Kun Huang

Publication Activity (10 Years)

Years Active: 2002-2022
Publications (10 Years): 31

Top Topics

Current Challenges

Morphological Features

Scientific Visualization

Top Venues

Genom. Proteom. Bioinform.

Publications

Michael F. Sharpnack, Travis S. Johnson, Robert Chalkley, Zhi Han, David Carbone, Kun Huang, Kai He
TSAFinder: exhaustive tumor-specific antigen detection with RNAseq. Bioinform. 38 (9) (2022)
Yingli Zuo, Yawen Wu, Zixiao Lu, Qi Zhu, Kun Huang, Daoqiang Zhang, Wei Shao
Identify Consistent Imaging Genomic Biomarkers for Characterizing the Survival-Associated Interactions Between Tumor-Infiltrating Lymphocytes and Tumors. MICCAI (2) (2022)
Feng Gao, Kun Huang, Yi Xing
Artificial Intelligence in Omics. Genom. Proteom. Bioinform. 20 (5) (2022)
Xiao Luo, Priyanka Gandhi, Susan Storey, Kun Huang
A Deep Language Model for Symptom Extraction From Clinical Text and its Application to Extract COVID-19 Symptoms From Social Media. IEEE J. Biomed. Health Informatics 26 (4) (2022)
Wei Shao, Xiao Luo, Zuoyi Zhang, Zhi Han, Vasu Chandrasekaran, Vladimir Turzhitsky, Vishal Bali, Anna R. Roberts, Megan Metzger, Jarod Baker, Carmen La Rosa, Jessica Weaver, Paul R. Dexter, Kun Huang
Application of unsupervised deep learning algorithms for identification of specific clusters of chronic cough patients from EMR data. BMC Bioinform. (3) (2022)
Yusong Liu, Tongxin Wang, Ben Duggan, Michael F. Sharpnack, Kun Huang, Jie Zhang, Xiufen Ye, Travis S. Johnson
SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. Briefings Bioinform. 23 (3) (2022)
Jing Su, Pengyue Zhang, Zuoyi Zhang, Michael Eadon, Xiaochun Li, Tian He, Stanley Taylor, Travis Johnson, Zhaorui Liu, Ziyang Tang, Baijian Yang, Qianqian Song, Kun Huang
PASC CKD: revealing the progression trajectories of sustained COVID-19-related renal injury using real-world evidence. AMIA (2021)
Zhi Huang, Zhi Han, Tongxin Wang, Wei Shao, Shunian Xiang, Paul Salama, Maher E. Rizkalla, Kun Huang, Jie Zhang
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining. Genom. Proteom. Bioinform. 19 (6) (2021)
Zixiao Lu, Xiaohui Zhan, Yi Wu, Jun Cheng, Wei Shao, Dong Ni, Zhi Han, Jie Zhang, Qianjin Feng, Kun Huang
: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images. Genom. Proteom. Bioinform. 19 (6) (2021)
Andreas S. Panayides, Amir A. Amini, Nenad D. Filipovic, Ashish Sharma, Sotirios A. Tsaftaris, Alistair A. Young, David J. Foran, Nhan Do, Spyretta Golemati, Tahsin M. Kurç, Kun Huang, Konstantina S. Nikita, Ben P. Veasey, Michalis E. Zervakis, Joel H. Saltz, Constantinos S. Pattichis
AI in Medical Imaging Informatics: Current Challenges and Future Directions. IEEE J. Biomed. Health Informatics 24 (7) (2020)
Kun Huang, Yifan Wang, Zihan Zhou, Tianjiao Ding, Shenghua Gao, Yi Ma
Learning to Parse Wireframes in Images of Man-Made Environments. CoRR (2020)
Arunima Srivastava, Michael Sharpnack, Kun Huang, Parag Mallick, Raghu Machiraju
PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms usingproteogenomics. PSB (2020)
Sundaresan Raman, Shantanu Singh, Thierry Pécot, Enrico Caserta, Kun Huang, Jens Rittscher, Gustavo Leone, Raghu Machiraju
Capturing variations in nuclear phenotypes. J. Comput. Sci. 36 (2019)
Zachary B. Abrams, Travis Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
A protocol to evaluate RNA sequencing normalization methods. BMC Bioinform. (24) (2019)
Hao Ding, Michael Sharpnack, Chao Wang, Kun Huang, Raghu Machiraju
Integrative cancer patient stratification via subspace merging. Bioinform. 35 (10) (2019)
Kun Huang, Yifan Wang, Zihan Zhou, Tianjiao Ding, Shenghua Gao, Yi Ma
Learning to Parse Wireframes in Images of Man-Made Environments. CVPR (2018)
Heng Huang, Li Shen, Paul M. Thompson, Kun Huang, Junzhou Huang, Lin Yang
Session introduction. PSB (2018)
Xing Tang, Arunima Srivastava, Huayang Liu, Raghu Machiraju, Kun Huang, Gustavo Leone
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. Bioinform. 34 (16) (2018)
Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju
Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles. PSB (2018)
Xing Tang, Arunima Srivastava, Huayang Liu, Raghu Machiraju, Kun Huang, Gustavo Leone
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. Bioinform. 33 (10) (2017)
Pacharmon Kaewprag, Cheryl Newton, Brenda Vermillion, Sookyung Hyun, Kun Huang, Raghu Machiraju
Predictive models for pressure ulcers from intensive care unit electronic health records using Bayesian networks. BMC Medical Informatics Decis. Mak. 17 (2) (2017)
Qihang Li, Kun Huang, Raghu Machiraju
Spatiotemporal Visualization of Gene Expression in the Developing Mouse Brain. EuroVis (Short Papers) (2017)
Chao Wang, Hai Su, Lin Yang, Kun Huang
Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations. PSB (2017)
Travis Johnson, Zachary B. Abrams, Yan Zhang, Kun Huang
Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing. PSB (2017)
Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. PLoS Comput. Biol. 12 (4) (2016)
Nan Meng, Raghu Machiraju, Kun Huang
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types. BMC Bioinform. 17 (S-17) (2016)
Kelly Regan, Zachary B. Abrams, Michael Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R. O. Payne
Session Introduction. PSB (2016)
Ayat Hatem, Kamer Kaya, Jeffrey D. Parvin, Kun Huang, Ümit V. Çatalyürek
MICA: MicroRNA integration for active module discovery. BCB (2015)
Hao Ding, Chao Wang, Kun Huang, Raghu Machiraju
GRAPHIE: graph based histology image explorer. BMC Bioinform. 16 (S11) (2015)
Nan Meng, Raghu Machiraju, Kun Huang
Identify Critical Genes in Development with Consistent H3K4me2 Patterns across Multiple Tissues. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Dong Xu, Kun Huang, Jeanette Schmidt
Guest Editors Introduction to the Special Issue on Software and Databases. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
A. Yates, Amy Webb, Michael Sharpnack, H. Chamberlin, Kun Huang, Raghu Machiraju
Visualizing Multidimensional Data with Glyph SPLOMs. Comput. Graph. Forum 33 (3) (2014)
Amy Webb, Aaron Albin, Zhan Ye, Majid Rastegar-Mojarad, Kun Huang, Jeffrey D. Parvin, Wolfgang Sadee, Lang Li, Simon M. Lin, Yang Xiang
Mining massive SNP data for identifying associated SNPs and uncovering gene relationships. BCB (2014)
Hao Ding, Chao Wang, Kun Huang, Raghu Machiraju
iGPSe: A visual analytic system for integrative genomic based cancer patient stratification. BMC Bioinform. 15 (2014)
Qihang Li, Gabriel Zachmann, David Feng, Kun Huang, Raghu Machiraju
2013 IEEE Scientific Visualization Contest Winner: Observing Genomics and Phenotypical Patterns in the Developing Mouse Brain. IEEE Computer Graphics and Applications 34 (5) (2014)
Hao Ding, Chao Wang, Kun Huang, Raghu Machiraju
iGPSe: A Visual Analytic System for Integrative Genomic Based Cancer Patient Stratification. CoRR (2014)
Vikram Kalluru, Raghu Machiraju, Kun Huang
Identify condition-specific gene co-expression networks. Int. J. Comput. Biol. Drug Des. 6 (1/2) (2013)
Chao Wang, Thierry Pécot, Debra L. Zynger, Raghu Machiraju, Charles L. Shapiro, Kun Huang
Research and applications: Identifying survival associated morphological features of triple negative breast cancer using multiple datasets. J. Am. Medical Informatics Assoc. 20 (4) (2013)
Jie Zhang, Shiwei Ni, Yang Xiang, Jeffrey D. Parvin, Yufeng Yang, Yongjian Zhou, Kun Huang
Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis. Int. J. Comput. Biol. Drug Des. 6 (1/2) (2013)
Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-wen Liu, Jeffrey D. Parvin, Kun Huang
Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability. PLoS Comput. Biol. 8 (8) (2012)
Zhi Han, Lu Tian, Thierry Pécot, Tim Hui-Ming Huang, Raghu Machiraju, Kun Huang
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data. BMC Bioinform. 13 (S-2) (2012)
Yang Xiang, David Fuhry, Ruoming Jin, Ye Zhao, Kun Huang
Visualizing Clusters in Parallel Coordinates for Visual Knowledge Discovery. PAKDD (1) (2012)
Thierry Pécot, Shantanu Singh, Enrico Caserta, Kun Huang, Raghu Machiraju, Gustavo Leone
Non parametric cell nuclei segmentation based on a tracking over depth from 3D fluorescence confocal images. ISBI (2012)
Pengyue Zhang, Raphaël Mourad, Yang Xiang, Kun Huang, Tim Hui-Ming Huang, Kenneth P. Nephew, Yunlong Liu, Lang Li
A dynamic time order network for time-series gene expression data analysis. BMC Syst. Biol. 6 (S-3) (2012)
Lee A. D. Cooper, Kun Huang, Manuel Ujaldon
Parallel Automatic Registration of Large Scale Microscopic Images on Multiprocessor CPUs and GPUs. IPDPS Workshops (2011)
Jie Zhang, Thomas Knobloch, Jeffrey D. Parvin, Christopher Weghorst, Kun Huang
Identifying smoking associated gene co-expression networks related to oral cancer initiation. BIBM Workshops (2011)
Jie Zhang, Shiwei Ni, Jeffrey D. Parvin, Yufeng Yang, Kun Huang
Predicting Parkinson's disease related genes using frequent gene co-expression analysis. BIBM Workshops (2011)
Shantanu Singh, Firdaus Janoos, Thierry Pécot, Enrico Caserta, Kun Huang, Jens Rittscher, Gustavo Leone, Raghu Machiraju
Non-parametric Population Analysis of Cellular Phenotypes. MICCAI (2) (2011)
Lee A. D. Cooper, Joel H. Saltz, Ümit V. Çatalyürek, Kun Huang
Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation. HISB (2011)
Cenny Taslim, Shili Lin, Kun Huang, Tim Hui-Ming Huang
Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model. GENSiPS (2011)
Hatice Gulcin Ozer, Yi-Wen Huang, Jiejun Wu, Jeffrey D. Parvin, Tim Hui-Ming Huang, Kun Huang
Comparing Multiple Chip-Sequencing Experiments. J. Bioinform. Comput. Biol. 9 (2) (2011)
Lee A. D. Cooper, Joel H. Saltz, Raghu Machiraju, Kun Huang
Two-point correlation as a feature for histology images: Feature space structure and correlation updating. CVPR Workshops (2010)
Philip R. O. Payne, Kun Huang, Kristin Keen-Circle, Abhisek Kundu, Jie Zhang, Tara Borlawsky
Multi-dimensional discovery of biomarker and phenotype complexes. BMC Bioinform. 11 (S-9) (2010)
Jie Zhang, Yang Xiang, Liya Ding, Kristin Keen-Circle, Tara Borlawsky, Hatice Gulcin Ozer, Ruoming Jin, Philip R. O. Payne, Kun Huang
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia. BMC Bioinform. 11 (S-9) (2010)
Antonio Ruiz, Manuel Ujaldon, Lee A. D. Cooper, Kun Huang
Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors. J. Signal Process. Syst. 55 (1-3) (2009)
Hatice Gulcin Ozer, Doruk Bozdag, Terry Camerlengo, Jiejun Wu, Yi-Wen Huang, Timothy D. R. Hartley, Jeffrey D. Parvin, Tim Hui-Ming Huang, Ümit V. Çatalyürek, Kun Huang
A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments. BICoB (2009)
Terry Camerlengo, Hatice Gulcin Ozer, Pearlly Yan, Jeffrey D. Parvin, Tim Hui-Ming Huang, Kun Huang, Mingxiang Teng, Lang Li, Yunlong Liu, Francisco Perez, Tahsin M. Kurç
Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. BIBM (2009)
Lee A. D. Cooper, Olcay Sertel, Jun Kong, Gerard Lozanski, Kun Huang, Metin N. Gurcan
Feature-based registration of histopathology images with different stains: An application for computerized follicular lymphoma prognosis. Comput. Methods Programs Biomed. 96 (3) (2009)
Firdaus Janoos, Kishore Mosaliganti, Xiaoyin Xu, Raghu Machiraju, Kun Huang, Stephen T. C. Wong
Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging. Medical Image Anal. 13 (1) (2009)
Jie Zhang, Kun Huang, Yang Xiang, Ruoming Jin
Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer Prognosis. IJCBS (2009)
Kishore Mosaliganti, Firdaus Janoos, M. Okan Irfanoglu, Randall Ridgway, Raghu Machiraju, Kun Huang, Joel H. Saltz, Gustavo Leone, Michael C. Ostrowski
Tensor classification of N-point correlation function features for histology tissue segmentation. Medical Image Anal. 13 (1) (2009)
Cenny Taslim, Jiejun Wu, Pearlly Yan, Greg Singer, Jeffrey D. Parvin, Tim Hui-Ming Huang, Shili Lin, Kun Huang
Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinform. 25 (18) (2009)
Kishore Mosaliganti, Raghu Machiraju, Kun Huang, Gustavo Leone
Geometry-driven Visualization of Microscopic Structures in Biology. Comput. Graph. Forum 27 (3) (2008)
Kishore Mosaliganti, Tony Pan, Randall Ridgway, Richard Sharp, Lee A. D. Cooper, Alex Gulacy, Ashish Sharma, M. Okan Irfanoglu, Raghu Machiraju, Tahsin M. Kurç, Alain de Bruin, Pamela Wenzel, Gustavo Leone, Joel H. Saltz, Kun Huang
An imaging workflow for characterizing phenotypical change in large histological mouse model datasets. J. Biomed. Informatics 41 (6) (2008)
Kishore Mosaliganti, Lee A. D. Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang, Joel H. Saltz
Reconstruction of Cellular Biological Structures from Optical Microscopy Data. IEEE Trans. Vis. Comput. Graph. 14 (4) (2008)
Kishore Mosaliganti, Raghu Machiraju, Kun Huang
Geometry-driven visualization of microscopic structures in biology. ISBI (2008)
Richard Sharp, Randall Ridgway, Kishore Mosaliganti, Pamela Wenzel, Tony Pan, Alain de Bruin, Raghu Machiraju, Kun Huang, Gustavo Leone, Joel H. Saltz
Volume Rendering Phenotype Differences in Mouse Placenta Microscopy Data. Comput. Sci. Eng. 9 (1) (2007)
Antonio Ruiz, Manuel Ujaldon, Jose Antonio Andrades, Jose Becerra, Kun Huang, Tony Pan, Joel H. Saltz
The GPU on biomedical image processing for color and phenotype analysis. BIBE (2007)
Kishore Mosaliganti, Firdaus Janoos, Richard Sharp, Randall Ridgway, Raghu Machiraju, Kun Huang, Pamela Wenzel, Alain de Bruin, Gustavo Leone, Joel H. Saltz
Detection and Visualization of Surface-Pockets to Enable Phenotyping Studies. IEEE Trans. Medical Imaging 26 (9) (2007)
Firdaus Janoos, M. Okan Irfanoglu, Kishore Mosaliganti, Raghu Machiraju, Kun Huang, Pamela Wenzel, Alain de Bruin, Gustavo Leone
Multi-Resolution Image Segmentation Using the 2-Point Correlation Functions. ISBI (2007)
Lee A. D. Cooper, Jun Liu, Kun Huang
Spatial Segmentation of Temporal Texture Using Mixture Linear Models. WDV (2006)
Wei Hong, John Wright, Kun Huang, Yi Ma
Multiscale Hybrid Linear Models for Lossy Image Representation. IEEE Trans. Image Process. 15 (12) (2006)
Jeff Prescott, Matthew Clary, Gregory J. Wiet, Tony Pan, Kun Huang
Automatic registration of large set of microscopic images using high-level features. ISBI (2006)
Kishore Mosaliganti, Tony Pan, Richard Sharp, Randall Ridgway, Srivathsan Iyengar, Alexandra Gulacy, Pamela Wenzel, Alain de Bruin, Raghu Machiraju, Kun Huang, Gustavo Leone, Joel H. Saltz
Registration and 3D visualization of large microscopy images. Medical Imaging: Image Processing (2006)
Allen Y. Yang, Kun Huang, Shankar R. Rao, Wei Hong, Yi Ma
Symmetry-based 3-D reconstruction from perspective images. Comput. Vis. Image Underst. 99 (2) (2005)
Shannon Hastings, Matheus Ribeiro, Stephen Langella, Scott Oster, Ümit V. Çatalyürek, Tony Pan, Kun Huang, Renato Ferreira, Joel H. Saltz, Tahsin M. Kurç
XML database support for distributed execution of data-intensive scientific workflows. SIGMOD Rec. 34 (3) (2005)
Wei Hong, John Wright, Kun Huang, Yi Ma
A Multi-Scale Hybrid Linear Model for Lossy Image Representation. ICCV (2005)
Ümit V. Çatalyürek, Shannon Hastings, Kun Huang, Vijay S. Kumar, Tahsin M. Kurç, Stephen Langella, Sivaramakrishnan Narayanan, Scott Oster, Tony Pan, Benjamin Rutt, Xi Zhang, Joel H. Saltz
Supporting Large Scale Medical and Scientific Datasets. PARCO (2005)
Kun Huang, Wei Hong, Yi Ma
Symmetry-based photo-editing. Pattern Recognit. 38 (6) (2005)
Kun Huang, Allen Y. Yang, Wei Hong, Yi Ma
Large-baseline Matching and Reconstruction from Symmetry Cells. ICRA (2004)
Wei Hong, Allen Y. Yang, Kun Huang, Yi Ma
On Symmetry and Multiple-View Geometry: Structure, Pose, and Calibration from a Single Image. Int. J. Comput. Vis. 60 (3) (2004)
Kun Huang, Allen Y. Yang, Yi Ma
Sparse representation of images with hybrid linear models. ICIP (2004)
Kun Huang, Yi Ma, René Vidal
Minimum Effective Dimension for Mixtures of Subspaces: A Robust GPCA Algorithm and Its Applications. CVPR (2) (2004)
Kun Huang, Andrew Wagner, Yi Ma
Identification of hybrid linear time-invariant systems via subspace embedding and segmentation (SES). CDC (2004)
Yi Ma, Kun Huang, René Vidal, Jana Kosecka, Shankar Sastry
Rank Conditions on the Multiple-View Matrix. Int. J. Comput. Vis. 59 (2) (2004)
Matheus Ribeiro, Tahsin M. Kurç, Tony Pan, Kun Huang, Ümit V. Çatalyürek, Xi Zhang, Stephen Langella, Shannon Hastings, Scott Oster, Renato Ferreira, Joel H. Saltz
Tools for efficient subsetting and pipelined processing of large scale, distributed biomedical image data. High Performance Computing Workshop (2004)
Allen Y. Yang, Shankar R. Rao, Kun Huang, Wei Hong, Yi Ma
Geometric Segmentation of Perspective Images Based on Symmetry Groups. ICCV (2003)
Kun Huang, Wei Hong, Yi Ma
Symmetry-Based Photo Editing. HLK (2003)
Kun Huang, Robert M. Fossum, Yi Ma
Generalized Rank Conditions in Multiple View Geometry with Applications to Dynamical Scenes. ECCV (2) (2002)