CBLAB

PUBLICATION

SCI/E publication 

• Dottie Y, Ram A, Sarah HS,  Likhitha C, Hafsa F, Junghyun J Abdullah AN, Grigore B, Jieting H, Ryan A, Sungmin P, Austin D N, Alex Z, Nicholas M, Jong Wha Joo, Reid FT, Houda A, Serghei M*, A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data, Nature Methods, 2023, PMID: 38293199 preprint (IF:48)

• Gayon Kim, Gyuyeon Jang, Jaeseung Song, Daeun Kim, Sora Lee, Jong Wha J. Joo, Wonhee Jang*, A transcriptome-wide association study of uterine fibroids to identify potential genetic markers and toxic chemicals, PLoS ONE, 2022 Sep;17(9). (IF:3.7)

• Jaeseung Song, Daeum Kim, Sora Lee, Junghyun Jung, Jong Wha J Joo, Wonhee Jang*, Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning, Communications Biology, 2022 Jun;5:615. (IF:5.9)

• Farhad Hormozdiari+, Junghyun Jung+, Eleazar Eskin, Jong Wha J Joo*, MARS: leveraging allelic heterogeneity to increase power of association testing, Genome Biology, 2021 Apr;22:128. (IF:17.906)

• Sung Min Park, Daeun Kim, Jaeseung Song, Jong Wha J. Joo*, An Integrative Transcriptome-wide Analysis of Amyotrophic Lateral Sclerosis for Identification for Potential Genetic Markers and Drug Candidates, J. Mol. Sci., 2021 Mar;22:3216. (IF:6.208)

• Juhun Choi+, Taegun Kim+, Junghyun Jung, Jong Wha J Joo*, Fully automated web-based tool identifying regulatory hotspots, BMC Genomics, 2020 Nov; 21:616. (IF:3.969)

• Yong-Sik Choi,Jin-Gu Kang, Jong Wha J. Joo, Jin-Woo Jung*, Real-time Informatized caption enhancement based on speaker pronunciation time database, Multimedia Tools and Applications, 2020 Sep;79:35667. (IF:2.757)

• Yue Wu+, Farhad Hormozdiari+, Jong Wha J Joo, Eleazar Eskin*, Improving imputation accuracy by inferring causal variants in genetic studies, Journal of Computational Biology, 2019 Nov;26(11);1203-1213. (IF:1.054)

• Song J, Kim D, Hong J, Kim GW, Jung J, Park S, Park HJ, Joo JWJ*, Jang W*. Meta-Analysis of Polymyositis and Dermatomyositis Microarray Data Reveals Novel Genetic Biomarkers, Genes (Basel). 2019 Oct 30;10(11). (IF:2.984)

• Junghyun Jung, Go Woon Kim, Byungjo Lee1, Jong Wha J. Joo*, Wonhee Jang*, Integrative genomic and transcriptomic analysis for genetic markers in Dupuytren's disease, BMC Medical Genomics, 2019 Jul; 12(98). (IF:2.570) 

• Junho Jeong+, Jong Wha J. Joo+, Yangsun Lee, Yunsik Son*, Secure Cloud Storage Service Using Bloom Filters for the Internet of Things, IEEE Access, 2019 Jan 7(1);60897-60907. (IF:3.557)

• Seungjin Na, Jae-Jin Lee, Jong Wha J. Joo, Kong-Joo Lee, Eunok Paek*, deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS, Scientific Reports, 2019 Jan;9:3176. (IF:4.122)

• Eun Yong Kang, Cue Hyunkyu Lee, Nicholas Furlotte, Jong Wha Joo, Emrah Kostem, Noah Zaitlen, Eleazar Eskin*, Buhm Han*, An association mapping framework to account for the sex difference in genetic architectures​, Genetics, 2018 Jul;209(3):685-698. (IF:4.644)​

• Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea J.-T. Ju, Ayellet V. Segrè, Jong Wha J. Joo, Hyejung Won, Sriram Sankararaman, Bogdan Pasaniuc, Sagiv Shifman , Eleazar Eskin*, Widespread Allelic HeteroBiogeneity in Complex Traits,  American Journal of Human Genetics, 2017 May;100(5):789-802. (IF:10.794)

• Farhad Hormozdiari, Ayellet V. Segre, Martijn van de Bunt, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Sriram Sankararaman, Bogdan Pasaniuc and Eleazar Eskin*, Colocalization of GWAS and eQTL detects Target Genes, American Journal of Human Genetics, 2016 Nov;99(6):1245-1260. (IF:10.794)

• Jong Wha J Joo, Eun Young Kang, Elin Org, Nick Furlotte, Brian Parks, Farhad Hormozsiari, Aldons J. Lusis, Eleazar Eskin*. Efficient and accurate multiple-phenotype regression method for high dimensional data considering population structure. Genetics, 2016 Dec, 204(4):1379-1390. (IF:4.866)

• Jong Wha J Joo, Farhad Hormozdiari, Buhm Han*, Eleazar Eskin*, Multiple Testing Correction in Linear Mixed Models, Genome Biology, 2016 Apr;17(1):62. (IF:11.91)

• Elin Org, Brian Parks, Jong Wha J Joo, Margarete Mehrabian, Yuna Blum, Eun Yong Kang, Benjamin Emert, Rob Knight, Thomas Drake, Eleazar Eskin, Aldons J. Lusis*, Genetic and environmental control of host-gut microbiota interaction. Genome Research, 2015 Oct; 25(10): 1558–69. (IF:14.63)

• Aldons J Lusis, Elin Org, Benjamin Emert, Jong Wha Joo, Margarete Mehrabian, William Schwartzman, Brian Parks, Richard Davis, Yuna Blum, John Furuta, Mohamad Navab, Alan Fogelman, Thomas Drake, Rob Knight, Robert Gunsalus, Stanley Hazen, Eleazar Eskin*, Microbiome/Metabolic Syndrome/Diabetes and CVD, The FASEB Journal, 2015 Apr; 29(1): 222.3. (IF:5.299)

• Farhad Hormozdiari+, Jong Wha J Joo+, Feng Guan, Rafail Ostrosky, Amit Sahai, Eleazar Eskin. Privacy Preserving Protocol for Detecting Genetic Relatives Using Rare Variants, Bioinformatics, 2014 Jun;30(12). (IF:4.981)

• Dan He+, Nicholas A Furlaotte+, Farhad Hormozdiari, Jong Wha Joo, Refail Ostrovsky, Amit Sahai*, Eleazar Eskin*. Identifying Genetic Relatives without Compromising Privacy, Genome Research, 2014, Apr;24(4):664-72. (IF:14.63)

• Jeffrey Ohmen, Eun Yong Kang, Xin Li, Jong Wha Joo, Farhad Hormozdiari, Qing Yin Zheng, Richard Davis, Aldones J. Lusis, Eleazar Eskin*, Rich Friedman*, Genome-Wide Association Study for Age-Related Hearing Loss (AHL) in the Mouse: A Meta-Analysis, J Assoc Res Otolaryngol, 2014, Jun;15(3):335-52. (IF:3.030)

• Jong Wha J Joo, Jae Hoon Sul, Buhm Han, Chun Ye, Eleazar Eskin*, Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies, Genome Biology, 2014 Apr;15(4):R61. (IF:10.81)

• Eun Yong Kang+, Buhm Han+, Nicholas Furlotte+, Jong Wha Joo, Diana Shih, Richard Davis, Jake Lusis, Eleazar Eskin*, Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,323 mouse samples, PLOS genetics, 2013 Jan;10(1). (IF:8.167)

• Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC*, Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits, Mamm Genome, 2012 Oct;23(9-10):680-92. (IF:2.078)

• Pao-Yang Chen, Suhua Feng, Jong Wha J Joo, Steve E. Jacobsen and Matteo Pellegrini*, A comparative analysis of DNA methylation across human embryonic stem cell lines, Genome Biology, 2011 Jul;12(7), R62. (IF:10.81)

• Jong Wha J Joo, Seungjin Na, Je-Hyun Baek, Cheolju Lee and Eunok Paek*, Target-Decoy with Mass Binning: A Simple and effective validation method for shotgun proteomics using high resolution mass spectrometry, Journal of Proteome Research, 2010 Feb;9(2): 1150-1156. (IF:4.245) 

Other publication

• Dottie Yu, Ram Ayyala, Hafsa Farooq, Sarah Sadek, Junghyun Jung, Jieting Hu, Tienze Tao, Ryan Alomair, Likhitha Chittampalli, Sungmin Park, Austin Nguyen, Nick Mancuso, Jong Wha Joo, Reid Thompson, Abhinav Nellore, Houda Alachkar and Serghei Mangul*, A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data, ICCABS 2023 Highlights

• Sung Min Park, Junghyun Jung, Jong Wha J. Joo*, Integrative Meta-Analysis of Transcriptome Data for Unmasking Biological Mechanism of Idiopathic Pulmonary Fibrosis, SCIS&ISIS2020

• Gi Ju Lee, Sung Min Park, Junghyun Jung, Jong Wha J. Joo*, A Fully Automated Parallel-Processing R Package for High-Dimensional Multiple-Phenotype Analysis Considering Population Structure, International Journal of Fuzzy Logic and Intelligent Systems, 2020 Sep;20(3):219-226 (SCOPUS, Impact Factor: 1.480)

• Jose a. lozano, Farhad hormozdiari, Jong wha (joanne) joo, Buhm han, Eleazar eskin* , The multivariate normal distribution framework for analyzing association studies, 2017, doi: https://doi.org/10.1101/208199 (Review)

• Robert Brown+, Jong Wha J. Joo+, Robert L. Smith, Bogdan Pasaniuc, Eleazar Eskin*, GGmend: A Mendelian randomization method for finding gene-on-gene regulatory effects in the presence of unobserved confounders, RECOMB Genetics, 2017(Book Chapter)

Under review

• Wonseok Oh, Junghyun Jung, Jong Wha J. Joo*, MR-GGI: Accurate inference of gene-gene interactions using Mendelian randomization, BMC Bioinformatics

PATENT

• Multivariant association test considering causal status, 10-2269208
• Fast multivariat association test utilizing importance sampling, S-A-2019-0016
• Augmented Reality-based Tourism Service System Using Smart Glass, 10-2019-0178708
• Object Removal and Partial Inpainting System using Deep Learning, 10-2019-0178707
• Real time Earthquake Detecting and Noticing service based on SNS, 10-2019-0178706
• An Efficient and Accurate Multivariate Association Study Using Importance Sampling, 10-2441856
• Efficient sampling for multivariate association study considering causal status, 10-2436956
• Provide NICE through The Web Service, C-2020-036036
• Fall Detection System Using Smartphone Applications, 10-2020-0187571
• Applications that use the Google Fit API to analyze users' lifestyle and provide customized content, 10-2020-0187569
• UI/UX Development for Editing Source Code Fault Detection Rules, 10-2020-0187572
• Applicant Tracking System (ATS) to help human resources staff work in conjunction with external services based on web interface, 10-2020-0187568
• Sound Quality Improvement Method of Voice and Video Using Deep Learning, 10-2538008
• Document-based chat services that add features using command, 10-2020-0187567
• Decentralized Delivery Order System Using Blockchain, 10-2020-0187573
• Provide fastMultiTrans throught The Web Serivce, C-2020-048259
• Imputing Phenotype Using Deep Learning, C-2021-029918
• Imputing Phenotype Using Meta-Learning, C-2021-029920
• Automating object detection in videos using ffmpeg and YOLO, 10-2022-0010850
• Medicine administration for Elderly, object detection and prediction for medicine based on deep learning using darknet and yolov4, 10-2625815
• posture detection and posture accuracy determination system that is effective in improving the physical health of the elderly using smart mirrors, 10-2023-0051191
• A mobile application using deep learning model to identify medication through pictures, 10-2023-0051193
• Web Service MarsNet, C-2024-000252
• Gene Regulatory Network Analysis using Mendelian Randomization, 10-2023-0188326
• Gene regulatory network construction program applying Mendelian random analysis method, C-2023-060598

SOFTWARE

• MARS is a novel computational approach that finds an association between variants in risk loci and a phenotype, considering the causal status of the variants.

• MultiTrans is an efficient and accurate multiple testing correction approach for linear mixed models. It transforms genotype data to account for genetic relatedness and heritability under linear mixed models.

• GAMMA, GRAMMER Generalized Analysis of Molecular variance for Mixed model Analysis is a method that can simultaneously analyze many phenotypes as well as correct for population structure.

• GenoCrypt GenoCrypt is a method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information.

• NICE, NICER Next-generation Intersample Correlation Emended (NICE) is a statistical test for correcting for expression heterogeneity inherent in expression dataset due to confounding from unmodeled factors. NICE estimates inter-sample correlation structure using only the genes with confounding effects and incorporates it as signatures of the systematic confounding effects to correct for it.

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