CPCB Ph.D. student Yutong Qiu has been awarded an SCS Cancer Research Fellowship. Yutong works on computational methods for understanding the human genome, including methods to identify variants within single genomes and populations of genomes. Her recent work is focused on construction and use of genome graphs for applications in cancer, especially more accurate subtyping of cancers from genomic features.
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The ability to efficiently query genomic variation data from
thousands of samples is critical to achieve the full potential of many medical
and scientific applications such as personalized medicine. We present
VariantStore, a system for efficiently …
Mutual information is widely used to characterize dependence
between biological signals, such as co-expression between genes or co-evolution
between amino acids. However, measurement error of the biological signals is
rarely considered in estimating …
Due to incomplete reference transcriptomes, incomplete
sequencing bias models, or other modeling defects, algorithms to infer isoform
expression from RNA-seq sometimes do not accurately model expression. We
present a computational method to detect …
Transcriptomic structural variants (TSVs) --- structural variants that affect expressed regions --- are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles …
Three-dimensional chromosome structure plays an integral role in
gene expression and regulation, replication timing, and other cellular
processes. Topologically associated domains (TADs), building blocks of
chromosome structure, are genomic regions …
Topological data analysis (TDA) is a mathematically well-founded
set of methods to derive robust information about the structure and topology of
data. It has been applied successfully in several biological contexts. Derived
primarily from algebraic …
Selected as one of the “(https://www.iscb.org/recomb-regsysgen2019-submissions/recomb-regsysgen2019-reading)[Top 10 Reading Papers]” at RECOMB/ISCB Regulatory & Systems Genomics 2019.