Research Presentation Nordborg Lab University of Southern California Helly Kwee August 21, 2003 Southern California Bioinformatics Summer Institute.

Slides:

Advertisements

Similar presentations

1 Inference of Regulatory Networks via Systems Genetics Ina Hoeschele.

Advertisements

Potato Mapping / QTLs Amir Moarefi VCR

GDR, the Genome Database for Rosaceae, in Chado and Tripal Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping Zheng,

Human Genome Project What did they do? Why did they do it? What will it mean for humankind? Animation OverviewAnimation Overview - Click.

Genetic Screening for Alzheimer’s Disease Thorstensen: Genetic Screening for Alzheimer's Disease 1.

The DNA Bead String Exercise Anita L DeStefano, PhD Department of Biostatistics BU School of Public Health Co-Director Biostatistics Program Associate.

Plant of the day! Pebble plants, Lithops, dwarf xerophytes Aizoaceae

BIOINFORMATICS Ency Lee.

By Angela Brooks and David Chapman Mentor: Dr. Garry Larson Molecular Medicine, City Of Hope Southern California Bioinformatics Institute 2004.

Aug. 20, JPL, SoCalBSI '091 The power of bioinformatics tools in cancer research Early Detection Research Network, JPL Mentors: Dr. Chris Mattmann,

Practical exercises in Plant Biodiversity and Breeding (BI1103) Jonas RoosTom MartinLuisa Ghelardini.

Bioinformatics “half a year in the lab can easily save you an afternoon in front of the computer….” (unknown)

Creating An Allele Index For NPGS: Bioinformatic Issues Edward Buckler USDA-ARS at Cornell University, Ithaca, NY.

A Genomic Survey of Polymorphism and Linkage Disequilibrium Imran Mohiuddin Magnus Nordborg, Ph.D. University of Southern California.

Abstract The goal of the Conifer Translational Genomics Network (CTGN) project is to provide tree breeders across the United States with new tools to enhance.

Structural and Functional Genomics of Tomato Barone et al Tomato (Solanum Lycopersicon) – economically important crop worldwide, – intensively investigated.

Predicting the Function of Single Nucleotide Polymorphisms Corey Harada Advisor: Eleazar Eskin.

Biology and Bioinformatics Gabor T. Marth Department of Biology, Boston College BI820 – Seminar in Quantitative and Computational Problems.

Light response QTL in Arabidopsis thaliana: LIGHT1 cloning Justin Borevitz Ecology & Evolution University of Chicago naturalvariation.org.

Richard, Rochelle, Zohal, Angie

Bioinformatics Tools for Microarray Analysis Connie Wu Dr. Jim Breaux Dr. Sandeep Gulati ViaLogy Southern California Bioinformatics Institute Summer 2004.

Inference of Genealogies for Recombinant SNP Sequences in Populations Yufeng Wu Computer Science and Engineering Department University of Connecticut

Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.

Building Bioinformatics Tools for Research Scientists Southern California Bioinformatics Summer Institute 2008 Andrew Clark Mentor: Dr. Ping Du, Allergan,

A Computational Analysis of the H Region of Mouse Olfactory Receptor Locus 28 Deanna Mendez SoCalBSI August 2004.

Genomic Region Analysis of Microsatellite Loci in Arabidopsis thaliana Abstract Microsatellite loci frequently occur throughout a genome in various locations.

Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.

LESSON 4: PowerPoint slides to accompany Using Bioinformatics: Genetic Testing.

Moving forward our shared data agenda: a view from the publishing industry ICSTI, March 2012.

Building Database Resources For Translational Research in Rosaceae Sook Jung, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping.

Gramene Objectives Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants.

Howard Hughes Medical Institute-NMSU Research Scholar

APPLICATION OF MOLECULAR MARKERS FOR CHARACTERIZATION OF LATVIAN CROP PLANTS Nils Rostoks University of Latvia Vienošanās Nr. 2009/0218/1DP/ /09/APIA/VIAA/099.

Diversity Bioinformatics Terry Casstevens Institute for Genomic Diversity, Cornell University GMOD Meeting at NESCent Durham, NC – June 29-30, 2006.

GDR in Drupal facilitating community building and efficient maintenance.

Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Stephen Ficklin 1, Taein Lee 1, Ping Zheng 1, Don Jones 2, Richard Percy 3, Dorrie Main 1 1. Washington State.

Korea BioInformation Center Byoung-Chul Kim

Announcements: Proposal resubmission deadline 4/23 (Thursday).

Gramene Objectives Provide researchers working on grasses and plants in general with a bird’s eye view of the grass genomes and their organization. Work.

Managing Next Generation Sequence Data with GMOD Dave Clements 1, Scott Cain 2, Paul Hohenlohe 3, Nicholas Stiffler 3, Paul Etter 3, Eric Johnson 3, William.

Kyle Tretina with a team led by Dr. Pattle P. Pun in collaboration with Mr. Ross Leung of CUHK Analysis of the Positively Selected and Non-Positively Selected.

NRSP10 Database Resources for Crop Genomics, Genetics and Breeding Research NRSP Crops Breeders Database Needs Focus Group Meeting July 30, 2015 Pullman,

Gramene: Interactions with NSF Project on Molecular and Functional Diversity in the Maize Genome Maize PIs (Doebley, Buckler, Fulton, Gaut, Goodman, Holland,

Copyright OpenHelix. No use or reproduction without express written consent1.

Description: Use the naturally occurring albino mutation of corn plants as an example of genetic biodiversity. Goals: Describe how the impact of humans.

C R O P S T O I N D U S T R Y WP 2 Tasks: 2-1 to 2-3 Task leader: Dimitra Milioni Crops2Industry “Non-food Crops-to-Industry schemes in EU27”

HW2: exome sequencing and complex disease Jacquemin Jonathan de Bournonville Sébastien.

The Future of Genetics Research Lesson 7. Human Genome Project 13 year project to sequence human genome and other species (fruit fly, mice yeast, nematodes,

“Jumping Genes” Lead The Way

IMDB: A Generic Insertional Mutagenesis Database Xiaokang Pan and Lincoln Stein Cold Spring Harbor Laboratory.

Sunflower Genomic Resources Consortium – Update Meeting (1)assemble, annotate, and curate the sunflower reference genome; (2)integrate the reference sequence.

Goal: Establish Aquilegia as an evolutionary model system 70 taxa (diverse in floral morphology & ecology) recent & rapid radiation (little genetic variation.

Research proposal 2009 信息技术会议 Bioinformatics Analysis & Identification of non-Synonymous SNPs in Candidate Genes for Ascites College of Animal Husbandry.

Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Stephen Ficklin 1, Taein Lee 1, Ping Zheng 1, Don Jones 2, Richard Percy 3, Dorrie Main 1 1. Washington State.

Graduate Research with Bioinformatics Research Mentors Nancy Warter-Perez, ECE Robert Vellanoweth Chem and Biochem Fellow Sean Caonguyen 8/20/08.

1 Finding disease genes: A challenge for Medicine, Mathematics and Computer Science Andrew Collins, Professor of Genetic Epidemiology and Bioinformatics.

1 Bioinformatics Tools for Genotyping Frances Tong Dr. Garry Larson, Ph.D City of Hope Department of Molecular Medicine Southern California Bioinformatics.

Bioinformatics Overview

Natural Variation and the Genetic Basis of

Introduction to bioinformatics lecture 11 SNP by Ms.Shumaila Azam

the Genome Database for Rosaceae: New Data and Functionality

Genome organization and Bioinformatics

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

Garrett McKinney University of Washington Seeb Lab

Linkage analysis and genetic mapping

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

Key CottonGen Features For more information contact:

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

Biotechnology & Bioinformatics

For more information contact:

Presentation transcript:

Research Presentation Nordborg Lab University of Southern California Helly Kwee August 21, 2003 Southern California Bioinformatics Summer Institute

Agenda Research area overview Projects Bioinformatics Tools Current State of Affairs Conclusion (Impacts)

Overview Genetic basis of adaptation Map loci conferring natural variation in Arabidopsis thaliana NSF 2010 Project

Projects Genomic survey of polymorphism in A. thaliana – Sequence ~2000 fragments from 96 accessions – Phenotype various traits – Association analysis Bioinformatics tools: – Publicly accessible database – Web-based viewers

Bioinformatics Tools Revised database schema Populating the database Revised web-based viewers – Genome – Polymorphism – Alignment

Database Contents

Code Revision I alignmentviewer.pl db.pm viewer.pm alignmentviewer.pl genomeviewer.pl polymorphismviewer.pl genomeviewer.pl polymorphismviewer. pl Module s

Screenshot-- Alignment Viewer

Screenshot– Genome Viewer Screenshot-- Genome Viewer

Screenshot-- Polymorphism Viewer

Impacts Insights into genetic basis of natural variation Genes responsible for agriculturally important traits Tools and methods --> applicable to economically important organisms Database as training tool

Questions ?

Acknowledgements Dr. Nordborg and his lab SoCalBSI faculty NSF and NIH