Rolando Garcia-Milian's blog

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   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.  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 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 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 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

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 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.

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.