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Open Access

Author:: Patel, Rushang Dilipkumar
Title:: REGULATION OF GENE TRANSCRIPTION BY THE ARYL HYDROCARBON RECEPTOR –NEW TARGETS AND MECHANISMS OF REGULATION.
Graduate Program:: Integrative Biosciences
Keywords:: Aryl hydrocarbon receptor
Dioxin
Inflammation
Toxicology
Nuclear receptor
Gene regulation
File:: Download ThesisMasterFinal.pdf
Committee Members:: Gary H Perdew, Committee Chair/Co-Chair
Curtis John Omiecinski, Committee Member
Jeffrey Maurice Peters, Committee Member
Robert Bruce Mitchell, Committee Member
Naomi S Altman, Committee Member
Peter John Hudson, Committee Member

Open Access

Author:: Sekhon, Rajandeep Singh
Title:: INVESTIGATION OF MOLECULAR MECHANISMS OF REGULATION OF MAIZE PERICARP COLOR1 BY AN EPIGENETIC MODIFIER UNSTABLE FACTOR FOR ORANGE1
Graduate Program:: Plant Biology
Keywords:: Tandem repeat
DNA methylation
Epigenetics
Gene regulation
Maize
Epiallele
File:: Download Thesis_Rajandeep_Sekhon.pdf
Committee Members:: Surinder Chopra, Committee Chair/Co-Chair
David M Braun, Committee Member
Majid R Foolad, Committee Member
Timothy W Mcnellis, Committee Member

Open Access

Author:: Chen, Kuanbei
Title:: Computational Approaches for Integrative Detection of Protein-DNA Interactions
Graduate Program:: Computer Science and Engineering
Keywords:: Computational Biology
Bioinformatics
Peak-Calling
ChIP-seq
Gene regulation
Comparative Genomics
File:: Download Kuan-Bei.dissertation.pdf
Committee Members:: Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Dr Yu Zhang, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Padma Raghavan, Committee Member
Kamesh Madduri, Committee Member

Open Access

Author:: Dogan, Nergiz
Title:: Elucidating Biological Function of Genomic DNA with Robust Signals of Biochemical Activity: Integrative Genome-wide Studies of Enhancers
Graduate Program:: Biochemistry, Microbiology, and Molecular Biology
Keywords:: Functional genomics
Gene regulation
TAL1
GATA1
Histone modifications
Enhancer assay
File:: Download Dogan_PhDThesis_final.pdf
Committee Members:: Ross Cameron Hardison, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Chair/Co-Chair
David Scott Gilmour, Committee Member
Robert Paulson, Committee Member
Philip L Reno, Committee Member
Anton Nekrutenko, Committee Member

Open Access

Author:: Miller, Jason Eli
Title:: Detection of mRNA decay machinery association with RNA during unstressed and stressed conditions
Graduate Program:: Biochemistry, Microbiology, and Molecular Biology
Keywords:: Gene regulation
RNA decay
RIP-seq
Oxidative Stress
Ccr4-NOT
File:: Download Miller_final_dissertation.pdf
Committee Members:: Joseph C. Reese, Dissertation Advisor/Co-Advisor
Joseph C. Reese, Committee Chair/Co-Chair
Benjamin Franklin Pugh, Committee Member
Ross Cameron Hardison, Committee Member
Michael Axtell, Outside Member
David Scott Gilmour, Committee Member

Open Access

Author:: Fisher, Michael James
Title:: AN IN VITRO BIOCHEMICAL STUDY OF THE DROSOPHILA NEGATIVE ELONGATION FACTOR
Graduate Program:: Biochemistry, Microbiology, and Molecular Biology
Keywords:: Transcription
Pausing
NELF
Drosophila
RNA Polymerase II
Gene regulation
File:: Download Michael_J_Fisher_Dissertation_Final.pdf
Committee Members:: David Gilmour, Dissertation Advisor/Co-Advisor
Paul Babitzke, Committee Chair/Co-Chair
Joseph Reese, Committee Member
Katsuhiko Murakami, Committee Member
Michael Axtell, Outside Member

Restricted (Penn State Only)

Author:: Das, Maitreya
Title:: Multi-modal assessment of impact of mutations on the genome
Graduate Program:: Molecular, Cellular, and Integrative Biosciences (PHD)
Keywords:: STARR-seq
Gene regulation
Enhancers
MPRA
Reproducibility
Neurodevelopmental Disorders
Non-coding elements
File:: Login to Download
Committee Members:: Yingwei Mao, Outside Unit & Field Member
Bernhard Luscher, Major Field Member
Santhosh Girirajan, Chair & Dissertation Advisor
Joyce Jose, Major Field Member
Melissa Rolls, Program Head/Chair

Open Access

Author:: Xu, Cheng
Title:: Systematic dissection of sequence features affecting the binding spcificity of a pioneer factor
Graduate Program:: Molecular, Cellular, and Integrative Biosciences (PHD)
Keywords:: Gene regulation
Transcription factor
Pioneer factor
Binding specificity
synthetic oligonucleotide library
FOXA1
AP-1
TF cooperativity
ChIP-ISO
File:: Download 202403_Thesis_Cheng_Xu_V4.pdf
Committee Members:: Robert Paulson, Outside Unit & Field Member
Xiaojun Lian, Major Field Member
Shaun Mahony, Major Field Member
Lu Bai, Chair & Dissertation Advisor
Melissa Rolls, Program Head/Chair

Open Access

Author:: Chatterjee, Debamalya
Title:: Functional Characterization of Rice MPK6 and Maize ufo1 Genes During Gametophyte and Seed Development
Graduate Program:: Agronomy (PHD)
Keywords:: Maize
Rice
Gametophyte
Seed development
Carbohydrate
Gene regulation
Endosperm development
Basal endosperm transfer layer
Kinase
Oryza sativa L.
Zea mays L.
File:: Download Thesis_Chatterjee_Debamalya_Final.pdf
Committee Members:: Majid Foolad, Major Field Member
Marvin Hall, Major Field Member
Charles Anderson, Outside Unit & Field Member
Erin Connolly, Program Head/Chair
Surinder Chopra, Chair & Dissertation Advisor
Yinong Yang, Dissertation Co-Advisor

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