Publications

Group highlights

(For a full list see below or go to Google Scholar)

Full List

Deep nonnegative matrix factorization using a variational autoencoder with application to single-cell RNA sequencing data
D. Jee, Y. Kong, and H. Chun
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2022)

Regulation of sclerostin by the SIRT1 stabiliztion pathwya in osteocytes
JM Kim, YS Yang, J Xie, O Lee, JH Kim, J Hong, B Boldyreff, O Filhol, H Chun, MB Greeblatt, G Gao, JH Shim
Cell Death & Differentiation (2022)

Impaired ERK MAPK activation in mature osteoblasts enhances bone formation via the mTOR pathway
JM Kim, YS Yang, J Hong, S Chaugule, H Chun, MCH van der Meulen, R Xu, MB Greenblatt, JH Shim
bioRxiv (2022)

A zero-inflated non-negative matrix factorization for the deconvolution of mixed signals of biological data
Y Kong, A Kozik, CH Nakatsu, YL Jones-Hall, and H Chun
International Journal of Biostatistics, (2021)

A RUNX2 stabilization pathway mediates physiologic and pathologic bone formation
Jung-Min Kim, Yeon-Suk Yang, Kwang Hwan Park, Xianpeng Ge, Ren Xu, Na Li, Minkyung Song, Hyonho Chun, Seoyeon Bok, Julia F Charles, Odile Filhol-Cochet, Brigitte Boldyreff, Teresa Dinter, B Yu Paul, Ning Kon, Wei Gu, Takeshi Takarada, Matthew B Greenblatt, Jae-Hyuck Shim
Nature communications 11, 1 (2020)

Proteomic and metabolomic profiling reveals the involvement of apoptosis in meat quality characteristics of ovine M. longissimus from different callipyge genotypes
Danyi Ma, Qianqian Yu, Vicki E Hendrick, Bruce R Cooper, Tiago Sobreira, Ji-Hwan Oh, Hyonho Chun, Yuan H Brad Kim
Meat Science (2020)

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
Hyunbin Kim, Andy Jinseok Lee, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dongwan Hong
Genome medicine 11, 1 (2019)

Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis
Ariangela J Kozik, Cindy H Nakatsu, Hyonho Chun, Yava L Jones-Hall
PloS one 14, 11 (2019)

Learning dispatching rules using random forest in flexible job shop scheduling problems
Sungbum Jun, Seokcheon Lee, Hyonho Chun
International Journal of Production Research 57, 10 (2019)

IL1R1 is required for celastrol’s leptin-sensitization and antiobesity effects
Xudong Feng, Dongxian Guan, Thomas Auen, Jae Won Choi, Mario Andres Salazar Hernandez, Jaemin Lee, Hyonho Chun, Farhana Faruk, Esther Kaplun, Zachary Herbert, Kyle D Copps, Umut Ozcan
Nature medicine 25, 4 (2019)

A Nonnegative Robust Linear Model for Deconvolution of Proportions
Hyonho Chun, Hyuna Yang
Contemporary Biostatistics with Biopharmaceutical Applications (2019)

Spatial autocorrelation in soil compaction and its impact on earthwork acceptance testing
Jiannan Cai, Qingyi Gao, Hyonho Chun, Hubo Cai, Tommy Nantung
Transportation Research Record 2673, 1 (2019)

Kernel partial correlation: a novel approach to capturing conditional independence in graphical models for noisy data
Jihwan Oh, Faye Zheng, RW Doerge, Hyonho Chun
Journal of Applied Statistics 45, 14 (2018)

Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures
Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong
Nucleic acids research 46, W1 (2018)

Robust precision matrix estimation via weighted median regression with regularization
Hyonho Chun, Myung Hee Lee, Sung‐Ho Kim, Jihwan Oh
Canadian Journal of Statistics 46, 2 (2018)

Optimal Sampling Strategy for Acceptance Decision in Highway Construction: a Cost–Benefit Analysis Approach
Jiannan Cai, Shuai Li, Qingyi Gao, Hyonho Chun, Tommy Nantung, Hubo Cai
Transportation Research Board 97th Annual MeetingTransportation Research Board (2018)

Age, sex, and TNF associated differences in the gut microbiota of mice and their impact on acute TNBS colitis
Ariangela J Kozik, Cindy H Nakatsu, Hyonho Chun, Yava L Jones-Hall
Experimental and molecular pathology 103, 3 (2017)

Metabolomics profiling to determine the effect of postmortem aging on color and lipid oxidative stabilities of different bovine muscles
Danyi Ma, Yuan H Brad Kim, Bruce Cooper, Ji-Hwan Oh, Hyonho Chun, Ju-Hui Choe, Jon P Schoonmaker, Kolapo Ajuwon, Byungrok Min
Journal of agricultural and food chemistry 65, 31 (2017)

Using pre-assessment and in-class questions to change student understanding of molecular movements
J Shi, Jennifer K Knight, Hyonho Chun, Nancy A Guild, Jennifer M Martin
Journal of microbiology & biology education 18, 1 (2017)

Graphical models via joint quantile regression with component selection
Hyonho Chun, Myung Hee Lee, James C Fleet, Ji Hwan Oh
Journal of Multivariate Analysis, 152 (2016)

Gene regulation network inference with joint sparse Gaussian graphical models
Hyonho Chun, Xianghua Zhang, Hongyu Zhao
Journal of Computational and Graphical Statistics 24, 4 (2015)

Effective simultaneous confidence bands for repeated measurements in linear mixed-effect models
Jungwon Mun, Hyonho Chun
Journal of Statistical Computation and Simulation 84, 8 (2014)

On an additive semigraphoid model for statistical networks with application to pathway analysis
Bing Li, Hyonho Chun, Hongyu Zhao
Journal of the American Statistical Association 109, 507 (2014)

Joint conditional Gaussian graphical models with multiple sources of genomic data
Hyonho Chun, Min Chen, Bing Li, Hongyu Zhao
Frontiers in genetics 4, (2013)

Sparse estimation of conditional graphical models with application to gene networks
Bing Li, Hyonho Chun, Hongyu Zhao
Journal of the American Statistical Association 107, 497 (2012)

Spls: sparse partial least squares (SPLS) regression and classification
Dongjun Chung, Hyonho Chun, Sunduz Keles
R package, version 2, (2012)

Identification of association between disease and multiple markers via sparse partial least‐squares regression
Hyonho Chun, David H Ballard, Judy Cho, Hongyu Zhao
Genetic epidemiology 35, 6 (2011)

Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4 in silico Network Challenge
Hyonho Chun, Jia Kang, Xianghua Zhang, Minghua Deng, Haisu Ma, Hongyu Zhao
Handbook of Statistical Bioinformatics, (2011)

Visualizing abnormal climate changes in Central America from 1995 to 2000
Sang-Hoon Cho, Hyonho Chun
Computational Statistics 25, 4 (2010)

Sparse partial least squares regression for simultaneous dimension reduction and variable selection
Hyonho Chun, Sündüz Keleş
Journal of the Royal Statistical Society B (Statistical Methodology) 72, 1 (2010)

Genome-wide association studies using single-nucleotide polymorphisms versus haplotypes: an empirical comparison with data from the North American Rheumatoid Arthritis Consortium
Heejung Shim, Hyonho Chun, Corinne D Engelman, Bret A Payseur
BMC proceedings 3, 1 (2009)

Expression quantitative trait loci mapping with multivariate sparse partial least squares regression
Hyonho Chun, Sündüz Keleş
Genetics 182, 1 (2009)

Comments on: Augmenting the bootstrap to analyze high dimensional genomic data
Sündüz Keleş, Hyonho Chun
Test 17, 1 (2008)

CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure
Pei Fen Kuan, Hyonho Chun, Sündüz Keleş
Biocomputing (2008)