Panel Discussion: Reference Databases Nathan Edwards Georgetown University Medical Center.

Slides:

Advertisements

Similar presentations

Protein Quantitation II: Multiple Reaction Monitoring

Advertisements

Huong Le Department of Molecular & Clinical Genetics, Royal Prince Alfred Hospital Click mouse to move to the next slide.

We processed six samples in triplicate using 11 different array platforms at one or two laboratories. we obtained measures of array signal variability.

MN-B-C 2 Analysis of High Dimensional (-omics) Data Kay Hofmann – Protein Evolution Group Week 5: Proteomics.

Phylogenetic Trees Understand the history and diversity of life. Systematics. –Study of biological diversity in evolutionary context. –Phylogeny is evolutionary.

Generalized Protein Parsimony and Spectral Counting for Functional Enrichment Analysis Nathan Edwards Department of Biochemistry and Molecular & Cellular.

Peptide Mass Fingerprinting

Bioinformatics “Other techniques raise more questions than they answer. Bioinformatics is what answers the questions those techniques generate.” SheAvery

PepArML: A model-free, result-combining peptide identification arbiter via machine learning Xue Wu, Chau-Wen Tseng, Nathan Edwards University of Maryland,

Introduction to Proteomics. First issue of Proteomics- Jan. 1, 2001.

1 Gene Finding Charles Yan. 2 Gene Finding Genomes of many organisms have been sequenced. We need to translate the raw sequences into knowledge. Where.

Computational Molecular Biology (Spring’03) Chitta Baral Professor of Computer Science & Engg.

Introduction to BioInformatics GCB/CIS535

Bio 465 Summary. Overview Conserved DNA Conserved DNA Drug Targets, TreeSAAP Drug Targets, TreeSAAP Next Generation Sequencing Next Generation Sequencing.

Genotyping of James Watson’s genome from Low-coverage Sequencing Data Sanjiv Dinakar and Yözen Hernández.

Protein Sequence Analysis - Overview Raja Mazumder Senior Protein Scientist, PIR Assistant Professor, Department of Biochemistry and Molecular Biology.

341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London

Mariya Smit and Holly Simon

Tryptic digestion Proteomics Workflow for Gel-based and LC-coupled Mass Spectrometry Protein or peptide pre-fractionation is a prerequisite for the reduction.

+ Hand Biometrics Measurement and biometric technologies for identification and security applications.

Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell A. Ståhlberg, C. Thomsen, D. Ruff, and P. Åman December 2012

In God We Trust.

Gene Technologies and Human ApplicationsSection 1 Secrets of the Human Genome Genomics is the study of entire genomes, especially by using technology to.

Chapter 13. The Impact of Genomics on Antimicrobial Drug Discovery and Toxicology CBBL - Young-sik Sohn-

Assay Development Breakout (red) Who was in the room? About half of attendees are active NGS users N=1 doing whole genome analyses Everyone else doing.

A New Oklahoma Bioinformatics Company. Microarray and Bioinformatics.

Top-down characterization of proteins in bacteria with unsequenced genomes Nathan Edwards Georgetown University Medical Center.

Finish up array applications Move on to proteomics Protein microarrays.

BIOINFORMATICS IN BIOCHEMISTRY Bioinformatics– a field at the interface of molecular biology, computer science, and mathematics Bioinformatics focuses.

Common parameters At the beginning one need to set up the parameters.

Analysis of Complex Proteomic Datasets Using Scaffold Free Scaffold Viewer can be downloaded at:

Protein Structure & Modeling Biology 224 Instructor: Tom Peavy Nov 18 & 23, 2009

Panel Discussion: Reference Databases Nathan Edwards Georgetown University Medical Center.

High throughput Protein Measurement Techniques Harin Kanani.

Finnish Genome Center Monday, 16 November Genotyping & Haplotyping.

Poster produced by Faculty & Curriculum Support (FACS), Georgetown University Medical Center Application of meta-search, grid-computing, and machine-learning.

Anis Karimpour-Fard ‡, Ryan T. Gill †,

Protein Sequence Analysis - Overview - NIH Proteomics Workshop 2007 Raja Mazumder Scientific Coordinator, PIR Research Assistant Professor, Department.

Genomics I: The Transcriptome RNA Expression Analysis Determining genomewide RNA expression levels.

Bioinformatics MEDC601 Lecture by Brad Windle Ph# Office: Massey Cancer Center, Goodwin Labs Room 319 Web site for lecture:

Reverse Interactomics

Clustering Algorithms to make sense of Microarray data: Systems Analyses in Biology Doug Welsh and Brian Davis BioQuest Workshop Beloit Wisconsin, June.

Bioinformatics Curriculum Issues, goals, curriculum.

EBI is an Outstation of the European Molecular Biology Laboratory. In silico analysis of accurate proteomics, complemented by selective isolation of peptides.

Data Management Support for Life Sciences or What can we do for the Life Sciences? Mourad Ouzzani

Doug Raiford Phage class: introduction to sequence databases.

Poster produced by Faculty & Curriculum Support (FACS), Georgetown University Medical Center Application of meta-search, grid-computing, and machine-learning.

Novel Peptide Identification using ESTs and Genomic Sequence Nathan Edwards Center for Bioinformatics and Computational Biology University of Maryland,

NCode TM miRNA Analysis Platform Identifies Differentially Expressed Novel miRNAs in Adenocarcinoma Using Clinical Human Samples Provided By BioServe.

Affymetrix User’s Group Meeting Boston, MA May 2005 Keynote Topics: 1. Human genome annotations: emergence of non-coding transcripts -tiling arrays: study.

Top-down characterization of proteins in bacteria with unsequenced genomes Colin Wynne Catherine Fenselau University of Maryland, College Park Nathan Edwards.

Higher Human Biology Unit 1 Human Cells KEY AREA 5: Human Genomics.

ISA Kim Hye mi. Introduction Input Spectrum data (Protein database) Peptide assignment Peptide validation manual validation PeptideProphet.

Global Variation in Copy Number in the Human Genome Speaker: Yao-Ting Huang Nature, Genome Research, Genome Research, 2006.

Prader Willi Syndrome & Necdin

BIOBASE Training TRANSFAC ® Containing data on eukaryotic transcription factors, their experimentally-proven binding sites, and regulated genes ExPlain™

Peptide de novo sequencing Peptide de novo sequencing is the analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum.

Post translational modification n- acetylation Peptide Mass Fingerprinting (PMF) is an analytical technique for identifying unknown protein. Proteins to.

Algorithms and Computation: Bottom-Up Data Analysis Workflows

Connecting Cancer Genomics to Cancer Biology using Proteomics

Scientists use several techniques to manipulate DNA.

Bioinformatics Solutions Inc.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Biometric technology.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Geneomics and Database Mining and Genetic Mapping

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Study overview. Study overview. (A) Terminal ilea from conventional and GF mice were quantitatively compared to produce the "ileum data set." Transcriptomics.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Presentation transcript:

Panel Discussion: Reference Databases Nathan Edwards Georgetown University Medical Center

Role of Reference Databases Provide “exemplar” for comparison w/ meta- data: Analytical signatures (spectra, fingerprints) Biological knowledge (DNA & protein seq., SNPs,...) Comparison turns measurements into identity......match measurements to exemplars (0,1,many) Identity (shades of grey!) depends on: the nature of the analytical measurement, the model for comparison, and the contents of the reference database. 2

Reference Database Use Cases Assay design Specific detection in device/kit (antibody, microarray) Signal is species specific Assay detection Non-specific design (mass spectrometry, sequencing) Detection by match to a reference database Assay validation In silico specificity guarantee? Guided specificity testing? In silico validation after update? 3

Assay Design Specificity: requires all sequences, but mislabeled or incorrect sequences may compromise the design the set of reference genomes will never be complete or "uniformly" sampled Homology and phylogeny may be able to compensate for missing sequences can inform clinical or in silico testing for specificity May lead to overly conservative designs… 4

Assay Detection Non-specific design generates sequence or signal from "any" organism Specificity by match to reference database Signal and/or reference may not be sequence! May require instrument error modeling May require statistical or error tolerant matches Competition for signal generation? Testing with mixed (abundance) samples is crucial – not a specificity issue, per se 5

Updated Assay Validation Specific assays: Target sequence may change (influenza) Updated reference may invalidate working designs Non-specific design assays: Authentication of detection reference Match algorithm changes may affect performance How is instrument/processing software validated across versions? 6