Future Medical Librarians at STEM Career Fair

24 May 2016 - 11:18am by Holly Grossetta Nardini

by Kate Nyhan

Librarian Kate Nyhan discusses a career in health sciences librarianship with four high school students.These future medical librarians are students at Wilbur Cross High School in New Haven attending a career fair to learn about STEM careers. Research and education librarian Holly Grossetta Nardini, reference librarian Melissa Funaro, and public health librarian Kate Nyhan (pictured) talked with students from New Haven's public schools about what medical librarians do, how informationists fit into the health care team, and how these young people can prepare for STEM careers like ours.

We were impressed with the confident kids at this STEM career fair. Many of them already have career goals, and lots of them discussed quite sophisticated strategies for seeking and evaluating information online. A good number of these students have visited the Cushing Center and learned about the history of science and medicine there.

The best part of this career fair was interactive: live searches in PubMed on health care topics relevant to these students. Speaking of which -- are you the track coach whose runners found an article suggesting that a short warm-up is as effective as a long one? I promise we talked to these young athletes about the importance of searching comprehensively. If they cherry-picked this evidence to get out of doing the long warm-up, remind them that evidence-based medicine is based on a thorough literature review!

Many thanks to Many Mentors, the Yale League of Black Scientists, and Wilbur Cross High School. We were glad to be part of the STEM career fair team, and we look forward to next year. And in the long term, we hope we can look forward to welcoming some of these talented students to the always rewarding profession of medical librarianship!


Cushing/Whitney Medical Library welcomes our new director, John Gallagher

10 May 2016 - 1:23pm by Andy Hickner

John Gallagher

The Cushing/Whitney Medical Library is delighted to announce the appointment of our new director, John Gallagher.

John joined the staff of the Yale Library in 1999 as a library services assistant in the Library Shelving Facility. He moved to the Medical Library in 2000 where he took the position of evening & weekend circulation supervisor, and was quickly promoted to the head of the circulation department. After completion of his Masters of Library Science in 2004, John was promoted again to the head of Access and Delivery Services. He was instrumental in pioneering and establishing the Scan on Demand service at the Cushing/Whitney Medical Library, which evolved into the Scan and Deliver service for the wider Yale Library system. He served as the library liaison to the Department of Orthopedics and Rehabilitation and co-chaired the library’s joint Department Committee for Best Practices, a university-wide initiative to foster and promote better management/labor relations and collaboration through interest-based problem solving. During this time, John also chaired a management/labor Access Services Assessment Task Force that reduced check-in errors at all libraries.

As deputy director for Public Services and later associate director, John oversaw the completion of a number of major medical library renovations, including a complete renovation of the Medical Historical Library’s rare book stacks and staff areas, the construction of a Secure Reading Room, and the construction of the Cushing Center.

In 2012, John was selected to participate in the National Library of Medicine/Association of Academic Health Sciences Libraries’ Leadership Fellowship Program. John's participation in this prestigious and highly competitive program gives testimony to the quality of his leadership abilities.

Susan Gibbons, University Librarian and Deputy Provost for Libraries & Scholarly Communication commented, "John’s appointment is fantastic. Not only do we add a talented colleague to the library’s senior leadership team, but John’s career demonstrates the opportunities for career advancement at Yale University Library."

Even with all his responsibilities, John has an open door policy and welcomes staff to share their thoughts, ideas and feelings with him. John is a mentor, teacher, friend and leader.  We welcome John as our new director!

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. 

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