Publications by authors named "Zhongming Zhao"

100Publications

A developmental stage specific network approach for studying dynamic transcription factor-microRNA co-regulation during craniofacial development.

Development 2020 Nov 24. Epub 2020 Nov 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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http://dx.doi.org/10.1242/dev.192948DOI Listing
November 2020

CSEA-DB: an omnibus for human complex trait and cell type associations.

Nucleic Acids Res 2020 Nov 19. Epub 2020 Nov 19.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkaa1064DOI Listing
November 2020

Machine learning to predict delayed cerebral ischemia and outcomes in subarachnoid hemorrhage.

Neurology 2020 Nov 12. Epub 2020 Nov 12.

Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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http://dx.doi.org/10.1212/WNL.0000000000011211DOI Listing
November 2020

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

Front Microbiol 2020 16;11:603509. Epub 2020 Oct 16.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States.

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http://dx.doi.org/10.3389/fmicb.2020.603509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596306PMC
October 2020

KinaseMD: kinase mutations and drug response database.

Nucleic Acids Res 2020 Nov 2. Epub 2020 Nov 2.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkaa945DOI Listing
November 2020

Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma.

Cancers (Basel) 2020 Sep 10;12(9). Epub 2020 Sep 10.

NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg L-1526, Luxembourg.

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http://dx.doi.org/10.3390/cancers12092583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563839PMC
September 2020

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

Genes (Basel) 2020 Aug 12;11(8). Epub 2020 Aug 12.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes11080931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465138PMC
August 2020

FOXK1 Participates in DNA Damage Response by Controlling 53BP1 Function.

Cell Rep 2020 Aug;32(6):108018

Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.108018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7458625PMC
August 2020

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours.

Epigenetics 2020 Jul 13:1-15. Epub 2020 Jul 13.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA.

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http://dx.doi.org/10.1080/15592294.2020.1790108DOI Listing
July 2020

H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer.

Mol Ther Nucleic Acids 2020 Sep 27;21:180-191. Epub 2020 May 27.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA. Electronic address:

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http://dx.doi.org/10.1016/j.omtn.2020.05.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321791PMC
September 2020

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.

Brief Bioinform 2020 Jun 24. Epub 2020 Jun 24.

Center for Precision Health, School of Biomedical Informatics.

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http://dx.doi.org/10.1093/bib/bbaa099DOI Listing
June 2020

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network.

Oncogene 2020 07 11;39(27):5031-5041. Epub 2020 Jun 11.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1038/s41388-020-1343-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334101PMC
July 2020

Landscape of drug-resistance mutations in kinase regulatory hotspots.

Brief Bioinform 2020 Jun 8. Epub 2020 Jun 8.

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http://dx.doi.org/10.1093/bib/bbaa108DOI Listing
June 2020

Correction to: The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics.

BMC Genomics 2020 05 6;21(1):342. Epub 2020 May 6.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-020-6753-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201704PMC
May 2020

Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.

BMC Med Inform Decis Mak 2020 04 28;20(1):77. Epub 2020 Apr 28.

Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.

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http://dx.doi.org/10.1186/s12911-020-1096-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187491PMC
April 2020

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

Genes (Basel) 2020 04 17;11(4). Epub 2020 Apr 17.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes11040437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231250PMC
April 2020

Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.

BMC Bioinformatics 2020 Apr 16;21(1):148. Epub 2020 Apr 16.

Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12859-020-3487-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161002PMC
April 2020

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

BMC Med Genomics 2020 04 3;13(Suppl 5):39. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12920-020-0675-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118807PMC
April 2020

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

BMC Med Genomics 2020 04 3;13(Suppl 5):47. Epub 2020 Apr 3.

Department of internal medicine, comprehensive cancer center, University of New Mexico, Albuquerque, NM, 87131, USA.

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http://dx.doi.org/10.1186/s12920-020-0678-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119270PMC
April 2020

Dense module searching for gene networks associated with multiple sclerosis.

BMC Med Genomics 2020 04 3;13(Suppl 5):48. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12920-020-0674-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118851PMC
April 2020

The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.

BMC Med Inform Decis Mak 2020 03 18;20(Suppl 2):51. Epub 2020 Mar 18.

Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.

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http://dx.doi.org/10.1186/s12911-020-1051-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079340PMC
March 2020

Diverse types of genomic evidence converge on alcohol use disorder risk genes.

J Med Genet 2020 Nov 13;57(11):733-743. Epub 2020 Mar 13.

School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA

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http://dx.doi.org/10.1136/jmedgenet-2019-106490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487038PMC
November 2020

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.

Bioinformatics 2020 05;36(10):3257-3259

School of Biomedical Informatics, Center for Precision Health.

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http://dx.doi.org/10.1093/bioinformatics/btaa113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214014PMC
May 2020

MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors.

Sci Rep 2020 01 21;10(1):852. Epub 2020 Jan 21.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41598-020-57834-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972857PMC
January 2020

Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression.

BMC Med 2020 01 6;18(1). Epub 2020 Jan 6.

Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China.

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http://dx.doi.org/10.1186/s12916-019-1469-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943904PMC
January 2020

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics.

BMC Genomics 2019 Dec 30;20(Suppl 12):1005. Epub 2019 Dec 30.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-019-6326-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936133PMC
December 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.

BMC Bioinformatics 2019 Dec 20;20(Suppl 24):676. Epub 2019 Dec 20.

Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12859-019-3240-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924135PMC
December 2019

MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse.

BMC Genomics 2019 Nov 14;20(1):852. Epub 2019 Nov 14.

Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.

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http://dx.doi.org/10.1186/s12864-019-6238-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854646PMC
November 2019

TSEA-DB: a trait-tissue association map for human complex traits and diseases.

Nucleic Acids Res 2020 01;48(D1):D1022-D1030

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkz957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145616PMC
January 2020

Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model.

Methods 2019 Oct 28. Epub 2019 Oct 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431277PMC
October 2019

VISDB: a manually curated database of viral integration sites in the human genome.

Nucleic Acids Res 2020 01;48(D1):D633-D641

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkz867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943068PMC
January 2020

Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice.

Brief Bioinform 2020 07;21(4):1465-1478

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bib/bbz082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412957PMC
July 2020

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

Genes (Basel) 2019 08 13;10(8). Epub 2019 Aug 13.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes10080611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723724PMC
August 2019

Changes in the Microbial Community Diversity of Oil Exploitation.

Genes (Basel) 2019 07 24;10(8). Epub 2019 Jul 24.

Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.

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http://dx.doi.org/10.3390/genes10080556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723437PMC
July 2019

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

BMC Med Genomics 2019 07 1;12(1):93. Epub 2019 Jul 1.

Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12920-019-0546-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604454PMC
July 2019

CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.

Bioinformatics 2019 12;35(24):5207-5215

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954662PMC
December 2019

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.

BMC Med Genomics 2019 05 23;12(1):70. Epub 2019 May 23.

Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12920-019-0535-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533741PMC
May 2019

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

Front Genet 2019 9;10:318. Epub 2019 Apr 9.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States.

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http://dx.doi.org/10.3389/fgene.2019.00318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467075PMC
April 2019

deTS: tissue-specific enrichment analysis to decode tissue specificity.

Bioinformatics 2019 10;35(19):3842-3845

School of Biomedical Informatics, Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761978PMC
October 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications.

BMC Genomics 2019 Feb 4;20(Suppl 1):80. Epub 2019 Feb 4.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-5369-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360715PMC
February 2019

Gene2vec: distributed representation of genes based on co-expression.

BMC Genomics 2019 Feb 4;20(Suppl 1):82. Epub 2019 Feb 4.

The University of Texas School of Biomedical Informatics, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-5370-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360648PMC
February 2019

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics.

BMC Genomics 2019 Feb 4;20(Suppl 1):79. Epub 2019 Feb 4.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-5373-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360716PMC
February 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine.

BMC Med Genomics 2019 01 31;12(Suppl 1):20. Epub 2019 Jan 31.

Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12920-018-0448-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357345PMC
January 2019

Network-based identification of critical regulators as putative drivers of human cleft lip.

BMC Med Genomics 2019 01 31;12(Suppl 1):16. Epub 2019 Jan 31.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0458-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357351PMC
January 2019

The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018).

BMC Med Inform Decis Mak 2019 01 31;19(Suppl 1):21. Epub 2019 Jan 31.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12911-019-0732-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354328PMC
January 2019

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

BMC Syst Biol 2019 Jan 24;13(1):14. Epub 2019 Jan 24.

The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210019, Jiangsu, China.

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http://dx.doi.org/10.1186/s12918-019-0682-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345063PMC
January 2019

Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data.

Brief Bioinform 2020 03;21(2):368-394

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston.

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http://dx.doi.org/10.1093/bib/bby120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373185PMC
March 2020

Next-Generation Sequencing in Human Genetic Studies: Genome Technologies and Applications to Human Genetic Studies.

Hum Hered 2018 9;83(3):105-106. Epub 2019 Jan 9.

Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA.

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https://www.karger.com/Article/FullText/494818
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http://dx.doi.org/10.1159/000494818DOI Listing
June 2019

Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types.

Cell Rep 2019 01;26(2):496-506.e3

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375892PMC
January 2019

TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer.

Cell Res 2019 03 3;29(3):248-250. Epub 2019 Jan 3.

Laboratory of Epigenetics, Liver Cancer Institute, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.

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http://www.nature.com/articles/s41422-018-0132-5
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http://dx.doi.org/10.1038/s41422-018-0132-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460428PMC
March 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.

BMC Bioinformatics 2018 Dec 28;19(Suppl 17):492. Epub 2018 Dec 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12859-018-2460-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309051PMC
December 2018

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

BMC Syst Biol 2018 12 21;12(Suppl 8):140. Epub 2018 Dec 21.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12918-018-0643-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302461PMC
December 2018

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

BMC Syst Biol 2018 12 21;12(Suppl 8):126. Epub 2018 Dec 21.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, 77030, TX, USA.

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http://dx.doi.org/10.1186/s12918-018-0650-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302366PMC
December 2018

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

BMC Syst Biol 2018 12 21;12(Suppl 8):128. Epub 2018 Dec 21.

The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210019, Jiangsu, China.

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https://bmcsystbiol.biomedcentral.com/articles/10.1186/s1291
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http://dx.doi.org/10.1186/s12918-018-0651-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302452PMC
December 2018

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

BMC Syst Biol 2018 12 21;12(Suppl 8):125. Epub 2018 Dec 21.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12918-018-0648-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302362PMC
December 2018

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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https://academic.oup.com/database/article/doi/10.1093/databa
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http://dx.doi.org/10.1093/database/bay121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310508PMC
January 2018

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 2017 Dec 23;5(4):302-327. Epub 2017 Nov 23.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1007/s40484-017-0119-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135253PMC
December 2017

Subtype-specific signaling pathways and genomic aberrations associated with prognosis of glioblastoma.

Neuro Oncol 2019 01;21(1):59-70

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.

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https://academic.oup.com/neuro-oncology/article/21/1/59/5059
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http://dx.doi.org/10.1093/neuonc/noy120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303485PMC
January 2019

Mega-analysis of Odds Ratio: A Convergent Method for a Deep Understanding of the Genetic Evidence in Schizophrenia.

Schizophr Bull 2019 04;45(3):698-708

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX.

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http://dx.doi.org/10.1093/schbul/sby085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483587PMC
April 2019

Repurposing sertraline sensitizes non-small cell lung cancer cells to erlotinib by inducing autophagy.

JCI Insight 2018 06 7;3(11). Epub 2018 Jun 7.

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

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http://dx.doi.org/10.1172/jci.insight.98921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124398PMC
June 2018

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

Transl Psychiatry 2018 05 24;8(1):105. Epub 2018 May 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41398-018-0154-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967316PMC
May 2018

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Cell Rep 2018 04;23(1):255-269.e4

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183043
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http://dx.doi.org/10.1016/j.celrep.2018.03.077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916795PMC
April 2018

Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor.

Brief Bioinform 2019 07;20(4):1502-1512

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bib/bby020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781582PMC
July 2019

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels.

Genome Med 2018 02 27;10(1):16. Epub 2018 Feb 27.

Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1186/s13073-018-0522-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828003PMC
February 2018

Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis.

Mech Dev 2018 04 21;150:21-27. Epub 2018 Feb 21.

Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mod.2018.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906164PMC
April 2018

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

Genome Med 2018 01 29;10(1). Epub 2018 Jan 29.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13073-018-0513-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789733PMC
January 2018

Splicing QTL of human adipose-related traits.

Sci Rep 2018 01 10;8(1):318. Epub 2018 Jan 10.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41598-017-18767-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762880PMC
January 2018

Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study.

Oncotarget 2017 Dec 24;8(66):110103-110117. Epub 2017 Nov 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.18632/oncotarget.22653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746368PMC
December 2017

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

Genes (Basel) 2017 Dec 28;9(1). Epub 2017 Dec 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes9010007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793160PMC
December 2017

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

Genes (Basel) 2017 Dec 5;8(12). Epub 2017 Dec 5.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes8120368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748686PMC
December 2017

Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition.

Nat Commun 2017 11 17;8(1):1604. Epub 2017 Nov 17.

Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1038/s41467-017-01781-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693921PMC
November 2017

TissGDB: tissue-specific gene database in cancer.

Nucleic Acids Res 2018 01;46(D1):D1031-D1038

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkx850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753286PMC
January 2018

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening.

BMC Genomics 2017 Oct 3;18(Suppl 6):678. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-017-4026-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629613PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

BMC Genomics 2017 Oct 3;18(Suppl 6):703. Epub 2017 Oct 3.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.

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http://dx.doi.org/10.1186/s12864-017-4018-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629612PMC
October 2017

Circular RNA expression profiles and features in human tissues: a study using RNA-seq data.

BMC Genomics 2017 Oct 3;18(Suppl 6):680. Epub 2017 Oct 3.

Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29 Jiangjun Avenue, Nanjing, Jiangsu, 211106, China.

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http://dx.doi.org/10.1186/s12864-017-4029-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629547PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.

BMC Syst Biol 2017 Oct 3;11(Suppl 5):88. Epub 2017 Oct 3.

The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12918-017-0461-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629615PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.

BMC Bioinformatics 2017 Oct 3;18(Suppl 11):405. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12859-017-1797-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629550PMC
October 2017

Distinct lithium-induced gene expression effects in lymphoblastoid cell lines from patients with bipolar disorder.

Eur Neuropsychopharmacol 2017 11 20;27(11):1110-1119. Epub 2017 Sep 20.

Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, United States. Electronic address:

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http://dx.doi.org/10.1016/j.euroneuro.2017.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5685885PMC
November 2017

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.

BMC Bioinformatics 2017 Sep 2;18(1):388. Epub 2017 Sep 2.

Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.

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http://dx.doi.org/10.1186/s12859-017-1796-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581471PMC
September 2017

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

BMC Med Inform Decis Mak 2017 Jul 5;17(Suppl 2):77. Epub 2017 Jul 5.

University of Texas, Health Science Center at Houston, of Biomedical Informatics, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12911-017-0462-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5506607PMC
July 2017

Advances on PPARγ Research in the Emerging Era of Precision Medicine.

Curr Drug Targets 2018 ;19(6):663-673

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States.

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http://dx.doi.org/10.2174/1389450118666170622091333DOI Listing
October 2019