Bioinformatics at the Medical Library

Simbonis Fellowship in Bioinformatics

12 November 2018 - 4:50pm by Dana Haugh

Simbonis Fellowship in Bioinformatics

Cushing/Whitney Medical Library

Yale University, New Haven, CT

 

Fixed Duration Position: 18 months from date of hire; non-renewable

Yale University offers an exciting opportunity for achievement and growth in New Haven, Connecticut. Conveniently located between Boston and New York, New Haven is the creative capital of Connecticut with cultural resources that include major art museums, theaters and music. New Haven is also a biotech and research hub and the location of one of the largest hospitals in the United States.

The Harvey Cushing/John Hay Whitney Medical Library

The Harvey Cushing/John Hay Whitney Medical Library serves the Yale Schools of Medicine, Nursing, Public Health, and the Yale-New Haven Hospital as well as Yale College and the Yale Graduate School. The Cushing/Whitney Medical Library is a dynamic and busy place; library staff work together as a team to provide responsive and effective information support to the Medical Center's missions of research, education, and patient care. Medical librarians provide individualized support through the library’s active personal librarian program. Electronic resources have grown to 22,717 e-journals, 48,911 e-books and 99 electronic databases. In addition, digitized collections, clinical synthesis tools, and evidence-based practice resources bring information to our community at the library, on campus and remotely. For additional information, see: https://library.medicine.yale.edu/

Position Description

The Simbonis Fellowship in Bioinformatics offers a recent Ph.D. or MS scientist a chance to explore a career in medical librarianship, by serving as an informationist in the established Bioinformatics Support Program at the Cushing/Whitney Medical Library. This fellowship is made possible through the generosity of the estate of Dr. Stanley Simbonis ’53, ‘57MD. Upon completion of this fellowship, the informationist would be poised to continue a career in the cutting-edge and expanding field of library bioinformatics support. 

The Cushing/Whitney Medical Library serves an array of academic and clinical programs. The Simbonis Fellow will have the opportunity to interact with faculty, staff, researchers, and students in the Schools of Medicine, Nursing, and Public Health as well as graduate students and post-docs. The library also supports Yale New Haven Hospital, and the Fellow will interact with clinicians, staff and researchers from the hospital. The Fellow will also have occasion to collaborate with colleagues from throughout the Yale University Library system.

The Cushing/Whitney Medical Library Bioinformatics Support Program is considered among the most comprehensive medical library bioinformatics programs. Geared towards biomedical researchers with little or no command-line skills, it supports Yale biomedical researchers by providing access to a suite of commercial and open source bioinformatics software for the analysis, annotation, and visualization of -omics and other types of data throughout the research data lifecycle. In addition, the program provides training and consultation on how to use these tools to hundreds of biomedical researchers every year. An integral part of the program is to assess the usage of the different resources and services provided by the program. 

Responsibilities

The Simbonis Fellowship is an 18-month appointment and focuses on growing services and innovating within the Biomedical Support Program at the Cushing/Whitney Medical Library while exploring new career opportunities.

Under the mentorship of the Biomedical Research Support Librarian, the Simbonis Fellow will gain broad experience in the growing field of bioinformatics support in libraries. Other activities will vary based on current library projects and the Fellow's interest and experience.

During their tenure at Yale, the Simbonis Fellow is expected to pursue mutually agreed-upon projects resulting in a publishable paper, a new library service (such as a webpage or research guide), or other relevant deliverables. The Simbonis Fellow will be introduced to a broad spectrum of professional activities and may have the opportunity to participate in library planning committees and task forces and engage in campus, regional, and national professional organizations and other collaborative activities. Fellows are expected to be professionally active and represent the library and the University in the academic, scholarly, and professional community. 

Specifically:

  • Observes, learns and then provides bioinformatics instruction in the form of training sessions on the use of databases and bioinformatics software and methods. These will be accomplished either by teaching or coordinating presentations from outside vendors and guest speakers for the benefit of the Yale biomedical community. 
  • Teaches Yale biomedical researchers and staff to use a range of free and commercial (licensed by the library) bioinformatics databases and software for retrieving, downloading, analyzing, and visualizing a wide variety of molecular data including (but not limited to) genomics, transcriptomics, proteomics, and metabolomics. 
  • Guides biomedical researchers through bioinformatics methods and analyses and prepares reports for group presentation or publication.
  • Participates in one-on-one and group consultations (in person or online) on a wide variety of bioinformatics topics under the mentorship of colleagues.
  • Provides reference and research services in response to requests for information related to bioinformatics and other biomedical subjects.
  • May evaluate, recommend, and support electronic resources, such as software applications, pertinent to the bioinformatics support program.
  • Provides support in assessing the efficacy/relevance of the program by collecting, analyzing, and reporting statistics which document the service levels and trends in service provision.
  • Helps the library gain insights into new potential uses and users of the bioinformatics resources, and information-seeking behaviors of scientists.

Qualifications

  • Master’s degree or Ph.D. in a biomedical or life sciences-related field.
  • Knowledge of the basic principles, theories, practices, techniques, and terminology of a biomedical-related discipline and an understanding of the standard methods, procedures, and techniques of research and analysis in that field.
  • Experience with genomics research and an understanding of fundamental biological concepts.
  • Excellent analytical, customer service, and interpersonal skills.
  • Effective oral and written communication skills.
  • Ability to work both independently and collegially in a demanding and rapidly changing environment.

Preferred:

  • Working experience in the analysis and interpretation of high-throughput biological data (e.g. sequencing, array-based technologies)
  • Ability to perform independent analyses and report findings to biomedical researchers
  • Publication(s) in relevant peer-reviewed journals

Salary and Benefits

The Simbonis Fellow will serve for eighteen months and will receive an award of $90,000 prorated over 18 months. Health insurance will be provided. Fellows can draw upon a wide range of expertise across Yale and the Yale University Library for support and will be offered mentorship and guidance.

Application Process

The Simbonis Fellowship is a competitive position. Applicants should submit a current resume or CV, a cover letter/statement of interest, and names and contact information for three professional references to Katie Hart via e-mail at katherine.hart@yale.edu. Applications will be reviewed on a rolling cycle until the position is filled. There is no application form. Please be sure to include “Simbonis Fellowship” in the e-mail subject line.

Background Check Requirements

All external candidates for employment will be subject to pre-employment background screening for this position, which may include motor vehicle and credit checks based on the position description and job requirements. Internal candidates may be subject to a motor vehicle or credit check for this position based on the position description and job requirements. All offers are contingent on successful completion of the required background check.

 

Yale University is an affirmative action/equal opportunity employer. Yale values diversity in its faculty, staff, and students and strongly encourages applications from women and members of underrepresented minority groups.

New Video: Bioinformatics at Yale

19 October 2017 - 10:18am by Caitlin Meyer

You probably know that the Cushing/Whitney Medical Library offers support for bioinformatics projects, but do you know exactly where we fit into the high-throughput omics research data cycle? In this new video produced by CWML staff, you can see a sampling of the tools and services we offer throughout the process.

Highlighted resources include:

Qlucore Omics Explorer, a tool that facilitates a dynamic analysis of omics data, applicable to various phases of a discovery cycle. Qlucore helps you visualize, QC, apply statistics, and create publication-ready graphics, such as 3D Principal Component Analysis, heat maps, and various 2D plots.

Partek Flow software, a program that is used for the analysis of next-generation sequencing data including RNA, small RNA, and DNA sequencing. Partek Flow provides a graphical user interface that allows building your own custom analysis pipelines for alignment, quantification, quality control, statistics, and visualization.

Ingenuity Pathway Analysis, a web-based software application for the analysis, integration, and interpretation of the data derived from omics experiments, ranging from microarrays and metabolomics to smaller scale experiments that generate gene and chemical lists.

And, finally, MetaCore, a systems biology analysis suite containing information that can be used to perform pathway enrichment, network building, target discovery, and more.

For more information on Bioinformatics at Yale, contact Rolando Garcia-Milian.

Qlucore Omics Explorer: A new tool for discovering and exploring omics data

11 January 2017 - 10:21am by Andy Hickner

(by Rolando Garcia Milian)

Qlucore Omics Explorer facilitates a dynamic, visualization-guided analysis of OMICs data, applicable to various phases of a discovery cycle. What differentiates Qlucore is the combination of speed, advanced analytics, seamless workflow, and simplicity. With Qlucore you can visualize, QC, apply statistics, and create publication-ready graphics, such as 3D Principal Component Analysis, heat maps, and various 2D plots.

For biological exploration, GO and enrichment analysis (perhaps the most user-friendly implementation of GSEA) are available. Use valuable public data (TCGA, GEO) to test your ideas, or generate/narrow new hypotheses, with an easy download and integration into your data analysis.  

This tool suite empowers researchers to participate in their data analysis,  exponentially shortening time to result and biological insight while improving accuracy of the findings.

We invite you to employ the  cutting edge high-throughput techniques without the learning curve associated with advanced statistics, scripting languages and painful integration of different tools and formats!

Supported data types include any matrix data including RNAseq, microarrays, proteomics, miRNA, methDNA, Mulitplex and FC (genomic data support is coming soon). Case studies are available.

Qlucore started as a collaborative research project at Lund University (Sweden) between the Departments of Mathematics and Clinical Genetics.

Register for a free account here.

Please contact Rolando Milian Rolando.milian@yale.edu for questions or comments on this tool. 

Track drugs from bench to patient with Pharmaprojects

10 January 2017 - 4:28pm by Andy Hickner

The Cushing/Whitney Medical Library has recently licensed Pharmaprojects from Informa PLC.  Pharmaprojects lets researchers track the progress of drugs from bench to patient by exploring drug development by global and country development status, and therapeutic class status.

This database covers the progress of new drug candidates as they enter commercial pharmaceutical research and development programs, and tracks their progress from early preclinical development right up to market launch, or to discontinuation if a drug fails at any stage.

Researchers can search drugs by chemical structure and other chemical attributes such as molecular weight or logP, or search by biological targets of the drugs.  Besides searching the database, users can export data and set up alerts.

Click on this link to register and create your account using your @yale.edu email: https://yale-pipeline.citeline.com

Training on how to use this resource is coming soon.

Please contact Rolando Milian for questions or comments on this database.

(2 X 2) 2 High-throughput Data Analysis Workshops X 2 on NCBI Public Databases.

19 September 2016 - 10:09am by Rolando Garcia-Milian

Cushing/Whitney Medical Library has organized these four workshops, two of them on high-throughput data analysis tools and two on NCBI public databases. Although these are free and open to any Yale affiliate, registration is required due to limited seating.  

Title:      NGS Data Analysis in Partek® Software: Onsite Workshop

Registration: http://schedule.yale.edu/event/2819565

Description:   

Morning Session (Overview, Hands On: Analysis on RNA-Seq Data): 9:00AM – 12:00PM

Free access to Partek Flow is provided by the Yale Medical Library. Register for an account here

This session will start with an overview of Partek Software solutions followed with a hands on RNA-Seq Data Analysis in Partek Flow. Topics will include how to use statistical tests to identify differentially expressed transcripts and alternative spliced genes among sample groups, how to generate a list of genes of interest and identify high level biological trends using Gene Ontology.

  • Import data (fastq, bam, text format)
  •  Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC)
  • Trim bases
  • Alignment
  • Gene/transcript abundance estimate (E/M)
  •  Differential expression detection (GSA, ANOVA)
  • Filter gene list
  • GO Enrichment Analysis
  • Visualization
    • Quality score distribution
    • Base composition
    • PCA scatterplot
    • Dotplot
    • Volcano plot
    • Hierarchical clustering
    • Chromosome view

Afternoon Session (Open Lab; Q&A): 1:30PM – 4:00PM

We hope to see you there!

 
Date & Time:     9:00am - 12:00pm, Thursday, September 29, 2016

Location:           C-103, SHM, 333 Cedar St

Campus:           Medical School

Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.

 

Title: Broadcast. Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST

Registration: http://schedule.yale.edu/event/2832345

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan, and provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject) and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources).

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Tuesday, October 4, 2016

 

Title: Broadcast. A Practical Guide to NCBI BLAST

Registration: http://schedule.yale.edu/event/2832347

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan and highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2- Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret.

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Wednesday, October 5, 2016

 

Title:      Make new discoveries with your OMICs data: Hypothesis testing and assumption-free exploration

Registration: http://schedule.yale.edu/event/2832289

Description:       

10AM- Noon:

  • Exemplary workflows for different experiment designs
  • Hypothesis testing and Assumption-free data exploration
  • Working with annotations, dynamic and interactive plots

Input data: any matrix multivariate data (RNAseq, Microarrays, Proteomics, miRNA, Metabolomics, Lipidomics, methDNA, Mulitplex and FACS, Clinical data, Biomarkers, etc.), as well as publicly available GEO data, gene sets files, gene ontology. Complete list is available here.

1-2PM:

Getting started session – take advantage of a trial access for Yale! Have a look the info uploaded to the Yale Library folder, including presentation, case studies, tutorials, etc.

Qlucore tools allow researchers to perform advanced visualization, exploration and statistical analysis of omics data with the help of an intuitive GUI. Targets of interest can be further explored in terms of biological insight using GO and GSEA.  Unmatched speed, immediate visual feedback, continuous visualization, and synchronized views significantly shorten both data-to-result and query-to-discovery times.

By combining right annotations with statistical methods, data selection tools, and the eliminated factors function, a very broad range of different experiment designs can be analyzed with exceptional productivity. This solution draws upon both innovative and classical approaches, fueled by best-in-class industrial and academic research.

Qlucore Omics Explorer helps you advance your research by:

  • boosting the speed of your analysis at least by 50%
  • generating new ideas, hypotheses, and giving you a new prospective on your data, and questions you ask of it
  • helping recognize significant insight that is specific to biological process, disease, or function, as well as assumption-free exploration
  • keeping your projects on track with simple QC checks on every step
  • providing publication ready graphics, and intermediate results for collaboration.

Qlucore Omics Explorer is used by big commercial companies as well as major research organizations and Universities across Europe and US. (e.g., Boehringer Ingelheim, Roche Diagnostics,  AstraZeneca, DFCI, BWH, Harvard, MD Anderson, MSKCC, MedImmune, Novo Nordisk, etc.).

Date & Time:     10:00am - 12:00pm, Thursday, October 27, 2016

Location:           C-103 - SHM 333 Cedar St

Campus:            Medical School

Presenter:          Yana Khalina-Stackpole, PhD, Business and Support manager, Qlucore

Fall Training Sessions on Bioinformatics at the Medical Library

6 September 2016 - 10:40pm by Rolando Garcia-Milian

The Yale Medical Library is offering a number of bioinformatics training session this Fall. These sessions are free and open to any Yale affiliate but registration is required due to limited seating.

Please contact Rolando.milian@yale.edu  for questions or comments.

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2800083

A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line terminal environment is required to run such programs. In this 2-hour session, you will learn the basics of a Unix command-line terminal, such as how to navigate the file system, the permission and security structure, and how to run programs from the command line. No previous Unix or command-line experience is required to attend this session.

Date: Thursday, October 6, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

Title: Introduction to Enrichment Analysis Tools

Registration required: http://schedule.yale.edu/event/1154118

Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce free tools for enrichment analysis as well as those licensed by the Medical Library

Date: Thursday, September 8, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St. Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 1 SNP Annotation

Registration required: http://schedule.yale.edu/event/2794996

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/PheGenI
  • EBI-Ensembl Variant Effect Predictor to annotate and determine the effect of variants on genes, transcripts, and protein sequence, as well as regulatory regions.
  • And more…

Date: Thursday, September 22, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 2 Structural Variants

Registration required: http://schedule.yale.edu/event/2795002

Structural variation encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, among others. In many cases, determining whether a particular genetic variant is pathogenic or benign and its correlation with respect to a patient's disease phenotype is challenging.

In this session we use online resources and tools to find, retrieve, annotate, and visualize structural variants

  • NCBI’s database of genomic structural variants dbVar
  • Database ofDatabasE of Chromosomal Imbalance and Phenotype in Humans
  • Genomic Variants DGVa
  • UCSC and Ensembl genome browsers

Date: Thursday, October 6, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Introduction to Genome Browsers. Part 1 Ensembl

Registration required: http://schedule.yale.edu/event/2795004

Ensembl provides access to genomic information with a number of visualization tools. By using Ensembl researchers can download data directly (e.g., genomic sequences), visualize many types of data (e.g., structural, variation, regulatory) directly on a genome assembly. In this session will review the basic functionalities and navigation of Ensembl by using specific examples. We will also use BioMart interface to answer questions and retrieve data and information from databases without the need of having any programming expertise.

Date: Thursday, October 20, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Understanding Research Impact

Registration required: http://schedule.yale.edu/event/2803327

Nowadays, it is not uncommon for employers, academic institutions, and funding agencies to ask for evidence of research impact before making important decisions, such as tenure promotions, academic honors, or grant awards. Therefore, it is important for researchers to understand what research impact is and what they can do to document, enhance, measure and present their research impact to those decision makers. This session introduces the core concepts of research impact, its deep roots and long tradition, the various quantitative metrics of impact, and an emerging practical framework for telling impact stories. This session also introduces how to publish and disseminate research work in ways that improve discoverability and therefore enhance impact.

Date: Thursday, November 10, 2016

Time: 10:30am - 11:30am

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

Title: My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI

Registration required: http://schedule.yale.edu/event/2795006

Although not required at this point, the NIH suggest the use of the Science Experts Network Curriculum Vitae (SciENcv), -a MyNCBI online tool- that serves as an interagency system designed to create biosketches for multiple federal agencies. This, along with the use of My Bibliography for grant activity reporting and NIH Public Access Policy compliance, increases the importance using MyNCBI as a tool for managing NIH-sponsored research. This workshop introduces researchers, research assistants and administrators on the effective use of these online tools and will cover the following among other topics:

  • How to create MyNCBI account and how to link it to the eRA Commons account
  • How to delegate your account
  • How to populate and manage My Bibliography
  • How to use My Bibliography for grant reporting/compliance
  • How to use SciENcv to create different biosketches (from scratch, from external source, etc)
  • How to create and ORCID ID* and how to link SciENcv to that ORCID ID

*ORCID stands for Open Research and Contribution ID. Some publishers and journals (Springer, Wiley, Journal of Neuroscience, The Journal of Immunology, etc.) are asking authors to submit their ORCD ID along with their manuscripts for publication.

Date: Thursday, December 1, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Campus: Medical School

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2803929

A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line terminal environment is required to run such programs. In this 2-hour session, you will learn the basics of a Unix command-line terminal, such as how to navigate the file system, the permission and security structure, and how to run programs from the command line. No previous Unix or command-line experience is required to attend this session.

Date: Thursday, December 8, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St.

Campus: Medical School

 

For a full list of training sessions including PubMed, EndNote, etc. , please visit the medical library calendar: http://library.medicine.yale.edu/classes

Access to Partek Flow for the analysis of NGS data available to Yale biomedical researchers

8 July 2016 - 2:11pm by Rolando Garcia-Milian

The Yale Medical Library is providing access to Partek Flow, a Graphical User Interface and user-friendly software for the analysis of RNA, SmallRNA, and DNA sequencing experiments. A webinar showing how to use this software will take place in SHM C-103 on August 4, 2016 (see details below).

Webinar: NGS Data Analysis in Partek Software

Registration here

Description: Why have over 5,000 scientific articles cited Partek software for turning their data into discovery? Because it empowers scientists to perform sophisticated statistical analyses with intuitive point-and-click actions, no command-line knowledge needed.

 Join us for a complimentary webinar to see how Partek Flow software can be used to analyze your RNA, SmallRNA, and DNA sequencing experiments. Using an RNA-Seq data set, we’ll demonstrate how to check read quality, align reads against a reference genome, quantify RNA transcript levels, and identify differentially expressed genes. We’ll show you how to save your analysis steps and parameters in your own start-to-finish, repeatable and shareable pipeline.

The webinar will conclude with a live Q&A session.

Flow that aligns RNA-Seq reads to a reference genome using the STAR aligner followed by quantification of reads to a transcriptome (from http://www.partek.com/pipelines)

Date & Time:      9:30am - 11:00am, Thursday, August 4, 2016

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

Campus:              Medical School

Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.

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.

SPONSORED BY
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