Over 50 students and faculty gathered in Clark Hall for the annual Foundations of Computational Biology and Bioinformatics Poster Session, the culminating event for the Foundations of Computational Biology and Bioinformatics course offered by The Department of Biomedical Engineering. The event was sponsored by The Department of Biomedical Engineering and The Institute for Computational Medicine and featured student projects for the spring 2019 term.

Foundations of Computational Biology and Bioinformatics is a required course for the undergraduate and graduate programs in computational medicine, an emerging discipline that applies quantitative approaches to understand, diagnose and treat human disease. Students of computational medicine learn to apply engineering, computer science, and mathematics to build computer models of disease, personalize these models using patient data, and apply them to diagnose and treat individual patients.

“The projects focus on computational medicine issues and data science including biological sequence analysis, machine learning and network modeling for cancer and infectious diseases,” said Rachel Karchin, professor of biomedical engineering, core ICM faculty member and instructor of the course. “This year, projects took advantage of large public data sets, including the Cancer Genome Atlas and the Stanford HIV database,” added Karchin.

During the evening students presented work from their capstone research projects in a poster session. Attendees mingled and explored the examples of computational medicine research. Student projects included:

Benchmarking of Clonal Deconvolution Tools
Yuncong Geng, Haoyang Mi, Yuanjia Wang (BME graduate students)

Identifying Significant Co-occurring or Mutually Exclusive Mutated Driver Genes Across Cancer Types
Luchao (Leon) Qi (BME graduate student) , Da Peng (BME graduate student) , Xi (Stanley) Wang (AMS third-year student)

Evolutionary Mutagenesis Tracking of Replication Fidelity Impacts in HIV Reverse Transcriptase
Alex Baca (chemical engineering graduate student), Andrew Masteller
(BME graduate student), Kavya Tumkur (CS second-year student)

MHC Class II Neoantigen Prediction Using Mass Spectrometry Data
Jenna Ballard (BME third-year student), Justin Huang
(BME third-year student), Gayatri Susarla (CS fourth-year student)

Evaluation of Performance on Clonal and Subclonal Clustering Algorithms
Jung Min Lee (BME third-year student), John Lin (BME fourth-year student), Alex Rodriguez (AMS fourth-year student), Victor Wang (data science graduate student)

Fast and Accurate Alignment-free and Annotation-free Transcriptome Assembly and Quantification from Short-Read RNA-Seq Data
Yoon Ki Joo (CHEMBE fourth-year student), Remy Schwab (BME graduate student), Ales Varabyou (CS graduate student)

Comparative Analysis of TCR Sequence Properties in Diabetes
Archana Balan, Kalen Clifton, Adriana Gonzalez (BME graduate students)

Cancer Driver Gene Prioritization Using a Network-Based Approach
Jitong Cai, Matthew Perrone, Ruitao Zhang, Yuchen Ge (BME graduate students)

Effects of Drug-Resistant Mutations on HIV-RT Mutation Spectrums and Replication Fidelity
Michael Morikubo, Han Kim, Jinrui Liu, Eric Chiang
(BME graduate students)