Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem. - Yutong Qiu; Cong Ma 008; Han Xie; Carl Kingsford (Algorithms Mol. Biol., 2020)

Exact transcript quantification over splice graphs. - Cong Ma 008; Hongyu Zheng 001; Carl Kingsford (Algorithms Mol. Biol., 2021)

Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. - Cong Ma 008; Uthsav Chitra; Shirley Zhang 001; Benjamin J. Raphael (RECOMB, 2022)

Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability. - Hongyu Zheng 001; Cong Ma 008; Carl Kingsford (J. Comput. Biol., 2022)

Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. - Uthsav Chitra; Brian J. Arnold; Hirak Sarkar; Cong Ma 008; Sereno Lopez-Darwin; Kohei Sanno; Benjamin J. Raphael (RECOMB, 2024)

Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. - Cong Ma 008; Metin Balaban; Jingxian Liu; Siqi Chen; Li Ding; Benjamin J. Raphael (RECOMB, 2024)