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
9. Cross-Species Prediction of Transcription Factor Binding Restricted (Penn State Only) Author: Agarwala, Vandana Title: Cross-Species Prediction of Transcription Factor Binding Area of Honors: Computer Science Keywords: Gene RegulationDeep LearningTransfer LearningDomain AdaptationComputational BiologyBioinformaticsMachine Learning File: Login to Download Thesis Supervisors: Shaun Mahony, Thesis SupervisorJohn Joseph Hannan, Thesis Honors Advisor
10. Characterizing the Microbial Community of Anaerobically Digested High Lignin Fermentation Byproduct and Composted Material with Corn Stover as the Feedstock Restricted (Penn State Only) Author: Sollenberger, Renee Title: Characterizing the Microbial Community of Anaerobically Digested High Lignin Fermentation Byproduct and Composted Material with Corn Stover as the Feedstock Area of Honors: Biological Engineering Keywords: BioinformaticsDiversity AnalysisCompostAnaerobic DigestionBiofuelsCorn StoverBioprocessing File: Login to Download Thesis Supervisors: Tom Richard, Thesis SupervisorAli Demirci, Thesis Honors Advisor