Bioinformatics

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 features leads to greater certainty in the clinical interpretation of these variants. As of January 6, 2015, there are 18 539 publicly available patient record, 51 496 phenotype observation in these patients, and 27 175 publicly available copy-number variants in this database. DECIPHER can be search by phenotype, by genomic position, band, gene, pathogenicity, variant consequence, etc. Results are presented as a table or can be visualized in a browser. This browser contains different tracks where variants can be visualized in the context of other data. Learn more on DECIPHER and how to use it to make sense of genetic variants at the workshop “Making Sense of Variation”.  You can also contact Rolando Garcia-Milian with questions on this or any other variation tool, References DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth, H.V. et al (2009). Am.J.Hum.Genet 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)

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 for an account or comments please contact Rolando Milian Title: 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, Protein and Metabolite Data Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis Pathway Analysis and Canonical Pathways Downstream Effects Analysis and identifying downstream functions and processes that are likely affected Upstream regulators Analysis Causal Network Analysis and identifying likely root regulators Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected Comparison analysis and comparing multiple observations Date & Time:      9:00am - 12:00pm, Tuesday, October 27, 2015 Location:              H-203, Jane Ellen Hope Building, 315 Cedar St, New Haven CT Presenter:          Field Scientist QIAGEN Informatics   Title:      MetaCore: Getting the most from your "omics" analysis (Introductory session) Description: The ability to generate massive amounts of data with "omics" analysis begs the need for a tool to analyze and prioritize the biological relevance of this information. GeneGo provides a solution for using "omics" gene lists to generate and prioritize hypotheses with MetaCore. This tutorial highlights how to work with different types of data (genomics, proteomics, metabolomics and interaction data) beginning with how to upload gene lists and expression data (if available). Here we demonstrate data manager capabilities including how to upload, batch upload, store, share and check data properties and signal distribution. We then focus on how MetaCore uses your gene list to extract functional relevance by determining the most enriched processes across several ontologies. This entails a detailed lesson on how to prioritize your hypothesis using the statistically significance enrichment histograms and associate highly interactive GeneGo Maps and pre-built networks. We further emphasize the role of expression data in your analysis and the ability to visually predict experimental results, associated disease and possible drug targets. Lastly we highlight the benefits of using MetaCore workflows to compare data sets and work with experiment intersections. Date & Time:      10:00am - 12:00pm, Tuesday, November 3, 2015 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters   Title:      MetaCore: Getting the most from your "omics" analysis (Advanced) Description: In the advanced tutorial, we will explore uses of our network building algorithms and methods for hypothesizing key hubs passed on data. We will begin this session with a discussion on using the Key Pathway Advisor to hypothesize key hubs regulating gene expression data. The session will then review ways of using the 11 network building algorithms in MetaCore. The first example will review how to build a network purely from the curated knowledge within MetaCore. Then we will go through an example of using omics data to build a network of interactions to better understand the relationships within our data. Date & Time:      1:00pm - 3:00pm, Tuesday, November 3, 2015 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters     Join the End-user Bioinformatics Group and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

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/GI- and uses a combination of BLAST and a multiple sequence alignment to produce its results. It first uses the query to search the non-redundant (nr) protein database. Then, it searches the reference database with BLASTP, followed by a multiple sequence alignment on the six sequences (the query and five subject sequences) using the COBALT multiple sequence alignment program. Screen capture showing the results of a SmartBLAST for TP53 (GI:187830777). Panel A shows the five matching sequences are represented as a phylogenetic tree and a graphical overview. The matches are color-coded: matches from the reference species are green, matches from the non-redundant protein database are blue, and your query is yellow. Panel B represents the results from the multiple alignments. Join the End-User Bioinformatics Network (EBNET) and become a member of a grass root community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

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, Protein and Metabolite Data Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis Pathway Analysis and Canonical Pathways Downstream Effects Analysis and identifying downstream functions and processes that are likely affected Upstream regulators Analysis Causal Network Analysis and identifying likely root regulators Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected Comparison analysis and comparing multiple observations Date & Time:  9:00am - 12:00pm, Wednesday, July 15, 2015 Location:         C-103 333 Cedar St, New Haven CT 06520 Campus:          Medical School Presenter:       Dr. Kate Wendelsdorf, Applied Advanced Genomics, QIAGEN Informatics   Advance Ingenuity Pathway Training: Integrated Analysis and Interpretation of Variant and Gene Expression Data from Breast Cancer Subtypes             Methods that jointly interpret genomes and transcriptome data from disease case samples may be able to identify disease-specific factors and pathogenicity mechanisms that may not be observable on a single data type. These insights can then be used create more effective screenings or treatments. Here we show how jointly analyzing tumor-specific genotypes and gene expression can indicate medically important differences among tumor subtypes. Pairing two tools from Ingenuity® Systems – Variant Analysis  (for interpreting human genome data) and IPA® (for transcriptome data) – we trace differences between breast tumors that spread quickly (Claudin-low) versus slowly (luminal) to sequence variation that likely governs Epithelial-to-Mesenchymal Transition (EMT). Variant Analysis was used to filter genomic variants in RNA seq data to a shortlist of those plausibly involved in driving tumor spread. IPA is then used to leverage gene expression patterns from the same dataset to identify molecular pathways involved in the metastatic phenotype of Claudin-low breast cancers. The seminar will demonstrate how using a combination of IPA features and QIAGEN tools can provide insight in to phenotype-causing pathways for experimental follow-up and hypothesis testing. Date & Time:  1:00pm - 4:00pm, Wednesday, July 15, 2015 Location:         C-103 333 Cedar St, New Haven CT 06520 Campus:          Medical School Presenter:       Dr. Wendelsdorf- QUIAGEN Category:        Bioinformatics     Managing your References with EndNote Description:     EndNote is a citation-management software application that makes saving citations and then citing them within documents easy. EndNote's pre-formatted style templates, specific to journal instructions, make it easy to insert references into your papers as you write them. In this class you will learn how to easily add citations into your EndNote library, attach PDFs, and insert references into your research papers. Date & Time:  2:00pm - 3:00pm, Wednesday, July 29, 2015 Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520 Campus:          Medical School Presenter:       Denise Hersey Category:        Reference Management Systems   Give your PubMed Skills a Tune Up Description:     PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it one time or another, but it may be time to brush up on your search skills to ensure that you have a relevant set of results.  In this class, we will go over PubMed search techniques, including how to quickly limit a search and the role of Medical Subject Headings (MeSH) in creating more effective searches. Participants will also learn time-saving features such as saving searches and how to link out to full-text. Date & Time:  6:00pm - 7:00pm, Wednesday, July 29, 2015 Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520 Campus:          Medical School Presenter:       Melissa Funaro Category:        Reference Management Systems     Webinar: Introduction to Cytoscape: network visualization software Description:     Cytoscape, an open source molecular interactions visualization tool, allows the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  This webinar will provide an introduction to some of the core functionality of Cytoscape, including the loading and manipulation of experimental data.  For example, you will learn how to change visual properties to easily distinguish biologically significant relationships.  Many additional features and advanced analyses are available through Cytoscape’s extensive list of apps. Examples of apps are MetScape (allows for visualizing and interpreting metabolomic data), Reactome FI (Reactome Functional Interaction and pathway enrichment tool), and BiNGO (Gene Ontology Tool). Date & Time:  11:30am - 12:30pm, Tuesday, August 11, 2015 Location:         Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520 Campus:          Medical School Presenter:       Marci Brandenburg, Bioinformationist, Taubman Health Sciences Library, University of Michigan Category:        Bioinformatics  

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 interdisciplinary panel of artists, scientists and members of medical community and selected for an YSM exhibition. Contest Deadline Friday, July 31 (deadline extended!), 2015 – 11:59 pm Winners will be notified Monday- August 31st, 2015 Awards Awards will be given to 3 - 1st Honors and 1 - Viewer’s choice and consist of 1 TB USB 3.0 M3 Portable External Hard Drive The images will also be posted online and a print exhibition will be on display in the foyer outside the Medical School Library Fall 2015 Eligibility Yale affiliates including, students, postdocs, faculty, assistants, physicians, etc. working in scientific and biomedical research. Rules of Submission 1.    Individuals may submit up to 2 images. 2.    There is no contest fee. 3.    The submitter must have been involved in the generation of the images and must obtain permission for its use in this contest from any colleagues who also participated. Acknowledgement of collaborators can be credited in the written description. 4.    Images must be submitted electronically USING THIS FORM  5.    In awarding of prizes, images will be judged on esthetics, originality, and composition.   If you have questions or need help, contact Rolando Garcia Milian or Terry Dagradi.