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Journal Articles
- 2024
[j45]Chen Zhao, Anqi Liu
, Xiao Zhang, Xuewei Cao, Zhengming Ding, Qiuying Sha, Hui Shen, Hong-Wen Deng, Weihua Zhou:
CLCLSA: Cross-omics linked embedding with contrastive learning and self attention for integration with incomplete multi-omics data. Comput. Biol. Medicine 170: 108058 (2024)- [j44]Chen Zhao, Kuan-Jui Su, Chong Wu, Xuewei Cao, Qiuying Sha, Wu Li, Zhe Luo, Qing Tian, Chuan Qiu, Lan Juan Zhao, Anqi Liu, Lindong Jiang, Xiao Zhang, Hui Shen, Weihua Zhou, Hong-Wen Deng:
Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data. Comput. Biol. Medicine 179: 108813 (2024) - [j43]Chuan Qiu, Kuanjui Su, Zhe Luo, Qing Tian, Lanjuan Zhao, Li Wu, Hong-Wen Deng, Hui Shen:
Developing and comparing deep learning and machine learning algorithms for osteoporosis risk prediction. Frontiers Artif. Intell. 7 (2024) - 2022
- [j42]Sho Tsukiyama, Md. Mehedi Hasan, Hong-Wen Deng, Hiroyuki Kurata:
BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches. Briefings Bioinform. 23(2) (2022) - [j41]Md. Faruk Hosen, S. M. Hasan Mahmud, Kawsar Ahmed, Wenyu Chen, Mohammad Ali Moni, Hong-Wen Deng, Watshara Shoombuatong, Md. Mehedi Hasan:
DeepDNAbP: A deep learning-based hybrid approach to improve the identification of deoxyribonucleic acid-binding proteins. Comput. Biol. Medicine 145: 105433 (2022) - [j40]Meng Song, Jonathan Greenbaum, Joseph Luttrell IV, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan-Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong-Wen Deng, Chaoyang Zhang:
An autoencoder-based deep learning method for genotype imputation. Frontiers Artif. Intell. 5 (2022) - [j39]Yu Deng, Ling Wang, Chen Zhao, Shaojie Tang, Xiaoguang Cheng, Hong-Wen Deng, Weihua Zhou:
A deep learning-based approach to automatic proximal femur segmentation in quantitative CT images. Medical Biol. Eng. Comput. 60(5): 1417-1429 (2022) - [j38]Zhong Chen, Wensheng Zhang, Hong-Wen Deng, Kun Zhang:
Effective Cancer Subtype and Stage Prediction via Dropfeature-DNNs. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 107-120 (2022) - 2021
- [j37]Md. Mehedi Hasan, Md. Ashad Alam, Watshara Shoombuatong, Hong-Wen Deng, Balachandran Manavalan, Hiroyuki Kurata:
NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning. Briefings Bioinform. 22(6) (2021) - [j36]Xiang-He Meng, Hong-Mei Xiao, Hong-Wen Deng:
Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants. Bioinform. 37(10): 1339-1344 (2021) - [j35]Md. Ashad Alam, Chuan Qiu, Hui Shen, Yu-Ping Wang, Hong-Wen Deng:
A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets, with application to adolescent brain development and osteoporosis. J. Biomed. Informatics 120: 103854 (2021) - [j34]Yuntong Bai, Yun Gong, Jianchao Bai, Jingyu Liu, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang:
A Joint Analysis of Multi-Paradigm fMRI Data With Its Application to Cognitive Study. IEEE Trans. Medical Imaging 40(3): 951-962 (2021) - 2020
- [j33]Fangtang Yu, Chao Xu, Hong-Wen Deng, Hui Shen:
A novel computational strategy for DNA methylation imputation using mixture regression model (MRM). BMC Bioinform. 21(1): 552 (2020) - [j32]Zhouxuan Li, Tao Xu, Kai Zhang, Hong-Wen Deng, Eric Boerwinkle, Momiao Xiong:
Causal Analysis of Health Interventions and Environments for Influencing the Spread of COVID-19 in the United States of America. Frontiers Appl. Math. Stat. 6: 611805 (2020) - 2019
- [j31]Yan Zhao, Yujie Ning, Feng Zhang, Miao Ding, Yan Wen, Liang Shi, Kunpeng Wang, Mengnan Lu, Jingyan Sun, Menglu Wu, Bolun Cheng, Mei Ma, Lu Zhang, Shiqiang Cheng, Hui Shen, Qing Tian, Xiong Guo, Hong-Wen Deng:
PCA-based GRS analysis enhances the effectiveness for genetic correlation detection. Briefings Bioinform. 20(6): 2291-2298 (2019) - [j30]Md. Ashad Alam, Osamu Komori, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang:
Robust kernel canonical correlation analysis to detect gene-gene co-associations: A case study in genetics. J. Bioinform. Comput. Biol. 17(4): 1950028:1-1950028:23 (2019) - 2018
- [j29]Chao Xu, Jian Fang, Hui Shen, Yu-Ping Wang, Hong-Wen Deng:
EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits. Bioinform. 34(12): 1996-2003 (2018) - [j28]Alexej Gossmann, Shaolong Cao, Damian Brzyski, Lan-Juan Zhao, Hong-Wen Deng, Yu-Ping Wang:
A Sparse Regression Method for Group-Wise Feature Selection with False Discovery Rate Control. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1066-1078 (2018) - [j27]Jian Fang, Ji-Gang Zhang, Hong-Wen Deng, Yu-Ping Wang:
Joint Detection of Associations Between DNA Methylation and Gene Expression From Multiple Cancers. IEEE J. Biomed. Health Informatics 22(6): 1960-1969 (2018) - [j26]Jian Fang, Chao Xu, Pascal Zille, Dongdong Lin, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang:
Fast and Accurate Detection of Complex Imaging Genetics Associations Based on Greedy Projected Distance Correlation. IEEE Trans. Medical Imaging 37(4): 860-870 (2018) - 2017
- [j25]Wenyu Wang, Jingcan Hao, Shuyu Zheng, Qianrui Fan, Awen He, Yan Wen, Xiong Guo, Cuiyan Wu, Sen Wang, Tielin Yang, Hui Shen, Xiangding Chen, Qing Tian, Lijun Tan, Hong-Wen Deng, Feng Zhang:
Tissue-specific pathway association analysis using genome-wide association study summaries. Bioinform. 33(2): 243-247 (2017) - [j24]Hao He, Dongdong Lin, Ji-Gang Zhang, Yu-Ping Wang, Hong-Wen Deng:
Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network. BMC Bioinform. 18(1): 149:1-149:6 (2017) - 2016
- [j23]Shaolong Cao, Huaizhen Qin, Alexej Gossmann, Hong-Wen Deng, Yu-Ping Wang:
Unified tests for fine-scale mapping and identifying sparse high-dimensional sequence associations. Bioinform. 32(3): 330-337 (2016) - [j22]Dongdong Lin, Ji-Gang Zhang, Jingyao Li, Chao Xu, Hong-Wen Deng, Yu-Ping Wang:
An integrative imputation method based on multi-omics datasets. BMC Bioinform. 17: 247 (2016) - [j21]Junbo Duan, Mingxi Wan, Hong-Wen Deng, Yu-Ping Wang:
A Sparse Model Based Detection of Copy Number Variations From Exome Sequencing Data. IEEE Trans. Biomed. Eng. 63(3): 496-505 (2016) - 2015
- [j20]Yan Wen, Jingcan Hao, Xiong Guo, Xiao Xiao, Cuiyan Wu, Sen Wang, Tielin Yang, Hui Shen, Xiangding Chen, Lijun Tan, Qing Tian, Hong-Wen Deng, Feng Zhang:
SWGDT: A sliding window-based genotype dependence testing tool for genome-wide susceptibility gene scan. J. Biomed. Informatics 57: 38-41 (2015) - [j19]Wenlong Tang, Chao Xu, Yu-Ping Wang, Hong-Wen Deng, Ji-Gang Zhang:
MicroRNA-mRNA interaction analysis to detect potential dysregulation in complex diseases. Netw. Model. Anal. Health Informatics Bioinform. 4(1) (2015) - 2014
- [j18]Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng:
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model. Bioinform. 30(13): 1876-1883 (2014) - [j17]Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng:
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model. Bioinform. 30(21): 3142 (2014) - [j16]Tao Yang, Hong-Wen Deng, Tianhua Niu:
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences. BMC Bioinform. 15: 3 (2014) - [j15]Junbo Duan, Ji-Gang Zhang, Mingxi Wan, Hong-Wen Deng, Yu-Ping Wang:
Population clustering based on copy number variations detected from next generation sequencing data. J. Bioinform. Comput. Biol. 12(4) (2014) - [j14]Junbo Duan, Hong-Wen Deng, Yu-Ping Wang:
Common Copy Number Variation Detection From Multiple Sequenced Samples. IEEE Trans. Biomed. Eng. 61(3): 928-937 (2014) - 2013
- [j13]Junbo Duan, Ji-Gang Zhang, Hong-Wen Deng, Yu-Ping Wang:
CNV-TV: A robust method to discover copy number variation from short sequencing reads. BMC Bioinform. 14: 150 (2013) - [j12]Dongdong Lin, Ji-Gang Zhang, Jingyao Li, Vince D. Calhoun, Hong-Wen Deng, Yu-Ping Wang:
Group sparse canonical correlation analysis for genomic data integration. BMC Bioinform. 14: 245 (2013) - 2011
- [j11]Yong Lin, Jian Li, Hui Shen, Lei Zhang, Christopher J. Papasian, Hong-Wen Deng:
Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinform. 27(15): 2031-2037 (2011) - [j10]Jinhua Sheng, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang:
Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1568-1579 (2011) - 2010
- [j9]Jie Chen, Ayten Yigiter, Yu-Ping Wang, Hong-Wen Deng:
A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process. EURASIP J. Bioinform. Syst. Biol. 2010 (2010) - 2009
- [j8]Runqing Yang, Xin Wang, Jian Li, Hong-Wen Deng:
Bayesian robust analysis for genetic architecture of quantitative traits. Bioinform. 25(8): 1033-1039 (2009) - [j7]Yan-Fang Guo, Jian Li, Yuan Chen, Li-Shu Zhang, Hong-Wen Deng:
A new permutation strategy of pathway-based approach for genome-wide association study. BMC Bioinform. 10: 429 (2009) - 2008
- [j6]Feng Zhang, Jianfeng Liu, Jie Chen, Hong-Wen Deng:
HAPSIMU: a genetic simulation platform for population-based association studies. BMC Bioinform. 9 (2008) - 2007
- [j5]Ji-Gang Zhang, Hong-Wen Deng:
Gene selection for classification of microarray data based on the Bayes error. BMC Bioinform. 8 (2007) - 2006
- [j4]Jin-Long Li, Miao-Xin Li, Yan-Fang Guo, H.-Y. Deng, Hong-Wen Deng:
JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation. Bioinform. 22(15): 1926-1927 (2006) - 2005
- [j3]Lan-Juan Zhao, Miao-Xin Li, Yan-Fang Guo, Fu-Hua Xu, Jin-Long Li, Hong-Wen Deng:
SNPP: automating large-scale SNP genotype data management. Bioinform. 21(2): 266-268 (2005) - [j2]Yan Lu, Peng-Yuan Liu, Peng Xiao, Hong-Wen Deng:
Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. Bioinform. 21(14): 3105-3113 (2005) - [j1]Jin-Long Li, Miao-Xin Li, H.-Y. Deng, P. E. Duffy, Hong-Wen Deng:
PhD: a web database application for phenotype data management. Bioinform. 21(16): 3443-3444 (2005)
Conference and Workshop Papers
- 2015
- [c9]Shaolong Cao, Huaizhen Qin, Alexej Gossmann, Hong-Wen Deng, Yu-Ping Wang:
Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations. BCB 2015: 241-249 - 2014
- [c8]Shaolong Cao, Huaizhen Qin, Jian Li, Hong-Wen Deng, Yu-Ping Wang:
Scaled sparse high-dimensional tests for localizing sequence variants. BCB 2014: 79-87 - 2013
- [c7]Shaolong Cao, Huaizhen Qin, Hong-Wen Deng, Yu-Ping Wang:
A generalized sparse regression model with adjustment of pedigree structure for variant detection from next generation sequencing data. BCB 2013: 191 - [c6]Junbo Duan, Mingxi Wan, Hong-Wen Deng, Yu-Ping Wang:
Modeling exome sequencing data with generalized Gaussian distribution with application to copy number variation detection. BIBM 2013: 1-7 - [c5]Dongdong Lin, Hao He, Jingyao Li, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang:
Network-based investigation of genetic modules associated with functional brain networks in schizophrenia. BIBM 2013: 9-16 - 2012
- [c4]Junbo Duan, Ji-Gang Zhang, Hongbao Cao, Hong-Wen Deng, Yu-Ping Wang:
Copy number variation estimation from multiple next-generation sequencing samples. BCB 2012: 555-557 - [c3]Junbo Duan, Ji-Gang Zhang, Hong-Wen Deng, Yu-Ping Wang:
Detection of common copy number variation with application to population clustering from next generation sequencing data. EMBC 2012: 1246-1249 - [c2]Hongbao Cao, Shufeng Lei, Hong-Wen Deng, Yu-Ping Wang:
Identification of genes for complex diseases by integrating multiple types of genomic data. EMBC 2012: 5541-5544 - 2011
- [c1]Junbo Duan, Ji-Gang Zhang, John Lefante, Hong-Wen Deng, Yu-Ping Wang:
Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization. BIBM Workshops 2011: 3-12
Informal and Other Publications
- 2024
- [i12]Anton Orlichenko, Gang Qu, Ziyu Zhou, Anqi Liu, Hong-Wen Deng, Zhengming Ding, Julia M. Stephen, Tony W. Wilson, Vince D. Calhoun, Yu-Ping Wang:
A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds. CoRR abs/2405.07977 (2024) - [i11]Anjum Shaik, Kristoffer Larsen, Nancy E. Lane, Chen Zhao, Kuan-Jui Su, Joyce H. Keyak, Qing Tian, Qiuying Sha, Hui Shen, Hong-Wen Deng, Weihua Zhou:
A Staged Approach using Machine Learning and Uncertainty Quantification to Predict the Risk of Hip Fracture. CoRR abs/2405.20071 (2024) - 2023
- [i10]Anton Orlichenko, Grant Daly, Anqi Liu, Hui Shen, Hong-Wen Deng, Yu-Ping Wang:
ImageNomer: developing an fMRI and omics visualization tool to detect racial bias in functional connectivity. CoRR abs/2302.00767 (2023) - [i9]Chen Zhao, Anqi Liu, Xiao Zhang, Xuewei Cao, Zhengming Ding, Qiuying Sha, Hui Shen, Hong-Wen Deng, Weihua Zhou:
CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data. CoRR abs/2304.05542 (2023) - [i8]Chen Zhao, Kuan-Jui Su, Chong Wu, Xuewei Cao, Qiuying Sha, Wu Li, Zhe Luo, Tian Qin, Chuan Qiu, Lan Juan Zhao, Anqi Liu, Lindong Jiang, Xiao Zhang, Hui Shen, Weihua Zhou, Hong-Wen Deng:
Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics. CoRR abs/2310.07990 (2023) - 2022
- [i7]Md. Ashad Alam, Hui Shen, Hong-Wen Deng:
A robust kernel machine regression towards biomarker selection in multi-omics datasets of osteoporosis for drug discovery. CoRR abs/2201.05060 (2022) - [i6]Chen Zhao, Joyce H. Keyak, Xuewei Cao, Qiuying Sha, Li Wu, Zhe Luo, Lanjuan Zhao, Qing Tian, Chuan Qiu, Ray Su, Hui Shen, Hong-Wen Deng, Weihua Zhou:
Multi-view information fusion using multi-view variational autoencoders to predict proximal femoral strength. CoRR abs/2210.00674 (2022) - [i5]Xuewei Cao, Joyce H. Keyak, Sigurdur Sigurdsson, Chen Zhao, Weihua Zhou, Anqi Liu, Thomas Lang, Hong-Wen Deng, Vilmundur Gudnason, Qiuying Sha:
Hip Fracture Prediction using the First Principal Component Derived from FEA-Computed Fracture Loads. CoRR abs/2210.01032 (2022) - 2021
- [i4]Chen Zhao, Haipeng Tang, Daniel McGonigle, Zhuo He, Chaoyang Zhang, Yu-Ping Wang, Hong-Wen Deng, Robert Bober, Weihua Zhou:
A new approach to extracting coronary arteries and detecting stenosis in invasive coronary angiograms. CoRR abs/2101.09848 (2021) - [i3]Yu Deng, Ling Wang, Chen Zhao, Shaojie Tang, Xiaoguang Cheng, Hong-Wen Deng, Weihua Zhou:
A Deep Learning-Based Approach to Extracting Periosteal and Endosteal Contours of Proximal Femur in Quantitative CT Images. CoRR abs/2102.01990 (2021) - 2020
- [i2]Md. Ashad Alam, Chuan Qiu, Hui Shen, Yu-Ping Wang, Hong-Wen Deng:
A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets. CoRR abs/2004.14031 (2020) - [i1]Chen Zhao, Joyce H. Keyak, Jinshan Tang, Tadashi S. Kaneko, Sundeep Khosla, Shreyasee Amin, Elizabeth J. Atkinson, Lan-Juan Zhao, Michael J. Serou, Chaoyang Zhang, Hui Shen, Hong-Wen Deng, Weihua Zhou:
A Deep Learning-Based Method for Automatic Segmentation of Proximal Femur from Quantitative Computed Tomography Images. CoRR abs/2006.05513 (2020)
Coauthor Index
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