Library profiled in spring 2016 issue of Nota Bene

10 May 2016 - 10:42am by Andy Hickner

Nota Bene

The spring 2016 issue of Nota Bene: News from the Yale Library is now available online. This issue has a particular focus on the work of the Harvey Cushing/John Hay Whitney Medical Library as it marks its 75th anniversary this year.  In addition to telling the story of the Medical Library, the issue profiles some of the current projects, resources, collections, and exhibits that are making an impact at Yale and in the medical community worldwide.

2016 Class Gift: The anatomy donor tree

3 May 2016 - 11:48am by Andy Hickner

(Guest post by the YSM, YSN, and PA Classes of 2016)

If you've visited the library recently, this unusual sculpture may have caught your eye as you entered.  The 2016 Class Gift is a collective effort between the Yale School of Medicine, School of Nursing, and Physician Associate Program.  The gift is a tree sculpture made from molds of the limbs of first-year students in the 3 programs, and serves as a reminder of the collaborative process between the bodies of students and donors in the anatomy course.  We invite everyone to write notes thanking the donors or describing what the service, donations, or anatomy course meant to them on ribbons and to pin them on the tree. 

Day of Data 2016 Spring Discussion Series: Outcome Defined Organization of Patient Profiles

25 April 2016 - 11:48am by Rolando Garcia-Milian

The Day of Data 2016 Spring Discussion Series will feature Dr. Alexander Cloninger. Dr. Cloninger has active applied collaborations with medical researchers at the Center for Outcomes Research and Evaluation at Yale and the National Institutes of Health. His current research deals with defining and analyzing patient similarity for the purposes of clustering and outcome prediction.

  • Thursday, May 5, 2016
  • 1:30 – 3:00 pm
  • Sterling Memorial Library Lecture Hall

Alex Cloninger is a Gibbs Assistant Professor in the Applied Mathematics Program at Yale, where he as been since 2014. He completed his Ph.D. at University of Maryland as a member of the Norbert Wiener Center for Harmonic Analysis, and his undergrad at Washington University in St. Louis. His research interests lie in the areas of machine learning and diffusion geometry, ranging from theory to implementation and data processing, with a focus on developing novel algorithms to work with medical data.

Yale Center for Research Computing
Yale Institution for Social and Policy Studies
Yale University Library
For more information, click here 


Four On-site Workshops on Next-Generation Sequencing Data Analysis Tools

20 April 2016 - 10:10am by Rolando Garcia-Milian

The End-user Bioinformatics Program at the Yale Cushing/Medical Library is hosting these four workshops on tools for the analysis of NGS data. Besides the two trainings on tools for functional analysis of NGS data already supported by the Medical Library (Ingenuity Pathway Analysis and MetaCore), we will have a presentation on Partek Flow, and another one on CLC Bio (QIAGEN). The medical library will ask for feedback on these tools for future support and licensing. If you are interested in attending any of these presentations, please register to reserve your seat. Please contact Rolando Milian for questions or comments.

Title:    Introductory Workshop to MetaCore and Key Pathway Advisor – Pathway Analysis of “Omics” Data
This hands-on training workshop will highlight basic functionalities as well as cover use cases to:

  • Predict upstream regulators of gene expression using causal reasoning
  • Use synergic enrichment analysis of upstream regulators and observed gene expression changes to identify key pathways associated with your data
  • Compare between experiments to uncover phenotypic differences using enrichment analyzes
  • Search and explore genes, proteins, diseases and compounds

Registration required
Date & Time:    9:00am - 11:00am, Thursday, April 28, 2016
Location:    Beaumont room (2nd floor), SHM, 333 Cedar St, New Haven CT 06510
Presenter:    Deborah Riley, PhD, Senior Solution Scientist – Thomson Reuters Life Sciences

Title:    Start-to-finish Analysis Software for NGS & Microarray Data.
(miRNA-Seq Analysis with Partek: Serum miRNA Study in Alcohol Use Disorder Subjects Suggests Alterations of CNS Structure and Function)     
During this seminar, we will feature a successful miRNA-Seq based study of extracellular miRNAs in 20 individuals diagnosed with alcohol use disorder (AUD).  We will demonstrate how to go from raw NGS data to biological interpretation using Partek software.  Analysis of the sequencing data using Partek Flow will include:

  • checking the quality of reads
  • generating aligned reads
  • quantifying miRNA levels
  • determining differentially expressed miRNAs

By integrating miRNA-Seq results in Partek Genomics Suite, we will demonstrate how differentially expressed miRNAs impact CNS structure and function using Partek Pathway.  Lastly, miRNA expression microarray data will be analyzed in Partek Genomics Suite to validate findings from the next generation sequencing data.
Registration required
Date & Time:    9:00am - 11:00am, Tuesday, May 3, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06520
Presenter:    Dr. Eric Seiser, Field Application Scientist, Partek Incorporated


Title:    Ingenuity Pathway Analysis Hands On Training
If you have gene (including RNAseq), protein and metabolic expression data, you should be using IPA to guide you with the biological interpretation of your data.  Using IPA you will learn how to rapidly understand:

  • Pathway involvement and change
  • Effected biological processes
  • Causal regulators and their directional effect on genes, functions and diseases across multiple time points or doses. You will also learn to explore IPA’s knowledge and discovery tools that allow you to relate the most recent literature findings to your research.  

Requirement:  Laptop and active IPA account (Request your account here)
Registration required
Presenter: Devendra Mistry, PhD, Field Application Scientist, Ingenuity Products, QIAGEN
Date & Time:    9:00am - 11:30am, Tuesday, May 10, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06510


Title: CLC Genomics Workbench
Overview of Application, Importing NGS read data, QC & Pre-processing

  • De novo assembly – Genomes & Transcriptomes. Characterizing Contigs, Joining & Finishing
  • Mapping/Alignment to Reference, Variant Calling, Annotation & Filtering
  • RNA Seq Analysis Workflow & Tools
  • Overview of Microbial Modules (Finishing & Microbial Genomics)
  • CLC Biomedical Workbench & Ingenuity Variant Analysis
  • Prebuilt intuitive pipeline for your human DNA-seq data that allows you to quickly go from reads or called variants to identifying and prioritizing the casual variants.

Registration required
Date & Time:    1:00pm - 3:00pm, Tuesday, May 10, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06510
Presenter:    Devendra Mistry, PhD, Field Application Scientist, Ingenuity Products, QIAGEN  

The Yale Medical Library is Providing Access to the Human Gene Mutation Database (HGMD®)

17 April 2016 - 9:45pm by Rolando Garcia-Milian

As part of its End-user Bioinformatics Program, the Cushing Whitney Medical Library is providing access to the the Human Gene Mutation Database (HGMD®) to all Yale affiliates. This database organizes all known genotypes responsible for causing human inherited disease along with disease-associated polymorphisms published in the peer-reviewed literature— HGMD mutation data are manually curated from the scientific literature.

HGMD is available in two versions: one public, one obtainable by subscription. The public version is maintained is only updated twice per annum and is permanently 3 years out of date. The professional version is available to both commercial and academic/non-profit users via subscription from BIOBASE (QIAGEN). Access to HGMD should be done by following this link ( and clicking on HGMD (access to BIOBASE Proteome or TRANSFAC continue to be provided by the medical library). VPN is required if connecting off-campus.

HGMD does not cover either somatic or mitochondrial mutations. For these, please visit COSMIC and MitoMap For pharmacological variants, PharmGKB The Medical Library offers regular training sessions on how to use these and other resources for variant annotation e.g. Database of Genomic Variants, DECIPHER and Copy Number Variation in Disease.

Please check the class calendar or contact Rolando Milian if you are interested in learning how to use these resources.

Geographic Information Systems Open House

15 April 2016 - 2:48pm by Mark Gentry

Miriam Olivares, GIS Librarian, now consults with Medical Library patrons on Wednesday afternoons.  We are kicking off this service with Open Houses on April 27 and May 4.  Drop in between 3pm and 5pm with your questions about geospatial applications in medicine and public health – or just come to hear more about this service.  Join us in our Gordon Conference Room (L101) at the front of the library, or get more information here.

Supply drive for mothers this week, sponsored by YSM students

12 April 2016 - 9:39am by Andy Hickner

Maybe you've noticed a donation box in the library lobby.  YSM students involved with AMWA (American Medical Women's Association) & ACOG (American College of Obstetrician's & Gynecologists) District I are gathering supplies for 2 organizations that provide supplies for survivors of domestic violence and other underserved women: The Women's Health Resource Center (NH) and The Women's Center of Rhode Island.  

The Women's Resource Center would like diapers & wipes, which are essential supplies for mothers' health

The Women's Center of RI would like:

  • Toiletries (shampoo, toothpaste, deodorant, etc)
  • Women's and infant's clothing & supplies (socks, winter boots, baby lotion)
  • Cleaning supplies (dish soap, sponges, laundry detergent)
  • Used cell phones to refurbish and give to survivors of domestic violence and sexual assault. 

The supply drive runs this week, Monday through Friday. 

Study space restrictions, week of April 4

4 April 2016 - 12:56pm by Andy Hickner

(by Katie Hart)

The Medical Library spaces are heavily booked this week. The Historical Library will be closed at some point almost every day, and the Morse Reading Room will be closed on Wednesday and Thursday afternoons. Study space in other parts of the library will be at a premium. Also, a brief reminder that Wednesday is the Annual Associates Lecture.

Here are a list of the closing times for our spaces:

Monday, 4/4: 

Historical Library,  3-7pm, “The Emperor’s New Genes: Science, Race, Justice, and the Allure of Objectivity” Lecture sponsored by HSHM and the office of the Provost 

Tuesday 4/5: 

Historical Library, 4:30-5:30pm, Class

Wednesday 4/6: 

Historical Library, 2-7pm,  Associates Lecture

Morse Reading Room, 3-8pm, Associates Reception

Thursday 4/7:

Historical Library, 9-11:30, Second Look groups

Morse Reading Room, 12:30-3:30pm, Second Look speed meetings with faculty

Friday 4/8: 

Historical Library, 9:30-11:30am, Dean’s office 

Historical Library, 12-3pm, Wellness Project Seminar “Cultivating Resilience in the Face of Burnout” 

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