BioMeCIS Lab @ UTA

OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases.

Nhat Tran, Jean Gao

Journal of Open Source Software · 09 May 2021

software

Package Docs Source

Renormalized Normalized Maximum Likelihood and Three-Part Code Criteria For Learning Gaussian Networks

Borzou Alipourfard, Jean X. Gao

arXiv · 29 Dec 2020

preprint

Solving All Regression Models For Learning Gaussian Networks Using Givens Rotations

Borzou Alipourfard, Jean X. Gao

arXiv · 29 Dec 2020

preprint

Layer-stacked Attention for Heterogeneous Network Embedding

Nhat Tran, Jean Gao

arXiv · 18 Sep 2020

preprint

Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of Diverse Multi-omics, Interactions, and Annotations Data

Nhat Tran, Jean Gao

Pacific Symposium on Biocomputing · 01 Dec 2019

conference

MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers

Nhat Tran, Vinay Abhyankar, KyTai Nguyen, Jon Weidanz, Jean Gao

BMC Bioinformatics · 21 Dec 2018

journal

One-step fabrication of flexible nanotextured PDMS as a substrate for selective cell capture

Mohammad R Hasan, Sai Santosh Sasank Peri, Viraj P Sabane, Nuzhat Mansur, Jean X Gao, Kytai T Nguyen, Jon A Weidanz, Samir M Iqbal, Vinay V Abhyankar

Biomedical Physics & Engineering Express · 22 Jan 2018

journal

Stable solution to l 2,1-based robust inductive matrix completion and its application in linking long noncoding RNAs to human diseases

Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, Chris Ding, Jean X. Gao

BMC Medical Genomics · 28 Dec 2017

journal

Multi-Block Bipartite Graph for Integrative Genomic Analysis

Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis K. Biswas, Chunyu Liu, Jean Gao

IEEE/ACM Transactions on Computational Biology and Bioinformatics · 01 Nov 2017

journal

Robust Inductive Matrix Completion strategy to explore associations between lincRNAs and human disease phenotypes

Ashis Kumer Biswas, Dong-Chul Kim, Mingon Kang, Jean X. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2016

conference

Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice

Mingon Kang, Liping Tang, Jean Gao

BMC Bioinformatics · 29 Feb 2016

journal

Inferring causal molecular networks: empirical assessment through a community-based effort

Steven M Hill, Laura M Heiser, Thomas Cokelaer, Michael Unger, Nicole K Nesser, Daniel E Carlin, Yang Zhang, Artem Sokolov, Evan O Paull, Chris K Wong, Kiley Graim, Adrian Bivol, Haizhou Wang, Fan Zhu, Bahman Afsari, Ludmila V Danilova, Alexander V Favorov, Wai Shing Lee, Dane Taylor, Chenyue W Hu, Byron L Long, David P Noren, Alexander J Bisberg, Gordon B Mills, Joe W Gray, Michael Kellen, Thea Norman, Stephen Friend, Amina A Qutub, Elana J Fertig, Yuanfang Guan, Mingzhou Song, Joshua M Stuart, Paul T Spellman, Heinz Koeppl, Gustavo Stolovitzky, Julio Saez-Rodriguez, Sach Mukherjee,

Nature Methods · 22 Feb 2016

journal

Which patellofemoral joint imaging features are associated with patellofemoral pain? Systematic review and meta-analysis

B.T. Drew, A.C. Redmond, T.O. Smith, F. Penny, P.G. Conaghan

Osteoarthritis and Cartilage · 01 Feb 2016

journal

An integrative genomic study for multimodal genomic data using multi-block bipartite graph

Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis K. Biswas, Chunyu Liu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2015

conference

Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to Psychiatric disorders

Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2015

conference

Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization

Ashis Kumer Biswas, Mingon Kang, Dong-Chul Kim, Chris H. Q. Ding, Baoju Zhang, Xiaoyong Wu, Jean X. Gao

Network Modeling Analysis in Health Informatics and Bioinformatics · 11 Jun 2015

journal

eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways

Mingon Kang, Chunling Zhang, Hyung-Wook Chun, Chris Ding, Chunyu Liu, Jean Gao

Bioinformatics · 01 Mar 2015

journal

Probabilistic partial least squares regression for quantitative analysis of Raman spectra

Shuo Li, James O. Nyagilo, Digant P. Dave, Wei Wang, Baoju Zhang, Jean Gao

International Journal of Data Mining and Bioinformatics · 01 Jan 2015

journal

NMF-Based LncRNA-Disease Association Inference and Bi-Clustering

Ashis Kumer Biswas, Jean X. Gao, Baoju Zhang, Xiaoyong Wu

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2014

conference

Multi-block and Multi-task Learning for Integrative Genomic Study

Mingon Kang, Dong-Chul Kim, Chunyu Liu, Baoju Zhang, Xiaoyong Wu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2014

conference

Integration of DNA Methylation, Copy Number Variation, and Gene Expression for Gene Regulatory Network Inference and Application to Psychiatric Disorders

Dong-Chul Kim, Mingon Kang, Baoju Zhang, Xiaoyong Wu, Chunyu Liu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2014

conference

Models and Methods for Quantitative Analysis of Surface-Enhanced Raman Spectra

Shuo Li, James O. Nyagilo, Digant P. Dave, Jean Gao

IEEE Journal of Biomedical and Health Informatics · 01 Mar 2014

journal

Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations

Dong-Chul Kim, Jiao Wang, Chunyu Liu, Jean Gao

BioMed Research International · 01 Jan 2014

journal

eQTL Mapping Study via Regularized Sparse Canonical Correlation Analysis

Mingon Kang, Shuo Li, Dongchul Kim, Chunyu Liu, Baoju Zhang, Xiaoyong Wu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2013

conference

Inference of gene regulatory networks by integrating gene expressions and genetic perturbations

Dong-Chul Kim, Chunyu Liu, Xiaoyong Wu, Baoju Zhang, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2013

conference

eQTL epistasis: Detecting complex interaction effects between multiple loci from eQTL data

Mingon Kang, Shuo Li, Chunyu Liu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2013

conference

QLZCClust: Quaternary lempel-Ziv complexity based clustering of the RNA-seq read block segments

Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu, Jean X. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2013

conference

CNCTDISCRIMINATOR: CODING AND NONCODING TRANSCRIPT DISCRIMINATOR — AN EXCURSION THROUGH HYPOTHESIS LEARNING AND ENSEMBLE LEARNING APPROACHES

ASHIS KUMER BISWAS, BAOJU ZHANG, XIAOYONG WU, JEAN X. GAO

Journal of Bioinformatics and Computational Biology · 16 Oct 2013

journal

Continuous Wavelet Transform Based Partial Least Squares Regression for Quantitative Analysis of Raman Spectrum

Shuo Li, James O. Nyagilo, Digant P. Dave, Jean X. Gao

IEEE Transactions on NanoBioscience · 01 Sep 2013

journal

Eigenspectra, a robust regression method for multiplexed Raman spectra analysis

Shuo Li, James O. Nyagilo, Digant P. Dave, Baoju Zhang, Jean Gao

International Journal of Data Mining and Bioinformatics · 01 Jan 2013

journal

Nonlinear RANSAC Optimization for Parameter Estimation with Applications to Phagocyte Transmigration

Mingon Kang, Jean Gao, Liping Tang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2011

conference

Fast Kernel Discriminant Analysis for Classification of Liver Cancer Mass Spectra

Jung Hun Oh, Jean Gao

IEEE/ACM Transactions on Computational Biology and Bioinformatics · 01 Nov 2011

journal

A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity

Dong-Chul Kim, Jean Gao, Xiaoyu Wang, Chin-Rang Yang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2011

conference

A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity

Dong-Chul Kim, Jean Gao, Xiaoyu Wang, Chin-Rang Yang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2011

conference

Probabilistic Partial Least Square Regression: A Robust Model for Quantitative Analysis of Raman Spectroscopy Data

Shuo Li, Jean Gao, James O. Nyagilo, Digant P. Dave

Institute of Electrical and Electronics Engineers (IEEE) · 01 Nov 2011

conference

Discovery of lung cancer pathways using Reverse Phase Protein Microarray and prior-knowledge based Bayesian networks

Dong-Chul Kim, Chin-Rang Yang, Xiaoyu Wang, Baoju Zhang, Xiaorong Wu, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Aug 2011

conference

Subcellular particles tracking in time-lapse confocal microscopy images

Shuo Li, K. Luby-Phelps, Baoju Zhang, Xiaorong Wu, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Aug 2011

conference

Branch-and-Bound for Model Selection and Its Computational Complexity

Ninad Thakoor, Jean Gao

IEEE Transactions on Knowledge and Data Engineering · 01 May 2011

journal

Eigenspectra, a robust regression method for multiplexed Raman spectra analysis

Shuo Li, Jean Gao, James O Nyagilo, Digant P Dave

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2010

conference

Computational modeling of phagocyte transmigration during biomaterial-mediated foreign body responses

Mingon Kang, Jean X. Gao, Liping Tang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Dec 2010

conference

Multibody Structure-and-Motion Segmentation by Branch-and-Bound Model Selection

Ninad Thakoor, Jean Gao, Venkat Devarajan

IEEE Transactions on Image Processing · 01 Jun 2010

journal

Learning biological network using mutual information and conditional independence

Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang, Jean Gao

BMC Bioinformatics · 29 Apr 2010

journal

Learning Proteomic Network Structure by a New Hill Climbing Algorithm

Dong-Chul Kim, Jean Gao, Chin-Rang Yang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2010

conference

Motion detection for subcellular structure trafficking

H. Iwaki, A. Kosaka, Shuo Li, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Sep 2009

conference

A kernel-based approach for detecting outliers of high-dimensional biological data

Jung Hun Oh, Jean Gao

BMC Bioinformatics · 29 Apr 2009

journal

An Extended Markov Blanket Approach to Proteomic Biomarker Detection From High-Resolution Mass Spectrometry Data

Jung Hun Oh, P. Gurnani, J. Schorge, K.P. Rosenblatt, J.X. Gao

IEEE Transactions on Information Technology in Biomedicine · 01 Mar 2009

journal

Multistage Branch-and-Bound Merging for Planar Surface Segmentation in Disparity Space

N. Thakoor, J. Gao, V. Devarajan

IEEE Transactions on Image Processing · 01 Nov 2008

journal

Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data

J. H. Oh, Y. B. Kim, P. Gurnani, K. P. Rosenblatt, J. X. Gao

Bioinformatics · 18 Jun 2008

journal

Branch-and-bound hypothesis selection for two-view multiple structure and motion segmentation

Ninad Thakoor, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jun 2008

conference

Wireless Sensor Network Lifetime Analysis Using Interval Type-2 Fuzzy Logic Systems

Haining Shu, Qilian Liang, Jean Gao

IEEE Transactions on Fuzzy Systems · 01 Apr 2008

journal

Application of Targeted Quantitative Proteomics Analysis in Human Cerebrospinal Fluid Using a Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Tandem Mass Spectrometer (LC MALDI TOF/TOF) Platform

Sheng Pan, John Rush, Elaine R. Peskind, Douglas Galasko, Kathryn Chung, Joseph Quinn, Joseph Jankovic, James B. Leverenz, Cyrus Zabetian, Catherine Pan, Yan Wang, Jung Hun Oh, Jean Gao, Jianpeng Zhang, Thomas Montine, Jing Zhang

Journal of Proteome Research · 11 Jan 2008

journal

Four-Dimensional Vascular Tree Reconstruction Using Moving Grid Deformation

Jiaxing Xue, Gary Arbique, Dan Hatef, Spencer Brown, Michel Saint-Cyr, Jean X. Gao

Academic Radiology · 01 Dec 2007

journal

Hidden Markov Model-Based Weighted Likelihood Discriminant for 2-D Shape Classification

Ninad Thakoor, Jean Gao, Sungyong Jung

IEEE Transactions on Image Processing · 01 Nov 2007

journal

Biomarker Selection for Predicting Alzheimer Disease Using High-Resolution MALDI-TOF Data

Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Oct 2007

conference

Phagocyte Transmigration Modeling Using System Dynamic Controls

Jiaxing Xue, Jean Gao, Liping Tang

Institute of Electrical and Electronics Engineers (IEEE) · 01 Oct 2007

conference

Tracking Interacting Subcellular Structures By Sequential Monte Carlo Method

Quan Wen, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Aug 2007

conference

Tracking Interacting Subcellular Structures By Sequential Monte Carlo Method

Quan Wen, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Aug 2007

conference

Three dimensional analysis of the vascular perfusion for anterolateral thigh perforator flaps

Jiaxing Xue, Jean Gao, Gary Arbique, Michel Saint-Cyr, Dan Hatef, Spencer Brown

SPIE-Intl Soc Optical Eng · 08 Mar 2007

conference

A Statistical Approach for Intensity Loss Compensation of Confocal Microscopy Images

Sowmya Gopinath, Ninad Thakoor, Jean Gao, Kate Luby-Phelps

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2007

journal

Defining Vascular Supply and Territory of Thinned Perforator Flaps: Part II. Superior Gluteal Artery Perforator Flap

Kimihiro Nojima, Spencer A. Brown, Cengiz Acikel, Jeffrey Janis, Gary Arbique, Tarek Abulezz, Jean Gao, Quan Wen, Kunihiro Kurihara, Rod J. Rohrich

Plastic and Reconstructive Surgery · 01 Nov 2006

journal

Peptide Identification by Tandem Mass Spectra: An Efficient Parallel Searching

Jung Hun Oh, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 11 Oct 2006

conference

A New Hybrid Approach for Unsupervised Gene Selection

Young Bun Kim, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Sep 2006

conference

Feature Selection, Matching, and Evaluation for Subcellular Structure Tracking

Quan Wen, Jean Gao, Kate Luby-Phelps

Institute of Electrical and Electronics Engineers (IEEE) · 01 Aug 2006

conference

A multi-Kalman filtering approach for video tracking of human-delineated objects in cluttered environments

Jean Gao, Akio Kosaka, Avinash C. Kak

Computer Vision and Image Understanding · 01 Jun 2006

journal

New Discoveries of Image Display Size on Observer Performance

Jean Gao

Academic Radiology · 01 Apr 2006

journal

Occlusion Resistant Shape Classifier based onWarped Optimal Path Matching

N. Thakoor, Sungyong Jung, Quan Wen, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2006

conference

A New Maximum-Relevance Criterion for Significant Gene Selection

Young Bun Kim, Jean Gao, Pawel Michalak

Lecture Notes in Computer Science · 01 Jan 2006

conference

Occlusion Resistant Shape Classifier based onWarped Optimal Path Matching

N. Thakoor, Sungyong Jung, Quan Wen, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2006

conference

Markov Chain Monte Carlo Data Association for Merge and Split Detection in Tracking Protein Clusters

Quan Wen, Jean Gao, K. Luby-Phelps

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2006

conference

Unsupervised Gene Selection For High Dimensional Data

Young Kim, Jean Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2006

conference

A Deformable Model for Automatic CT Liver Extraction1

Jean Gao, Akio Kosaka, Avinash Kak

Academic Radiology · 01 Sep 2005

journal

A TWO-WAY SEARCHING ALGORITHM FOR DE NOVO PEPTIDE SEQUENCING VIA TANDEM MASS SPECTROMETRY

JUNG HUN OH, YOUNG BUN KIM, JEAN GAO

World Scientific Pub Co Pte Ltd · 01 May 2005

journal

A TWO-WAY SEARCHING ALGORITHM FOR DE NOVO PEPTIDE SEQUENCING VIA TANDEM MASS SPECTROMETRY

JUNG HUN OH, YOUNG BUN KIM, JEAN GAO

World Scientific Pub Co Pte Ltd · 01 May 2005

conference

EMERGING PATTERN BASED SUBSPACE CLUSTERING OF MICROARRAY GENE EXPRESSION DATA USING MIXTURE MODELS

YOUNG BUN KIM, JUNG HUN OH, JEAN GAO

World Scientific Pub Co Pte Ltd · 01 May 2005

conference

Shape-based 3D vascular tree extraction for perforator flaps

Quan Wen, Jean Gao

SPIE-Intl Soc Optical Eng · 29 Apr 2005

conference

Diagnosis of Early Relapse in Ovarian Cancer Using Serum Proteomic Profiling

Jung Hun Oh, Jean Gaol, Animesh Nandi, Prem Gurnani, Lynne Knowles, John Schorge, Kevin P. Rosenblatt

Genome Informatics · 01 Jan 2005

journal

Automatic video object shape extraction and its classification with camera in motion

N. Thakoor, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2005

conference

Multicategory Classification using Extended SVM-RFE and Markov Blanket on SELDI-TOF Mass Spectrometry Data

Jung Hun Oh, J. Gao, A. Nandi, P. Gurnani, L. Knowles, J. Schorge, K.P. Rosenblatt

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2005

conference

Shape classifier based on generalized probabilistic descent method with hidden Markov descriptor

N. Thakoor, J. Gao

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2005

conference

A particle filter framework using optimal importance function for protein molecules tracking

Q. Wen, J. Gao, A. Kosaka, H. Iwaki, K. Luby-Phelps, D. Mundy

Institute of Electrical and Electronics Engineers (IEEE) · 01 Jan 2005

conference

Publications

2021

2020

2019

2018

2017

2016

2015

2014

2013

2011

2010

2009

2008

2007

2006

2005