THE GENOME INITIATIVE AT UC DAVIS

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THE GENOME INITIATIVE AT UC DAVIS
Objective To increase international
leadership at UC Davis in organismal biology
To ensure research campus-wide remains current
To provide limiting technologies at cost
through technology service cores To create
the Genome Center 10 lab 7 bioinformatics
faculty 5 service cores Rationale Technolog
y antenna in genomics for campus
http//www.genomecenter.ucdavis.edu
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GENOME AND MEDICAL BIOSCIENCES BUILDING
Molecular Medicine Genomics Bioinformatics Pharm
acology Biomedical Engineering Enabling Genomics
Facility Imaging Vivarium 70 Faculty 25
new 700 people Six floors 225,000 sq
ft 98M On budget September 2004 Garimendi funded
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First Floor
GENOMICS CENTER First floor 10,000 sq feet

Building support
Proteomics Research Service Core Facility
Offices
Demo Lab
Auditorium
Metabolomics Research Service Core Facility
Cafe
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First floor metabolomics lab and service
core Open design to house mass spectrometers Minim
al benches, utilities in ceiling
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Fourth Floor

GENOMICS BIOINFORMATICS CENTER Fourth floor (
¼ fifth floor)
Expression Analysis
Bioinformatics
Offices Admin
Comparative Genomics Research Expression
Service Core Facility
Genetics Research Service Core Facility
Offices
Meeting Room
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Fourth floor Shared wet labs 32 workspaces per
lab Two to three groups per lab
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Bioinformatics lab 32 cubicles Machine room
300 cpu in clusters
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ORGANIZATIONAL STRUCTURE FOR SERVICE CORES DNA
TECHNOLOGIES, EXPRESSION ANALYSIS, PROTEOMICS,
METABOLOMICS, BIOINFORMATICS
GENOME CENTER DIRECTOR
SENIOR FACULTY LEADERSHIP STRATEGIC
OVERSIGHT TROUBESHOOTING
CORE MANAGER DAY-TO-DAY MANAGEMENT DAILY
OPERATIONS
JUNIOR FACULTY TECHNOLOGY DEVELOPMENT
CAMPUS FACULTY TECHNOLOGY REQUESTS
TECHNICAL SUPPORT STAFF DAILY OPERATIONS
Recharges based on costs of consumables, labor,
and service contract minimal
equipment and administrative overhead
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GENOTYPING OPPORTUNITIES AT DAVIS
Fragment microsatellite Taq-Man
Microarray SNP analysis
GC DNA Technology Core
CAES Genomics Facility
SOM/GC Affymetrix Core
Lucy Whittier Molecular Diagnostic Core
Veterinary Genetics Laboratory
CCM Mouse Biology Program
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DNA TECHNOLOGIES SERVICE CORE
HIGH THROUGHPUT GENOTYPING FINGERPRINTING (NOT
SEQUENCING)
AVAILABLE Spectrumedix Reveal
TDGGE Fluorescence Polarization Luminex Flow
System Affymetrix Microarrays
Illumina Bead Array UNDER CONSIDERATION ABI
3730 SNPlex Spectrumedix SSCP AVAILABLE
ELSEWHERE ABI9700 TaqMan (SOM) CE
Microsatellite (CGF) MANAGER Charlie Nicolet
REVEAL
FP
LUMINEX
ILLUMINA
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EXPRESSION ANALYSIS SERVICE CORE
AVAILABLE Oligonucleotide/spotted
arrays Affymetrix oligonucleotide arrays
(SOM/GC) Luminex microbeads UNDER
CONSIDERATION Inkjet oligonucleotide in situ
synthesizer AVAILABLE ELSEWHERE ABI9700 TaqMan
(SOM)
Oligonucleotide arrayer
Agilent scanner
Affymetrix washstations high throughput scanner
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PROTEOMICS SERVICE CORE
Analysis of macromolecular complexes Identificatio
n of constitutions Post-translation
modifications Sample preparation Mass spec
analysis Data analysis MANAGER Brett
Phinney
Julie Leary Lab
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METABOLOMICS SERVICE CORE

• GC-TOF 50 per sample
• Start July 2005
• Full QC under SOPs
• LIMS and database
• Metabolic annotations under MIAMET
• LC-MS start Fall 2005
• QCs, LIMS and database to be done
• MANAGER
• Vladimir Tolstikov

Max-Planck-Institute of Molecular Plant
Physiology, Potsdam
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BIOINFORMATICS SERVICE CORE
DATA ACQUISITION, CURATION, INTEROGATION,
DISTRIBUTION SUPPORT FOR GENOTYPING, EXPRESSION,
PROTEOMICS, METABOLOMICS
CORES EXPERIMENTAL DESIGN AND INTERPRETATION LABOR
ATORY LIMS INDEPENDENT DATABASE SUPPORT AREAS
OF INTEREST MANAGER ASSOCIATION STUDIES
UNDER RECRUITMENT MICROARRAY
DATA STRUCTURAL MODELING METABOLITE PROFILES
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FACULTY INVOLVEMENT IN THE GENOME CENTER
MULTIPLE LEVELS OF PARTICIPATION GENOME
CENTER FACULTY 9 TECHNOLOGY-DRIVEN BIOLOGISTS
8 BIOINFORMATICS MICROBIAL, PLANT,
ANIMAL/HUMAN INTERESTS LOCATED PRIMARILY IN
CENTER LEADERSHIP AND DEVELOPMENT OF CORES
GENOME CENTER MEMBERS GENOMICS FACULTY
THROUGHOUT CAMPUS FREQUENT USERS OF CORES
RECRUITMENT OF GENOME CENTER
FACULTY MEMBERS OF CAMPUS ADVISORY COMMITTEE
BIOLOGY FACULTY THROUGHOUT CAMPUS OCCASIONAL AD
HOC USERS
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Unique multidisciplinary combination of
faculty Integration of wet lab and experimental
approaches Faculty half wet lab, half
computational Shared wet lab and computational
resources Two gathering areas per floor
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GENOME CENTER RECRUITMENTS 2004 Interviewed end
January early May 2004
Portfolio of positions, simultaneous
offers Criteria Excellent science
Technology or computationally-driven biologists
Nucleate/complement larger efforts on campus
E.g. Areas of strength plant genomics,
cancer, chromosome biology,
infectious disease E.g. Areas of
opportunity microbial genomics,
mammalian genetics, foods for health Center focus
on the phenotypic consequences of genetic
variation
Wet lab Bioinformatics Total Interviewed
20 13 33 Recommended for
recruitment 7 5 12 Formal
Offers 5 5 10 Declined
1 0 1 Accepted
4 5 9
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WET LAB/EXPERIMENTAL FACULTY 2004 RECRUITS
Peggy Farnham, U. Wisconsin, McArdle Cancer
Center Pharmacology. ChIP chip,
DNA-protein interactions, liver cancer. Julie
Leary, UC Berkeley. Chemistry MCB. Mass
Spec, Proteomics, Post-translation
modification. Oliver Fiehn, Max Plank, Potsdam.
Mol. Cell. Biology. Mass Spec, Metabolomics.
Plant mouse liver profiling. Michael Wright,
Inst. Systems Biology, Seattle. Pharmacology.
Mass spec. Proteomics prostate cancer.
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BIOINFORMATICS FACULTY 2004 RECRUITS
Patrice Koehl, Stanford Genome Center. Computer
Science Molecular modeling, protein folding,
database inferences Ian Korf, Sanger Center,
Cambridge, UK. Mol. Cell. Biology Genome
annotation, eukaryotic comparative
genomics. Bruce Rannala, University of Alberta.
Evolution Ecology Bayesian evolutionary
inference. Yong Duan, U. Delaware. Applied
Science Molecular modeling, protein-ligand
interactions. Bertram Ludascher, San Diego
Supercomputer Center. Computer
Science. Database structures and interactivity.
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FACULTY RECRUITMENTS 2004 - 2005
More focused High throughput genotyping,
Statistical genetics (human), Microbial
comparative genomics (infectious disease)
Metabolic pathway analysis Analysis of large
complex datasets
Wet lab Computational Interviewed
14 Formal Offers 6 Declined
2 Pending 2 Accepted 2
2.5 FTE remain. Wet lab analysis of metabolic
pathways
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FACULTY 2004 - 2005 RECRUITMENTS
Accepted Katy Pollard, UC Santa Cruz.
Statistics. Analysis of high dimensional
datasets, microarrays, comparative genomics.
David Segal, U. Arizona. Pharmacology.
Therapeutic applications of zinc finger proteins,
gene replacement. Pending Jonathan Eisen,
TIGR. EVE Med. Micro. Comparative microbial
genomics. DNA repair. Luca Comai, U.
Washington. Plant Biology. Consequences of
polyploidy. High throughput genetic analysis.
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THE PHENOTYPIC CONSEQUENCES OF NATURAL GENETIC
VARIATION
COMPUTATIONAL WET LAB
SEQUENCE STRUCTURE ACTIVITY PATHWAY PHENOTYPE
POPULATION
Ian Korf Craig Benham
Peggy Farnham David Segal
Yong Duan Patrice Koehl Katy Pollard
Julie Leary Mike Wright Oliver Fiehn
Open
Open
Bertram Ludaescher
Richard Michelmore
(Jonathan Eisen) (Luca Comai)
Bruce Rannala
ENABLE COMPARATIVE FUNCTIONAL GENOMICS ACROSS
CAMPUS
1/3 Assistant, 1/3 Associate, 1/3 Full
Professor
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PRIORITIES FOR NEXT TWELVE MONTHS
Complete move into GBSF Establish labs and
internal infrastructure Develop interactions with
existing faculty and facilities Establish five
service cores (Techs, Equipment,
Recharges) Complete recruitment and relocation of
new recruits Last round of recruitment (Fall
2005?, Pathway Analysis) Submit Center grant
proposals
http//www.genomecenter.ucdavis.edu