Selected Research Papers by the CSSB lab in the past 5 years
S. Lee, J. Bang, Y. Kim, H. Choi, S.Y Oh, J.H. Won. Learning massive-scale partial correlation networks in clinical multi-omics studies with HP-ACCORD. Available in arXiv, accepted in Annals of Applied Statistics.
H. Koh, A. Pilbrow, S. Tan, Q. Zhao, P. Benke, B. Burla, F. Torta, J. Pickering, R. Troughton, C. Pemberton, W. Soo, L.H. Ling, R. Doughty, H. Choi, M. Wenk, A.M. Richards, M. Chan. An integrated signature of extracellular matrix proteins and a diastolic function imaging parameter predicts post-MI long-term outcomes. Frontiers in Cardiovascular Medicine 2023. Paper featuring the upgraded iOmicsPASSplus software.
S. Ko, G.X.L. Li, H. Choi*, J. Won*. Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx. Brief. Bioinfo. 2021; 22(6):bbab256.
S. Ghosh, A. Datta, H. Choi. multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data. Nat. Comms 2021; 12(1): 1-11.
G. Teo, W.S. Chew, B. Burla, D. Herr, E.S. Tai, M.R. Wenk, F.T. Torta, H. Choi. MRMkit: automated data processing for large-scale targeted metabolomics analysis. Analytical Chemistry 2021; 92(20): 13677-13682.
P. Narayanaswamy#, G. Teo#, J.R. Ow, A. Lau, P. Kaldis, S. Tate, and H. Choi. MetaboKit: a comprehensive data extraction tool for untargeted metabolomics. Mol. Omics 2020; 16(5): 436-447.
G.X.L. Li, D. Munro, D. Fermin, C. Vogel, H. Choi. A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes. Hum. Mutation. 2020; 41(5): 934-945.
H.W.L. Koh, D. Fermin, C. Vogel, K.P. Choi, R. Ewing, H. Choi. iOmicsPASS: network-based integration of multi-omics data for predictive subnetwork discovery. npj Systems Biology and Applications 2019, 5:22.
H.W.L. Koh, Y. Zhang, C. Vogel, H. Choi. EBprotV2: a Perseus plugin for statistical analysis of labeling-based quantitative proteomics data. J. Proteome Res. 2018, 18 (2), 748-752.
S. Ghosh, A. Datta, K. Tan, H. Choi, SLIDE - a web-based tool for interactive visualization of large-scale -omics data. Bioinformatics 2018, 35 (2), 346-348.
G.X. Li, C. Vogel, H. Choi. PTMscape: an open source tool to predict generic post-translational modifications and map hotspots of modification crosstalk. Molecular Omics 2018, 14:197-209.
G.S. Teo, Y. Zhang, C. Vogel*, H. Choi*. PECAplus: a comprehensive package of software tools for time-specific, biological function-level detection of dynamic regulatory changes. npj Systems Biology and Applications 2017, 4 (1), 3.
Selected Papers from collaboration
Narayanaswamy et al., LipiSonics: An enhanced high-throughput lipidomics workflow using acoustic ejection mass spectrometry. Preprint at ChemRxiv.
W.K. Tham et al., Ultrafast measurement of circulating ceramides in human cohorts. Analytical Chemistry 2025.
S. Cho et al., Cross-covariance matrix estimation for directional integration of dual-omics data. J. Statist. Comput. Sim. 2025, 95(8), 1763-1787.
J. Chang et al., Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci. Rep. 2023; 13(1): 19281.
T. Tumkaya et al., Most primary olfactory neurons have individually neutral effects on behavior. Elife 2022; 11:e71238.
S. Tan et al., Variability of the plasma lipidome and subclinical coronary atherosclerosis. Arterioscler. Thromb. Vasc. Biol. 2022; 42(1):100-112.
A. Targa el al., Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene. EMBO J. 2021;40(21):e107839.
J. Ow et al., Remodeling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of CDK1 and hepatocyte division. Elife 2020, 9, e63835.
M. Dewhurst et al., Loss of hepatocyte cell division leads to liver inflammation and fibrosis. PLoS Genetics 2020, 16 (11), e1009084.