Works matching AU Zhongming Zhao

Results: 339

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

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

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

Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf090

By:

Liu, Wendao;
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

Classification of schizophrenia, bipolar disorder and major depressive disorder with comorbid traits and deep learning algorithms.

Published in:

Schizophrenia, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41537-025-00564-7

By:

Chen, Xiangning;
Lu, Yimei;
Cue, Joan Manuel;
Han, Mira V.;
Nimgaonkar, Vishwajit L.;
Weinberger, Daniel R.;
Han, Shizhong;
Zhao, Zhongming;
Chen, Jingchun

Publication type:

Article

A Convergent Study of Genetic Variants Associated With Crohn's Disease: Evidence From GWAS, Gene Expression, Methylation, eQTL and TWAS.

Published in:

Frontiers in Genetics, 2019, p. N.PAG, doi. 10.3389/fgene.2019.00318

By:

Dai, Yulin;
Pei, Guangsheng;
Zhao, Zhongming;
Jia, Peilin

Publication type:

Article

A gene regulatory network approach harmonizes genetic and epigenetic signals and reveals repurposable drug candidates for multiple sclerosis.

Published in:

Human Molecular Genetics, 2023, v. 32, n. 6, p. 998, doi. 10.1093/hmg/ddac265

By:

Manuel, Astrid M;
Dai, Yulin;
Jia, Peilin;
Freeman, Leorah A;
Zhao, Zhongming

Publication type:

Article

Identifying candidate genes and drug targets for Alzheimer's disease by an integrative network approach using genetic and brain region-specific proteomic data.

Published in:

Human Molecular Genetics, 2022, v. 31, n. 19, p. 3341, doi. 10.1093/hmg/ddac124

By:

Liu, Andi;
Manuel, Astrid M;
Dai, Yulin;
Fernandes, Brisa S;
Enduru, Nitesh;
Jia, Peilin;
Zhao, Zhongming

Publication type:

Article

Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice.

Published in:

Human Molecular Genetics, 2021, v. 30, n. 19, p. 1881, doi. 10.1093/hmg/ddab151

By:

Yoshioka, Hiroki;
Li, Aimin;
Suzuki, Akiko;
Ramakrishnan, Sai Shankar;
Zhao, Zhongming;
Iwata, Junichi

Publication type:

Article

microRNA regulation in cancer: One arm or two arms?

Published in:

International Journal of Cancer, 2015, v. 137, n. 6, p. 1516, doi. 10.1002/ijc.29512

By:

Mitra, Ramkrishna;
Sun, Jingchun;
Zhao, Zhongming

Publication type:

Article

Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38800-2

By:

Feofanova, Elena V.;
Brown, Michael R.;
Alkis, Taryn;
Manuel, Astrid M.;
Li, Xihao;
Tahir, Usman A.;
Li, Zilin;
Mendez, Kevin M.;
Kelly, Rachel S.;
Qi, Qibin;
Chen, Han;
Larson, Martin G.;
Lemaitre, Rozenn N.;
Morrison, Alanna C.;
Grieser, Charles;
Wong, Kari E.;
Gersztern, Robert E.;
Zhao, Zhongming;
Lasky-Su, Jessica;
Lin, Honghuang

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

Bundling evaluating changes in ecosystem service under karst rocky desertification restoration: projects a case study of Huajiang-Guanling, Guizhou province, Southwest China.

Published in:

Environmental Earth Sciences, 2022, v. 81, n. 10, p. 1, doi. 10.1007/s12665-022-10400-1

By:

Xu, Guoyu;
Xiong, Kangning;
Shu, Tian;
Shi, Yunjie;
Chen, Lisha;
Zheng, Lilin;
Fan, Hongxiang;
Zhao, Zhongming;
Yang, Zhenhua

Publication type:

Article

De novo mutations disturb early brain development more frequently than common variants in schizophrenia.

Published in:

American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2023, v. 192, n. 3/4, p. 62, doi. 10.1002/ajmg.b.32932

By:

Itai, Toshiyuki;
Jia, Peilin;
Dai, Yulin;
Chen, Jingchun;
Chen, Xiangning;
Zhao, Zhongming

Publication type:

Article

Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study.

Published in:

American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2017, v. 174, n. 4, p. 413, doi. 10.1002/ajmg.b.32530

By:

Jia, Peilin;
Zhao, Zhongming;
Hulgan, Todd;
Bush, William S.;
Samuels, David C.;
Bloss, Cinnamon S.;
Heaton, Robert K.;
Ellis, Ronald J.;
Schork, Nicholas;
Marra, Christina M.;
Collier, Ann C.;
Clifford, David B.;
Gelman, Benjamin B.;
Sacktor, Ned;
Morgello, Susan;
Simpson, David M.;
McCutchan, J. Allen;
Barnholtz‐Sloan, Jill S.;
Franklin, Donald R.;
Rosario, Debralee

Publication type:

Article

Association study of 83 candidate genes for bipolar disorder in chromosome 6q selected using an evidence-based prioritization algorithm.

Published in:

American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2013, v. 162B, n. 8, p. 898, doi. 10.1002/ajmg.b.32200

By:

Bigdeli, T. Bernard;
Maher, Brion S.;
Zhao, Zhongming;
Sun, Jingchun;
Medeiros, Helena;
Akula, Nirmala;
McMahon, Francis J.;
Carvalho, Celia;
Ferreira, Susana R.;
Azevedo, Maria H.;
Knowles, James A.;
Pato, Michele T.;
Pato, Carlos N.;
Fanous, Ayman H.

Publication type:

Article

Genetic Overlap of Schizophrenia and Bipolar Disorder in a High-Density Linkage Survey in the Portuguese Island Population.

Published in:

American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2012, v. 159B, n. 4, p. 383, doi. 10.1002/ajmg.b.32041

By:

Fanous, Ayman H.;
Middleton, Frank A.;
Gentile, Karen;
Amdur, Richard L.;
Maher, Brion S.;
Zhongming Zhao;
Jingchun Sun;
Medeiros, Helena;
Carvalho, Celia;
Ferreira, Susana R.;
Macedo, Antonio;
Knowles, James A.;
Azevedo, Maria H.;
Pato, Michele T.;
Pato, Carlos N.

Publication type:

Article

Chronic kidney disease prediction using boosting techniques based on clinical parameters.

Published in:

PLoS ONE, 2023, v. 18, n. 12, p. 1, doi. 10.1371/journal.pone.0295234

By:

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

Publication type:

Article

Federated learning based futuristic biomedical big-data analysis and standardization.

Published in:

PLoS ONE, 2023, v. 18, n. 10, p. 1, doi. 10.1371/journal.pone.0291631

By:

Fathima, Afifa Salsabil;
Basha, Syed Muzamil;
Ahmed, Syed Thouheed;
Mathivanan, Sandeep Kumar;
Rajendran, Sukumar;
Mallik, Saurav;
Zhao, Zhongming

Publication type:

Article

Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 4, p. 2202, doi. 10.3390/ijms22042202

By:

Yoshioka, Hiroki;
Wang, Yin-Ying;
Suzuki, Akiko;
Shayegh, Meysam;
Gajera, Mona V.;
Zhao, Zhongming;
Iwata, Junichi;
Gupta, Bhagwati

Publication type:

Article

DTome: a web-based tool for drug-target interactome construction.

Published in:

BMC Bioinformatics, 2012, v. 13, n. Suppl 9, p. 1, doi. 10.1186/1471-2105-13-S9-S7

By:

Jingchun Sun;
Yonghui Wu;
Hua Xu;
Zhongming Zhao

Publication type:

Article

Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach.

Published in:

2011

By:

Siyuan Zheng;
Zhongming Zhao

Publication type:

Abstract

CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-65

By:

Leng Han;
Zhongming Zhao

Publication type:

Article

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 414, doi. 10.1186/1471-2105-8-414

By:

Jingchun Sun;
Yan Sun;
Guohui Ding;
Qi Liu;
Chuan Wang;
Youyu He;
Tieliu Shi;
Yixue Li;
Zhongming Zhao

Publication type:

Article

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 9, p. 1, doi. 10.1371/journal.pcbi.1004497

By:

Cheng, Feixiong;
Liu, Chuang;
Lin, Chen-Ching;
Zhao, Junfei;
Jia, Peilin;
Li, Wen-Hsiung;
Zhao, Zhongming

Publication type:

Article

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004202

By:

Sun, Jingchun;
Zhao, Min;
Jia, Peilin;
Wang, Lily;
Wu, Yonghui;
Iverson, Carissa;
Zhou, Yubo;
Bowton, Erica;
Roden, Dan M.;
Denny, Joshua C.;
Aldrich, Melinda C.;
Xu, Hua;
Zhao, Zhongming

Publication type:

Article

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pcbi.1003460

By:

Jia, Peilin;
Zhao, Zhongming

Publication type:

Article

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002587

By:

Jia, Peilin;
Wang, Lily;
Fanous, Ayman H.;
Pato, Carlos N.;
Edwards, Todd L.;
Zhongming Zhao

Publication type:

Article

Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002488

By:

Jingchun Sun;
Xue Gong;
Purow, Benjamin;
Zhongming Zhao

Publication type:

Article

SURE-based optimum-length S-G filter to reconstruct NDVI time series iteratively with outliers removal.

Published in:

International Journal of Wavelets, Multiresolution & Information Processing, 2020, v. 18, n. 2, p. N.PAG, doi. 10.1142/S0219691320500010

By:

Tang, Liang;
Zhao, Zhongming;
Tang, Ping;
Yang, Haijun

Publication type:

Article

Aging- and alcohol-associated spatial transcriptomic signature in mouse acute pancreatitis reveals heterogeneity of inflammation and potential pathogenic factors.

Published in:

Journal of Molecular Medicine, 2024, v. 102, n. 8, p. 1051, doi. 10.1007/s00109-024-02460-6

By:

Tindall, Rachel R.;
Yang, Yuntao;
Hernandez, Isabella;
Qin, Amy;
Li, Jiajing;
Zhang, Yinjie;
Gomez, Thomas H.;
Younes, Mamoun;
Shen, Qiang;
Bailey-Lundberg, Jennifer M.;
Zhao, Zhongming;
Kraushaar, Daniel;
Castro, Patricia;
Cao, Yanna;
Zheng, W. Jim;
Ko, Tien C.

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

Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05120-6

By:

Fan, Huihui;
Wang, Feng;
Zeng, Andy;
Murison, Alex;
Tomczak, Katarzyna;
Hao, Dapeng;
Jelloul, Fatima Zahra;
Wang, Bofei;
Barrodia, Praveen;
Liang, Shaoheng;
Chen, Ken;
Wang, Linghua;
Zhao, Zhongming;
Rai, Kunal;
Jain, Abhinav K.;
Dick, John;
Daver, Naval;
Futreal, Andy;
Abbas, Hussein A.

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

Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network.

Published in:

Translational Psychiatry, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41398-018-0154-2

By:

Jia, Peilin;
Chen, Xiangning;
Fanous, Ayman H.;
Zhao, Zhongming

Publication type:

Article