Publications
Publications
Preprint and in preparation
Ma, C., & Kingsford, C. (2019). Estimating mutual information under measurement error. bioRxiv, 852384.
Peer-reviewed journal articles
Chitra U, Arnold BJ, Sarkar H, Sanno K, Ma C, Lopez-Darwin S, Raphael BJ. Mapping the topography of spatial gene expression with interpretable deep learning. Nature Methods. 2025 Feb;22(2):298-309.
Mo CK, Liu J, Chen S, Storrs E, Targino da Costa AL, Houston A, Wendl MC, Jayasinghe RG, Iglesia MD, Ma C, Herndon JM. Tumour evolution and microenvironment interactions in 2D and 3D space. Nature. 2024 Oct;634(8036):1178-86.
Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L, Raphael BJ. Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics. Nature Methods. 2024 Dec;21(12):2239-47
Terekhanova NV, Karpova A, Liang WW, Ma C, et al. Epigenetic regulation during cancer transitions across 11 tumor types. Nature 623, 432–441 (2023). https://doi.org/10.1038/s41586-023-06682-5.
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature. 2023 Apr;616(7955):113-122. doi: 10.1038/s41586-023-05795-1. Epub 2023 Mar 15. PMID: 36922587; PMCID: PMC10076218.
Ma C, Chitra U, Zhang S, Raphael BJ. Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics. Cell Syst. 2022 Oct 19;13(10):786-797.e13. doi: 10.1016/j.cels.2022.09.002. PMID: 36265465; PMCID: PMC9814896.
Ma C*, Zheng H*. & Kingsford C. Exact transcript quantification over splice graphs. Algorithms Mol Biol 16, 5 (2021). https://doi.org/10.1186/s13015-021-00184-7.
Ma C, Kingsford C. Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification. Cell Syst. 2019 Dec 18;9(6):589-599.e7. doi: 10.1016/j.cels.2019.10.005. Epub 2019 Nov 27. PMID: 31786209; PMCID: PMC6938679.
Qiu Y.*, Ma C.*, Xie H. et al. Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem. Algorithms Mol Biol 15, 9 (2020). https://doi.org/10.1186/s13015-020-00170-5.
Ma C, Shao M, Kingsford C. SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biol 19, 52 (2018). https://doi.org/10.1186/s13059-018-1421-5.
Wu F, Ma C., Tan C. Network motifs modulate druggability of cellular targets. Sci Rep 6, 36626 (2016). https://doi.org/10.1038/srep36626.