Works matching AU Zhao, Zhongming

Results: 342

An informatics research agenda to support precision medicine: seven key areas.

Published in:

2016

By:

Tenenbaum, Jessica D.;
Avillach, Paul;
Benham-Hutchins, Marge;
Breitenstein, Matthew K.;
Crowgey, Erin L.;
Hoffman, Mark A.;
Xia Jiang;
Madhavan, Subha;
Mattison, John E.;
Nagarajan, Radhakrishnan;
Ray, Bisakha;
Shin, Dmitriy;
Visweswaran, Shyam;
Zhongming Zhao;
Freimuth, Robert R.;
Jiang, Xia;
Zhao, Zhongming

Publication type:

journal article

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.

Published in:

2016

By:

Feixiong Cheng;
Junfei Zhao;
Fooksa, Michaela;
Zhongming Zhao;
Cheng, Feixiong;
Zhao, Junfei;
Zhao, Zhongming

Publication type:

journal article

Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension.

Published in:

2016

By:

Hemnes, Anna R.;
Min Zhao;
West, James;
Newman, John H.;
Rich, Stuart;
Archer, Stephen L.;
Robbins, Ivan M.;
Blackwell, Timothy S.;
Cogan, Joy;
Loyd, James E.;
Zhongming Zhao;
Gaskill, Christa;
Jetter, Christopher;
Kropski, Jonathan A.;
Majka, Susan M.;
Austin, Eric D.;
Zhao, Min;
Zhao, Zhongming

Publication type:

journal article

MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer.

Published in:

2016

By:

Edmonds, Mick D.;
Boyd, Kelli L.;
Moyo, Tamara;
Mitra, Ramkrishna;
Duszynski, Robert;
Arrate, Maria Pia;
Xi Chen;
Zhongming Zhao;
Blackwell, Timothy S.;
Andl, Thomas;
Eischen, Christine M.;
Chen, Xi;
Zhao, Zhongming

Publication type:

journal article

Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data.

Published in:

2017

By:

Cui Tao;
Yang Gong;
Hua Xu;
Zhongming Zhao;
Tao, Cui;
Gong, Yang;
Xu, Hua;
Zhao, Zhongming

Publication type:

Editorial

Genetic, Transcriptomic, and Epigenomic Insights into Sjögren's Disease: An Integrative Network Investigation and Immune Diseases Comparison.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4637, doi. 10.3390/ijms26104637

By:

Enduru, Nitesh;
Manuel, Astrid M.;
Zhao, Zhongming

Publication type:

Article

Enhanced and Interpretable Prediction of Multiple Cancer Types Using a Stacking Ensemble Approach with SHAP Analysis.

Published in:

Bioengineering (Basel), 2025, v. 12, n. 5, p. 472, doi. 10.3390/bioengineering12050472

By:

Ganie, Shahid Mohammad;
Dutta Pramanik, Pijush Kanti;
Zhao, Zhongming

Publication type:

Article

Mutations in GDF6 are associated with vertebral segmentation defects in Klippel-Feil syndrome.

Published in:

Human Mutation, 2008, v. 29, n. 8, p. 1017, doi. 10.1002/humu.20741

By:

Tassabehji, May;
Fang, Zhi Ming;
Hilton, Emma N.;
McGaughran, Julie;
Zhao, Zhongming;
de Bock, Charles E.;
Howard, Emma;
Malass, Michael;
Donnai, Dian;
Diwan, Ashish;
Manson, Forbes D.C.;
Murrell, Dédée;
Clarke, Raymond A.

Publication type:

Article

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles.

Published in:

Bioinformatics, 2015, v. 31, n. 15, p. 2591, doi. 10.1093/bioinformatics/btv150

By:

Quan Wang;
Hui Yu;
Zhongming Zhao;
Peilin Jia

Publication type:

Article

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 84, doi. 10.1093/bioinformatics/btu603

By:

Xu, Yaomin;
Guo, Xingyi;
Sun, Jiayang;
Zhao, Zhongming

Publication type:

Article

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 686, doi. 10.1093/bioinformatics/btq728

By:

Wang, Lily;
Jia, Peilin;
Wolfinger, Russell D.;
Chen, Xi;
Grayson, Britney L.;
Aune, Thomas M.;
Zhao, Zhongming

Publication type:

Article

dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks.

Published in:

Bioinformatics, 2011, v. 27, n. 1, p. 95, doi. 10.1093/bioinformatics/btq615

By:

Jia, Peilin;
Zheng, Siyuan;
Long, Jirong;
Zheng, Wei;
Zhao, Zhongming

Publication type:

Article

A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2595, doi. 10.1093/bioinformatics/btp428

By:

Jingchun Sun;
Jia, Peilin;
Fanous, Ayman H.;
Webb, Bradley T.;
Van den Oord, Edwin J.C.G.;
Xiangning Chen;
Bukszar, Jozsef;
Kendler, Kenneth S.;
Zhongming Zhao

Publication type:

Article

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.

Published in:

Quantitative Biology, 2017, v. 5, n. 4, p. 302, doi. 10.1007/s40484-017-0119-0

By:

Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults.

Published in:

Fluids & Barriers of the CNS, 2017, p. 1, doi. 10.1186/s12987-017-0058-1

By:

Patton, Stephanie M.;
Quan Wang;
Hulgan, Todd;
Connor, James R.;
Jia, Peilin;
Zhongming Zhao;
Letendre, Scott L.;
Ellis, Ronald J.;
Bush, William S.;
Samuels, David C.;
Franklin, Donald R.;
Kaur, Harpreet;
Iudicello, Jennifer;
Grant, Igor;
Kallianpur, Asha R.

Publication type:

Article

MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data.

Published in:

Genes, 2023, v. 14, n. 6, p. 1222, doi. 10.3390/genes14061222

By:

Wang, Mingqiang;
Deng, Wankun;
Samuels, David C.;
Zhao, Zhongming;
Simon, Lukas M.

Publication type:

Article

PPIGCF: A Protein–Protein Interaction-Based Gene Correlation Filter for Optimal Gene Selection.

Published in:

Genes, 2023, v. 14, n. 5, p. 1063, doi. 10.3390/genes14051063

By:

Pati, Soumen Kumar;
Gupta, Manan Kumar;
Banerjee, Ayan;
Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments.

Published in:

Genes, 2022, v. 13, n. 7, p. 1210, doi. 10.3390/genes13071210

By:

Dai, Yulin;
Yu, Hui;
Yan, Qiheng;
Li, Bingrui;
Liu, Andi;
Liu, Wendao;
Jiang, Xiaoqian;
Kim, Yejin;
Guo, Yan;
Zhao, Zhongming

Publication type:

Article

siRNA Mediate RNA Interference Concordant with Early On-Target Transient Transcriptional Interference.

Published in:

Genes, 2021, v. 12, n. 8, p. 1290, doi. 10.3390/genes12081290

By:

Fang, Zhiming;
Zhao, Zhongming;
Eapen, Valsamma;
Clarke, Raymond A.

Publication type:

Article

Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death.

Published in:

Genes, 2021, v. 12, n. 8, p. 1183, doi. 10.3390/genes12081183

By:

Dai, Jun;
Leung, Ming;
Guan, Weihua;
Guo, Han-Tian;
Krasnow, Ruth E.;
Wang, Thomas J.;
El-Rifai, Wael;
Zhao, Zhongming;
Reed, Terry

Publication type:

Article

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods.

Published in:

Genes, 2021, v. 12, n. 5, p. 665, doi. 10.3390/genes12050665

By:

Yu, Hui;
Guo, Yan;
Chen, Jingchun;
Chen, Xiangning;
Jia, Peilin;
Zhao, Zhongming;
Zou, Quan

Publication type:

Article

Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches.

Published in:

Genes, 2021, v. 12, n. 5, p. 635, doi. 10.3390/genes12050635

By:

Jeong, Hyun-Hwan;
Jia, Johnathan;
Dai, Yulin;
Simon, Lukas M.;
Zhao, Zhongming;
Cai, James

Publication type:

Article

A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data.

Published in:

Genes, 2020, v. 11, n. 8, p. 931, doi. 10.3390/genes11080931

By:

Mallik, Saurav;
Seth, Soumita;
Bhadra, Tapas;
Zhao, Zhongming

Publication type:

Article

Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue.

Published in:

Genes, 2020, v. 11, n. 4, p. 1, doi. 10.3390/genes11040437

By:

Yan Guo;
Xia Ning;
Mathé, Ewy;
Kai Wang;
Lang Li;
Chi Zhang;
Zhongming Zhao

Publication type:

Article

Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles.

Published in:

Genes, 2019, v. 10, n. 8, p. 611, doi. 10.3390/genes10080611

By:

Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

Changes in the Microbial Community Diversity of Oil Exploitation.

Published in:

Genes, 2019, v. 10, n. 8, p. 556, doi. 10.3390/genes10080556

By:

Liu, Jingjing;
Wu, Jing;
Lin, Jiawei;
Zhao, Jian;
Xu, Tianyi;
Yang, Qichang;
Zhao, Jing;
Zhao, Zhongming;
Song, Xiaofeng

Publication type:

Article

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

Published in:

Genes, 2018, v. 9, n. 1, p. 7, doi. 10.3390/genes9010007

By:

Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells.

Published in:

Genes, 2017, v. 8, n. 12, p. 368, doi. 10.3390/genes8120368

By:

Yuan Cao;
Junjie Zhu;
Peilin Jia;
Zhongming Zhao

Publication type:

Article

Patterns and processes of somatic mutations in nine major cancers.

Published in:

BMC Medical Genomics, 2014, v. 7, n. 1, p. 1, doi. 10.1186/1755-8794-7-11

By:

Peilin Jia;
William Pao;
Zhongming Zhao

Publication type:

Article

Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells.

Published in:

2019

By:

Yang, Qichang;
Wu, Jing;
Zhao, Jian;
Xu, Tianyi;
Zhao, Zhongming;
Song, Xiaofeng;
Han, Ping

Publication type:

Correction Notice

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: systems biology on diverse data types.

Published in:

BMC Systems Biology, 2018, v. 12, n. 8, p. N.PAG, doi. 10.1186/s12918-018-0648-9

By:

Wang, Kai;
Liu, Xiaoming;
Guo, Yan;
Wu, Zhijin;
Zhi, Degui;
Ruan, Jianhua;
Zhao, Zhongming

Publication type:

Article

Circular RNA expression profiles during the differentiation of mouse neural stem cells.

Published in:

BMC Systems Biology, 2018, v. 12, n. 8, p. N.PAG, doi. 10.1186/s12918-018-0651-1

By:

Yang, Qichang;
Wu, Jing;
Zhao, Jian;
Xu, Tianyi;
Zhao, Zhongming;
Song, Xiaofeng;
Han, Ping

Publication type:

Article

Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm.

Published in:

BMC Systems Biology, 2018, v. 12, n. 8, p. N.PAG, doi. 10.1186/s12918-018-0650-2

By:

Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

Multiple transcription factors contribute to inter-chromosomal interaction in yeast.

Published in:

BMC Systems Biology, 2018, v. 12, n. 8, p. N.PAG, doi. 10.1186/s12918-018-0643-1

By:

Dai, Yulin;
Li, Chao;
Pei, Guangsheng;
Dong, Xiao;
Ding, Guohui;
Zhao, Zhongming;
Li, Yixue;
Jia, Peilin

Publication type:

Article

The challenges and opportunities of scRNA-seq in COVID-19 research and clinical translation.

Published in:

Virology Journal, 2022, v. 19, n. 1, p. 1, doi. 10.1186/s12985-022-01923-x

By:

Liu, Wendao;
Ye, Xiaohua;
An, Zhiqiang;
Zhao, Zhongming

Publication type:

Article

Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 8, p. 1, doi. 10.1186/1471-2164-13-S8-S16

By:

Zhongming Zhao;
An-Yuan Guo;
Van den Oord, Edwin JCG;
Aliev, Fazil;
Peilin Jia;
Edenberg, Howard J.;
Riley, Brien P.;
Dick, Danielle M.;
Bettinger, Jill C.;
Davies, Andrew G.;
Grotewiel, Michael S.;
Schuckit, Marc A.;
Agrawal, Arpana;
Kramer, John;
Nurnberger Jr, John I.;
Kendler, Kenneth S.;
Webb, Bradley T.;
Miles, Michael F.

Publication type:

Article

Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 8, p. 1, doi. 10.1186/1471-2164-13-S8-S7

By:

Junfeng Xia;
Leng Han;
Zhongming Zhao

Publication type:

Article

Genomics in 2012: challenges and opportunities in the next generation sequencing era.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 8, p. 1, doi. 10.1186/1471-2164-13-S8-S1

By:

Zhongming Zhao;
Yufei Huang;
Bing Zhang;
Yu Shyr;
Hua Xu

Publication type:

Article

RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 8, p. 1, doi. 10.1186/1471-2164-13-S8-S2

By:

Junzhe Xu;
Jingchun Sun;
Jingchun Chen;
Lily Wang;
Anna Li;
Helm, Matthew;
Dubovsky, Steven L.;
Bacanu, Silviu-Alin;
Zhongming Zhao;
Xiangning Chen

Publication type:

Article

Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 6, p. 1, doi. 10.1186/1471-2164-13-S6-S15

By:

Peilin Jia;
Zhongming Zhao

Publication type:

Article

Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome.

Published in:

BMC Genomics, 2011, v. 12, n. Suppl 5, p. 1, doi. 10.1186/1471-2164-12-S5-S15

By:

Zhixi Su;
Junfeng Xia;
Zhongming Zhao

Publication type:

Article

A comparative study of cancer proteins in the human protein-protein interaction network.

Published in:

BMC Genomics, 2010, v. 11, p. 1, doi. 10.1186/1471-2164-11-S3-S5

By:

Jingchun Sun;
Zhongming Zhao

Publication type:

Article

Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05448-0

By:

Valenzuela, Olga;
Cannataro, Mario;
Rusur, Irena;
Wang, Jianxin;
Zhao, Zhongming;
Rojas, Ignacio

Publication type:

Article

Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing.

Published in:

Cancer Immunology, Immunotherapy, 2022, v. 71, n. 6, p. 1479, doi. 10.1007/s00262-021-03084-2

By:

Ravirala, Divya;
Pei, Guangsheng;
Zhao, Zhongming;
Zhang, Xiaoliu

Publication type:

Article

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).

Published in:

Bioinformatics, 2005, v. 21, n. 10, p. 2517, doi. 10.1093/bioinformatics/bti377

By:

Fengkai Zhang;
Zhongming Zhao

Publication type:

Article

Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains.

Published in:

Open Forum Infectious Diseases, 2019, v. 6, n. 2, p. N.PAG, doi. 10.1093/ofid/ofz013

By:

Endres, Bradley T;
Begum, Khurshida;
Sun, Hua;
Walk, Seth T;
Memariani, Ali;
Lancaster, Chris;
Gonzales-Luna, Anne J;
Dotson, Kierra M;
Bassères, Eugénie;
Offiong, Charlene;
Tupy, Shawn;
Kuper, Kristi;
Septimus, Edward;
Arafat, Raouf;
Alam, M Jahangir;
Zhao, Zhongming;
Hurdle, Julian G;
Savidge, Tor C;
Garey, Kevin W

Publication type:

Article

Frontiers in Integrative Genomics and Translational Bioinformatics.

Published in:

BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/725491

By:

Zhao, Zhongming;
Jin, Victor X.;
Huang, Yufei;
Guda, Chittibabu;
Ruan, Jianhua

Publication type:

Article

Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations.

Published in:

BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/491502

By:

Chen, Yukun;
Sun, Jingchun;
Huang, Liang-Chin;
Xu, Hua;
Zhao, Zhongming

Publication type:

Article

Integrative genomics and computational systems medicine.

Published in:

2014

By:

McDermott, Jason E;
Huang, Yufei;
Zhang, Bing;
Xu, Hua;
Zhao, Zhongming

Publication type:

Journal Article

Network-assisted prediction of potential drugs for addiction.

Published in:

2014

By:

Sun, Jingchun;
Huang, Liang-Chin;
Xu, Hua;
Zhao, Zhongming

Publication type:

Journal Article