Research
I am interested in supervising excellent students on a variety of computational biology and bioinformatics projects. These are some bioinformatics-related project topics, as well as the computational
skills you will acquire along the way:
* separation of strains in communities of eukaryotic or prokaryotic organisms, on
the basis of SNPs and SVs
computer skills: Java, visualization libraries, statistics
* identification of plasmids in very large microbial (bacterial and archaeal) datasets
computer skills: machine learning, Linux command line, Python programming
* reconstruction of 16S sequences in metagenomic data to identify the microbial taxonomic
strains
computer skills: Linux command line, Python programming
* separation of phages and CRISPR elements in mixed bacterial-phage datasets on the
basis of the assembly graph
computer skills: visualization libraries, Python
* modeling tools for omics datasets; integration of genomics, metabolomics, transciptomics
and protein-protein interaction networks.
computer skills: machine learning (bayesian networks), clustering (PCA, tSNE, UMAP),
R or Python programming
* visualization tools
computer skills: Java, visualization libraries
* deep learning and machine learning applications to molecular biology problems
computer skills: Python, Keras libraries
* reproducibiliity of data science
computer skills:Linux command line, Docker containers
I work with environmental data, as well as cancer data (PCAWG and TCGA).
William "Bill" Andreopoulos group
Former and Present Students
Venkat Teja Golamaru (CS297/CS298)
Fei Pan (CS297/CS298)
Meet Patel (CS297/CS298)
Stephen Nguyen (CS297/CS298)
Vedashree Bhandare (CS297/CS298)
Niraj Pandkar (CS280)
Anirudh Mallya (CS280)
Gagandeep Singh (CS180)
Nhung (Nina) Luong