Rolando Garcia-Milian's blog

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. 

The Yale Medical Library will be hosting a National Center for Biotechnology Information workshop series (broadcasted from the University of Michigan Medical Center). Please register (next to each workshop title) since seating is limited Navigating NCBI Molecular Data through the Integrated Entrez System and BLAST (May 5, 9:00am - 11:30am EDT)  Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT)  Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT)  Each workshop consists of four 2.5-hour hands-on sessions emphasizing a different set of NCBI resources. Each session uses specific examples to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks. Attendees will learn among others: The content of the sequence databases and uses these as exemplar Entrez molecular databases. The importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene. Aspects of the Entrez interface to collect and download a specific set of records, to narrow the search, and to use the pre-computed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. The practical aspects of working with NCBI BLAST, the most popular sequence similarity service in the world. How to use the features of the updated service including direct access from the Entrez sequence databases. The integrated databases to find phenotypes, literature, sequences (genome, mRNA and protein), and variations. How to map variations onto genes, transcripts, proteins, and genomic regions. Gain experience using additional tools and viewers associated with Entrez. These include the Graphical Sequence Viewer, the Variation Viewer, Gene View in dbSNP, and the 1000 Genomes Browser. NCBI's Entrez as a discovery system. Image courtesy of Dr. Peter Cooper, NCBI.

The NIH Genomic Data Sharing Policy becomes effective with NIH grant applications submitted for the January 25, 2015, due date and thereafter.  Investigators preparing grant applications for those due dates should prepare now if the work proposed involves the generation or use of large-scale genomic data (Suplemental Information to the NIH Genomic Data Sharing).  Applicants preparing such grant applications are expected to: state in the cover letter that the studies proposed will generate large-scale human and/or non-human genomic data include a genomic data sharing plan in the application. if sharing of human data is not possible, provide a justification explaining why they cannot share these data and provide an alternative data sharing plan. Applicants who plan to use controlled-access human genomic data from NIH-designated data repositories as a secondary user to achieve the specific aims in the application should: briefly address their plans for requesting access to the data state their intention to abide by the NIH Genomic Data User Code of Conduct, in the Research Plan of the application. Applicants preparing applications that involve research funded prior to the Policy's effective date should: make every effort to include a genomic data sharing plan in the application that outlines plans to comply with the expectations outlined in the Policy plan to transition to a consent for future research uses and broad sharing, if possible if the studies involve human participants and were initiated before the Policy's effective date and used consents that do not meet the expectations of the GDS Policy. Additional questions: Genomic Data Sharing Policy Team NIH Office of Science Policy Telephone: 301-496-9838 Email: GDS@nih.gov