Zhongming Zhao

171 papers B 1C 12Misc 2Journal 127Unranked 27
YearRankTypeTitle / Venue / Authors
2026 J jnl
MethConvTransformer: A Deep Learning Framework for Cross-Tissue Alzheimer's Disease Detection.
CoRR
Gang Qu, Guanghao Li, Zhongming Zhao
2025 J jnl
BrainGeneBot: a framework for variant prioritization and generative pretrained transformer-informed interpretation across polygenic risk score studies.
Briefings Bioinform.
Gang Qu, Nitesh Enduru, Xinyi Liu, Xiaoqian Jiang, Zhongming Zhao
2025 J jnl
Deciphering RNA modification and post-transcriptional regulation with NetRNApan.
Briefings Bioinform.
Haodong Xu, Wankun Deng, Ruifeng Hu, Binfeng Liu, Wenchao Zhang, Lujuan Wang, Lin Qi, Xiaolei Ren, Chao Tu, Zhihong Li, Zhongming Zhao
2025 J jnl
Explainable Hybrid Model for Presaging Tumor Stage Classification with Survival Survey.
SN Comput. Sci.
Sweta Manna, Sujoy Mistry, Zhongming Zhao, Keshav Dahal
2025 J jnl
Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model.
Bioinform.
Wendao Liu, Zhongming Zhao
2025 — conf
Thought Graph: Balancing Specificity and Uncertainty in LLM-Based Gene Set Annotation.
ICHI
Kyle Cox, Gang Qu, Chi-Yang Hsu, Jiawei Xu, Yingtong Zhou, Zhen Tan, Mengzhou Hu, Tianlong Chen, Ziniu Hu, Zhongming Zhao, Ying Ding
2025 J jnl
iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics.
Briefings Bioinform.
Kanglin Hsieh, Kai Zhang, Yan Chu, Lishan Yu, Xiaoyang Li, Nuo Hu, Isha Kawosa, Patrick G. Pilié, Pratip K. Bhattacharya, Degui Zhi, Xiaoqian Jiang, Zhongming Zhao, Yulin Dai
2024 J jnl
An improved method for diagnosis of Parkinson's disease using deep learning models enhanced with metaheuristic algorithm.
BMC Medical Imaging
Babita Majhi, Aarti Kashyap, Siddhartha Suprasad Mohanty, Sujata Dash, Saurav Mallik, Aimin Li, Zhongming Zhao
2024 J jnl
Correction: VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images.
BMC Medical Imaging
Anindita Saha, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Rakesh Kumar Yadav, Saurav Mallik, Zhongming Zhao
2024 — conf
Deep Transfer Learning for Kidney Disease Detection Using CT Scan Images.
BIBM
Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao
2024 J jnl
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup.
J. Am. Medical Informatics Assoc.
Nephi A. Walton, Radhakrishnan Nagarajan, Chen Wang, 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, Ece D. Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
2024 J jnl
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.
Bioinform.
Anindita Nath, Savannah Mwesigwa, Yulin Dai, Xiaoqian Jiang, Zhongming Zhao
2024 J jnl
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.
CoRR
Anindita Nath, Savannah Mwesigwa, Yulin Dai, Xiaoqian Jiang, Zhongming Zhao
2024 J jnl
Improved liver disease prediction from clinical data through an evaluation of ensemble learning approaches.
BMC Medical Informatics Decis. Mak.
Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao
2024 J jnl
MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons.
Briefings Bioinform.
Mengqiu Zheng, Shaofeng Lin, Kunqi Chen, Ruifeng Hu, Liming Wang, Zhongming Zhao, Haodong Xu
2024 J jnl
VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images.
BMC Medical Imaging
Anindita Saha, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Rakesh Kumar Yadav, Saurav Mallik, Zhongming Zhao
2023 J jnl
Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020.
BMC Bioinform.
Olga Valenzuela, Mario Cannataro, Irena Rusur, Jianxin Wang, Zhongming Zhao, Ignacio Rojas
2023 J jnl
Benchmark of embedding-based methods for accurate and transferable prediction of drug response.
Briefings Bioinform.
Peilin Jia, Ruifeng Hu, Zhongming Zhao
2023 J jnl
Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome.
Patterns
Hao-Dong Xu, Johnathan Jia, Hyun-Hwan Jeong, Zhongming Zhao
2023 J jnl
Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data.
Frontiers Bioinform.
Saurav Mallik, Soumita Seth, Amalendu Si, Tapas Bhadra, Zhongming Zhao
2023 J jnl
SMLBT: secure machine learning and blockchain-based telemedicine model for the remote areas of developing countries.
Int. J. Comput. Biol. Drug Des.
Milon Biswas, Atanu Shome, Prodipta Promit Mukherjee, Loveleen Gaur, Zhongming Zhao
2022 J jnl
Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer.
BMC Bioinform.
Tapas Bhadra, Saurav Mallik, Neaj Hasan, Zhongming Zhao
2022 J jnl
Designing optimal convolutional neural network architecture using differential evolution algorithm.
Patterns
Arjun Ghosh, Nanda Dulal Jana, Saurav Mallik, Zhongming Zhao
2022 — conf
Detection of Chronic Kidney Disease Using Neuro-Fuzzy Rule-based Classifier.
BIBM
Supantha Das, Arnab Hazra, Soumen Kumar Pati, Soumadip Ghosh, Saurav Mallik, Suharta Banerjee, Ayan Mukherji, Aimin Li, Zhongming Zhao
2022 — conf
Grid-Search Integrated Optimized Support Vector Machine Model for Breast Cancer Detection.
BIBM
Partho Ghose, Selina Sharmin, Loveleen Gaur, Zhongming Zhao
2022 J jnl
KCOSS: an ultra-fast k-mer counter for assembled genome analysis.
Bioinform.
Deyou Tang, Yucheng Li, Daqiang Tan, Juan Fu, Yelei Tang, Jiabin Lin, Rong Zhao, Hongli Du, Zhongming Zhao
2022 J jnl
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes.
Genom. Proteom. Bioinform.
Hao-Dong Xu, Zhongming Zhao
2022 J jnl
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.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tapas Bhadra, Saurav Mallik, Amir Sohel, Zhongming Zhao
2022 J jnl
WebCSEA: web-based cell-type-specific enrichment analysis of genes.
Nucleic Acids Res.
Yulin Dai, Ruifeng Hu, Andi Liu, Kyung Serk Cho, Astrid Marilyn Manuel, Xiaoyang Li, Xianjun Dong, Peilin Jia, Zhongming Zhao
2021 J jnl
Artificial image objects for classification of schizophrenia with GWAS-selected SNVs and convolutional neural network.
Patterns
Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin Zhan, Changrong Ji, Jingchun Chen
2021 J jnl
CSEA-DB: an omnibus for human complex trait and cell type associations.
Nucleic Acids Res.
Yulin Dai, Ruifeng Hu, Astrid Marilyn Manuel, Andi Liu, Peilin Jia, Zhongming Zhao
2021 J jnl
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.
Briefings Bioinform.
Hao-Dong Xu, Peilin Jia, Zhongming Zhao
2021 J jnl
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.
Nucleic Acids Res.
Guangsheng Pei, Ruifeng Hu, Peilin Jia, Zhongming Zhao
2021 J jnl
Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity.
Briefings Bioinform.
Peilin Jia, Astrid Marilyn Manuel, Brisa S. Fernandes, Yulin Dai, Zhongming Zhao
2021 J jnl
EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data.
Patterns
Fangfang Yan, Zhongming Zhao, Lukas M. Simon
2021 J jnl
Integration of millions of transcriptomes using batch-aware triplet neural networks.
Nat. Mach. Intell.
Lukas M. Simon, Yin-Ying Wang, Zhongming Zhao
2021 J jnl
KinaseMD: kinase mutations and drug response database.
Nucleic Acids Res.
Ruifeng Hu, Hao-Dong Xu, Peilin Jia, Zhongming Zhao
2021 J jnl
Landscape of drug-resistance mutations in kinase regulatory hotspots.
Briefings Bioinform.
Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao
2021 — conf
Mining Cancer Cell Line-Based Drugs to Benefit KRAS
BIBM
Aman Chandra Kaushik, Aamir Mehmood, Ajay Kumar, Ankit Babu, Dong-Qing Wei, Zhongming Zhao
2021 — conf
Negatively-Associated Maximal Frequent Geneset Mining on DNA Methylation Profile.
BIBM
Saurav Mallik, Souvik Rakshit, Ujjwal Maulik, Zhongming Zhao
2020 J jnl
6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.
Bioinform.
Hao-Dong Xu, Ruifeng Hu, Peilin Jia, Zhongming Zhao
2020 J jnl
Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020.
BMC Bioinform.
Yan Guo, Li Shen, Xinghua Shi, Kai Wang, Yulin Dai, Zhongming Zhao
2020 J jnl
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Nat.
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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel González-Pérez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
2020 J jnl
Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.
BMC Bioinform.
Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy A. Mathé, Lai Wei, Kai Wang
2020 J jnl
Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.
BMC Medical Informatics Decis. Mak.
Xia Ning, Chi Zhang, Kai Wang, Zhongming Zhao, Ewy A. Mathé
2020 J jnl
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice.
Briefings Bioinform.
Aimin Li, Peilin Jia, Saurav Mallik, Rong Fei, Hiroki Yoshioka, Akiko Suzuki, Junichi Iwata, Zhongming Zhao
2020 J jnl
Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation.
CoRR
Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean I. Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim
2020 J jnl
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data.
Briefings Bioinform.
Saurav Mallik, Zhongming Zhao
2020 J jnl
In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells.
BMC Bioinform.
Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik, Zhongming Zhao
2020 J jnl
Informatics and machine learning methods for health applications.
BMC Medical Informatics Decis. Mak.
Li Shen, Xinghua Shi, Zhongming Zhao, Kai Wang
2020 J jnl
SURE-based optimum-length S-G filter to reconstruct NDVI time series iteratively with outliers removal.
Int. J. Wavelets Multiresolution Inf. Process.
Liang Tang, Zhongming Zhao, Ping Tang, Haijun Yang
2020 J jnl
TSEA-DB: a trait?tissue association map for human complex traits and diseases.
Nucleic Acids Res.
Peilin Jia, Yulin Dai, Ruifeng Hu, Guangsheng Pei, Astrid Marilyn Manuel, Zhongming Zhao
2020 J jnl
The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.
BMC Medical Informatics Decis. Mak.
Xia Ning, Chi Zhang, Kai Wang, Zhongming Zhao, Ewy A. Mathé
2020 J jnl
VISDB: a manually curated database of viral integration sites in the human genome.
Nucleic Acids Res.
Deyou Tang, Bingrui Li, Tianyi Xu, Ruifeng Hu, Daqiang Tan, Xiaofeng Song, Peilin Jia, Zhongming Zhao
2019 — conf
A Multi-classifier Model to Identify Mitochondrial Respiratory Gene Signatures in Human Cancer.
BIBM
Saurav Mallik, Soumita Seth, Tapas Bhadra, Namrata Tomar, Zhongming Zhao
2019 J jnl
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.
Bioinform.
Peilin Jia, Guangsheng Pei, Zhongming Zhao
2019 — ch.
Computational Approaches for Modeling Signal Transduction Networks.
Encyclopedia of Bioinformatics and Computational Biology (2)
Zhongming Zhao, Junfeng Xia
2019 J jnl
Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells.
BMC Syst. Biol.
Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song, Ping Han
2019 J jnl
Distance based knowledge retrieval through rule mining for complex biomarker recognition from tri-omics profiles.
Int. J. Comput. Biol. Drug Des.
Saurav Mallik, Zhongming Zhao
2019 J jnl
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor.
Briefings Bioinform.
Hua Sun, Pora Kim, Peilin Jia, Aekyung Park, Han Liang, Zhongming Zhao
2019 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.
BMC Bioinform.
Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy A. Mathé, Lai Wei, Kai Wang
2019 J jnl
The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018).
BMC Medical Informatics Decis. Mak.
Yaoyun Zhang, Cui Tao, Yang Gong, Kai Wang, Zhongming Zhao
2019 J jnl
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery.
Briefings Bioinform.
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
2019 J jnl
deTS: tissue-specific enrichment analysis to decode tissue specificity.
Bioinform.
Guangsheng Pei, Yulin Dai, Zhongming Zhao, Peilin Jia
2018 J jnl
ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence.
Database J. Biol. Databases Curation
Ruifeng Hu, Yulin Dai, Peilin Jia, Zhongming Zhao
2018 J jnl
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.
Briefings Bioinform.
Pora Kim, Peilin Jia, Zhongming Zhao
2018 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.
BMC Bioinform.
Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi
2018 J jnl
TissGDB: tissue-specific gene database in cancer.
Nucleic Acids Res.
Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, Zhongming Zhao
2017 J jnl
Impacts of somatic mutations on gene expression: an association perspective.
Briefings Bioinform.
Peilin Jia, Zhongming Zhao
2017 J jnl
Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data.
BMC Medical Informatics Decis. Mak.
Cui Tao, Yang Gong, Hua Xu, Zhongming Zhao
2017 J jnl
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
BMC Bioinform.
Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang
2017 Misc conf
No-Boundary Thinking in Bioinformatics.
PSB
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
2017 — conf
Representation Learning for Retinal Vasculature Embeddings.
FIFI/OMIA@MICCAI
Luca Giancardo, Kirk Roberts, Zhongming Zhao
2017 J jnl
SZGR 2.0: a one-stop shop of schizophrenia candidate genes.
Nucleic Acids Res.
Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao
2017 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.
BMC Bioinform.
Zhandong Liu, W. Jim Zheng, Genevera I. Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
2017 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.
BMC Syst. Biol.
W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu
2017 J jnl
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.
Quant. Biol.
Saurav Mallik, Zhongming Zhao
2017 — conf
TrapRM: Transcriptomic and proteomic rule mining using weighted shortest distance based multiple minimum supports for multi-omics dataset.
BIBM
Saurav Mallik, Zhongming Zhao
2017 J jnl
mutLBSgeneDB: mutated ligand binding site gene DataBase.
Nucleic Acids Res.
Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao
2016 J jnl
A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.
J. Am. Medical Informatics Assoc.
Feixiong Cheng, Junfei Zhao, Michaela Fooksa, Zhongming Zhao
2016 J jnl
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.
Briefings Bioinform.
Feixiong Cheng, Junfei Zhao, Zhongming Zhao
2016 J jnl
Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.
BMC Syst. Biol.
Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
2016 J jnl
An informatics research agenda to support precision medicine: seven key areas.
J. Am. Medical Informatics Assoc.
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, Shyam Visweswaran, Zhongming Zhao, Robert R. Freimuth
2016 J jnl
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach.
BMC Syst. Biol.
Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao
2016 J jnl
Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types.
Briefings Bioinform.
Wei Jiang, Ramkrishna Mitra, Chen-Ching Lin, Quan Wang, Feixiong Cheng, Zhongming Zhao
2016 J jnl
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis.
PLoS Comput. Biol.
Feixiong Cheng, James L. Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H. Rubin
2016 J jnl
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.
Nucleic Acids Res.
Min Zhao, Pora Kim, Ramkrishna Mitra, Junfei Zhao, Zhongming Zhao
2016 J jnl
Two Algorithms for the Detection and Tracking of Moving Vehicle Targets in Aerial Infrared Image Sequences.
Remote. Sens.
Yutian Cao, Gang Wang, Dongmei Yan, Zhongming Zhao
2016 J jnl
ccmGDB: a database for cancer cell metabolism genes.
Nucleic Acids Res.
Pora Kim, Feixiong Cheng, Junfei Zhao, Zhongming Zhao
2015 J jnl
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types.
PLoS Comput. Biol.
Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao
2015 J jnl
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.
BMC Syst. Biol.
Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun
2015 J jnl
Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm.
BioData Min.
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, Donald F. McMullen, Bindu Nanduri, Andy D. Perkins, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Karl Walker, Donald C. Wunsch, Donghai Xiong, Shuzhong Zhang, Yu Zhang, Zhongming Zhao, Jason H. Moore
2015 J jnl
Continuous Change Detection and Classification Using Hidden Markov Model: A Case Study for Monitoring Urban Encroachment onto Farmland in Beijing.
Remote. Sens.
Yuan Yuan, Yu Meng, Lei Lin, Hichem Sahli, Anzhi Yue, Jingbo Chen, Zhongming Zhao, Yun-long Kong, Dong-xu He
2015 J jnl
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
PLoS Comput. Biol.
Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao
2015 J jnl
EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles.
Bioinform.
Quan Wang, Hui Yu, Zhongming Zhao, Peilin Jia
2015 J jnl
SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations.
BMC Bioinform.
Junfei Zhao, Feixiong Cheng, Zhongming Zhao
2015 J jnl
Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.
Bioinform.
Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao
2014 J jnl
Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses.
BMC Bioinform.
Hui Yu, Zhongming Zhao
2014 J jnl
Integrated Approach in Systems Biology.
Comput. Math. Methods Medicine
Huiru Zheng, Rui Jiang, Zhongming Zhao
2014 J jnl
Parcel-Based Change Detection in Land-Use Maps by Adopting the Holistic Feature.
IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens.
Bin Wu, Jian Yang, Zhongming Zhao, Yu Meng, Anzhi Yue, Jingbo Chen, Dong-xu He, Xingchun Liu, Shunxi Liu
2014 J jnl
The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer.
Int. J. Comput. Biol. Drug Des.
Ramkrishna Mitra, Zhongming Zhao
2014 J jnl
VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.
PLoS Comput. Biol.
Peilin Jia, Zhongming Zhao
2013 J jnl
A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling.
BMC Bioinform.
Huy Vuong, Zhongming Zhao
2013 J jnl
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.
Briefings Bioinform.
Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao, Zhongming Zhao
2013 J jnl
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.
BMC Bioinform.
Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
2013 — conf
Correlating adverse drug reactions with biological pathways in humans.
BIBM
Huiru Zheng, Haiying Wang, Hua Xu, Zhongming Zhao, Francisco Azuaje
2013 J jnl
Differential coexpression network modules observed in human hepatocellular carcinoma progression.
BMC Bioinform.
Hui Yu, Zhongming Zhao
2013 J jnl
Dynamic protein interaction modules in human hepatocellular carcinoma progression.
BMC Syst. Biol.
Hui Yu, Chen-Ching Lin, Yuan-Yuan Li, Zhongming Zhao
2013 J jnl
Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer.
BMC Bioinform.
Ramkrishna Mitra, Jingchun Sun, Min Zhao, Zhongming Zhao
2013 J jnl
Network analysis of gene fusions in human cancer.
BMC Bioinform.
Morgan Harrell, Junfeng Xia, Zhongming Zhao
2013 — conf
Network-based mutation analysis of putative cancer genes from next-generation sequencing data.
BIBM
Peilin Jia, Zhongming Zhao
2013 J jnl
No-boundary thinking in bioinformatics research.
BioData Min.
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, Joan Peckham, Andy D. Perkins, Shawn W. Polson, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Donald C. Wunsch, Donghai Xiong, Shuzhong Zhang, Zhongming Zhao
2013 J jnl
TSGene: a web resource for tumor suppressor genes.
Nucleic Acids Res.
Min Zhao, Jingchun Sun, Zhongming Zhao
2012 — conf
A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data.
GENSiPS
Qingguo Wang, Zhongming Zhao
2012 — conf
A network and functional investigation of illicit drugs and their targets.
BIBM Workshops
Ravi V. Atreya, Jingchun Sun, Zhongming Zhao
2012 J jnl
Advances in systems biology: computational algorithms and applications.
BMC Syst. Biol.
Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang
2012 J jnl
BioEve Search: A Novel Framework to Facilitate Interactive Literature Search.
Adv. Bioinformatics
Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, Zhongming Zhao
2012 — conf
Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspective.
GENSiPS
Min Zhao, Jingchun Sun, Zhongming Zhao
2012 J jnl
DTome: a web-based tool for drug-target interactome construction.
BMC Bioinform.
Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao
2012 J jnl
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer.
BMC Syst. Biol.
Peilin Jia, Yang Liu, Zhongming Zhao
2012 J jnl
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs.
J. Am. Medical Informatics Assoc.
Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun, Zhongming Zhao, Xue-wen Chen, Michael E. Matheny, Hua Xu
2012 J jnl
Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia.
PLoS Comput. Biol.
Peilin Jia, Lily Wang, Ayman H. Fanous, Carlos N. Pato, Todd L. Edwards, Zhongming Zhao
2012 Misc conf
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation.
Pacific Symposium on Biocomputing
Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu
2012 J jnl
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma.
PLoS Comput. Biol.
Jingchun Sun, Xue Gong, Benjamin Purow, Zhongming Zhao
2011 J jnl
A comprehensive network and pathway analysis of candidate genes in major depressive disorder.
BMC Syst. Biol.
Peilin Jia, Chung-Feng Kao, Po-Hsiu Kuo, Zhongming Zhao
2011 J jnl
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.
Bioinform.
Lily Wang, Peilin Jia, Russell D. Wolfinger, Xi Chen, Britney L. Grayson, Thomas M. Aune, Zhongming Zhao
2011 — conf
Development and implementation of a novel computational tool for an efficient construction of drug-target interactome.
BIBM Workshops
Jingchun Sun, Paul Hart, Zhongming Zhao
2011 — conf
Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region?
ICIC (3)
Zhixi Su, Junfeng Xia, Zhongming Zhao
2011 J jnl
Do cancer proteins really interact strongly in the human protein-protein interaction network?
Comput. Biol. Chem.
Junfeng Xia, Jingchun Sun, Peilin Jia, Zhongming Zhao
2011 J jnl
Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors.
Int. J. Comput. Biol. Drug Des.
Xue Gong, Jingchun Sun, Zhongming Zhao
2011 J jnl
Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach.
BMC Bioinform.
Siyuan Zheng, Zhongming Zhao
2011 J jnl
MentalSquares: A generic bipolar Support Vector Machine for psychiatric disorder classification, diagnostic analysis and neurobiological data mining.
Int. J. Data Min. Bioinform.
Wen-Ran Zhang, Anand K. Pandurangi, Karl E. Peace, Yan-Qing Zhang, Zhongming Zhao
2011 J jnl
Multiple-cue saliency measurement and optimized image composition for image retargeting.
J. Comput. Appl. Math.
Xiaonan Luo, Zhongming Zhao, Zhuo Su, Yun Liang
2011 — conf
Network-assisted causal gene detection in genome-wide association studies: an improved module search algorithm.
GENSiPS
Peilin Jia, Zhongming Zhao
2011 J jnl
Virus interactions with human signal transduction pathways.
Int. J. Comput. Biol. Drug Des.
Zhongming Zhao, Junfeng Xia, Öznur Tastan, Irtisha Singh, Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman
2011 J jnl
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
Bioinform.
Peilin Jia, Siyuan Zheng, Jirong Long, Wei Zheng, Zhongming Zhao
2010 J jnl
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia.
BMC Syst. Biol.
An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao
2010 — ed.
Advanced Intelligent Computing Theories and Applications, 6th International Conference on Intelligent Computing, ICIC 2010, Changsha, China, August 18-21, 2010. Proceedings
ICIC (1)
De-Shuang Huang, Zhongming Zhao, Vitoantonio Bevilacqua, Juan Carlos Figueroa García
2010 J jnl
Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes.
BMC Bioinform.
Hung-Chung Huang, Siyuan Zheng, Zhongming Zhao
2010 J jnl
Assessing gene length biases in gene set analysis of Genome-Wide Association Studies.
Int. J. Comput. Biol. Drug Des.
Peilin Jia, Jian Tian, Zhongming Zhao
2010 J jnl
Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.
Artif. Intell. Medicine
Jingchun Sun, Leng Han, Zhongming Zhao
2010 — conf
Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines.
ICIC (1)
Leng Han, Siyuan Zheng, Shuying Sun, Tim Hui-Ming Huang, Zhongming Zhao
2010 J jnl
Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues.
Int. J. Comput. Biol. Drug Des.
Kellie J. Archer, Zhongming Zhao, Tobias Guennel, Daniel G. Maluf, Robert A. Fisher, Valeria R. Mas
2010 — conf
Investigating microRNA-transcription factor mediated regulatory network in glioblastoma.
BIBM Workshops
Xue Gong, Peilin Jia, Zhongming Zhao
2010 J jnl
Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia.
BMC Bioinform.
Peilin Jia, Zhongming Zhao
2009 J jnl
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case.
Bioinform.
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
2009 J jnl
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
BMC Bioinform.
Leng Han, Zhongming Zhao
2009 J jnl
ERGR: An ethanol-related gene resource.
Nucleic Acids Res.
An-Yuan Guo, Bradley Todd Webb, Michael F. Miles, Mark P. Zimmerman, Kenneth S. Kendler, Zhongming Zhao
2009 — conf
Global Network Features of Cancer Genes in the Human Interactome.
IJCBS
Jingchun Sun, Peilin Jia, Zhongming Zhao
2009 — conf
Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks.
IJCBS
Peilin Jia, Jingchun Sun, Leng Han, Zhongming Zhao
2009 — conf
SmartWarf - A portable automated warfarin dosing tool.
CTS
Zhongming Zhao, Shivi Kansal, Bonny L. Bukaveckas
2008 B conf
A fast two-step deblurring method for satellite images.
SMC
Fen Chen, Zhensong Wang, Zhongming Zhao
2008 — conf
An SVM-Based Algorithm for Classifying Promoter-Associated CpG Islands in the Human and Mouse Genomes.
ICIC (2)
Leng Han, Ruolin Yang, Bing Su, Zhongming Zhao
2008 — conf
Building Change Detection Based on Similarity Calibration.
FSKD (3)
Yu Meng, Zhongming Zhao, Xin Du, Shu Peng
2008 — conf
FindSUMO: A PSSM-Based Method for Sumoylation Site Prediction.
ICIC (2)
Christopher J. Friedline, Xueping Zhang, Zendra E. Zehner, Zhongming Zhao
2008 — conf
Schizophrenia Genes: Characteristics of Function and Protein Interaction Networks.
BMEI (1)
Jingchun Sun, Leng Han, Zhongming Zhao
2007 J jnl
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
BMC Bioinform.
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
2005 C conf
A fused road detection approach in high resolution multi-spectrum remote sensing imagery.
IGARSS
Dongmei Yan, Zhongming Zhao, Zhong Chen
2005 — conf
A new identification method for artificial objects based on various features.
Color Imaging: Processing, Hardcopy, and Applications
Linli Cui, Ping Tang, Zhongming Zhao, Jun Shi
2005 C conf
Clouds and cloud shadows removal from high-resolution remote sensing images.
IGARSS
Fen Chen, Zhongming Zhao, Ling Peng, Dongmei Yan
2005 C conf
Image compression based on unrestrained sized wavelet transform.
IGARSS
Renxi Chen, Zhongming Zhao, Zhong Chen
2005 C conf
Multi-scale segmentation of the high resolution remote sensing image.
IGARSS
Zhong Chen, Zhongming Zhao, Dongmei Yan, Renxi Chen
2005 J jnl
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
Bioinform.
Fengkai Zhang, Zhongming Zhao
2005 C conf
The indigenous remote sensing image processing system and its exertion strategy.
IGARSS
Ling Peng, Zhongming Zhao, Ziqi Guo, Qian Yao, Fen Chen, Jianglin Ma
2004 C conf
An algorithm for eliminating the isolated regions based on connected area in image classification.
IGARSS
Jianghong Song, Zhongming Zhao, Qingye Zeng, Yanfeng Wei
2004 C conf
An integrated classification strategy of hyperspectral imaging spectrometer data.
IGARSS
Linli Cui, Wenyi Fan, Zhongming Zhao, Jun Shi, Ling Peng
2004 C conf
Remote sensing study based on IRSA Remote Sensing Image Processing System.
IGARSS
Ling Peng, Zhongming Zhao, Linli Cui, Lu Wang
2004 C conf
Texture image segmentation based on wavelet-domain hidden Markov models.
IGARSS
Ling Peng, Zhongming Zhao, Jianglin Ma
2004 C conf
Urban building extraction from high-resolution satellite panchromatic image using clustering and edge detection.
IGARSS
Yanfeng Wei, Zhongming Zhao, Jianghong Song
2003 C conf
Automatic change detection of artificial objects in multitemporal high spatial resolution remotely sensed imagery.
IGARSS
Jianwei Ma, Zhongming Zhao, Ge Zhao, Ping Tang
2003 C conf
Road detection from Quickbird fused image using IHS transform and morphology.
IGARSS
Dongmei Yan, Zhongming Zhao