1. On the Origin of Sequences: Computational Analysis of Somatic Hypermutation for Probabilistic Immunoglobulin Predecessor Identification Open Access Author: Lengerich, Benjamin J Title: On the Origin of Sequences: Computational Analysis of Somatic Hypermutation for Probabilistic Immunoglobulin Predecessor Identification Area of Honors: Computer Science Keywords: Computer ScienceMachine LearningBioinformaticsSomatic HypermutationImmunoglobulin Predecessor Identification File: Download Lengerich_Benjamin_thesis.pdf Thesis Supervisors: Raj Acharya, Thesis SupervisorDr. Jesse Louis Barlow, Thesis Honors Advisor
2. Random Forest Classification in Copy Number Variation Discovery Open Access Author: Jayakar, Gopal Title: Random Forest Classification in Copy Number Variation Discovery Area of Honors: Biochemistry and Molecular Biology Keywords: CNVMachine LearningSequencingGenomicsBioinformaticsRandom Forest File: Download Thesis_Jayakar.pdf Thesis Supervisors: Santhosh Girirajan, Thesis SupervisorSanthosh Girirajan, Thesis Honors AdvisorShaun Mahony, Faculty Reader
3. The Effect of Overlapping Generations on Inferences of Genetic Population Structure Open Access Author: Setar, Nathaniel Title: The Effect of Overlapping Generations on Inferences of Genetic Population Structure Area of Honors: Statistics Keywords: Population GeneticsfastSTRUCTUREOverlapping GenerationsCoralBioinformatics File: Download Thesis_Final_Setar.pdf Thesis Supervisors: Iliana Brigitta Baums, Thesis SupervisorLe Bao, Thesis Honors Advisor
4. Structural and Functional Analysis of Two Novel Iron- and Oxygen-Dependent Halogenases Open Access Author: Wertz, Adam Title: Structural and Functional Analysis of Two Novel Iron- and Oxygen-Dependent Halogenases Area of Honors: Biochemistry and Molecular Biology Keywords: Enzyme StructureHalogenasesBesDWel05HomologyBioinformatics File: Download Thesis_FINAL_Wertz__1_.pdf Thesis Supervisors: Amie Kathleen Boal, Thesis SupervisorDavid Scott Gilmour, Thesis Honors Advisor
5. Genome-Metagenome Similarity Graph: a Novel Data Structure for Containment-Based Metagenome Comparison Open Access Author: Thomas, Isaac Title: Genome-Metagenome Similarity Graph: a Novel Data Structure for Containment-Based Metagenome Comparison Area of Honors: Computer Science Keywords: MetagenomicsBioinformaticsMathematicsComputer ScienceMetagenomic Similarity File: Download SHCThesis_IsaacThomas_Final.pdf Thesis Supervisors: David Koslicki, Thesis SupervisorJohn Joseph Hannan, Thesis Honors Advisor
6. An Enhancer-Based Deep Learning Approach for Studying Viral Regulation Open Access Author: Cooper, Rachel Title: An Enhancer-Based Deep Learning Approach for Studying Viral Regulation Area of Honors: Computer Science Keywords: Deep LearningBioinformaticsGene RegulationEnhancersVirusHSV-1 File: Download Cooper_Rachel_An_Enhancer-Based_Deep_Learning_Approach_For_Studying_Viral_Regulation.pdf Thesis Supervisors: Shaun Mahony, Thesis SupervisorJohn Joseph Hannan, Thesis Honors Advisor
7. L2-UniFrac Open Access Author: Millward, Andrew Title: L2-UniFrac Area of Honors: Computer Science Keywords: UniFracBioinformaticsComparative MetagenomicsRepresentative MicrobiomeDistance MetricDifferential Abundance File: Download L2_Unifrac-Andrew_Millward-Schreyer.pdf Thesis Supervisors: David Koslicki, Thesis SupervisorDanfeng Zhang, Thesis Honors AdvisorPaul Medvedev, Faculty Reader
8. Whole-genome sequence-based molecular characterization of antimicrobial genes in Salmonella enterica subsp. Dublin and Salmonella enterica subsp. Heidelberg isolated from veal calves Open Access Author: Reiss, Hailey Title: Whole-genome sequence-based molecular characterization of antimicrobial genes in Salmonella enterica subsp. Dublin and Salmonella enterica subsp. Heidelberg isolated from veal calves Area of Honors: Immunology and Infectious Disease Keywords: SalmonellaSalmonella DublinSalmonella HeidelbergPennsylvaniaVealGenomicsBioinformaticsWhole-genome sequence analysisAntimicrobial resistance File: Download reiss_hailey_thesis_iid.pdf Thesis Supervisors: Bhushan M Jayarao, Thesis SupervisorRobert Paulson, Thesis Honors Advisor
