Cong Ma Completes Her Ph.D.

Will join Ben Raphael’s group at Princeton

Cong Ma joined the CPCB Ph.D. program in the School of Computer Science at Carnegie Mellon in 2015. She joined the Kingsford group the same year to work on new algorithms for high-throughput sequencing.

Cong had an outstanding research career during her time at CMU. She developed the first approach for calling structural variants (SVs) from RNA-seq, which she dubbed “transcriptomic structural variants.” This research and its subsequent follow up work is unique in that it formalized the structural variant problem as several rearrangement problems where genomic permutations that best matched the observed reads are found via integer linear programming.

More recently, she introduced the idea of an expression coverage “anomaly”, a new way to identify unexplained expression signals, introducing a new analysis approach, and new computational problems coupled with rigorous methods. She also, with fellow Ph.D. student Hongyu Zheng, developed a new approach to expression quantification called graph quantification that avoids using a linearized reference that is typically incomplete.

Her work has been published in Genome Biology, Cell Systems and other venues. She has presented her work at the Cold Spring Harbor Lab’s Genome Informatics conference and elsewhere.

Links to her publications can be found here.