Changjin Hong, Ph.D.

Postdoctoral Associate, Johnson Lab


B.S., Electrical Engineering, Hanyang University, South Korea
Ph.D., Electrical Engineering, University of Minnesota, Twin Cities, MN

Contact Information


Research Interests

Probabilistic Short Read Alignments with Next Generation Sequencing (NGS) Data. To develop a probabilistic mapping algorithm to achieve a high-quality NGS alignments. The applications I primarily focus on include bisulfited reads for methylation profiling, RNA editing, and Single-nucleotide polymorphism(SNP) analysis.

Rapid Diagnosis of Pathogen with Clinical Samples. To design a statistical framework and develop a highly scalable algorithm to rapidly identify non-human sequences with the minimum read depth.

Genome-wide Methylation Data Analysis. To apply Kalman filter to bisulfited reads alignments and quantify a true methylation proifle across cells. Furthermore, a time-dependent autoregressive–moving-average model (ARMA) is applied to analyze a differentially methylated region (DMR).


A Novel Update Propagation Module for the Data Provenance Problem: A Contemplating Vision on Realizing Data Provenance from Models to Storage. Abed E. Lawabni, Changjin Hong, David H-C. Du, and Ahmed H. Tewfik, IEEE Mass Storage Systems 2005, pp.61-9, 2005.

Efficient Updating of Biological Sequence Analyses. Changjin Hong and Ahmed H. Tewfik, IEEE Journal of Selected Topics in Signal Processing, Volume 2, Issue 3 pp.365-77, Jun. 2008.

Heuristic Reusable Dynamic Programming: Efficient Updates of Local Sequence Alignment. Changjin Hong and Ahmed H. Tewfik, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 6, Issue 4, pp.570-82, Oct. 2009.

Co-clustering Phenome-genome for Phenotype Classification and Disease Gene Discovery. Hwang, TaeHyun; Atluri, Gowtham; Xie, Maoqiang; Dey, Sanjoy; Hong, Changjin; Kumar, Vipin; Kuang, Rui, Nucl. Acids Res., 2012.

Module-based Subnetwork Alignments Reveal Novel Transcriptional Regulators in Malaria Parasite Plasmodium falciparum.  Hong Cai*, Changjin Hong*, Jianying Gu*, Timothy G. Lilburn, Rui Kuang, Yufeng Wang, BMC system biology, 2012.