Iterative normalization of cDNA microarray data. - Yue Joseph Wang; Jianping Lu; Richard Lee 002; Zhiping Gu; Robert Clarke (IEEE Trans. Inf. Technol. Biomed., 2002)

Partially-independent component analysis for tissue heterogeneity correction in microarray gene expression analysis. - Yue Joseph Wang; Junying Zhang; Javed I. Khan; Robert Clarke; Zhiping Gu (NNSP, 2003)

Discriminatory Mining of Gene Expression Microarray Data. - Zuyi Wang; Yue Joseph Wang; Jianping Lu; Sun-Yuan Kung; Junying Zhang; Richard Lee 002; Jianhua Xuan; Javed I. Khan; Robert Clarke (J. VLSI Signal Process., 2003)

Robust Feature Selection by Weighted Fisher Criterion for Multiclass Prediction in Gene Expression Profiling. - Jianhua Xuan; Yibin Dong; Javed I. Khan; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (ICPR (2), 2004)

Gene selection in class space for molecular classification of cancer. - Junying Zhang; Yue Joseph Wang; Javed I. Khan; Robert Clarke (Sci. China Ser. F Inf. Sci., 2004)

Gene Selection by Weighted Fisher criterion for Multiclass Prediction. - Jianhua Xuan; Yibin Dong; Javed I. Khan; Robert Clarke; Eric P. Hoffman; Yue Wang 021 (Advances in Bioinformatics and Its Applications, 2005)

Normalization of Microarray Data by Iterative Nonlinear Regression. - Jianhua Xuan; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (BIBE, 2005)

Secure Mutual Distrust Transaction Tracking Using Cryptographic Elements. - Angela S. L. Wong; Matthew Sorell; Robert Clarke (IWDW, 2005)

ModVis: An information visualization tool for gene module discovery. - Justin Molineaux; Jianhua Xuan; Ting Gong; Yitan Zhu; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (CAINE, 2006)

Inference of Gene Regulatory Networks from Time Course Gene Expression Data Using Neural Networks and Swarm Intelligence. - Habtom W. Ressom; Yuji Zhang 001; Jianhua Xuan; Yue Joseph Wang; Robert Clarke (CIBCB, 2006)

Latent Variable and nICA Modeling of Pathway Gene Module Composite. - Ting Gong; Yitan Zhu; Jianhua Xuan; Huai Li; Robert Clarke; Eric P. Hoffman; Yue Wang 021 (EMBC, 2006)

Inferring Network Interactions Using Recurrent Neural Networks and Swarm Intelligence. - Habtom W. Ressom; Yuji Zhang 001; Jianhua Xuan; Yue Wang 021; Robert Clarke (EMBC, 2006)

Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data. - Zuyi Wang; Yue Joseph Wang; Jianhua Xuan; Yibin Dong; Marina Bakay; Yuanjian Feng; Robert Clarke; Eric P. Hoffman (Bioinform., 2006)

Stability-Based Dimension Estimation of ICA with Application to Microarray Data Analysis. - Chen Wang 001; Jianhua Xuan; Ting Gong; Robert Clarke; Eric P. Hoffman; Yue Joseph Wang (BIOCOMP, 2007)

Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis. - Li Chen 018; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman; Jianhua Xuan (ICMLA, 2007)

VISDA: an open-source caBIGTM analytical tool for data clustering and beyond. - Jiajing Wang; Huai Li; Yitan Zhu; Malik Yousef; Michael Nebozhyn; Michael M. Showe; Louise C. Showe; Jianhua Xuan; Robert Clarke; Yue Joseph Wang (Bioinform., 2007)

Gene Selection for Multiclass Prediction by Weighted Fisher Criterion. - Jianhua Xuan; Yue Joseph Wang; Yibin Dong; Yuanjian Feng; Bin Wang 064; Javed I. Khan; Marina Bakay; Zuyi Wang; Lauren Pachman; Sara Winokur; Yi-Wen Chen; Robert Clarke; et al. (EURASIP J. Bioinform. Syst. Biol., 2007)

Annotating breast cancer microarray samples using ontologies. - Hongfang Liu; Xin Li; Victoria Y. Yoon; Robert Clarke (AMIA, 2008)

Reliability Analysis of Transcriptional Regulatory Networks. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Eric P. Hoffman; Robert Clarke (BCBGC, 2008)

Inferring Condition-Specific miRNA-Gene Modules from miRNA and mRNA Profiling Data. - Jianghui Xiong; Chen Wang 001; Bai Zhang; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke; Jianhua Xuan (BCBGC, 2008)

Identification of Condition-specific Regulatory Modules by Multi-level Motif and mRNA Expression Analysis. - Li Chen 018; Jianhua Xuan; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (BIOCOMP, 2008)

Exploring Transcriptional Modules Through Integrative Gene Clustering Guided by Transcription Factor Binding Information. - Ting Gong; Jianhua Xuan; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (BIOCOMP, 2008)

Reverse Engineering Module Networks by PSO-RNN Hybrid Modeling. - Yuji Zhang 001; Jianhua Xuan; Benildo de los Reyes; Robert Clarke; Habtom W. Ressom (BIOCOMP, 2008)

Network-Constrained Support Vector Machine for Classification. - Li Chen 018; Jianhua Xuan; Yue Joseph Wang; Rebecca B. Riggins; Robert Clarke (ICMLA, 2008)

Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information. - Ting Gong; Jianhua Xuan; Li Chen 018; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (ISBRA, 2008)

Integrative Network Component Analysis for Regulatory Network Reconstruction. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Po Zhao; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman (ISBRA, 2008)

Knowledge-guided multi-scale independent component analysis for biomarker identification. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Ie-Ming Shih; Yue Joseph Wang; Zhen Zhang; Eric P. Hoffman; Robert Clarke (BMC Bioinform., 2008)

Motif-directed network component analysis for regulatory network inference. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Po Zhao; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman (BMC Bioinform., 2008)

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. - Yuji Zhang 001; Jianhua Xuan; Benildo de los Reyes; Robert Clarke; Habtom W. Ressom (BMC Bioinform., 2008)

caBIGTM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data. - Yitan Zhu; Huai Li; David J. Miller 001; Zuyi Wang; Jianhua Xuan; Robert Clarke; Eric P. Hoffman; Yue Joseph Wang (BMC Bioinform., 2008)

A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction Networks. - Ting Gong; Jianhua Jason Xuan; Rebecca B. Riggins; Robert Clarke (IJCBS, 2009)

Differential dependency network analysis to identify condition-specific topological changes in biological networks. - Bai Zhang; Huai Li; Rebecca B. Riggins; Ming Zhan; Jianhua Xuan; Zhen Zhang; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (Bioinform., 2009)

Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. - Li Chen 018; Jianhua Xuan; Yue Joseph Wang; Eric P. Hoffman; Rebecca B. Riggins; Robert Clarke (Int. J. Comput. Biol. Drug Des., 2009)

Biomarker identification by knowledge-driven multilevel ICA and motif analysis. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Yue Joseph Wang; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Robert Clarke; Eric P. Hoffman (Int. J. Data Min. Bioinform., 2009)

Module-based biomarker discovery in breast cancer. - Yuji Zhang 001; Jianhua Jason Xuan; Robert Clarke; Habtom W. Ressom (BIBM, 2010)

Identification of Transcriptional Regulatory Networks by Learning the Marginal Function of Outlier Sum Statistic. - Jinghua Gu; Jianhua Xuan; Yue Joseph Wang; Rebecca B. Riggins; Robert Clarke (ICMLA, 2010)

Multilevel support vector regression analysis to identify condition-specific regulatory networks. - Li Chen 018; Jianhua Xuan; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (Bioinform., 2010)

Knowledge-guided gene ranking by coordinative component analysis. - Chen Wang 001; Jianhua Xuan; Huai Li; Yue Joseph Wang; Ming Zhan; Eric P. Hoffman; Robert Clarke (BMC Bioinform., 2010)

Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases. - Guoqiang Yu; Yuanjian Feng; David J. Miller 001; Jianhua Xuan; Eric P. Hoffman; Robert Clarke; Ben Davidson; Ie-Ming Shih; Yue Joseph Wang (J. Mach. Learn. Res., 2010)

GIST: A Gibbs sampler to identify intracellular signal transduction pathways. - Jinghua Gu; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Yue Wang 021; Robert Clarke; Jianhua Xuan (EMBC, 2011)

PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. - Guoqiang Yu; Huai Li; Sook Shin Ha; Ie-Ming Shih; Robert Clarke; Eric P. Hoffman; Subha Madhavan; Jianhua Xuan; Yue Joseph Wang (Bioinform., 2011)

DDN: a caBIG® analytical tool for differential network analysis. - Bai Zhang; Ye Tian; Lu Jin; Huai Li; Ie-Ming Shih; Subha Madhavan; Robert Clarke; Eric P. Hoffman; Jianhua Xuan; Leena Hilakivi-Clarke; Yue Joseph Wang (Bioinform., 2011)

Motif-guided sparse decomposition of gene expression data for regulatory module identification. - Ting Gong; Jianhua Xuan; Li Chen 018; Rebecca B. Riggins; Huai Li; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (BMC Bioinform., 2011)

Identifying cancer biomarkers by network-constrained support vector machines. - Li Chen 018; Jianhua Xuan; Rebecca B. Riggins; Robert Clarke; Yue Joseph Wang (BMC Syst. Biol., 2011)

Accurate identification of significant aberrations in contaminated cancer genome. - Xuchu Hou; Guoqiang Yu; Xiguo Yuan; Bai Zhang; Ie-Ming Shih; Zhen Zhang; Robert Clarke; Subha Madhavan (GENSiPS, 2012)

Sampling-Based Subnetwork Identification from Microarray Data and Protein-Protein Interaction Network. - Xiao Wang 031; Jinghua Gu; Jianhua Xuan; Ayesha N. Shajahan; Robert Clarke; Li Chen 018 (ICMLA (2), 2012)

Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis. - Xi Chen 056; Chen Wang 001; Ayesha N. Shajahan; Rebecca B. Riggins; Robert Clarke; Jianhua Xuan (ISBRA, 2012)

Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. - Chen Wang 001; Jianhua Xuan; Ie-Ming Shih; Robert Clarke; Yue Joseph Wang (Signal Process., 2012)

Reconstructing transcriptional regulatory networks by probabilistic network component analysis. - Jinghua Gu; Jianhua Xuan; Xiao Wang 031; Ayesha N. Shajahan; Leena Hilakivi-Clarke; Robert Clarke (BCB, 2013)

A novel statistical approach to identify co-regulatory gene modules. - Xi Chen 056; Jianhua Xuan; Xu Shi; Ayesha N. Shajahan-Haq; Leena Hilakivi-Clarke; Robert Clarke (BIBM, 2013)

Commercial aspects of contract cheating. - Robert Clarke; Thomas Lancaster (ITiCSE, 2013)

mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks. - Xu Shi; Jinghua Gu; Xi Chen 056; Ayesha N. Shajahan; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (BMC Syst. Biol., 2013)

Module-based breast cancer classification. - Yuji Zhang 001; Jianhua Xuan; Robert Clarke; Habtom W. Ressom (Int. J. Data Min. Bioinform., 2013)

The CAM software for nonnegative blind source separation in R-Java. - Niya Wang; Fan Meng; Li Chen 018; Subha Madhavan; Robert Clarke; Eric P. Hoffman; Jianhua Xuan; Yue Joseph Wang (J. Mach. Learn. Res., 2013)

Reconstruction of Transcriptional Regulatory Networks by Stability-Based Network Component Analysis. - Xi Chen 056; Jianhua Xuan; Chen Wang 001; Ayesha N. Shajahan; Rebecca B. Riggins; Robert Clarke (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

An Initial Analysis of the Contextual Information Available within Auction Posts on Contract Cheating Agency Websites. - Thomas Lancaster; Robert Clarke (AINA Workshops, 2014)

Statistical Identification of Co-regulatory Gene Modules using Multiple ChIP-Seq Experiments. - Xi Chen 056; Xu Shi; Ayesha N. Shajahan-Haq; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (BIOINFORMATICS, 2014)

A Markov random field-based Bayesian model to identify genes with differential methylation. - Xiao Wang 031; Jinghua Gu; Jianhua Xuan; Robert Clarke; Leena Hilakivi-Clarke (CIBCB, 2014)

An Observational Analysis of the Range and Extent of Contract Cheating from Online Courses Found on Agency Websites. - Thomas Lancaster; Robert Clarke (CISIS, 2014)

BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. - Xi Chen 056; Xu Shi; Ayesha N. Shajahan; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (EMBC, 2014)

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. - Jinghua Gu; Jianhua Xuan; Rebecca B. Riggins; Li Chen 018; Yue Joseph Wang; Robert Clarke (Bioinform., 2014)

AISAIC: a software suite for accurate identification of significant aberrations in cancers. - Bai Zhang; Xuchu Hou; Xiguo Yuan; Ie-Ming Shih; Zhen Zhang; Robert Clarke; Roger R. Wang; Yi Fu; Subha Madhavan; Yue Joseph Wang; Guoqiang Yu (Bioinform., 2014)

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data. - Jinghua Gu; Xiao Wang 031; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (BMC Bioinform., 2014)

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (BMC Syst. Biol., 2014)

Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses. - Ye Tian; Sean S. Wang; Zhen Zhang; Olga C. Rodriguez; Emanuel Petricoin III; Ie-Ming Shih; Daniel Chan; Maria Avantaggiati; Guoqiang Yu; Shaozhen Ye; Robert Clarke; Chao Wang 005; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. - Xu Shi; Robert O. Barnes; Li Chen 018; Ayesha N. Shajahan-Haq; Leena Hilakivi-Clarke; Robert Clarke; Yue Joseph Wang; Jianhua Xuan (Bioinform., 2015)

KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (Bioinform., 2015)

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. - Niya Wang; Ting Gong; Robert Clarke; Lulu Chen; Ie-Ming Shih; Zhen Zhang; Douglas A. Levine; Jianhua Xuan; Yue Joseph Wang (Bioinform., 2015)

Risk prediction for cardiovascular disease using ECG data in the China kadoorie biobank. - Yanting Shen; Yang Yang 125; Sarah Parish; Zhengming Chen; Robert Clarke; David A. Clifton (EMBC, 2016)

G-DOC Plus - an integrative bioinformatics platform for precision medicine. - Krithika Bhuvaneshwar; Anas Belouali; Varun Singh; Robert M. Johnson; Lei Song; Adil Alaoui; Michael Harris; Robert Clarke; Louis M. Weiner; Yuriy Gusev; Subha Madhavan (BMC Bioinform., 2016)

Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants. - Ibrahim Youssef; Robert Clarke; Ie-Ming Shih; Yue Joseph Wang; Guoqiang Yu (Comput. Biol. Medicine, 2016)

PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. - Xi Chen 056; Xu Shi; Leena Hilakivi-Clarke; Ayesha N. Shajahan-Haq; Robert Clarke; Jianhua Xuan (Bioinform., 2017)

DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. - Xiao Wang 031; Jinghua Gu; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (Bioinform., 2017)

CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. - Xi Chen 056; Jinghua Gu; Xiao Wang 031; Jin-Gyoung Jung; Tian-Li Wang; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (Bioinform., 2018)

SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. - Xu Shi; Xiao Wang 031; Tian-Li Wang; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (Bioinform., 2018)

Remote sensing and identification of volcanic plumes using fixed-wing UAVs over Volcán de Fuego, Guatemala. - Ben Schellenberg; Tom Richardson 002; Matt Watson 001; Colin Greatwood; Robert Clarke; Rick Thomas; Kieran Wood; Jim Freer; Helen Thomas; Emma J. Liu; Francis Salama; Gustavo Chigna (J. Field Robotics, 2019)

On-Board Real-Time Trajectory Planning for Fixed Wing Unmanned Aerial Vehicles in Extreme Environments. - Ben Schellenberg; Tom Richardson 002; Arthur Richards; Robert Clarke; Matt Watson 001 (Sensors, 2019)

debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues. - Lulu Chen; Chiung-Ting Wu; Niya Wang; David M. Herrington; Robert Clarke; Yue Wang 021 (Bioinform., 2020)

Visual Odometry Using Pixel Processor Arrays for Unmanned Aerial Systems in GPS Denied Environments. - Alexander McConville; Laurie Bose; Robert Clarke; Walterio W. Mayol-Cuevas; Jianing Chen; Colin Greatwood; Stephen J. Carey; Piotr Dudek; Thomas Richardson 002 (Frontiers Robotics AI, 2020)

BVLOS UAS Operations in Highly-Turbulent Volcanic Plumes. - Kieran Wood; Emma J. Liu; Tom Richardson 002; Robert Clarke; Jim Freer; Alessandro Aiuppa; Gaetano Giudice; Marcello Bitetto; Kila Mulina; Ima Itikarai (Frontiers Robotics AI, 2020)

The Design of Prometheus: A Reconfigurable UAV for Subterranean Mine Inspection. - Liam Brown; Robert Clarke; Aliakbar Akbari; Ujjar Bhandari; Sara Bernardini; Puneet S. Chhabra; Ognjen Marjanovic; Thomas Richardson 002; Simon Watson 001 (Robotics, 2020)

IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. - Xu Shi; Andrew F. Neuwald; Xiao Wang 031; Tian-Li Wang; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (Bioinform., 2021)

ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. - Xi Chen 056; Xu Shi; Andrew F. Neuwald; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (BMC Bioinform., 2021)

Stroke risk prediction using machine learning: a prospective cohort study of 0.5 million Chinese adults. - Matthew Chun; Robert Clarke; Benjamin J. Cairns; David A. Clifton; Derrick Bennett; Yiping Chen; Yu Guo; Pei Pei; Jun Lv; Canqing Yu; Ling Yang; Liming Li; et al. (J. Am. Medical Informatics Assoc., 2021)

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. - Xi Chen 056; Andrew F. Neuwald; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (PLoS Comput. Biol., 2021)

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution. - Lulu Chen; Chiung-Ting Wu; Chia-Hsiang Lin; Rujia Dai; Chunyu Liu 001; Robert Clarke; Guoqiang Yu; Jennifer E. Van Eyk; David M. Herrington; Yue Wang 021 (Bioinform., 2022)

Mathematical Models of Death Signaling Networks. - Madhumita Srinivasan; Robert Clarke; Pavel Kraikivski (Entropy, 2022)

Reinforcement Learning Derived High-Alpha Aerobatic Manoeuvres for Fixed Wing Operation in Confined Spaces. - Robert Clarke; Liam Fletcher; Sebastian East; Thomas Richardson 002 (Algorithms, 2023)

CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. - Chiung-Ting Wu; Dongping Du; Lulu Chen; Rujia Dai; Chunyu Liu 001; Guoqiang Yu; Saurabh Bhardwaj; Sarah J. Parker; Zhen Zhang; Robert Clarke; David M. Herrington; Yue Wang 021 (Bioinform., 2024)

AutoNet-Generated Deep Layer-Wise Convex Networks for ECG Classification. - Yanting Shen; Lei Lu; Tingting Zhu 001; Xinshao Wang; Lei A. Clifton; Zhengming Chen; Robert Clarke; David A. Clifton (IEEE Trans. Pattern Anal. Mach. Intell., 2024)

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data. - Xu Shi; Xiao Wang 031; Lu Jin; Leena Halakivi-Clarke; Robert Clarke; Andrew F. Neuwald; Jianhua Xuan (PLoS Comput. Biol., 2025)