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. 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
3. 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
4. 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
5. 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