QCI has been evaluated in collaboration with Emory University School of Medicine and Dartmouth-Hitchcock Medical Center, among 50 other groups. Clinical Insight®... Read More
Apr 17, 2015
Scientists may not consider themselves artists, however, there are times when science and research experiments lead to incredibly beautiful visual results. We invite Yale biomedical researchers (undergrads, graduate students, postdocs, faculty, associate researchers, etc.) at Yale to “Discover the Beauty of Science” by submitting up to two images per individual. Share with us the visual results of your work where science crosses over to art. Your images will be reviewed by an... Read More
Apr 16, 2015
Sponsored by the Cushing/Whitney Medical Library
Date & Time: 9:00am - 12:30pm, Friday, June 5, 2015
Location: The Anlyan Center Auditorium (N 107), 300 Cedar Street New Haven, CT 06520
Campus: Medical School
Presenter: Dr. Alex Kaplun, Field Applications Scientist, BIOBASE
Registration: Free and open to Yale affiliates – limited seating-
PROTEOME™’s powerful ontology search... Read More