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3. DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

open_access
Open Access
Author:
Bonnell, Victoria
Title:
DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum
Graduate Program:
Biochemistry, Microbiology, and Molecular Biology
Keywords:
Molecular Parasitology
Gene Regulation
Transcription Factor Binding
Malaria
Sequence-specific Transcription Factors
File:
Download BONNELL_Dissertation_HighResVersion_FINAL_March2023_FormatFixed.pdf
Committee Members:
Elizabeth Mcgraw, Outside Unit & Field Member
Shaun Mahony, Major Field Member
Scott Lindner, Major Field Member
Manuel Llinas, Chair & Dissertation Advisor
Wendy Hanna-Rose, Program Head/Chair
Lu Bai, Major Field Member
B. Franklin Pugh, Special Member

4. Computational Methods For Characterizing The Sequence And Chromatin Determinants Of Transcription Factor Binding

open_access
Open Access
Author:
Srivastava, Divyanshi
Title:
Computational Methods For Characterizing The Sequence And Chromatin Determinants Of Transcription Factor Binding
Graduate Program:
Bioinformatics and Genomics (PhD)
Keywords:
Transcription Factors
Gene Regulation
Chromatin
Neural Networks
Neural Networks for Biological Sequences
Interpretable Models For DNA Sequences
Protein-DNA Binding
File:
Download Srivastava-Dissertation-Revised-2021-July.pdf
Committee Members:
Frank Pugh, Major Field Member
Shaun Mahony, Chair & Dissertation Advisor
Ross Hardison, Outside Field Member
Daniel Kifer, Outside Unit Member
George Perry, Program Head/Chair

5. Investigating the druggability and biological roles of Apicomplexan AP2 transcription factors in the human malaria parasite Plasmodium falciparum

open_access
Open Access
Author:
Russell, Timothy
Title:
Investigating the druggability and biological roles of Apicomplexan AP2 transcription factors in the human malaria parasite Plasmodium falciparum
Graduate Program:
Biochemistry, Microbiology, and Molecular Biology
Keywords:
Plasmodium falciparum
ApiAP2 proteins
Gene Regulation
Antimalarial drugs
File:
Download TRussell_Thesis_document.pdf
Committee Members:
David Gilmour, Major Field Member
Scott Showalter, Outside Unit & Field Member
Scott Lindner, Major Field Member
Manuel Llinas, Chair & Dissertation Advisor
Wendy Hanna-Rose, Program Head/Chair
C Okafor, Major Field Member
Frank Pugh, Special Member

6. Cross-Species Prediction of Transcription Factor Binding

restricted_to_institution
Restricted (Penn State Only)
Author:
Agarwala, Vandana
Title:
Cross-Species Prediction of Transcription Factor Binding
Graduate Program:
Statistics
Keywords:
Bioinformatics
Deep Learning
Gene Regulation
Domain Adaptation
Transfer Learning
Computational Biology
Machine Learning
File:
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Committee Members:
Shaun Mahony, Thesis Advisor/Co-Advisor
Qunhua Li, Thesis Advisor/Co-Advisor
Ephraim Hanks, Professor in Charge/Director of Graduate Studies
Xiang Zhu, Committee Member