Publications

Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.
Cong Ma, Uthsav Chitra, Shirley Zhang, and Benjamin Raphael
Cell Systems 13.10 (2022): 786–797

Estimating mutual information under measurement error
Cong Ma and Carl Kingsford
bioRxiv, doi 10.1101/852384

Deriving ranges of optimal estimated transcript expression due to non-identifiability.
Hongyu Zheng, Cong Ma, and Carl Kingsford
RECOMB 2021

Exact transcript quantification over splice graphs.
Cong Ma, Hongyu Zheng, and Carl Kingsford
WABI 2020

Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem
Yutong Qiu and Cong Ma and Han Xie and Carl Kingsford
19th International Workshop on Algorithms in Bioinformatics (WABI 2019)

Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.
Cong Ma and Carl Kingsford
Cell Systems 9.6 (2019): 589-599

SQUID: transcriptomic structural variation detection from RNA-seq.
Cong Ma, Mingfu Shao, and Carl Kingsford
Genome Biology 19.1 (2018): 52

Network motifs modulate druggability of cellular targets.
Fan Wu, Cong Ma, and Cheemeng Tan
Scientific Reports 6 (2016): 36626

Talks

Belayer: Model- ing discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics. RECOMB (2022)

Exact Transcript Quantification Over Splice Graphs. WABI (2020)

SQUID: transcriptomic structural variation detection from RNA-seq. ISMB (2018)

SQUID: transcriptomic structural variation detection from RNA-seq. CSHL Genome Informatics (2017)

Posters

Belayer: Model- ing discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics. Damon Runyon Fellows Retreat (2022)

Copy number and tumor clone infer- ence in bulk, single-cell and spatial sequencing data. NCI Informatics Technology for Cancer Research (2022)

Detecting anomalies in RNA-seq quantification. RECOMB (2019)