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© Kumar and Parkhurst, 2011
Lost in (Variation) Space
3
Phylomedicine
© Kumar and Parkhurst, 2011
Phylomedicine: Evolutionary Telescope
Conservation
Divergence
(2011) 27:377-386
Mission
– Our mission is to harness molecular evolutionary knowledge and techniques to advance research and development in biomedicine to biodiversity.
– We are accomplishing this mission by making fundamental discoveries, developing informatics resources, and training the next generation of young scientists.
Evolution
Medicine Genomics
Informatics
iGEM
Mission
• Discovering the Rules of Life– Patterns and processes that have shaped the
blueprint of life (DNA) and diversity of life on earth
•Genes and Genomes•Species
Mission
• Building evolutionary Tools for Life– Predictive models and translational
technologies•Genome Medicine•Biological Diversity
P4 paradigm
Patterns
Processes
Predictions
Products
The faculty
Scholarship impact
18,000
19,000
20,000
21,000
22,000
23,000
20142015
2016
New Citations 2014-2016
Does not include Masatoshi Nei (adjunct professor)
Worldwide usage of iGEM tools
• MEGA, HyPhy, TimeTree, and others
Research support
$-
$500,000
$1,000,000
$1,500,000
$2,000,000
$2,500,000
$3,000,000
FY15 FY16 FY17
$1,171,424
$2,248,543 $2,530,944 *
EXTRAMURAL FUNDING(EXCLUDES SUBCONTRACTS)
All grants are new to Temple (i.e., FY 2015 onwards). Includes only grants coded into ORG 13410
Awards by agency
2%1%
55%28%
14%
Awards (FY15 - FY17)
FoundationNASANIHNSFPA-CURE
Example Grant Titles
• Diseases– Cancer/Mendelian Diseases
• Evolutionary Bioinformatics of Tumor Profiles• Computational Diagnosis of Non-Synonymous Variations Using
Structural Dynamics
– Complex Diseases• Methods for Evolutionary Informed Network Analysis to Discover
Disease Variation• eQTL Mega-Analysis for Functional Assessment of Multi-Enhancer Gene
Regulation
– Infectious diseases• Modeling Epidemic Infectious Diseases Using Sequence Analysis• Biological Properties Of HIV-1 V3 Evolutionary Variants
Example Grant examples
• Tools– Databases
• TimeTree: Enabling Discoveries Across Disciplines Through a Synthesis of Time-Calibrated Evolutionary Histories
• FlyExpress: Fruitfly gene expression patterns
– Software• Improved Tools for Population Genomics• (Hyphy) Comprehensive, Fast, and User-Friendly Software for
Evolutionary Analysis• (MEGA) Comparative Molecular Sequence Analysis
iGEM in education
• iGEM faculty are educating and training the future workforce.
• We are developing – certificate programs, – participating in masters' and doctoral degree
programs, – offering advanced courses, and – providing one-on-one research mentoring to
• undergraduate, • graduate, and • postgraduate students.
iGEM in education
• CERTIFICATE IN GENOME MEDICINE– This certificate is designed for undergraduate
students to become conversant in state-of-the-art genomics and computational biology approach to study and remedy human diseases.
• BS IN DATA SCIENCE (GENOMICS AND BIOINFORMATICS)– The Bachelors of Science in Data Science with a
concentration in Genomics and Bioinformatics is to prepare the next generation workforce for managing, processing, and analyzing large quantities of data collected in biology and genomics.
Class room instruction
Graduate training
• GRADUATE STUDENT TRAINING PORTALS– Innovative web resources highlighting iGEM faculty
expertise in the following areas have been designed and implemented to attract potential graduate students to iGEM:
• EVOLUTIONARY MEDICINE• GENOMIC EPIDEMIOLOGY• POPULATION GENETICS• More to come…
• Designed and implemented Professional Science Masters (PSM) websites– Bioinformatics, Biotechnology, and Bioinnovation
iGEM Members
• Core faculty = 10– 4 New (Kumar, Hedges, Escalante, Pond) – 1 Adjunct Carnell Professor (Nei)– 3 New CCGG (Hey, Liberles, Schraiber) – 2 Existing (Kulathinal, Spigler)
• Others = 40+– Research Faculty = 5– Postdocs = 9– Doctoral students = 7– Undergrads and MS = ~20
Thank you!
