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Tao Y, Rajaraman A, Cui X, Cui Z, Eaton J, Kim H, Ma J*, and Schwartz R*.
Assessing the contribution of tumor mutational phenotypes to cancer progression risk.
PLOS Computational Biology, 17(3):e1008777, 2021
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Zhang Y, Xiao Y, Yang M, and Ma J.
Cancer mutational signatures representation by large-scale context embedding.
ISMB, 2020.
Bioinformatics, 36(Supplement_1):i309-i316, 2020.
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Rajaraman A and Ma J.
Towards recovering allele-specific cancer genome graphs.
RECOMB, 2017.
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Li Y, Zhou S, Schwartz DC, and Ma J.
Allele-specific quantification of structural variations in cancer genomes.
Cell Systems, 3(1):21-34, 2016.
RECOMB, 2016.
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Hou JP†, Emad A†, Puleo GJ, Ma J*, and Milenkovic O*.
A new correlation clustering method for cancer mutation analysis.
Bioinformatics, 32(24):3717-28, 2016.
- Hou JP and Ma J.
DawnRank: Discovering personalized driver genes in cancer.
Genome Medicine, 6:56, 2014.
- Liu Y, Gu Q, Hou JP, Han J, and Ma J.
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.
BMC Bioinformatics, 15:37, 2014.
- Li Y, Chien J, Smith DI, and Ma J.
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Bioinformatics, 27(12):1708-10, 2011.