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Journal Articles
- 2024
[j118]Anindita Saha
, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Rakesh Kumar Yadav, Saurav Mallik, Zhongming Zhao:
VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images. BMC Medical Imaging 24(1): 120 (2024)- [j117]Anindita Saha, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Rakesh Kumar Yadav, Saurav Mallik, Zhongming Zhao:
Correction: VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images. BMC Medical Imaging 24(1): 128 (2024) - [j116]Babita Majhi, Aarti Kashyap, Siddhartha Suprasad Mohanty, Sujata Dash, Saurav Mallik, Aimin Li, Zhongming Zhao:
An improved method for diagnosis of Parkinson's disease using deep learning models enhanced with metaheuristic algorithm. BMC Medical Imaging 24(1): 156 (2024) - [j115]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:
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J. Am. Medical Informatics Assoc. 31(2): 536-541 (2024) - [j114]Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao:
Improved liver disease prediction from clinical data through an evaluation of ensemble learning approaches. BMC Medical Informatics Decis. Mak. 24(1): 160 (2024) - 2023
- [j113]Peilin Jia, Ruifeng Hu, Zhongming Zhao:
Benchmark of embedding-based methods for accurate and transferable prediction of drug response. Briefings Bioinform. 24(3) (2023) - [j112]Olga Valenzuela, Mario Cannataro, Irena Rusur, Jianxin Wang, Zhongming Zhao, Ignacio Rojas:
Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020. BMC Bioinform. 24-S(1): 361 (2023) - [j111]Saurav Mallik, Soumita Seth, Amalendu Si, Tapas Bhadra, Zhongming Zhao:
Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data. Frontiers Bioinform. 3 (2023) - [j110]Guangsheng Pei, Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao:
deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues. Genom. Proteom. Bioinform. 21(2): 370-384 (2023) - [j109]Milon Biswas, Atanu Shome, Prodipta Promit Mukherjee, Loveleen Gaur, Zhongming Zhao:
SMLBT: secure machine learning and blockchain-based telemedicine model for the remote areas of developing countries. Int. J. Comput. Biol. Drug Des. 15(6): 503-517 (2023) - [j108]Hao-Dong Xu, Johnathan Jia, Hyun-Hwan Jeong, Zhongming Zhao:
Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome. Patterns 4(2): 100674 (2023) - 2022
- [j107]Deyou Tang, Yucheng Li, Daqiang Tan, Juan Fu, Yelei Tang, Jiabin Lin, Rong Zhao, Hongli Du, Zhongming Zhao:
KCOSS: an ultra-fast k-mer counter for assembled genome analysis. Bioinform. 38(4): 933-940 (2022) - [j106]Tapas Bhadra, Saurav Mallik, Neaj Hasan, Zhongming Zhao:
Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. BMC Bioinform. 23-S(3): 153 (2022) - [j105]Hao-Dong Xu, Zhongming Zhao:
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes. Genom. Proteom. Bioinform. 20(5): 1002-1012 (2022) - [j104]Yulin Dai, Ruifeng Hu, Andi Liu, Kyung Serk Cho, Astrid Marilyn Manuel, Xiaoyang Li, Xianjun Dong, Peilin Jia, Zhongming Zhao:
WebCSEA: web-based cell-type-specific enrichment analysis of genes. Nucleic Acids Res. 50(W1): 782- (2022) - [j103]Arjun Ghosh, Nanda Dulal Jana, Saurav Mallik, Zhongming Zhao:
Designing optimal convolutional neural network architecture using differential evolution algorithm. Patterns 3(9): 100567 (2022) - [j102]Tapas Bhadra, Saurav Mallik, Amir Sohel, Zhongming Zhao:
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. 19(3): 1354-1364 (2022) - 2021
- [j101]Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao:
Landscape of drug-resistance mutations in kinase regulatory hotspots. Briefings Bioinform. 22(3) (2021) - [j100]Hao-Dong Xu, Peilin Jia, Zhongming Zhao:
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Briefings Bioinform. 22(3) (2021) - [j99]Peilin Jia, Astrid Marilyn Manuel, Brisa S. Fernandes, Yulin Dai, Zhongming Zhao:
Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. Briefings Bioinform. 22(6) (2021) - [j98]Ruifeng Hu, Hao-Dong Xu, Peilin Jia, Zhongming Zhao:
KinaseMD: kinase mutations and drug response database. Nucleic Acids Res. 49(Database-Issue): D552-D561 (2021) - [j97]Yulin Dai, Ruifeng Hu, Astrid Marilyn Manuel, Andi Liu, Peilin Jia, Zhongming Zhao:
CSEA-DB: an omnibus for human complex trait and cell type associations. Nucleic Acids Res. 49(Database-Issue): D862-D870 (2021) - [j96]Guangsheng Pei, Ruifeng Hu, Peilin Jia, Zhongming Zhao:
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner. Nucleic Acids Res. 49(Webserver-Issue): 131-139 (2021) - [j95]Lukas M. Simon, Yin-Ying Wang, Zhongming Zhao:
Integration of millions of transcriptomes using batch-aware triplet neural networks. Nat. Mach. Intell. 3(8): 705-715 (2021) - [j94]Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin Zhan, Changrong Ji, Jingchun Chen:
Artificial image objects for classification of schizophrenia with GWAS-selected SNVs and convolutional neural network. Patterns 2(8): 100303 (2021) - [j93]Fangfang Yan, Zhongming Zhao, Lukas M. Simon:
EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. Patterns 2(8): 100311 (2021) - 2020
- [j92]Saurav Mallik, Zhongming Zhao:
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data. Briefings Bioinform. 21(2): 368-394 (2020) - [j91]Aimin Li, Peilin Jia, Saurav Mallik, Rong Fei, Hiroki Yoshioka, Akiko Suzuki, Junichi Iwata, Zhongming Zhao:
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Briefings Bioinform. 21(4): 1465-1478 (2020) - [j90]Hao-Dong Xu, Ruifeng Hu, Peilin Jia, Zhongming Zhao:
6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. Bioinform. 36(10): 3257-3259 (2020) - [j89]Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy A. Mathé, Lai Wei, Kai Wang:
Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. BMC Bioinform. 21(1): 148 (2020) - [j88]Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik, Zhongming Zhao:
In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. BMC Bioinform. 21-S(21): 499 (2020) - [j87]Yan Guo, Li Shen, Xinghua Shi, Kai Wang, Yulin Dai, Zhongming Zhao:
Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020. BMC Bioinform. 21-S(21): 563 (2020) - [j86]Liang Tang, Zhongming Zhao, Ping Tang, Haijun Yang:
SURE-based optimum-length S-G filter to reconstruct NDVI time series iteratively with outliers removal. Int. J. Wavelets Multiresolution Inf. Process. 18(2): 2050001:1-2050001:17 (2020) - [j85]Xia Ning, Chi Zhang, Kai Wang, Zhongming Zhao, Ewy A. Mathé:
Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions. BMC Medical Informatics Decis. Mak. 20(1): 77 (2020) - [j84]Xia Ning, Chi Zhang, Kai Wang, Zhongming Zhao, Ewy A. Mathé:
The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions. BMC Medical Informatics Decis. Mak. 20-S(2): 51 (2020) - [j83]Li Shen, Xinghua Shi, Zhongming Zhao, Kai Wang:
Informatics and machine learning methods for health applications. BMC Medical Informatics Decis. Mak. 20-S(11): 342 (2020) - [j82]Peilin Jia, Yulin Dai, Ruifeng Hu, Guangsheng Pei, Astrid Marilyn Manuel, Zhongming Zhao:
TSEA-DB: a trait?tissue association map for human complex traits and diseases. Nucleic Acids Res. 48(Database-Issue): D1022-D1030 (2020) - [j81]Deyou Tang, Bingrui Li, Tianyi Xu, Ruifeng Hu, Daqiang Tan, Xiaofeng Song, Peilin Jia, Zhongming Zhao:
VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Res. 48(Database-Issue): D633-D641 (2020) - [j80]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 Gonzalez-Perez, 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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - 2019
- [j79]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:
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Briefings Bioinform. 20(3): 842-856 (2019) - [j78]Hua Sun, Pora Kim, Peilin Jia, Aekyung Park, Han Liang, Zhongming Zhao:
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. Briefings Bioinform. 20(4): 1502-1512 (2019) - [j77]Guangsheng Pei, Yulin Dai, Zhongming Zhao, Peilin Jia:
deTS: tissue-specific enrichment analysis to decode tissue specificity. Bioinform. 35(19): 3842-3845 (2019) - [j76]Peilin Jia, Guangsheng Pei, Zhongming Zhao:
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. Bioinform. 35(24): 5207-5215 (2019) - [j75]Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy A. Mathé, Lai Wei, Kai Wang:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. BMC Bioinform. 20-S(24): 676 (2019) - [j74]Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song, Ping Han:
Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells. BMC Syst. Biol. 13(1): 14:1 (2019) - [j73]Saurav Mallik, Zhongming Zhao:
Distance based knowledge retrieval through rule mining for complex biomarker recognition from tri-omics profiles. Int. J. Comput. Biol. Drug Des. 12(2): 105-127 (2019) - [j72]Yaoyun Zhang, Cui Tao, Yang Gong, Kai Wang, Zhongming Zhao:
The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018). BMC Medical Informatics Decis. Mak. 19-S(1): 21:1-21:3 (2019) - 2018
- [j71]Pora Kim, Peilin Jia, Zhongming Zhao:
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. Briefings Bioinform. 19(3): 450-460 (2018) - [j70]Ruifeng Hu, Yulin Dai, Peilin Jia, Zhongming Zhao:
ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence. Database J. Biol. Databases Curation 2018: bay121 (2018) - [j69]Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinform. 19-S(17): 492:1-492:3 (2018) - [j68]Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, Zhongming Zhao:
TissGDB: tissue-specific gene database in cancer. Nucleic Acids Res. 46(Database-Issue): D1031-D1038 (2018) - 2017
- [j67]Peilin Jia, Zhongming Zhao:
Impacts of somatic mutations on gene expression: an association perspective. Briefings Bioinform. 18(3): 413-425 (2017) - [j66]Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang:
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinform. 18(1): 388 (2017) - [j65]Zhandong Liu, W. Jim Zheng, Genevera I. Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinform. 18(S-11): 405:1-405:3 (2017) - [j64]W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst. Biol. 11(S-5): 88:1-88:3 (2017) - [j63]Cui Tao, Yang Gong, Hua Xu, Zhongming Zhao:
Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. BMC Medical Informatics Decis. Mak. 17(2): 77:1-77:3 (2017) - [j62]Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao:
mutLBSgeneDB: mutated ligand binding site gene DataBase. Nucleic Acids Res. 45(Database-Issue): D256-D263 (2017) - [j61]Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao:
SZGR 2.0: a one-stop shop of schizophrenia candidate genes. Nucleic Acids Res. 45(Database-Issue): D915-D924 (2017) - [j60]Saurav Mallik, Zhongming Zhao:
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. 5(4): 302-327 (2017) - 2016
- [j59]Feixiong Cheng, Junfei Zhao, Zhongming Zhao:
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Briefings Bioinform. 17(4): 642-656 (2016) - [j58]Wei Jiang, Ramkrishna Mitra, Chen-Ching Lin, Quan Wang, Feixiong Cheng, Zhongming Zhao:
Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. Briefings Bioinform. 17(6): 996-1008 (2016) - [j57]Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan:
Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. BMC Syst. Biol. 10(S-3): 61 (2016) - [j56]Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao:
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst. Biol. 10(S-3): 65 (2016) - [j55]Feixiong Cheng, Junfei Zhao, Michaela Fooksa, Zhongming Zhao:
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. 23(4): 681-691 (2016) - [j54]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:
An informatics research agenda to support precision medicine: seven key areas. J. Am. Medical Informatics Assoc. 23(4): 791-795 (2016) - [j53]Pora Kim, Feixiong Cheng, Junfei Zhao, Zhongming Zhao:
ccmGDB: a database for cancer cell metabolism genes. Nucleic Acids Res. 44(Database-Issue): 959-968 (2016) - [j52]Min Zhao, Pora Kim, Ramkrishna Mitra, Junfei Zhao, Zhongming Zhao:
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res. 44(Database-Issue): 1023-1031 (2016) - [j51]Feixiong Cheng, James L. Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H. Rubin:
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput. Biol. 12(9) (2016) - [j50]Yutian Cao, Gang Wang, Dongmei Yan, Zhongming Zhao:
Two Algorithms for the Detection and Tracking of Moving Vehicle Targets in Aerial Infrared Image Sequences. Remote. Sens. 8(1): 28 (2016) - 2015
- [j49]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:
Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. BioData Min. 8: 7 (2015) - [j48]Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao:
Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. Bioinform. 31(1): 84-93 (2015) - [j47]Quan Wang, Hui Yu, Zhongming Zhao, Peilin Jia:
EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles. Bioinform. 31(15): 2591-2594 (2015) - [j46]Junfei Zhao, Feixiong Cheng, Zhongming Zhao:
SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations. BMC Bioinform. 16(S15): P21 (2015) - [j45]Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun:
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Syst. Biol. 9(S-4): S2 (2015) - [j44]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:
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. 11(6) (2015) - [j43]Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao:
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types. PLoS Comput. Biol. 11(9) (2015) - [j42]Yuan Yuan, Yu Meng, Lei Lin, Hichem Sahli, Anzhi Yue, Jingbo Chen, Zhongming Zhao, Yun-long Kong, Dong-xu He:
Continuous Change Detection and Classification Using Hidden Markov Model: A Case Study for Monitoring Urban Encroachment onto Farmland in Beijing. Remote. Sens. 7(11): 15318-15339 (2015) - 2014
- [j41]Hui Yu, Zhongming Zhao:
Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses. BMC Bioinform. 15(S-10): P33 (2014) - [j40]Huiru Zheng, Rui Jiang, Zhongming Zhao:
Integrated Approach in Systems Biology. Comput. Math. Methods Medicine 2014: 656473:1-656473:2 (2014) - [j39]Ramkrishna Mitra, Zhongming Zhao:
The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. Int. J. Comput. Biol. Drug Des. 7(4): 384-393 (2014) - [j38]Peilin Jia, Zhongming Zhao:
VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data. PLoS Comput. Biol. 10(2) (2014) - [j37]Bin Wu, Jian Yang, Zhongming Zhao, Yu Meng, Anzhi Yue, Jingbo Chen, Dong-xu He, Xingchun Liu, Shunxi Liu:
Parcel-Based Change Detection in Land-Use Maps by Adopting the Holistic Feature. IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens. 7(8): 3482-3490 (2014) - 2013
- [j36]Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao, Zhongming Zhao:
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Briefings Bioinform. 14(4): 506-519 (2013) - [j35]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:
No-boundary thinking in bioinformatics research. BioData Min. 6: 19 (2013) - [j34]Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao:
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinform. 14(S-11): S1 (2013) - [j33]Hui Yu, Zhongming Zhao:
Differential coexpression network modules observed in human hepatocellular carcinoma progression. BMC Bioinform. 14(S-17): A11 (2013) - [j32]Morgan Harrell, Junfeng Xia, Zhongming Zhao:
Network analysis of gene fusions in human cancer. BMC Bioinform. 14(S-17): A13 (2013) - [j31]Ramkrishna Mitra, Jingchun Sun, Min Zhao, Zhongming Zhao:
Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer. BMC Bioinform. 14(S-17): A14 (2013) - [j30]Huy Vuong, Zhongming Zhao:
A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling. BMC Bioinform. 14(S-17): A15 (2013) - [j29]Hui Yu, Chen-Ching Lin, Yuan-Yuan Li, Zhongming Zhao:
Dynamic protein interaction modules in human hepatocellular carcinoma progression. BMC Syst. Biol. 7(S-5): S2 (2013) - [j28]Min Zhao, Jingchun Sun, Zhongming Zhao:
TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res. 41(Database-Issue): 970-976 (2013) - 2012
- [j27]Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, Zhongming Zhao:
BioEve Search: A Novel Framework to Facilitate Interactive Literature Search. Adv. Bioinformatics 2012: 509126:1-509126:12 (2012) - [j26]Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao:
DTome: a web-based tool for drug-target interactome construction. BMC Bioinform. 13(S-9): S7 (2012) - [j25]Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang:
Advances in systems biology: computational algorithms and applications. BMC Syst. Biol. 6(S-3): S1 (2012) - [j24]Peilin Jia, Yang Liu, Zhongming Zhao:
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. BMC Syst. Biol. 6(S-3): S13 (2012) - [j23]Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun, Zhongming Zhao, Xue-wen Chen, Michael E. Matheny, Hua Xu:
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [j22]Peilin Jia, Lily Wang, Ayman H. Fanous, Carlos N. Pato, Todd L. Edwards, Zhongming Zhao:
Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia. PLoS Comput. Biol. 8(7) (2012) - [j21]Jingchun Sun, Xue Gong, Benjamin Purow, Zhongming Zhao:
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput. Biol. 8(7) (2012) - 2011
- [j20]Peilin Jia, Siyuan Zheng, Jirong Long, Wei Zheng, Zhongming Zhao:
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinform. 27(1): 95-102 (2011) - [j19]Lily Wang, Peilin Jia, Russell D. Wolfinger, Xi Chen, Britney L. Grayson, Thomas M. Aune, Zhongming Zhao:
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinform. 27(5): 686-692 (2011) - [j18]Siyuan Zheng, Zhongming Zhao:
Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach. BMC Bioinform. 12(S-7): A4 (2011) - [j17]Peilin Jia, Chung-Feng Kao, Po-Hsiu Kuo, Zhongming Zhao:
A comprehensive network and pathway analysis of candidate genes in major depressive disorder. BMC Syst. Biol. 5(S-3): S12 (2011) - [j16]Junfeng Xia, Jingchun Sun, Peilin Jia, Zhongming Zhao:
Do cancer proteins really interact strongly in the human protein-protein interaction network? Comput. Biol. Chem. 35(3): 121-125 (2011) - [j15]Zhongming Zhao, Junfeng Xia, Öznur Tastan, Irtisha Singh, Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman:
Virus interactions with human signal transduction pathways. Int. J. Comput. Biol. Drug Des. 4(1): 83-105 (2011) - [j14]Xue Gong, Jingchun Sun, Zhongming Zhao:
Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors. Int. J. Comput. Biol. Drug Des. 4(2): 111-126 (2011) - [j13]Wen-Ran Zhang, Anand K. Pandurangi, Karl E. Peace, Yan-Qing Zhang, Zhongming Zhao:
MentalSquares: A generic bipolar Support Vector Machine for psychiatric disorder classification, diagnostic analysis and neurobiological data mining. Int. J. Data Min. Bioinform. 5(5): 532-557 (2011) - [j12]Xiaonan Luo, Zhongming Zhao, Zhuo Su, Yun Liang:
Multiple-cue saliency measurement and optimized image composition for image retargeting. J. Comput. Appl. Math. 236(5): 704-713 (2011) - 2010
- [j11]Jingchun Sun, Leng Han, Zhongming Zhao:
Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artif. Intell. Medicine 48(2-3): 99-106 (2010) - [j10]Peilin Jia, Zhongming Zhao:
Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia. BMC Bioinform. 11(S-4): O1 (2010) - [j9]Hung-Chung Huang, Siyuan Zheng, Zhongming Zhao:
Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes. BMC Bioinform. 11(S-4): P23 (2010) - [j8]An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao:
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst. Biol. 4: 10 (2010) - [j7]Kellie J. Archer, Zhongming Zhao, Tobias Guennel, Daniel G. Maluf, Robert A. Fisher, Valeria R. Mas:
Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. Int. J. Comput. Biol. Drug Des. 3(1): 52-67 (2010) - [j6]Peilin Jia, Jian Tian, Zhongming Zhao:
Assessing gene length biases in gene set analysis of Genome-Wide Association Studies. Int. J. Comput. Biol. Drug Des. 3(4): 297-310 (2010) - 2009
- [j5]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:
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case. Bioinform. 25(19): 2595-2602 (2009) - [j4]Leng Han, Zhongming Zhao:
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinform. 10 (2009) - [j3]An-Yuan Guo, Bradley Todd Webb, Michael F. Miles, Mark P. Zimmerman, Kenneth S. Kendler, Zhongming Zhao:
ERGR: An ethanol-related gene resource. Nucleic Acids Res. 37(Database-Issue): 840-845 (2009) - 2007
- [j2]Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao:
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinform. 8 (2007) - 2005
- [j1]Fengkai Zhang, Zhongming Zhao:
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinform. 21(10): 2517-2519 (2005)
Conference and Workshop Papers
- 2022
- [c40]Supantha Das, Arnab Hazra, Soumen Kumar Pati, Soumadip Ghosh, Saurav Mallik, Suharta Banerjee, Ayan Mukherji, Aimin Li, Zhongming Zhao:
Detection of Chronic Kidney Disease Using Neuro-Fuzzy Rule-based Classifier. BIBM 2022: 2839-2845 - [c39]Partho Ghose, Selina Sharmin, Loveleen Gaur, Zhongming Zhao:
Grid-Search Integrated Optimized Support Vector Machine Model for Breast Cancer Detection. BIBM 2022: 2846-2852 - 2021
- [c38]Aman Chandra Kaushik, Aamir Mehmood, Ajay Kumar, Ankit Babu, Dong-Qing Wei, Zhongming Zhao:
Mining Cancer Cell Line-Based Drugs to Benefit KRAS(G12D) Pancreatic Adenocarcinoma Patients. BIBM 2021: 2423-2428 - [c37]Saurav Mallik, Souvik Rakshit, Ujjwal Maulik, Zhongming Zhao:
Negatively-Associated Maximal Frequent Geneset Mining on DNA Methylation Profile. BIBM 2021: 2443-2450 - 2019
- [c36]Saurav Mallik, Soumita Seth, Tapas Bhadra, Namrata Tomar, Zhongming Zhao:
A Multi-classifier Model to Identify Mitochondrial Respiratory Gene Signatures in Human Cancer. BIBM 2019: 1928-1935 - 2017
- [c35]Saurav Mallik, Zhongming Zhao:
TrapRM: Transcriptomic and proteomic rule mining using weighted shortest distance based multiple minimum supports for multi-omics dataset. BIBM 2017: 2187-2194 - [c34]Luca Giancardo, Kirk Roberts, Zhongming Zhao:
Representation Learning for Retinal Vasculature Embeddings. FIFI/OMIA@MICCAI 2017: 243-250 - [c33]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:
No-Boundary Thinking in Bioinformatics. PSB 2017: 646-648 - 2013
- [c32]Peilin Jia, Zhongming Zhao:
Network-based mutation analysis of putative cancer genes from next-generation sequencing data. BIBM 2013: 41 - [c31]Huiru Zheng, Haiying Wang, Hua Xu, Zhongming Zhao, Francisco Azuaje:
Correlating adverse drug reactions with biological pathways in humans. BIBM 2013: 197-200 - 2012
- [c30]Ravi V. Atreya, Jingchun Sun, Zhongming Zhao:
A network and functional investigation of illicit drugs and their targets. BIBM Workshops 2012: 564-569 - [c29]Qingguo Wang, Zhongming Zhao:
A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data. GENSiPS 2012: 38-41 - [c28]Min Zhao, Jingchun Sun, Zhongming Zhao:
Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspective. GENSiPS 2012: 101-102 - [c27]Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu:
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. Pacific Symposium on Biocomputing 2012: 422-433 - 2011
- [c26]Jingchun Sun, Paul Hart, Zhongming Zhao:
Development and implementation of a novel computational tool for an efficient construction of drug-target interactome. BIBM Workshops 2011: 274-279 - [c25]Peilin Jia, Zhongming Zhao:
Network-assisted causal gene detection in genome-wide association studies: an improved module search algorithm. GENSiPS 2011: 131-134 - [c24]Zhixi Su, Junfeng Xia, Zhongming Zhao:
Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region? ICIC (3) 2011: 253-258 - 2010
- [c23]Xue Gong, Peilin Jia, Zhongming Zhao:
Investigating microRNA-transcription factor mediated regulatory network in glioblastoma. BIBM Workshops 2010: 258-263 - [c22]Leng Han, Siyuan Zheng, Shuying Sun, Tim Hui-Ming Huang, Zhongming Zhao:
Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines. ICIC (1) 2010: 277-284 - 2009
- [c21]Zhongming Zhao, Shivi Kansal, Bonny L. Bukaveckas:
SmartWarf - A portable automated warfarin dosing tool. CTS 2009: 348-355 - [c20]Jingchun Sun, Peilin Jia, Zhongming Zhao:
Global Network Features of Cancer Genes in the Human Interactome. IJCBS 2009: 412-416 - [c19]Peilin Jia, Jingchun Sun, Leng Han, Zhongming Zhao:
Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks. IJCBS 2009: 442-447 - 2008
- [c18]Jingchun Sun, Leng Han, Zhongming Zhao:
Schizophrenia Genes: Characteristics of Function and Protein Interaction Networks. BMEI (1) 2008: 437-441 - [c17]Yu Meng, Zhongming Zhao, Xin Du, Shu Peng:
Building Change Detection Based on Similarity Calibration. FSKD (3) 2008: 527-531 - [c16]Leng Han, Ruolin Yang, Bing Su, Zhongming Zhao:
An SVM-Based Algorithm for Classifying Promoter-Associated CpG Islands in the Human and Mouse Genomes. ICIC (2) 2008: 975-981 - [c15]Christopher J. Friedline, Xueping Zhang, Zendra E. Zehner, Zhongming Zhao:
FindSUMO: A PSSM-Based Method for Sumoylation Site Prediction. ICIC (2) 2008: 1004-1011 - [c14]Fen Chen, Zhensong Wang, Zhongming Zhao:
A fast two-step deblurring method for satellite images. SMC 2008: 814-819 - 2005
- [c13]Linli Cui, Ping Tang, Zhongming Zhao, Jun Shi:
A new identification method for artificial objects based on various features. Color Imaging: Processing, Hardcopy, and Applications 2005: 589-597 - [c12]Renxi Chen, Zhongming Zhao, Zhong Chen:
Image compression based on unrestrained sized wavelet transform. IGARSS 2005: 3 - [c11]Dongmei Yan, Zhongming Zhao, Zhong Chen:
A fused road detection approach in high resolution multi-spectrum remote sensing imagery. IGARSS 2005: 1557-1560 - [c10]Ling Peng, Zhongming Zhao, Ziqi Guo, Qian Yao, Fen Chen, Jianglin Ma:
The indigenous remote sensing image processing system and its exertion strategy. IGARSS 2005: 3163-3166 - [c9]Zhong Chen, Zhongming Zhao, Dongmei Yan, Renxi Chen:
Multi-scale segmentation of the high resolution remote sensing image. IGARSS 2005: 3682-3684 - [c8]Fen Chen, Zhongming Zhao, Ling Peng, Dongmei Yan:
Clouds and cloud shadows removal from high-resolution remote sensing images. IGARSS 2005: 4256-4259 - 2004
- [c7]Yanfeng Wei, Zhongming Zhao, Jianghong Song:
Urban building extraction from high-resolution satellite panchromatic image using clustering and edge detection. IGARSS 2004: 2008-2010 - [c6]Jianghong Song, Zhongming Zhao, Qingye Zeng, Yanfeng Wei:
An algorithm for eliminating the isolated regions based on connected area in image classification. IGARSS 2004: 3058-3061 - [c5]Linli Cui, Wenyi Fan, Zhongming Zhao, Jun Shi, Ling Peng:
An integrated classification strategy of hyperspectral imaging spectrometer data. IGARSS 2004: 3283-3285 - [c4]Ling Peng, Zhongming Zhao, Jianglin Ma:
Texture image segmentation based on wavelet-domain hidden Markov models. IGARSS 2004: 3829-3832 - [c3]Ling Peng, Zhongming Zhao, Linli Cui, Lu Wang:
Remote sensing study based on IRSA Remote Sensing Image Processing System. IGARSS 2004: 4829-4832 - 2003
- [c2]Jianwei Ma, Zhongming Zhao, Ge Zhao, Ping Tang:
Automatic change detection of artificial objects in multitemporal high spatial resolution remotely sensed imagery. IGARSS 2003: 3356-3358 - [c1]Dongmei Yan, Zhongming Zhao:
Road detection from Quickbird fused image using IHS transform and morphology. IGARSS 2003: 3967-3969
Editorship
- 2010
- [e1]De-Shuang Huang, Zhongming Zhao, Vitoantonio Bevilacqua, Juan Carlos Figueroa García:
Advanced Intelligent Computing Theories and Applications, 6th International Conference on Intelligent Computing, ICIC 2010, Changsha, China, August 18-21, 2010. Proceedings. Lecture Notes in Computer Science 6215, Springer 2010, ISBN 978-3-642-14921-4 [contents]
Reference Works
- 2019
- [r1]Zhongming Zhao, Junfeng Xia:
Computational Approaches for Modeling Signal Transduction Networks. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 856-863
Informal and Other Publications
- 2024
- [i2]Anindita Nath, Savannah Mwesigwa, Yulin Dai, Xiaoqian Jiang, Zhongming Zhao:
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console. CoRR abs/2404.04299 (2024) - 2020
- [i1]Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean I. Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim:
Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation. CoRR abs/2009.10931 (2020)
Coauthor Index
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