Young CMU students succeed in prestigious conference papers

Two first year students in our Computational Biology Ph.D. program and one recent graduate of the M.S. in Computational Biology program have had papers accepted for ISMB 2018, a top conference in Computational Biology and Bioinformatics.

Xiangrui Zeng’s paper, titled “An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification, proposes an integrated method called Fast Alignment Maximum Likelihood (FAML).  Because it is more robust and performs well with fewer input subtograms, the FAML method can serve as a key component for improved construction of structural models.  Yixiu Zhao, a third-year undergraduate in Computer Science also collaborated on this paper.   Both are members of Min Xu’s research group.

In his paper, “Predicting CTCF-mediated chromatin loops using CTCF-MP”, Ruochi Zhang discusses a new machine learning algorithm to demonstrate that sequence-based features have the capability to predict if a pair of convergent CTCF motifs would form a chromatin loop.  He is a member of Jian Ma’s group.

Jesse’s paper, “Deconvolution and phylogeny inference of structural variations in tumor genomic samples”, describes a method he developed during his MS studies to reconstruct the progression of cancers via accumulating genetic variations, specifically improving on prior work by incorporating complex genomic rearrangements that are crucial to how many tumors develop and adapt over time.  Jingyi Wang, a recent graduate of Carnegie Mellon’s MS in Biomedical Engineering program, also collaborated on the paper.