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Author:

Lawson, Heather Alane

Title:

Molecular Evolutionary Underpinnings of Craniofacial Growth and Development

Graduate Program:

Anthropology

Keywords:

genomics
primate
molecular evolution
craniofacial
genotype
phenotype

File:

Download Lawson2008.pdf

Committee Members:

Kenneth Monrad Weiss, Committee Chair/Co-Chair
Anton Nekrutenko, Committee Member
Ross Cameron Hardison, Committee Member
Webb Colby Miller, Committee Member
Joan Therese Richtsmeier, Committee Member
Alan Walker, Committee Member

Author:

Swanson, John-David

Title:

Flower development in Theobroma cacao L.: An assessment of morphological and molecular conservation of floral development between Arabidopsis thaliana and Theobroma cacao

Graduate Program:

Integrative Biosciences

Keywords:

Flower development
Theobroma cacao
Arabidopsis
morphology
genomics

File:

Download SwansonPhDthesisFinal.pdf

Committee Members:

Mark Guiltinan, Committee Chair/Co-Chair
John Edward Carlson, Committee Chair/Co-Chair
Hong Ma, Committee Member
David Russell Hunter, Committee Member

Author:

Guo, Li

Title:

Molecular Genetic Analysis of Development and Pathogenicity in the Filamentous Fungus Fusarium verticillioides

Graduate Program:

Plant Pathology

Keywords:

Fusarium verticillioides
fumonisins
reactive oxygen species
hyphal fusion
genomics
maize
ear rot

File:

Download Li_Guo_Dissertation_FINAL.pdf

Committee Members:

Gretchen Anna Kuldau, Dissertation Advisor/Co-Advisor
Gretchen Anna Kuldau, Committee Chair/Co-Chair
Seogchan Kang, Committee Member
David Michael Geiser, Committee Member
Yinong Yang, Committee Member
Dawn S Luthe, Committee Member
Anthony Glenn, Committee Member

Author:

Meisel, Richard P

Title:

GENE DUPLICATION AND CHROMOSOMAL REARRANGEMENT IN DROSOPHILA GENOMES

Graduate Program:

Genetics

Keywords:

population genetics
genomics
chromosomal rearrangement
gene duplication
Drosophila
meiotic drive
sex chromosomes

File:

Download __meisel_thesis_2008_07_08_.pdf

Committee Members:

Claude W De Pamphilis, Committee Chair/Co-Chair
Stephen Wade Schaeffer, Committee Member
Hiroshi Akashi, Committee Member
Bruce A Mc Pheron, Committee Member
Wojciech Makalowski, Committee Member

Author:

Richards, Jessica Yung

Title:

Chemical communication and genomics of swarming behavior in honey bees (apis mellifera L.)

Graduate Program:

Entomology

Keywords:

honey bee
Apis mellifera
swarming
chemical communication
genomics

File:

Download JYR_Thesis_2013.pdf

Committee Members:

Christina M Grozinger, Thesis Advisor/Co-Advisor
James Homer Tumlinson Iii, Thesis Advisor/Co-Advisor
Edwin George Rajotte, Thesis Advisor/Co-Advisor
Anita Collins, Thesis Advisor/Co-Advisor

Author:

Chang, Gue Su

Title:

Integrated Genomics Approach To Uncovering Gene Regulation and Epigenetics Across Eukaryotes

Graduate Program:

Integrative Biosciences

Keywords:

genomics
eukaryote transcriptional regulation
epigenetics
bioinformatics
high throughput sequencing

File:

Download Thesis-Chang_Gue_Su.pdfDownload Thesis-Chang_Gue_Su-Tables.xls

Committee Members:

Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Istvan Albert, Committee Member
Yu Zhang, Committee Member

Author:

Ma, Zhaorong

Title:

Functional and Evolutionary Genomics of Plant Small RNAs

Graduate Program:

Integrative Biosciences

Keywords:

genomics
small RNAs
microRNAs
comparative genomics
evolutionary genomics
targeted enrichment
targeted genomic enrichment

File:

Download Zhaorong_Ma_final_dissertation.pdf

Committee Members:

Michael Axtell, Dissertation Advisor/Co-Advisor
Michael Axtell, Committee Chair/Co-Chair
Claude Walker Depamphilis, Committee Member
Naomi S Altman, Committee Member
Ross Cameron Hardison, Committee Member

Author:

Olson, Thomas Lynn

Title:

Identification of Somatic Mutations in LGL Leukemia through Whole Genome Sequencing and Correlation of STAT3 Y640F Mutation with Treatment Response to Methotrexate.

Graduate Program:

Molecular Medicine

Keywords:

large granular lymphocytes
leukemia
STAT3
TBET
genomics

File:

Download Thomas_L_Olson.pdf

Committee Members:

"Thomas P Loughran, Jr", Dissertation Advisor/Co-Advisor
Rosalyn Bryson Irby, Committee Chair/Co-Chair
Thomas E Spratt, Committee Member
Richard James Courtney, Committee Member
Bruce A Stanley, Special Member

Author:

Loquasto, Joseph Robert

Title:

Assessing the diverstiy of the monomorphic subspecies Bifidobacterium animalis subsp. lactis

Graduate Program:

Food Science

Keywords:

bifidobacteria
probiotics
genomics
dairy products

File:

Download Loquasto-Dissertation.pdf

Committee Members:

Robert F Roberts, Committee Chair/Co-Chair
Edward G Dudley, Committee Member
Rodolphe Barrangou, Committee Member
Eric Thomas Harvill, Committee Member

Author:

Mishra, Tejaswini

Title:

Integrative genome-wide studies to elucidate regulation of lineage choice in hematopoiesis

Graduate Program:

Cell and Developmental Biology

Keywords:

hematopoiesis
genomics
gene regulation;RNA-seq;erythroblast;megakaryocyte

File:

Download Dissertation_TejaswiniMishra.pdf

Committee Members:

Ross Cameron Hardison, Dissertation Advisor/Co-Advisor
Michael Axtell, Committee Member
Benjamin Franklin Pugh, Committee Member
Robert Paulson, Committee Member
Debashis Ghosh, Committee Member

Author:

Shipley, Mackenzie Marie

Title:

Examining the Link Between Viral Genotype and Disease Phenotype Using Clinical Cases of HSV-1 and a Human Neuronal Model

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

herpes simplex virus
genomics
infection
genital
neonatal
neurobiology

File:

Download ShipleyMM_PSU_Dissertation2018_Final.pdf

Committee Members:

Moriah Louise Szpara, Dissertation Advisor/Co-Advisor
Moriah Louise Szpara, Committee Chair/Co-Chair
Melissa Rolls, Committee Member
Richard J. Frisque, Committee Member
John Warren Wills, Outside Member
Lorraine C Santy, Committee Member

Author:

Yang, Tao

Title:

STATISTICAL METHODS FOR COMAPRING NEXT-GENERATION SEQUENCING DATA REPRODUCIBILITY, SIMILARITY AND DIFFERENTIATION

Graduate Program:

Bioinformatics and Genomics

Keywords:

sequencing
reproducibility
quality control
ChIP-seq
Hi-C
differential interaction
genomics

File:

Download TaoYang_dissertation_2018_FinalVersion.pdf

Committee Members:

Qunhua Li, Dissertation Advisor/Co-Advisor
Qunhua Li, Committee Chair/Co-Chair
Shaun Mohany, Committee Member
Yu Zhang, Committee Member
Ross Hardison, Outside Member
Feng Yue, Dissertation Advisor/Co-Advisor

Author:

Gonzalez Angel, Ana Maria

Title:

Genomic and Transcriptomic Insights on the -Orbicella- Species Complex

Graduate Program:

Biology

Keywords:

Coral Reefs
Orbicella
genomics
transcriptomics
speciation
reproductive isolation

File:

Download 2019_11_24_DoctoralDissertation_AMGA_final.pdf

Committee Members:

Monica Medina, Dissertation Advisor/Co-Advisor
James Harold Marden, Committee Chair/Co-Chair
Stephen Wade Schaeffer, Committee Member
Istvan Albert, Outside Member
Stephen Wade Schaeffer, Program Head/Chair

Author:

Reich, Hannah Gallogly

Title:

The importance of trace metals in coral-algal symbiosis

Graduate Program:

Biology

Keywords:

coral-algal symbiosis
Symbiodiniaceae
Trace metals
Metal quota
Iron limitation
Coral bleaching
genomics
Algal culturing
Dinoflagellate
Micronutrients
Physiology

File:

Download reich_dissertation_03202020.pdf

Committee Members:

Todd C Lajeunesse, Dissertation Advisor/Co-Advisor
Iliana Brigitta Baums, Committee Chair/Co-Chair
Roberto Iglesias-Prieto, Committee Member
Erin L Connolly, Outside Member
Tracy Langkilde, Program Head/Chair

Author:

Lasisi, Tina Tina

Title:

The genetic architecture and evolutionary function of human scalp hair morphology

Graduate Program:

Anthropology

Keywords:

hair morphology
human evolution
biological anthropology
human scalp hair
human genetics
genetics
genomics
phenotypic variation

File:

Download Lasisi_2021_Dissertation.pdf

Committee Members:

Nina G Jablonski, Dissertation Advisor/Co-Advisor
Nina G Jablonski, Committee Chair/Co-Chair
George H Perry, Committee Member
Tim Ryan, Major Field Member
Mark Shriver, Dissertation Advisor/Co-Advisor
Mark Shriver, Committee Chair/Co-Chair
William Lawrence Kenney, Jr., Outside Member
George Havenith, Special Member
Tim Ryan, Program Head/Chair

Author:

Benson, Christopher

Title:

Genomic and transcriptomic insight into the evolution and breeding of turfgrass species, Poa annua and Bouteloua dactyloides

Graduate Program:

Plant Biology

Keywords:

Poa annua
turfgrass
genetics
genomics
polyploidy
sequencing
breeding
annual bluegrass
annual meadowgrass
pistil smut
Bouteloua dactyloides
Buffalograss
Salmacisia buchloëana
the genome balance hypothesis
dioecy
tilletia
golf
putting green
homoeolog
polyploid plasticity hypothesis
chromosome modification
chromosome restructuring
fractionation
retrotransposon
synteny
RNA-seq
comparative genomics
pan-genome
transposable element
host manipulation
amphihapoid
haploid plants
allotetraploid
DNA methylation
Poa infirma
Poa supina

File:

Download Benson_dissertation.pdf

Committee Members:

Sally Mackenzie, Major Field Member
David Huff, Chair & Dissertation Advisor
Claude Depamphilis, Outside Field Member
Gary Felton, Outside Unit Member
Teh-Hui Kao, Program Head/Chair

Author:

Manickavasagam Pounraja, Vijay Kumar

Title:

Computational methods for dissecting the genetic basis of neurodevelopmental disorders

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

exome-sequencing
CNV
machine learning
rare variant genetics
genomics
neurodevelopmental disorders
random forest
apriori algorithm
rare combinations
combinatorial analysis

File:

Download Vijay_Kumar_Dissertation.pdf

Committee Members:

Naomi Altman, Major Field Member
Vasant Honavar, Outside Field Member
Yifei Huang, Major Field Member
Santhosh Girirajan, Chair & Dissertation Advisor
Reka Albert, Outside Unit Member
George Perry, Program Head/Chair

Author:

Mandell, Zachary

Title:

MECHANISMS OF INTRINSIC TRANSCRIPTION TERMINATION AND RIBONUCLEOLYTIC DECAY IN Bacillus subtilis

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

transcription
genomics
transcriptomics
RNA biology
translation
Microbiology

File:

Download Electronic_Dissertation.pdf

Committee Members:

Paul Babitzke, Chair & Dissertation Advisor
Istvan Albert, Major Field Member
Timothy Meredith, Outside Field Member
Philip Bevilacqua, Outside Unit Member
Katsuhiko Murakami, Major Field Member
Wendy Hanna-Rose, Program Head/Chair

Author:

Silva Gallardo, Constanza Paulina

Title:

The impact of nicotine exposure and cigarette smoking on gene expression and behavior from a translational perspective

Graduate Program:

Biobehavioral Health

Keywords:

gene expression
genomics
smoking
nicotine
translational
cigarette smoking
reduced nicotine-content cigarettes
RNA-Seq
DNA methylation
sex differences

File:

Download Silva-Dissertation.pdfDownload Appendix-A_Tables.zipDownload Appendix-B_Tables.zipDownload Appendix-C_Tables.zip

Committee Members:

Dajiang Liu, Outside Unit Member
David Vandenbergh, Major Field Member
Steven Branstetter, Outside Field Member
Helen Kamens, Chair & Dissertation Advisor
Thomas Gould, Program Head/Chair

Author:

Ray, Allyson

Title:

Deformed wing virus in the Western Honey Bee (Apis mellifera) : Genotypic and Phenotypic Variation Across Contexts and Scales

Graduate Program:

Molecular, Cellular, and Integrative Biosciences

Keywords:

deformed wing virus
Varroa destructor
Apis mellifera
epidemiology
virus evolution
experimental evolution
viral variation
virulence
transcriptomics
genomics

File:

Login to Download

Committee Members:

David Kennedy, Outside Field Member
Moriah Szpara, Outside Unit & Field Member
Elizabeth Mcgraw, Major Field Member
Christina Grozinger, Co-Chair & Dissertation Advisor
Jason Rasgon, Co-Chair & Dissertation Advisor
Melissa Rolls, Program Head/Chair

Author:

Stankiewicz, Kathryn

Title:

Coral biology and evolution through the lens of genomics and population genetics

Graduate Program:

Biology

Keywords:

genomics
bioinformatics
corals
population genetics
hybridization
recombination
comparative genomics
Delta K
STRUCTURE

File:

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Committee Members:

David Toews, Major Field Member
Istvan Albert, Outside Unit & Field Member
Iliana Baums, Major Field Member & Dissertation Advisor
Todd Lajeunesse, Chair of Committee
Stephen Wade Schaeffer, Professor in Charge/Director of Graduate Studies

Author:

Bresnahan, Sean

Title:

Molecular Mechanisms of Phenotypic Variation in Honey Bees (Apis mellifera)

Graduate Program:

Molecular, Cellular, and Integrative Biosciences

Keywords:

phenotypic plasticity
genomics
transcriptomics
epigenomics
honey bee
caste determination
individual variation
pheromones
genomic imprinting
histone post-translational modifications
RNA methylation
gene networks
allele-specific expression
diapause

File:

Download STB_dissertation_062124_corrected.pdf

Committee Members:

Melissa Rolls, Program Head/Chair
Amro Zayed, Special Member
Shaun Mahony, Outside Unit & Field Member
Michael Axtell, Co-Chair & Dissertation Advisor
Christina Grozinger, Co-Chair & Dissertation Advisor
Heather Hines, Major Field Member

Author:

Dweikat, Sarah

Title:

Multi-Parameter Phenotype-Based Investigations of Attenuation in Herpes Simplex Virus

Graduate Program:

Molecular, Cellular, and Integrative Biosciences

Keywords:

hsv
neonatal
genomics
phenotypic diversity
minor variants

File:

Login to Download

Committee Members:

Melissa Rolls, Program Head/Chair
David Kennedy, Major Field Member
Moriah Szpara, Chair & Dissertation Advisor
Lisa Akhtar, Special Member
Ilias Georgakopoulos-Soares, Outside Unit Member
Troy Sutton, Outside Field Member

Author:

Hernandez, Margarita

Title:

Noventa Millas: Migration history, genomic ancestry, and health outcomes among Cuban refugees/immigrants and Cuban-Americans in the United States

Graduate Program:

Anthropology

Keywords:

anthropology
genomics
biocultural anthropology
Latiné
mixed-methods
community based research

File:

Download DISSERTATION_FINAL.pdf

Committee Members:

Tim Ryan, Program Head/Chair
Lindsay Fernandez-Rhodes, Outside Unit & Field Member
Mary Shenk, Dissertation Co-Advisor
George Perry, Chair & Dissertation Advisor
Mark Shriver, Major Field Member

Author:

Apsley, Abner

Title:

A Critical Analysis of the Biomolecular Variation of Immune Cells Across Time and Stressful Environmental Exposures Using Multiomic Methods

Graduate Program:

Molecular, Cellular, and Integrative Biosciences

Keywords:

genomics
multiomics
multiomic integration
stress
early-life adversity
immune system
immune cells
epigenomics
DNA methylation
transcriptomics
metabolomics
NMR
RNA-seq

File:

Download DissertationSupplement.xlsxDownload Dissertation_Apsley_03_28_2025.pdf

Committee Members:

Melissa Rolls, Program Head/Chair
David Almeida, Outside Unit Member
Yogasudha Veturi, Major Field Member
Idan Shalev, Chair & Dissertation Advisor
Molly Hall, Outside Field Member