Kun Huang

Orcid: 0000-0002-8530-370X

Affiliations:
  • Indiana University School of Medicine, Department of Biostatistics & Health Data Science, USA
  • The Ohio State University, Department of Computer Science and Engineering / Department of Biomedical Informatics, Columbus, OH, USA
  • University of Illinois at Urbana-Champaign, IL, USA (former)


According to our database1, Kun Huang authored at least 111 papers between 2002 and 2022.

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Bibliography

2022
Artificial Intelligence in Omics.
Genom. Proteom. Bioinform., October, 2022

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, 2022

Application of unsupervised deep learning algorithms for identification of specific clusters of chronic cough patients from EMR data.
BMC Bioinform., 2022

TSAFinder: exhaustive tumor-specific antigen detection with RNAseq.
Bioinform., 2022

SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression.
Briefings Bioinform., 2022

Identify Consistent Imaging Genomic Biomarkers for Characterizing the Survival-Associated Interactions Between Tumor-Infiltrating Lymphocytes and Tumors.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2022, 2022

2021
Weakly Supervised Deep Ordinal Cox Model for Survival Prediction From Whole-Slide Pathological Images.
IEEE Trans. Medical Imaging, 2021

A Computational Framework to Analyze the Associations Between Symptoms and Cancer Patient Attributes Post Chemotherapy Using EHR Data.
IEEE J. Biomed. Health Informatics, 2021

Analyzing the symptoms in colorectal and breast cancer patients with or without type 2 diabetes using EHR data.
Health Informatics J., 2021

<i>BrcaSeg</i>: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images.
Genom. Proteom. Bioinform., 2021

TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.
Genom. Proteom. Bioinform., 2021

Applying interpretable deep learning models to identify chronic cough patients using EHR data.
Comput. Methods Programs Biomed., 2021

TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery.
BMC Bioinform., 2021

Towards Fair Cross-Domain Adaptation via Generative Learning.
Proceedings of the IEEE Winter Conference on Applications of Computer Vision, 2021

PASC CKD: revealing the progression trajectories of sustained COVID-19-related renal injury using real-world evidence.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020
Integrative Analysis of Pathological Images and Multi-Dimensional Genomic Data for Early-Stage Cancer Prognosis.
IEEE Trans. Medical Imaging, 2020

AI in Medical Imaging Informatics: Current Challenges and Future Directions.
IEEE J. Biomed. Health Informatics, 2020

Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers.
Medical Image Anal., 2020

Low-Rank Reorganization via Proportional Hazards Non-negative Matrix Factorization Unveils Survival Associated Gene Clusters.
CoRR, 2020

PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms usingproteogenomics.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Microsatellite Instability Prediction of Uterine Corpus Endometrial Carcinoma Based on H&E Histology Whole-Slide Imaging.
Proceedings of the 17th IEEE International Symposium on Biomedical Imaging, 2020

2019
Capturing variations in nuclear phenotypes.
J. Comput. Sci., 2019

Generalized gene co-expression analysis via subspace clustering using low-rank representation.
BMC Bioinform., 2019

A protocol to evaluate RNA sequencing normalization methods.
BMC Bioinform., 2019

LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection.
Bioinform., 2019

Integrative cancer patient stratification via subspace merging.
Bioinform., 2019

Topological Methods for Visualization and Analysis of High Dimensional Single-Cell RNA Sequencing Data.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Diagnosis-Guided Multi-modal Feature Selection for Prognosis Prediction of Lung Squamous Cell Carcinoma.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2019, 2019

Identifying Symptom Clusters in Breast Cancer and Colorectal Cancer Patients using EHR Data.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018
Identification of topological features in renal tumor microenvironment associated with patient survival.
Bioinform., 2018

Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Session introduction.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Ordinal Multi-modal Feature Selection for Survival Analysis of Early-Stage Renal Cancer.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, 2018

Learning to Parse Wireframes in Images of Man-Made Environments.
Proceedings of the 2018 IEEE Conference on Computer Vision and Pattern Recognition, 2018

Genetic Mutations Associated with Histopathology Changes in Kidney Cancer.
Proceedings of the AMIA 2018, 2018

2017
Predictive models for pressure ulcers from intensive care unit electronic health records using Bayesian networks.
BMC Medical Informatics Decis. Mak., 2017

annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.
Bioinform., 2017

Spatiotemporal Visualization of Gene Expression in the Developing Mouse Brain.
Proceedings of the 19th Eurographics Conference on Visualization, 2017

Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Open Data for Discovery Science.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes.
PLoS Comput. Biol., 2016

Precision Medicine: What Challenges Are We Facing?
Genom. Proteom. Bioinform., 2016

Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types.
BMC Bioinform., 2016

Session Introduction.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015
GRAPHIE: graph based histology image explorer.
BMC Bioinform., December, 2015

Guest Editors Introduction to the Special Issue on Software and Databases.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Identify Critical Genes in Development with Consistent H3K4me2 Patterns across Multiple Tissues.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

MICA: MicroRNA integration for active module discovery.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014
Visualizing Multidimensional Data with Glyph SPLOMs.
Comput. Graph. Forum, 2014

2013 IEEE Scientific Visualization Contest Winner: Observing Genomics and Phenotypical Patterns in the Developing Mouse Brain.
IEEE Computer Graphics and Applications, 2014

iGPSe: A visual analytic system for integrative genomic based cancer patient stratification.
BMC Bioinform., 2014

Mining massive SNP data for identifying associated SNPs and uncovering gene relationships.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013
Research and applications: Identifying survival associated morphological features of triple negative breast cancer using multiple datasets.
J. Am. Medical Informatics Assoc., 2013

Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis.
Int. J. Comput. Biol. Drug Des., 2013

Identify condition-specific gene co-expression networks.
Int. J. Comput. Biol. Drug Des., 2013

2012
Transactional Database Transformation and Its Application in Prioritizing Human Disease Genes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability.
PLoS Comput. Biol., 2012

Merging network patterns: a general framework to summarize biomedical network data.
Netw. Model. Anal. Health Informatics Bioinform., 2012

k-Neighborhood decentralization: A comprehensive solution to index the UMLS for large scale knowledge discovery.
J. Biomed. Informatics, 2012

A dynamic time order network for time-series gene expression data analysis.
BMC Syst. Biol., 2012

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.
BMC Bioinform., 2012

Visualizing Clusters in Parallel Coordinates for Visual Knowledge Discovery.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2012

Non parametric cell nuclei segmentation based on a tracking over depth from 3D fluorescence confocal images.
Proceedings of the 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2012

2011
Comparing Multiple Chip-Sequencing Experiments.
J. Bioinform. Comput. Biol., 2011

Non-parametric Population Analysis of Cellular Phenotypes.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2011, 2011

Detecting cellular events in brain cortex using time-lapse microscopy.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

Parallel Automatic Registration of Large Scale Microscopic Images on Multiprocessor CPUs and GPUs.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011

Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation.
Proceedings of the 2011 IEEE International Conference on Healthcare Informatics, 2011

Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

Predicting Parkinson's disease related genes using frequent gene co-expression analysis.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

Identifying smoking associated gene co-expression networks related to oral cancer initiation.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia.
BMC Bioinform., 2010

Multi-dimensional discovery of biomarker and phenotype complexes.
BMC Bioinform., 2010

Two-point correlation as a feature for histology images: Feature space structure and correlation updating.
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2010

2009
Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors.
J. Signal Process. Syst., 2009

Tensor classification of N-point correlation function features for histology tissue segmentation.
Medical Image Anal., 2009

Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging.
Medical Image Anal., 2009

Feature-based registration of histopathology images with different stains: An application for computerized follicular lymphoma prognosis.
Comput. Methods Programs Biomed., 2009

Comparative study on ChIP-seq data: normalization and binding pattern characterization.
Bioinform., 2009

Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer Prognosis.
Proceedings of the International Joint Conferences on Bioinformatics, 2009

A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments.
Proceedings of the Bioinformatics and Computational Biology, 2009

Clinical Attribute Network for Chronic Lymphocytic Leukemia.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

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.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008
Reconstruction of Cellular Biological Structures from Optical Microscopy Data.
IEEE Trans. Vis. Comput. Graph., 2008

An imaging workflow for characterizing phenotypical change in large histological mouse model datasets.
J. Biomed. Informatics, 2008

Geometry-driven Visualization of Microscopic Structures in Biology.
Comput. Graph. Forum, 2008

Geometry-driven visualization of microscopic structures in biology.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

2007
Detection and Visualization of Surface-Pockets to Enable Phenotyping Studies.
IEEE Trans. Medical Imaging, 2007

Volume Rendering Phenotype Differences in Mouse Placenta Microscopy Data.
Comput. Sci. Eng., 2007

Multi-Resolution Image Segmentation Using the 2-Point Correlation Functions.
Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2007

The GPU on biomedical image processing for color and phenotype analysis.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Multiscale Hybrid Linear Models for Lossy Image Representation.
IEEE Trans. Image Process., 2006

Registration and 3D visualization of large microscopy images.
Proceedings of the Medical Imaging 2006: Image Processing, 2006

Automatic registration of large set of microscopic images using high-level features.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006

Spatial Segmentation of Temporal Texture Using Mixture Linear Models.
Proceedings of the Dynamical Vision, ICCV 2005 and ECCV 2006 Workshops, 2006

2005
XML database support for distributed execution of data-intensive scientific workflows.
SIGMOD Rec., 2005

Symmetry-based photo-editing.
Pattern Recognit., 2005

Symmetry-based 3-D reconstruction from perspective images.
Comput. Vis. Image Underst., 2005

Supporting Large Scale Medical and Scientific Datasets.
Proceedings of the Parallel Computing: Current & Future Issues of High-End Computing, 2005

A Multi-Scale Hybrid Linear Model for Lossy Image Representation.
Proceedings of the 10th IEEE International Conference on Computer Vision (ICCV 2005), 2005

2004
Rank Conditions on the Multiple-View Matrix.
Int. J. Comput. Vis., 2004

On Symmetry and Multiple-View Geometry: Structure, Pose, and Calibration from a Single Image.
Int. J. Comput. Vis., 2004

Large-baseline Matching and Reconstruction from Symmetry Cells.
Proceedings of the 2004 IEEE International Conference on Robotics and Automation, 2004

Sparse representation of images with hybrid linear models.
Proceedings of the 2004 International Conference on Image Processing, 2004

Tools for efficient subsetting and pipelined processing of large scale, distributed biomedical image data.
Proceedings of the Grid Computing: The New Frontier of High Performance Computing [post-proceedings of the High Performance Computing Workshop, 2004

Minimum Effective Dimension for Mixtures of Subspaces: A Robust GPCA Algorithm and Its Applications.
Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2004), with CD-ROM, 27 June, 2004

Identification of hybrid linear time-invariant systems via subspace embedding and segmentation (SES).
Proceedings of the 43rd IEEE Conference on Decision and Control, 2004

2003
Geometric Segmentation of Perspective Images Based on Symmetry Groups.
Proceedings of the 9th IEEE International Conference on Computer Vision (ICCV 2003), 2003

2002
Generalized Rank Conditions in Multiple View Geometry with Applications to Dynamical Scenes.
Proceedings of the Computer Vision, 2002


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