37 Publications (Page 1 of 2)
2021
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification.
Wang, Tongxin⋅Shao, Wei⋅Huang, Zhi⋅Tang, Haixu⋅Zhang, Jie⋅Ding, Zhengming and Huang, Kun
Nature communications, vol. 12, (no. 1), pp. 3445, June 8, 2021. | Journal Article
 
ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways.
Huang, Xiaoqing⋅Huang, Kun⋅Johnson, Travis⋅Radovich, Milan⋅Zhang, Jie⋅Ma, Jianzhu and Wang, Yijie
NAR genomics and bioinformatics, vol. 3, (no. 4), pp. lqab097, December 2021. | Journal Article
 
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery.
Liu, Yusong⋅Ye, Xiufen⋅Yu, Christina Y⋅Shao, Wei⋅Hou, Jie⋅Feng, Weixing⋅Zhang, Jie and Huang, Kun
BMC bioinformatics, vol. 22, pp. 111, October 25, 2021. | Journal Article
 
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.
Huang, Zhi⋅Han, Zhi⋅Wang Resource, Tongxin⋅Shao, Wei⋅Xiang, Shunian⋅Salama, Paul⋅Rizkalla, Maher⋅Huang, Kun and Zhang, Jie
Genomics, proteomics & bioinformatics, March 8, 2021. | Journal Article
 
Weakly Supervised Deep Ordinal Cox Model for Survival Prediction from Whole-slide Pathological Images.
Shao, Wei⋅Wang, Tongxin⋅Huang, Zhi⋅Han, Zhi⋅Zhang, Jie and Huang, Kun
IEEE transactions on medical imaging, vol. PP, July 15, 2021. | Journal Article
2020
A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma.
Zhan, Xiaohui⋅Liu, Yusong⋅Yu, Christina Y⋅Wang, Tian-Fu⋅Zhang, Jie⋅Ni, Dong and Huang, Kun
BMC medical genomics, vol. 13, pp. 190, December 28, 2020. | Journal Article
 
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations
Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Z, Huang⋅Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅TS, Johnson⋅Johnson, Travis S⋅Johnson, Travis S⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Z, Han⋅Han, Zhi⋅Han, Zhi⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅B, Helm⋅Helm, Bryan⋅Helm, Bryan⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅C, Zhang⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅P, Salama⋅Salama, Paul⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅M, Rizkalla⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅CY, Yu⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅J, Cheng⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅S, Xiang⋅Xiang, Shunian⋅Xiang, Shunian⋅X, Zhan⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅J, Zhang⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Huang, Kun⋅K, Huang⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun and Huang, Kun
BMC Medical Genomics, vol. 13, pp. 1-12, 2020. | Journal Article
 
Deep-Learning-Based Characterization of Tumor-Infiltrating Lymphocytes in Breast Cancers From Histopathology Images and Multiomics Data.
Lu, Zixiao⋅Xu, Siwen⋅Shao, Wei⋅Wu, Yi⋅Zhang, Jie⋅Han, Zhi⋅Feng, Qianjin and Huang, Kun
JCO clinical cancer informatics, vol. 4, pp. 480-490, May 2020. | Journal Article
 
Liquid biopsy in the clinical management of bladder cancer: current status and future developments.
Kouba, Erik⋅Kouba, Erik⋅Lopez-Beltran, Antonio⋅Lopez-Beltran, Antonio⋅Montironi, Rodolfo⋅Montironi, Rodolfo⋅Massari, Francesco⋅Massari, Francesco⋅Huang, Kun⋅Huang, Kun⋅Santoni, Matteo⋅Santoni, Matteo⋅Chovanec, Michal⋅Chovanec, Michal⋅Cheng, Michael⋅Cheng, Michael⋅Scarpelli, Marina⋅Scarpelli, Marina⋅Zhang, Jie⋅Zhang, Jie⋅Cimadamore, Alessia⋅Cimadamore, Alessia⋅Cheng, Liang and Cheng, Liang
Expert review of molecular diagnostics, vol. 20, (no. 2), pp. 255-264, February 2020. | Journal Article
 
Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers
Shao, Wei⋅Shao, Wei⋅Wang, Tongxin⋅Wang, Tongxin⋅Sun, Liang⋅Sun, Liang⋅Dong, Tianhan⋅Dong, Tianhan⋅Han, Zhi⋅Han, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Daoqiang⋅Zhang, Daoqiang⋅Huang, Kun and Huang, Kun
Medical Image Analysis, vol. 65, Oct 2020. | Journal Article
 
Vascular amyloid accumulation alters the gabaergic synapse and induces hyperactivity in a model of cerebral amyloid angiopathy.
Cisternas, P.⋅Cisternas, Pablo⋅Taylor, Xavier⋅Taylor, X.⋅Perkins, Abigail⋅Perkins, A.⋅Maldonado, O.⋅Maldonado, Orlando⋅Allman, E.⋅Allman, Elysabeth⋅Cordova, R.⋅Cordova, Ricardo⋅Marambio, Yamil⋅Marambio, Y.⋅Munoz, B.⋅Munoz, Braulio⋅Pennington, Taylor⋅Pennington, T.⋅Xiang, S.⋅Xiang, Shunian⋅Zhang, Jie⋅Zhang, J.⋅Vidal, R.⋅Vidal, Ruben⋅Atwood, Brady⋅Atwood, B.⋅Lasagna-Reeves, C.A. and Lasagna-Reeves, Cristian A
Aging cell, vol. 19, (no. 10), pp. e13233, October 2020. | Journal Article
2019
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Wang, Tongxin⋅Wang, Tongxin⋅Johnson, Travis S⋅Johnson, Travis⋅Shao, Wei⋅Shao, Wei⋅Lu, Zixiao⋅Lu, Zixiao⋅Helm, Bryan R⋅Helm, Bryan⋅Zhang, Jie⋅Zhang, Jie⋅Huang, Kun and Huang, Kun
Genome Biology (Online Edition), vol. 20, (no. 1), pp. 165, 2019-12-00. | Journal Article
 
Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer.
Zhan, Xiaohui⋅Zhan, Xiaohui⋅Cheng, Jun⋅Cheng, Jun⋅Huang, Zhi⋅Huang, Zhi⋅Han, Zhi⋅Han, Zhi⋅Helm, Bryan⋅Helm, Bryan⋅Liu, Xiaowen⋅Liu, Xiaowen⋅Zhang, Jie⋅Zhang, Jie⋅Wang, Tian-Fu⋅Wang, Tian-Fu⋅Ni, Dong⋅Ni, Dong⋅Huang, Kun and Huang, Kun
Molecular & cellular proteomics : MCP, vol. 18, (no. 8S1), pp. S37-S51, August 9, 2019. | Journal Article
 
Generalized gene co-expression analysis via subspace clustering using low-rank representation
Wang, Tongxin⋅Zhang, Jie and Huang, Kun
BMC bioinformatics, vol. 20, (no. Suppl 7), pp. 196, 2019-May-01. | Journal Article
 
Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients
Han, Yatong⋅Han, Yatong⋅Ye, Xiufen⋅Ye, Xiufen⋅Wang, Chao⋅Wang, Chao⋅Liu, Yusong⋅Liu, Yusong⋅Zhang, Siyuan⋅Zhang, Siyuan⋅Feng, Weixing⋅Feng, Weixing⋅Huang, Kun⋅Huang, Kun⋅Zhang, Jie and Zhang, Jie
Biology Direct, vol. 14, 2019. | Journal Article
 
LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection.
Johnson, Travis S⋅Johnson, Travis S⋅Wang, Tongxin⋅Wang, Tongxin⋅Huang, Zhi⋅Huang, Zhi⋅Yu, Christina Y⋅Yu, Christina Y⋅Wu, Yi⋅Wu, Yi⋅Han, Yatong⋅Han, Yatong⋅Zhang, Yan⋅Zhang, Yan⋅Huang, Kun⋅Huang, Kun⋅Zhang, Jie and Zhang, Jie
Bioinformatics (Oxford, England), vol. 35, (no. 22), pp. 4696-4706, November 1, 2019. | Journal Article
 
Topological Methods for Visualization and Analysis of High Dimensional Single-Cell RNA Sequencing Data.
Wang, Tongxin⋅Wang, Tongxin⋅Wang, Tongxin⋅Johnson, Travis⋅Johnson, Travis⋅Johnson, Travis⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Huang, Kun⋅Huang, Kun and Huang, Kun
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, vol. 24, pp. 350-361, 2019. | Journal Article
2018
Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Hankey, William⋅Hankey, William⋅McIlhatton, Michael A⋅McIlhatton, Michael A⋅Ebede, Kenechi⋅Kenechi, Ebede⋅Kennedy, Brian⋅Kennedy, Brian⋅Hancioglu, Baris⋅Zhang, Jie⋅Zhang, Jie⋅Brock, Guy N⋅Brock, Guy N⋅Huang, Kun⋅Huang, Kun⋅Groden, Joanna and Groden, Joanna
Cancer Research, vol. 78, (no. 3), pp. 617-630, Feb 1, 2018. | Journal Article
2017
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns
Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Johnson, Travis⋅Johnson, Travis⋅Johnson, Travis⋅Johnson, Travis⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Xuan⋅Zhang, Xuan⋅Zhang, Xuan⋅Zhang, Xuan⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun and Huang, Kun
BioMed Research International, vol. 2017, 2017. | Journal Article
 
Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers
Zhang, Jie⋅Zhang, Jie⋅Huang, Kun and Huang, Kun
BMC Genomics, vol. 18, pp. 1-14, 2017. | Journal Article
2016
Exome‐wide single‐base substitutions in tissues and derived cell lines of the constitutive Fhit knockout mouse
Paisie, Carolyn A⋅Paisie, Carolyn A⋅Schrock, Morgan S⋅Schrock, Morgan S⋅Karras, Jenna R⋅Karras, Jenna R⋅Zhang, Jie⋅Zhang, Jie⋅Miuma, Satoshi⋅Miuma, Satoshi⋅Ouda, Iman M⋅Ouda, Iman M⋅Waters, Catherine E⋅Waters, Catherine E⋅Saldivar, Joshua C⋅Saldivar, Joshua C⋅Druck, Teresa⋅Druck, Teresa⋅Huebner, Kay and Huebner, Kay
Cancer Science, vol. 107, (no. 4), pp. 535, April 2016. | Journal Article
 
Fhit loss‐associated initiation and progression of neoplasia in vitro
Karras, Jenna R⋅Karras, Jenna R⋅Schrock, Morgan S⋅Schrock, Morgan S⋅Batar, Bahadir⋅Batar, Bahadir⋅Zhang, Jie⋅Zhang, Jie⋅La Perle, Krista⋅La Perle, Krista⋅Druck, Teresa⋅Druck, Teresa⋅Huebner, Kay and Huebner, Kay
Cancer Science, vol. 107, (no. 11), pp. 1598, November 2016. | Journal Article
 
Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers
Zhang, Jie and Huang, Kun
Cancer Informatics, vol. 2014, (no. Suppl. 3), pp. 146, 2016-07-24. | Journal Article
 
Visceral Adipose MicroRNA 223 Is Upregulated in Human and Murine Obesity and Modulates the Inflammatory Phenotype of Macrophages
Deiuliis, Jeffrey A⋅Deiuliis, Jeffrey A⋅Deiuliis, Jeffrey A⋅Syed, Rafay⋅Duggineni, Dheeraj⋅Duggineni, Dheeraj⋅Duggineni, Dheeraj⋅Rutsky, Jessica⋅Rutsky, Jessica⋅Rutsky, Jessica⋅Rengasamy, Palanivel⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun⋅Needleman, Bradley⋅Needleman, Bradley⋅Needleman, Bradley⋅Mikami, Dean⋅Mikami, Dean⋅Mikami, Dean⋅Perry, Kyle⋅Perry, Kyle⋅Perry, Kyle⋅Hazey, Jeffrey⋅Hazey, Jeffrey⋅Hazey, Jeffrey⋅Rajagopalan, Sanjay⋅Rajagopalan, Sanjay and Rajagopalan, Sanjay
PLoS One, vol. 11, (no. 11), Nov 2016. | Journal Article
2014
Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers
Zhang, Jie⋅Zhang, Jie⋅Huang, Kun and Huang, Kun
Cancer Informatics, pp. 137-146, 2014. | Journal Article