Award Abstract # 0543586
Statistical and Computational Methods for the Study of Gene Families

NSF Org: DBI
Division of Biological Infrastructure
Recipient: TRUSTEES OF INDIANA UNIVERSITY
Initial Amendment Date: June 29, 2006
Latest Amendment Date: June 29, 2006
Award Number: 0543586
Award Instrument: Standard Grant
Program Manager: Reed Beaman
DBI
 Division of Biological Infrastructure
BIO
 Directorate for Biological Sciences
Start Date: July 1, 2006
End Date: June 30, 2010 (Estimated)
Total Intended Award Amount: $360,177.00
Total Awarded Amount to Date: $360,177.00
Funds Obligated to Date: FY 2006 = $360,177.00
History of Investigator:
  • Matthew Hahn (Principal Investigator)
    mwh@indiana.edu
Recipient Sponsored Research Office: Indiana University
107 S INDIANA AVE
BLOOMINGTON
IN  US  47405-7000
(317)278-3473
Sponsor Congressional District: 09
Primary Place of Performance: Indiana University
107 S INDIANA AVE
BLOOMINGTON
IN  US  47405-7000
Primary Place of Performance
Congressional District:
09
Unique Entity Identifier (UEI): YH86RTW2YVJ4
Parent UEI:
NSF Program(s): ADVANCES IN BIO INFORMATICS
Primary Program Source: app-0106 
Program Reference Code(s): 1165, 9183, 9184, BIOT
Program Element Code(s): 116500
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

Indiana University is awarded a grant to develop a statistical framework that would allow for inferences regarding gene family evolution among species. In order to take full advantage of the data being produced by various genome sequencing projects, this project aims to extend the statistical and computational tools necessary for biological researchers to study gene families. There are three main goals of this proposal: 1) Development of improved statistical tools. This work will enable more refined estimates of gene duplication and deletion parameters between species, and will provide new ways in which to study gene families within single genomes. The inclusion of methods for detecting and incorporating whole genome duplications will greatly extend statistical inferences. 2) Creation of easy-to-use software. A free software package will be implemented that can be used by researchers studying whole genomes or individual gene families. Statistical tools created in this project will be quickly disseminated to the community via this package. 3) Providing annotated gene families for Drosophila. The sequencing of 12 Drosophila species will be a boon to comparative genomics studies. By working with FlyBase to provide a well-annotated set of gene families from across these species, we will present new ways for biologists to connect this information with functional and comparative genomic data. The products of this research will provide a broad statistical and computational framework for all future studies of gene families. The research will also provide a diverse training environment for undergraduates, graduate students, and postdoctoral researchers in molecular evolution, statistics, and bioinformatics. The participation of under-represented groups and women via multiple scholarship programs will ensure that this specific research priority is achieved. The research will also be used in the development of classes and programs for understanding the relationship between biodiversity and genetic variation, and in graduate education for bioinformatics students.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 22)
Schrider, D. R.;Costello, J. C.;Hahn, M W; "All human-specific gene losses are present in the genome as pseudogenes" Journal of Computational Biology , v.16 , 2009 , p.1419
Casola, C., C.L. Ganote, and M.W. Hahn "Nonallelic gene conversion in the genus Drosophila" Genetics , v.185 , 2010 , p.95
Casola, C;Hahn, M W; "Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods" Journal of Molecular Evolution , v.68 , 2009 , p.679
Drosophila Comparative Genome Sequencing and Analysis Consortium "Evolution of genes and genomes on the Drosophila phylogeny." Nature , v.450 , 2007 , p.203
Han, M.V.;Hahn, M.W.; "Identifying parent-daughter relationships among duplicated genes" Pacific Symposium on Biocomputing , v.14 , 2009 , p.114-125
J.C. Costello, M.V. Han, and M.W. Hahn "Limitations of pseudogenes in identifying gene losses" RECOMB-Comparative Genomics , 2008 , p.14
J.P. Demuth and M.W. Hahn "Life and death of gene families" BioEssays , v.31 , 2009 , p.29
J.P. Demuth, T. De Bie, J. Stajich, N. Cristianini, and M.W. Hahn "The evolution of mammalian gene families." Public Library of Science ONE , v.1 , 2006 , p.e85
Kostka, D., M.W. Hahn, and K.S. Pollard "Non-coding sequences near duplicated genes evolve rapidly" Genome Biology and Evolution , 2010 10.1093/gbe/evq037
McGrath, C L;Casola, C;Hahn, M W; "Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes" Genetics , v.182 , 2009 , p.615
Meisel, R.P., M.V. Han, and M.W. Hahn "A complex suite of forces drives gene traffic from Drosophila X chromosomes" Genome Biology and Evolution , v.1 , 2009 , p.176
(Showing: 1 - 10 of 22)

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