Methods to probe cancer genomes
Natalie Sauerwald (2020). Algorithms for the study of chromosomal structure variability. Ph.D. Dissertation.
Prashant Pandey, Yinjie Gao, Carl Kingsford (2019). VariantStore: A Large-Scale Genomic Variant Search Index. bioRxiv 888297.
Cong Ma, Carl Kingsford (2019). Estimating mutual information under measurement error. bioRxiv 852384.
Cong Ma, Carl Kingsford (2019). Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification. Cell Systems 9:1-11.
Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford (2019). Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 18:1–18:19 (2019); journal version in Alg Mol Bio (2020).
Natalie Sauerwald, Akshat Singhal, Carl Kingsford (2019). Analysis of the structural variability of topologically associated domains as revealed by Hi-C. Nuc. Acids Res. Genomics and Bioinformatics 2(1):lqz008 (2020).
Natalie Sauerwald, Yihang Shen, Carl Kingsford (2019). Topological data analysis reveals principles of chromosome structure throughout cellular differentiation. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 23:1–23:16 (2019).
Heewook Lee, Carl Kingsford (2018). Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami. HLA Typing, pages 235-247.
Heewook Lee, Carl Kingsford (2018). Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery. Genome Biology 19:16.
Natalie Sauerwald, Carl Kingsford (2018). Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics (ISMB) 34(13):i475-i483.