Works by Zhongming Zhao

Results: 343

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

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

iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics Open Access.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 3, p. 1, doi. 10.1093/bib/bbaf296

By:

Hsieh, Kang-Lin;
Zhang, Kai;
Chu, Yan;
Yu, Lishan;
Li, Xiaoyang;
Hu, Nuo;
Kawosa, Isha;
Pilié, Patrick G;
Bhattacharya, Pratip K;
Zhi, Degui;
Jiang, Xiaoqian;
Zhao, Zhongming;
Dai, Yulin

Publication type:

Article

Features and Trend of Loss of Promoter-Associated CpG Islands in the Human and Mouse Genomes.

Published in:

Molecular Biology & Evolution, 2007, v. 24, n. 9, p. 1991, doi. 10.1093/molbev/msm128

By:

Jiang, Cizhong;
Han, Leng;
Su, Bing;
Li, Wen-Hsiung;
Zhao, Zhongming

Publication type:

Article

Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions.

Published in:

Molecular Biology & Evolution, 2007, v. 24, n. 1, p. 23, doi. 10.1093/molbev/msl156

By:

Zhongming Zhao;
Cizhong Jiang

Publication type:

Article

MET Exon 14 Skipping in Non-Small Cell Lung Cancer.

Published in:

Oncologist, 2016, v. 21, n. 4, p. 481, doi. 10.1634/theoncologist.2015-0510

By:

Heist, Rebecca S.;
Shim, Hyo Sup;
Gingipally, Shalini;
Mino‐Kenudson, Mari;
Le, Long;
Gainor, Justin F.;
Zheng, Zongli;
Aryee, Martin;
Xia, Junfeng;
Jia, Peilin;
Jin, Hailing;
Zhao, Zhongming;
Pao, William;
Engelman, Jeffrey A.;
Iafrate, A. John

Publication type:

Article

Early Detection of Parkinson's Disease Using Fusion of Discrete Wavelet Transformation and Histograms of Oriented Gradients.

Published in:

Mathematics (2227-7390), 2022, v. 10, n. 22, p. 4218, doi. 10.3390/math10224218

By:

Das, Himanish Shekhar;
Das, Akalpita;
Neog, Anupal;
Mallik, Saurav;
Bora, Kangkana;
Zhao, Zhongming

Publication type:

Article

Machine Learning Based Approach for Automated Cervical Dysplasia Detection Using Multi-Resolution Transform Domain Features.

Published in:

Mathematics (2227-7390), 2022, v. 10, n. 21, p. 4126, doi. 10.3390/math10214126

By:

Bora, Kangkana;
Mahanta, Lipi B.;
Borah, Kasmika;
Chyrmang, Genevieve;
Barua, Barun;
Mallik, Saurav;
Das, Himanish Shekhar;
Zhao, Zhongming

Publication type:

Article

Unsupervised Learning for Feature Representation Using Spatial Distribution of Amino Acids in Aldehyde Dehydrogenase (ALDH2) Protein Sequences.

Published in:

Mathematics (2227-7390), 2022, v. 10, n. 13, p. 2228, doi. 10.3390/math10132228

By:

Khandelwal, Monika;
Sheikh, Sabha;
Rout, Ranjeet Kumar;
Umer, Saiyed;
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

MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.

Published in:

Scientific Reports, 2015, p. 8004, doi. 10.1038/srep08004

By:

Bandyopadhyay, Sanghamitra;
Ghosh, Dip;
Mitra, Ramkrishna;
Zhao, Zhongming

Publication type:

Article

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data.

Published in:

GigaScience, 2020, v. 9, n. 12, p. 1, doi. 10.1093/gigascience/giaa122

By:

Simon, Lukas M;
Yan, Fangfang;
Zhao, Zhongming

Publication type:

Article

ImmuneApp for HLA-I epitope prediction and immunopeptidome analysis.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53296-0

By:

Xu, Haodong;
Hu, Ruifeng;
Dong, Xianjun;
Kuang, Lan;
Zhang, Wenchao;
Tu, Chao;
Li, Zhihong;
Zhao, Zhongming

Publication type:

Article

ImmuneApp for HLA-I epitope prediction and immunopeptidome analysis.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53296-0

By:

Xu, Haodong;
Hu, Ruifeng;
Dong, Xianjun;
Kuang, Lan;
Zhang, Wenchao;
Tu, Chao;
Li, Zhihong;
Zhao, Zhongming

Publication type:

Article

Integrated analysis of racial disparities in genomic architecture identifies a trans‐ancestry prognostic subtype in bladder cancer.

Published in:

Molecular Oncology, 2023, v. 17, n. 4, p. 564, doi. 10.1002/1878-0261.13360

By:

Zhang, Baifeng;
Jia, Peilin;
Wang, Jiayin;
Pei, Guangsheng;
Wang, Changxi;
Pei, Shimei;
Li, Xiangchun;
Zhao, Zhongming;
Yi, Xin;
Guan, Xin‐yuan;
Huang, Yi

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

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

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

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

Genetic overlap between Alzheimer's disease and immune‐mediated diseases: An atlas of shared genetic determinants and biological convergence.

Published in:

Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2024, v. 20, p. 1, doi. 10.1002/alz.089871

By:

Enduru, Nitesh;
Fernandes, Brisa S.;
Bahrami, Shahram;
Dai, Yulin;
Andreassen, Ole;
Zhao, Zhongming

Publication type:

Article

Innately expressed estrogen-related receptors in the skeletal muscle are indispensable for exercise fitness.

Published in:

FASEB Journal, 2023, v. 37, n. 2, p. 1, doi. 10.1096/fj.202201518R

By:

Sopariwala, Danesh H.;
Rios, Andrea S.;
Guangsheng Pei;
Roy, Anirban;
da Silva, Meiricris Tomaz;
Hao Thi Thu Nguyen;
Saley, Addison;
Van Drunen, Rachel;
Kralli, Anastasia;
Mahan, Kristin;
Zhongming Zhao;
Kumar, Ashok;
Narkar, Vihang A.

Publication type:

Article

Hepatic circadian and differentiation factors control liver susceptibility for fatty liver disease and tumorigenesis.

Published in:

FASEB Journal, 2022, v. 36, n. 9, p. 1, doi. 10.1096/fj.202101398R

By:

Fekry, Baharan;
Ribas‐Latre, Aleix;
Drunen, Rachel Van;
Santos, Rafael Bravo;
Shivshankar, Samay;
Dai, Yulin;
Zhao, Zhongming;
Yoo, Seung‐hee;
Chen, Zheng;
Sun, Kai;
Sladek, Frances M.;
Younes, Mamoun;
Eckel‐Mahan, Kristin

Publication type:

Article

Estrogen-related receptor α is involved in angiogenesis and skeletal muscle revascularization in hindlimb ischemia.

Published in:

FASEB Journal, 2021, v. 35, n. 5, p. 1, doi. 10.1096/fj.202001794RR

By:

Sopariwala, Danesh H.;
Likhite, Neah;
Gungsheng Pei;
Haroon, Fnu;
Lin, Lisa;
Yadav, Vikas;
Zhongming Zhao;
Narkar, Vihang A.

Publication type:

Article

Hypoxia-inducible factor-dependent induction of myeloid-derived netrin-1 attenuates natural killer cell infiltration during endotoxin-induced lung injury.

Published in:

FASEB Journal, 2021, v. 35, n. 4, p. 1, doi. 10.1096/fj.202002407R

By:

Berg, Nathaniel K.;
Jiwen Li;
Boyun Kim;
Mills, Tingting;
Guangsheng Pei;
Zhongming Zhao;
Xiangyun Li;
Xu Zhang;
Wei Ruan;
Eltzschig, Holger K.;
Xiaoyi Yuan

Publication type:

Article

Connectivity Map Analysis of Nonsense-Mediated Decay-Positive BMPR2-Related Hereditary Pulmonary Arterial Hypertension Provides Insights into Disease Penetrance.

Published in:

American Journal of Respiratory Cell & Molecular Biology, 2012, v. 47, n. 1, p. 20, doi. 10.1165/rcmb.2011-0251OC

By:

Flynn, Charles;
Siyuan Zheng;
Ling Yan;
Hedges, Lora;
Womack, Bethany;
Fessel, Josh;
Cogan, Joy;
Austin, Eric;
Loyd, James;
West, James;
Zhongming Zhao;
Hamid, Rizwan

Publication type:

Article

Improved liver disease prediction from clinical data through an evaluation of ensemble learning approaches.

Published in:

BMC Medical Informatics & Decision Making, 2024, v. 24, n. 1, p. 1, doi. 10.1186/s12911-024-02550-y

By:

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

Publication type:

Article

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

GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae500

By:

Nath, Anindita;
Mwesigwa, Savannah;
Dai, Yulin;
Jiang, Xiaoqian;
Zhao, Zhongming

Publication type:

Article

KCOSS: an ultra-fast k-mer counter for assembled genome analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 933, doi. 10.1093/bioinformatics/btab797

By:

Tang, Deyou;
Li, Yucheng;
Tan, Daqiang;
Fu, Juan;
Tang, Yelei;
Lin, Jiabin;
Zhao, Rong;
Du, Hongli;
Zhao, Zhongming

Publication type:

Article

Genome-wide CRISPR screen reveals the synthetic lethality between BCL2L1 inhibition and radiotherapy.

Published in:

Life Science Alliance, 2024, v. 7, n. 4, p. 1, doi. 10.26508/lsa.202302353

By:

Ling Yin;
Xiaoding Hu;
Guangsheng Pei;
Mengfan Tang;
You Zhou;
Huimin Zhang;
Min Huang;
Siting Li;
Jie Zhang;
Citu Citu;
Zhongming Zhao;
Debeb, Bisrat G.;
Xu Feng;
Junjie Chen

Publication type:

Article

Adipose tissue-specific ablation of Ces1d causes metabolic dysregulation in mice.

Published in:

Life Science Alliance, 2022, v. 5, n. 8, p. 1, doi. 10.26508/lsa.202101209

By:

Gang Li;
Xin Li;
Li Yang;
Shuyue Wang;
Yulin Dai;
Fekry, Baharan;
Veillon, Lucas;
Lin Tan;
Berdeaux, Rebecca;
Eckel-Mahan, Kristin;
Lorenzi, Philip L.;
Zhongming Zhao;
Lehner, Richard;
Kai Sun

Publication type:

Article

An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change.

Published in:

Biomedicines, 2021, v. 9, n. 6, p. 657, doi. 10.3390/biomedicines9060657

By:

Xu, Tianyi;
Wang, LiPing;
Jia, Peilin;
Song, Xiaofeng;
Zhao, Zhongming

Publication type:

Article

A Method for Bridging Population-Specific Genotypes to Detect Gene Modules Associated with Alzheimer's Disease.

Published in:

Cells (2073-4409), 2022, v. 11, n. 14, p. N.PAG, doi. 10.3390/cells11142219

By:

Dai, Yulin;
Jia, Peilin;
Zhao, Zhongming;
Gottlieb, Assaf

Publication type:

Article

Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.603509

By:

Liu, Teng;
Jia, Peilin;
Fang, Bingliang;
Zhao, Zhongming

Publication type:

Article

Enhancing the utility of polygenic scores in Alzheimer's disease through systematic curation and annotation.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1507395

By:

Mwesigwa, Savannah;
Dai, Yulin;
Enduru, Nitesh;
Zhao, Zhongming

Publication type:

Article

TSGene: a web resource for tumor suppressor genes.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D970, doi. 10.1093/nar/gks937

By:

Min Zhao;
Jingchun Sun;
Zhongming Zhao

Publication type:

Article

Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 20, p. 6985, doi. 10.1093/nar/gkq579

By:

Chmielecki, Juliann;
Peifer, Martin;
Jia, Peilin;
Socci, Nicholas D.;
Hutchinson, Katherine;
Viale, Agnes;
Zhao, Zhongming;
Thomas, Roman K.;
Pao, William

Publication type:

Article

ERGR: An ethanol-related gene resource.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D840, doi. 10.1093/nar/gkn816

By:

Guo, An-Yuan;
Webb, Bradley T.;
Miles, Michael F.;
Zimmerman, Mark P.;
Kendler, Kenneth S.;
Zhao, Zhongming

Publication type:

Article

Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes.

Published in:

European Journal of Human Genetics, 2012, v. 20, n. 10, p. 1078, doi. 10.1038/ejhg.2012.47

By:

Webb, Bradley T;
Guo, An-Yuan;
Maher, Brion S;
Zhao, Zhongming;
van den Oord, Edwin J;
Kendler, Kenneth S;
Riley, Brien P;
Gillespie, Nathan A;
Prescott, Carol A;
Middeldorp, Christel M;
Willemsen, Gonneke;
de Geus, Eco JC;
Hottenga, Jouke-Jan;
Boomsma, Dorret I;
Slagboom, Eline P;
Wray, Naomi R;
Montgomery, Grant W;
Martin, Nicholas G;
Wright, Margie J;
Heath, Andrew C

Publication type:

Article

The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Data-driven analytics in biomedical genomics.

Published in:

2020

By:

Shi, Xinghua;
Zhao, Zhongming;
Wang, Kai;
Shen, Li

Publication type:

Editorial

Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders.

Published in:

BMC Medical Genomics, 2020, v. 13, p. 1, doi. 10.1186/s12920-020-00832-8

By:

Dai, Yulin;
O'Brien, Timothy D.;
Pei, Guangsheng;
Zhao, Zhongming;
Jia, Peilin

Publication type:

Article

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics.

Published in:

2020

By:

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

Publication type:

Editorial

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate.

Published in:

BMC Medical Genomics, 2020, v. 13, p. 1, doi. 10.1186/s12920-020-0675-4

By:

Yan, Fangfang;
Dai, Yulin;
Iwata, Junichi;
Zhao, Zhongming;
Jia, Peilin

Publication type:

Article

Dense module searching for gene networks associated with multiple sclerosis.

Published in:

BMC Medical Genomics, 2020, v. 13, p. 1, doi. 10.1186/s12920-020-0674-5

By:

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

Publication type:

Article

MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12920-019-0546-z

By:

Suzuki, Akiko;
Li, Aimin;
Gajera, Mona;
Abdallah, Nada;
Zhang, Musi;
Zhao, Zhongming;
Iwata, Junichi

Publication type:

Article

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12920-019-0535-2

By:

Gajera, Mona;
Desai, Neha;
Suzuki, Akiko;
Li, Aimin;
Zhang, Musi;
Jun, Goo;
Jia, Peilin;
Zhao, Zhongming;
Iwata, Junichi

Publication type:

Article