Automatic change detection of artificial objects in multitemporal high spatial resolution remotely sensed imagery. - Jianwei Ma; Zhongming Zhao; Ge Zhao; Ping Tang (IGARSS, 2003)

Road detection from Quickbird fused image using IHS transform and morphology. - Dongmei Yan; Zhongming Zhao (IGARSS, 2003)

An integrated classification strategy of hyperspectral imaging spectrometer data. - Linli Cui; Wenyi Fan; Zhongming Zhao; Jun Shi; Ling Peng (IGARSS, 2004)

Remote sensing study based on IRSA Remote Sensing Image Processing System. - Ling Peng; Zhongming Zhao; Linli Cui; Lu Wang (IGARSS, 2004)

Texture image segmentation based on wavelet-domain hidden Markov models. - Ling Peng; Zhongming Zhao; Jianglin Ma (IGARSS, 2004)

An algorithm for eliminating the isolated regions based on connected area in image classification. - Jianghong Song; Zhongming Zhao; Qingye Zeng; Yanfeng Wei (IGARSS, 2004)

Urban building extraction from high-resolution satellite panchromatic image using clustering and edge detection. - Yanfeng Wei; Zhongming Zhao; Jianghong Song (IGARSS, 2004)

A new identification method for artificial objects based on various features. - Linli Cui; Ping Tang; Zhongming Zhao; Jun Shi (Color Imaging: Processing, Hardcopy, and Applications, 2005)

Image compression based on unrestrained sized wavelet transform. - Renxi Chen; Zhongming Zhao; Zhong Chen (IGARSS, 2005)

Clouds and cloud shadows removal from high-resolution remote sensing images. - Fen Chen; Zhongming Zhao; Ling Peng; Dongmei Yan (IGARSS, 2005)

Multi-scale segmentation of the high resolution remote sensing image. - Zhong Chen; Zhongming Zhao; Dongmei Yan; Renxi Chen (IGARSS, 2005)

The indigenous remote sensing image processing system and its exertion strategy. - Ling Peng; Zhongming Zhao; Ziqi Guo; Qian Yao; Fen Chen; Jianglin Ma (IGARSS, 2005)

A fused road detection approach in high resolution multi-spectrum remote sensing imagery. - Dongmei Yan; Zhongming Zhao; Zhong Chen (IGARSS, 2005)

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). - Fengkai Zhang; Zhongming Zhao (Bioinform., 2005)

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. - Jingchun Sun; Yan Sun; Guohui Ding 001; Qi Liu 024; Chuan Wang; Youyu He; Tieliu Shi; Yixue Li; Zhongming Zhao (BMC Bioinform., 2007)

Schizophrenia Genes: Characteristics of Function and Protein Interaction Networks. - Jingchun Sun; Leng Han; Zhongming Zhao (BMEI (1), 2008)

Building Change Detection Based on Similarity Calibration. - Yu Meng; Zhongming Zhao; Xin Du; Shu Peng (FSKD (3), 2008)

FindSUMO: A PSSM-Based Method for Sumoylation Site Prediction. - Christopher J. Friedline; Xueping Zhang; Zendra E. Zehner; Zhongming Zhao (ICIC (2), 2008)

An SVM-Based Algorithm for Classifying Promoter-Associated CpG Islands in the Human and Mouse Genomes. - Leng Han; Ruolin Yang 003; Bing Su; Zhongming Zhao (ICIC (2), 2008)

A fast two-step deblurring method for satellite images. - Fen Chen; Zhensong Wang; Zhongming Zhao (SMC, 2008)

SmartWarf - A portable automated warfarin dosing tool. - Zhongming Zhao; Shivi Kansal; Bonny L. Bukaveckas (CTS, 2009)

Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks. - Peilin Jia; Jingchun Sun; Leng Han; Zhongming Zhao (IJCBS, 2009)

Global Network Features of Cancer Genes in the Human Interactome. - Jingchun Sun; Peilin Jia; Zhongming Zhao (IJCBS, 2009)

A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case. - Jingchun Sun; Peilin Jia; Ayman H. Fanous; Bradley Todd Webb; Edwin J. C. G. van den Oord; Xiangning Chen; József Bukszár; Kenneth S. Kendler; Zhongming Zhao (Bioinform., 2009)

CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? - Leng Han; Zhongming Zhao (BMC Bioinform., 2009)

ERGR: An ethanol-related gene resource. - An-Yuan Guo; Bradley Todd Webb; Michael F. Miles; Mark P. Zimmerman; Kenneth S. Kendler; Zhongming Zhao (Nucleic Acids Res., 2009)

Investigating microRNA-transcription factor mediated regulatory network in glioblastoma. - Xue Gong; Peilin Jia; Zhongming Zhao (BIBM Workshops, 2010)

Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines. - Leng Han; Siyuan Zheng; Shuying Sun; Tim Hui-Ming Huang; Zhongming Zhao (ICIC (1), 2010)

Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. - Jingchun Sun; Leng Han; Zhongming Zhao (Artif. Intell. Medicine, 2010)

Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes. - Hung-Chung Huang; Siyuan Zheng; Zhongming Zhao (BMC Bioinform., 2010)

Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia. - Peilin Jia; Zhongming Zhao (BMC Bioinform., 2010)

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. - An-Yuan Guo; Jingchun Sun; Peilin Jia; Zhongming Zhao (BMC Syst. Biol., 2010)

Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. - Kellie J. Archer; Zhongming Zhao; Tobias Guennel; Daniel G. Maluf; Robert A. Fisher; Valeria R. Mas (Int. J. Comput. Biol. Drug Des., 2010)

Assessing gene length biases in gene set analysis of Genome-Wide Association Studies. - Peilin Jia; Jian Tian; Zhongming Zhao (Int. J. Comput. Biol. Drug Des., 2010)

Development and implementation of a novel computational tool for an efficient construction of drug-target interactome. - Jingchun Sun; Paul Hart; Zhongming Zhao (BIBM Workshops, 2011)

Network-assisted causal gene detection in genome-wide association studies: an improved module search algorithm. - Peilin Jia; Zhongming Zhao (GENSiPS, 2011)

Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region? - Zhixi Su; Junfeng Xia; Zhongming Zhao (ICIC (3), 2011)

dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. - Peilin Jia; Siyuan Zheng; Jirong Long; Wei Zheng; Zhongming Zhao (Bioinform., 2011)

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. - Lily Wang 001; Peilin Jia; Russell D. Wolfinger; Xi Chen; Britney L. Grayson; Thomas M. Aune; Zhongming Zhao (Bioinform., 2011)

Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach. - Siyuan Zheng; Zhongming Zhao (BMC Bioinform., 2011)

A comprehensive network and pathway analysis of candidate genes in major depressive disorder. - Peilin Jia; Chung-Feng Kao; Po-Hsiu Kuo; Zhongming Zhao (BMC Syst. Biol., 2011)

Do cancer proteins really interact strongly in the human protein-protein interaction network? - Junfeng Xia; Jingchun Sun; Peilin Jia; Zhongming Zhao (Comput. Biol. Chem., 2011)

Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors. - Xue Gong; Jingchun Sun; Zhongming Zhao (Int. J. Comput. Biol. Drug Des., 2011)

Virus interactions with human signal transduction pathways. - Zhongming Zhao; Junfeng Xia; Öznur Tastan; Irtisha Singh; Meghana Kshirsagar 001; Jaime G. Carbonell; Judith Klein-Seetharaman (Int. J. Comput. Biol. Drug Des., 2011)

MentalSquares: A generic bipolar Support Vector Machine for psychiatric disorder classification, diagnostic analysis and neurobiological data mining. - Wen-Ran Zhang; Anand K. Pandurangi; Karl E. Peace; Yan-Qing Zhang 001; Zhongming Zhao (Int. J. Data Min. Bioinform., 2011)

Multiple-cue saliency measurement and optimized image composition for image retargeting. - Xiaonan Luo; Zhongming Zhao; Zhuo Su 001; Yun Liang 003 (J. Comput. Appl. Math., 2011)

A network and functional investigation of illicit drugs and their targets. - Ravi V. Atreya; Jingchun Sun; Zhongming Zhao (BIBM Workshops, 2012)

A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data. - Qingguo Wang; Zhongming Zhao (GENSiPS, 2012)

Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspective. - Min Zhao 006; Jingchun Sun; Zhongming Zhao (GENSiPS, 2012)

Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. - Yonghui Wu; Mei Liu; W. Jim Zheng; Zhongming Zhao; Hua Xu 001 (Pacific Symposium on Biocomputing, 2012)

BioEve Search: A Novel Framework to Facilitate Interactive Literature Search. - Syed Toufeeq Ahmed; Hasan Davulcu; Sukru Tikves; Radhika Nair; Zhongming Zhao (Adv. Bioinformatics, 2012)

DTome: a web-based tool for drug-target interactome construction. - Jingchun Sun; Yonghui Wu; Hua Xu 001; Zhongming Zhao (BMC Bioinform., 2012)

Advances in systems biology: computational algorithms and applications. - Yufei Huang 001; Zhongming Zhao; Hua Xu 001; Yu Shyr; Bing Zhang 003 (BMC Syst. Biol., 2012)

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. - Peilin Jia; Yang Liu; Zhongming Zhao (BMC Syst. Biol., 2012)

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. - Mei Liu; Yonghui Wu; Yukun Chen 001; Jingchun Sun; Zhongming Zhao; Xue-wen Chen 001; Michael E. Matheny; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2012)

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia. - Peilin Jia; Lily Wang 001; Ayman H. Fanous; Carlos N. Pato; Todd L. Edwards; Zhongming Zhao (PLoS Comput. Biol., 2012)

Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. - Jingchun Sun; Xue Gong; Benjamin Purow; Zhongming Zhao (PLoS Comput. Biol., 2012)

Network-based mutation analysis of putative cancer genes from next-generation sequencing data. - Peilin Jia; Zhongming Zhao (BIBM, 2013)

Correlating adverse drug reactions with biological pathways in humans. - Huiru Zheng; Haiying Wang 001; Hua Xu 001; Zhongming Zhao; Francisco Azuaje (BIBM, 2013)

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. - Qingguo Wang; Junfeng Xia; Peilin Jia; William Pao; Zhongming Zhao (Briefings Bioinform., 2013)

No-boundary thinking in bioinformatics research. - Xiuzhen Huang; Barry Bruce; Alison Buchan; Clare Bates Congdon; Carole L. Cramer; Steven F. Jennings; Hongmei Jiang; Zenglu Li; Gail McClure; Rick McMullen; Jason H. Moore; Bindu Nanduri; et al. (BioData Min., 2013)

Network analysis of gene fusions in human cancer. - Morgan Harrell; Junfeng Xia; Zhongming Zhao (BMC Bioinform., 2013)

Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer. - Ramkrishna Mitra; Jingchun Sun; Min Zhao 006; Zhongming Zhao (BMC Bioinform., 2013)

A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling. - Huy Vuong; Zhongming Zhao (BMC Bioinform., 2013)

Differential coexpression network modules observed in human hepatocellular carcinoma progression. - Hui Yu; Zhongming Zhao (BMC Bioinform., 2013)

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. - Min Zhao 006; Qingguo Wang; Quan Wang 004; Peilin Jia; Zhongming Zhao (BMC Bioinform., 2013)

Dynamic protein interaction modules in human hepatocellular carcinoma progression. - Hui Yu 014; Chen-Ching Lin; Yuan-Yuan Li; Zhongming Zhao (BMC Syst. Biol., 2013)

TSGene: a web resource for tumor suppressor genes. - Min Zhao 006; Jingchun Sun; Zhongming Zhao (Nucleic Acids Res., 2013)

Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses. - Hui Yu; Zhongming Zhao (BMC Bioinform., 2014)

Integrated Approach in Systems Biology. - Huiru Zheng; Rui Jiang 001; Zhongming Zhao (Comput. Math. Methods Medicine, 2014)

The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. - Ramkrishna Mitra; Zhongming Zhao (Int. J. Comput. Biol. Drug Des., 2014)

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data. - Peilin Jia; Zhongming Zhao (PLoS Comput. Biol., 2014)

Parcel-Based Change Detection in Land-Use Maps by Adopting the Holistic Feature. - Bin Wu; Jian Yang; Zhongming Zhao; Yu Meng 002; Anzhi Yue; Jingbo Chen; Dong-xu He; Xingchun Liu; Shunxi Liu (IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens., 2014)

Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. - Xiuzhen Huang; Steven F. Jennings; Barry Bruce; Alison Buchan; Liming Cai; Pengyin Chen; Carole L. Cramer; Weihua Guan; Uwe Hilgert; Hongmei Jiang; Zenglu Li; Gail McClure; et al. (BioData Min., 2015)

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles. - Quan Wang 004; Hui Yu; Zhongming Zhao; Peilin Jia (Bioinform., 2015)

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. - Yaomin Xu; Xingyi Guo; Jiayang Sun; Zhongming Zhao (Bioinform., 2015)

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. - Liang-Chin Huang; Ergin Soysal; W. Jim Zheng; Zhongming Zhao; Hua Xu 001; Jingchun Sun (BMC Syst. Biol., 2015)

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types. - Feixiong Cheng; Chuang Liu; Chen-Ching Lin; Junfei Zhao; Peilin Jia; Wen-Hsiung Li; Zhongming Zhao (PLoS Comput. Biol., 2015)

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. - Jingchun Sun; Min Zhao 006; Peilin Jia; Lily Wang 001; Yonghui Wu; Carissa Iverson; Yubo Zhou; Erica A. Bowton; Dan M. Roden; Joshua C. Denny; Melinda C. Aldrich; Hua Xu 001; et al. (PLoS Comput. Biol., 2015)

Continuous Change Detection and Classification Using Hidden Markov Model: A Case Study for Monitoring Urban Encroachment onto Farmland in Beijing. - Yuan Yuan 026; Yu Meng 002; Lei Lin 002; Hichem Sahli; Anzhi Yue; Jingbo Chen; Zhongming Zhao; Yun-long Kong; Dong-xu He (Remote. Sens., 2015)

SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations. - Junfei Zhao; Feixiong Cheng; Zhongming Zhao (BMC Bioinform., 2015)

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. - Feixiong Cheng; Junfei Zhao; Zhongming Zhao (Briefings Bioinform., 2016)

Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. - Wei Jiang 023; Ramkrishna Mitra; Chen-Ching Lin; Quan Wang 004; Feixiong Cheng; Zhongming Zhao (Briefings Bioinform., 2016)

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. - Feixiong Cheng; Chuang Liu; Bairong Shen; Zhongming Zhao (BMC Syst. Biol., 2016)

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. - Zhongming Zhao; Yunlong Liu; Yufei Huang 001; Kun Huang; Jianhua Ruan (BMC Syst. Biol., 2016)

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. - Feixiong Cheng; Junfei Zhao; Michaela Fooksa; Zhongming Zhao (J. Am. Medical Informatics Assoc., 2016)

An informatics research agenda to support precision medicine: seven key areas. - Jessica D. Tenenbaum; Paul Avillach; Marge M. Benham-Hutchins; Matthew K. Breitenstein; Erin L. Crowgey; Mark A. Hoffman; Xia Jiang; Subha Madhavan; John E. Mattison; Radhakrishnan Nagarajan; Bisakha Ray; Dmitriy Shin; et al. (J. Am. Medical Informatics Assoc., 2016)

ccmGDB: a database for cancer cell metabolism genes. - Pora Kim; Feixiong Cheng; Junfei Zhao; Zhongming Zhao (Nucleic Acids Res., 2016)

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. - Min Zhao 006; Pora Kim; Ramkrishna Mitra; Junfei Zhao; Zhongming Zhao (Nucleic Acids Res., 2016)

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. - Feixiong Cheng; James L. Murray; Junfei Zhao; Jinsong Sheng; Zhongming Zhao; Donald H. Rubin (PLoS Comput. Biol., 2016)

Two Algorithms for the Detection and Tracking of Moving Vehicle Targets in Aerial Infrared Image Sequences. - Yutian Cao; Gang Wang; Dongmei Yan; Zhongming Zhao (Remote. Sens., 2016)

TrapRM: Transcriptomic and proteomic rule mining using weighted shortest distance based multiple minimum supports for multi-omics dataset. - Saurav Mallik; Zhongming Zhao (BIBM, 2017)

Representation Learning for Retinal Vasculature Embeddings. - Luca Giancardo; Kirk Roberts; Zhongming Zhao (FIFI/OMIA@MICCAI, 2017)

No-Boundary Thinking in Bioinformatics. - Jason H. Moore; Steven F. Jennings; Casey S. Greene; Lawrence E. Hunter; Andy D. Perkins; ClarLynda R. Williams-DeVane; Donald C. Wunsch; Zhongming Zhao; Xiuzhen Huang (PSB, 2017)

Impacts of somatic mutations on gene expression: an association perspective. - Peilin Jia; Zhongming Zhao (Briefings Bioinform., 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. - Zhandong Liu; W. Jim Zheng; Genevera I. Allen; Yin Liu; Jianhua Ruan; Zhongming Zhao (BMC Bioinform., 2017)

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. - Hao Wang; Jiamao Luo; Chun Liu; Huilin Niu; Jing Wang 026; Qi Liu 024; Zhongming Zhao; Hua Xu 001; Yanqing Ding; Jingchun Sun; Qingling Zhang 003 (BMC Bioinform., 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. - W. Jim Zheng; Jianhua Ruan; Hua Xu 001; Zhongming Zhao; Zhangdong Liu (BMC Syst. Biol., 2017)

Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. - Cui Tao; Yang Gong; Hua Xu 001; Zhongming Zhao (BMC Medical Informatics Decis. Mak., 2017)

SZGR 2.0: a one-stop shop of schizophrenia candidate genes. - Peilin Jia; Guangchun Han; Junfei Zhao; Pinyi Lu; Zhongming Zhao (Nucleic Acids Res., 2017)

mutLBSgeneDB: mutated ligand binding site gene DataBase. - Pora Kim; Junfei Zhao; Pinyi Lu; Zhongming Zhao (Nucleic Acids Res., 2017)

Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles. - Saurav Mallik; Zhongming Zhao (Quant. Biol., 2017)

Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. - Pora Kim; Peilin Jia; Zhongming Zhao (Briefings Bioinform., 2018)

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence. - Ruifeng Hu 002; Yulin Dai; Peilin Jia; Zhongming Zhao (Database J. Biol. Databases Curation, 2018)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. - Xiaoming Liu; Lei Xie 006; Zhijin Wu; Kai Wang 063; Zhongming Zhao; Jianhua Ruan; Degui Zhi (BMC Bioinform., 2018)

TissGDB: tissue-specific gene database in cancer. - Pora Kim; Aekyung Park; Guangchun Han; Hua Sun 003; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2018)

A Multi-classifier Model to Identify Mitochondrial Respiratory Gene Signatures in Human Cancer. - Saurav Mallik; Soumita Seth; Tapas Bhadra; Namrata Tomar; Zhongming Zhao (BIBM, 2019)

Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. - Hua Sun 003; Pora Kim; Peilin Jia; Aekyung Park; Han Liang; Zhongming Zhao (Briefings Bioinform., 2019)

Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. - Jessica D. Tenenbaum; Krithika Bhuvaneshwar; Jane P. Gagliardi; Kate Fultz Hollis; Peilin Jia; Liang Ma; Radhakrishnan Nagarajan; Gopalkumar Rakesh; Vignesh Subbian; Shyam Visweswaran; Zhongming Zhao; Leon Rozenblit (Briefings Bioinform., 2019)

CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. - Peilin Jia; Guangsheng Pei; Zhongming Zhao (Bioinform., 2019)

deTS: tissue-specific enrichment analysis to decode tissue specificity. - Guangsheng Pei; Yulin Dai; Zhongming Zhao; Peilin Jia (Bioinform., 2019)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. - Zhongming Zhao; Yulin Dai; Chi Zhang; Ewy A. Mathé; Lai Wei; Kai Wang 063 (BMC Bioinform., 2019)

Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells. - Qichang Yang; Jing Wu; Jian Zhao 034; Tianyi Xu; Zhongming Zhao; Xiaofeng Song; Ping Han (BMC Syst. Biol., 2019)

Distance based knowledge retrieval through rule mining for complex biomarker recognition from tri-omics profiles. - Saurav Mallik; Zhongming Zhao (Int. J. Comput. Biol. Drug Des., 2019)

The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018). - Yaoyun Zhang; Cui Tao; Yang Gong; Kai Wang 063; Zhongming Zhao (BMC Medical Informatics Decis. Mak., 2019)

Computational Approaches for Modeling Signal Transduction Networks. - Zhongming Zhao; Junfeng Xia (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. - Aimin Li; Peilin Jia; Saurav Mallik; Rong Fei; Hiroki Yoshioka; Akiko Suzuki; Junichi Iwata; Zhongming Zhao (Briefings Bioinform., 2020)

Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data. - Saurav Mallik; Zhongming Zhao (Briefings Bioinform., 2020)

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. - Hao-Dong Xu; Ruifeng Hu 002; Peilin Jia; Zhongming Zhao (Bioinform., 2020)

Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020. - Yan Guo; Li Shen 001; Xinghua Shi; Kai Wang 063; Yulin Dai; Zhongming Zhao (BMC Bioinform., 2020)

In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. - Monalisa Mandal; Sanjeeb Kumar Sahoo; Priyadarsan Patra; Saurav Mallik; Zhongming Zhao (BMC Bioinform., 2020)

Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. - Zhongming Zhao; Yulin Dai; Chi Zhang; Ewy A. Mathé; Lai Wei; Kai Wang 063 (BMC Bioinform., 2020)

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation. - Kanglin Hsieh; Yinyin Wang; Luyao Chen; Zhongming Zhao; Sean I. Savitz; Xiaoqian Jiang; Jing Tang 002; Yejin Kim 001 (CoRR, 2020)

SURE-based optimum-length S-G filter to reconstruct NDVI time series iteratively with outliers removal. - Liang Tang; Zhongming Zhao; Ping Tang; Haijun Yang (Int. J. Wavelets Multiresolution Inf. Process., 2020)

Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions. - Xia Ning; Chi Zhang; Kai Wang 063; Zhongming Zhao; Ewy A. Mathé (BMC Medical Informatics Decis. Mak., 2020)

Informatics and machine learning methods for health applications. - Li Shen 001; Xinghua Shi; Zhongming Zhao; Kai Wang 063 (BMC Medical Informatics Decis. Mak., 2020)

TSEA-DB: a trait?tissue association map for human complex traits and diseases. - Peilin Jia; Yulin Dai; Ruifeng Hu 002; Guangsheng Pei; Astrid Marilyn Manuel; Zhongming Zhao (Nucleic Acids Res., 2020)

VISDB: a manually curated database of viral integration sites in the human genome. - Deyou Tang; Bingrui Li; Tianyi Xu; Ruifeng Hu 002; Daqiang Tan; Xiaofeng Song; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions. - Xia Ning; Chi Zhang; Kai Wang 063; Zhongming Zhao; Ewy A. Mathé (BMC Medical Informatics Decis. Mak., 2020)

Mining Cancer Cell Line-Based Drugs to Benefit KRAS(G12D) Pancreatic Adenocarcinoma Patients. - Aman Chandra Kaushik; Aamir Mehmood; Ajay Kumar; Ankit Babu; Dong-Qing Wei; Zhongming Zhao (BIBM, 2021)

Negatively-Associated Maximal Frequent Geneset Mining on DNA Methylation Profile. - Saurav Mallik; Souvik Rakshit; Ujjwal Maulik; Zhongming Zhao (BIBM, 2021)

Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. - Peilin Jia; Astrid Marilyn Manuel; Brisa S. Fernandes; Yulin Dai; Zhongming Zhao (Briefings Bioinform., 2021)

Landscape of drug-resistance mutations in kinase regulatory hotspots. - Pora Kim; Hanyang Li; Junmei Wang; Zhongming Zhao (Briefings Bioinform., 2021)

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. - Hao-Dong Xu; Peilin Jia; Zhongming Zhao (Briefings Bioinform., 2021)

KinaseMD: kinase mutations and drug response database. - Ruifeng Hu 002; Hao-Dong Xu; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

CSEA-DB: an omnibus for human complex trait and cell type associations. - Yulin Dai; Ruifeng Hu 002; Astrid Marilyn Manuel; Andi Liu; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner. - Guangsheng Pei; Ruifeng Hu 002; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

Integration of millions of transcriptomes using batch-aware triplet neural networks. - Lukas M. Simon; Yin-Ying Wang; Zhongming Zhao (Nat. Mach. Intell., 2021)

Artificial image objects for classification of schizophrenia with GWAS-selected SNVs and convolutional neural network. - Xiangning Chen; Daniel G. Chen; Zhongming Zhao; Justin Zhan; Changrong Ji; Jingchun Chen (Patterns, 2021)

EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. - Fangfang Yan; Zhongming Zhao; Lukas M. Simon (Patterns, 2021)

Detection of Chronic Kidney Disease Using Neuro-Fuzzy Rule-based Classifier. - Supantha Das; Arnab Hazra; Soumen Kumar Pati; Soumadip Ghosh; Saurav Mallik; Suharta Banerjee; Ayan Mukherji; Aimin Li; Zhongming Zhao (BIBM, 2022)

Grid-Search Integrated Optimized Support Vector Machine Model for Breast Cancer Detection. - Partho Ghose; Selina Sharmin; Loveleen Gaur; Zhongming Zhao (BIBM, 2022)

KCOSS: an ultra-fast k-mer counter for assembled genome analysis. - Deyou Tang; Yucheng Li; Daqiang Tan; Juan Fu; Yelei Tang; Jiabin Lin; Rong Zhao; Hongli Du; Zhongming Zhao (Bioinform., 2022)

Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. - Tapas Bhadra; Saurav Mallik; Neaj Hasan; Zhongming Zhao (BMC Bioinform., 2022)

WebCSEA: web-based cell-type-specific enrichment analysis of genes. - Yulin Dai; Ruifeng Hu 002; Andi Liu; Kyung Serk Cho; Astrid Marilyn Manuel; Xiaoyang Li; Xianjun Dong; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2022)

Designing optimal convolutional neural network architecture using differential evolution algorithm. - Arjun Ghosh; Nanda Dulal Jana; Saurav Mallik; Zhongming Zhao (Patterns, 2022)

Unsupervised Feature Selection Using an Integrated Strategy of Hierarchical Clustering With Singular Value Decomposition: An Integrative Biomarker Discovery Method With Application to Acute Myeloid Leukemia. - Tapas Bhadra; Saurav Mallik; Amir Sohel; Zhongming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes. - Hao-Dong Xu; Zhongming Zhao (Genom. Proteom. Bioinform., 2022)

SMLBT: secure machine learning and blockchain-based telemedicine model for the remote areas of developing countries. - Milon Biswas; Atanu Shome; Prodipta Promit Mukherjee; Loveleen Gaur; Zhongming Zhao (Int. J. Comput. Biol. Drug Des., 2023)

Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome. - Hao-Dong Xu; Johnathan Jia; Hyun-Hwan Jeong; Zhongming Zhao (Patterns, 2023)

deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues. - Guangsheng Pei; Fangfang Yan; Lukas M. Simon; Yulin Dai; Peilin Jia; Zhongming Zhao (Genom. Proteom. Bioinform., 2023)

Benchmark of embedding-based methods for accurate and transferable prediction of drug response. - Peilin Jia; Ruifeng Hu 002; Zhongming Zhao (Briefings Bioinform., 2023)

Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data. - Saurav Mallik; Soumita Seth; Amalendu Si; Tapas Bhadra; Zhongming Zhao (Frontiers Bioinform., 2023)

Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020. - Olga Valenzuela; Mario Cannataro; Irena Rusur; Jianxin Wang 001; Zhongming Zhao; Ignacio Rojas (BMC Bioinform., 2023)

Deep Transfer Learning for Kidney Disease Detection Using CT Scan Images. - Shahid Mohammad Ganie; Pijush Kanti Dutta Pramanik; Zhongming Zhao (BIBM, 2024)

MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons. - Mengqiu Zheng; Shaofeng Lin; Kunqi Chen; Ruifeng Hu 002; Liming Wang; Zhongming Zhao; Haodong Xu (Briefings Bioinform., 2024)

GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console. - Anindita Nath; Savannah Mwesigwa; Yulin Dai; Xiaoqian Jiang; Zhongming Zhao (CoRR, 2024)

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. - Nephi A. Walton; Radhakrishnan Nagarajan; Chen Wang 001; Murat Sincan; Robert R. Freimuth; David B. Everman; Derek C. Walton; Scott P. McGrath; Dominick J. Lemas; Panayiotis V. Benos; Alexander V. Alekseyenko; Qianqian Song; et al. (J. Am. Medical Informatics Assoc., 2024)

An improved method for diagnosis of Parkinson's disease using deep learning models enhanced with metaheuristic algorithm. - Babita Majhi; Aarti Kashyap; Siddhartha Suprasad Mohanty; Sujata Dash; Saurav Mallik; Aimin Li; Zhongming Zhao (BMC Medical Imaging, 2024)

VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images. - Anindita Saha; Shahid Mohammad Ganie; Pijush Kanti Dutta Pramanik; Rakesh Kumar Yadav; Saurav Mallik; Zhongming Zhao (BMC Medical Imaging, 2024)

Correction: VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images. - Anindita Saha; Shahid Mohammad Ganie; Pijush Kanti Dutta Pramanik; Rakesh Kumar Yadav; Saurav Mallik; Zhongming Zhao (BMC Medical Imaging, 2024)

Improved liver disease prediction from clinical data through an evaluation of ensemble learning approaches. - Shahid Mohammad Ganie; Pijush Kanti Dutta Pramanik; Zhongming Zhao (BMC Medical Informatics Decis. Mak., 2024)

Thought Graph: Balancing Specificity and Uncertainty in LLM-Based Gene Set Annotation. - Kyle Cox; Gang Qu; Chi-Yang Hsu; Jiawei Xu 006; Yingtong Zhou; Zhen Tan 001; Mengzhou Hu; Tianlong Chen 001; Ziniu Hu; Zhongming Zhao; Ying Ding 001 (ICHI, 2025)

iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics. - Kanglin Hsieh; Kai Zhang; Yan Chu 005; Lishan Yu; Xiaoyang Li; Nuo Hu; Isha Kawosa; Patrick G. Pilié; Pratip K. Bhattacharya; Degui Zhi; Xiaoqian Jiang; Zhongming Zhao; et al. (Briefings Bioinform., 2025)

Explainable Hybrid Model for Presaging Tumor Stage Classification with Survival Survey. - Sweta Manna; Sujoy Mistry; Zhongming Zhao; Keshav Dahal (SN Comput. Sci., 2025)