Transcriptomic discovery of a theranostic signature (SERPINE1/MMP3/COL1A1/SPP1) for head and neck squamous cell carcinomas and identification of antrocinol as a candidate drug

[1]  A. Wu,et al.  Large-scale transcriptomic analysis of coding and non-coding pathological biomarkers, associated with the tumor immune microenvironment of thyroid cancer and potential target therapy exploration , 2022, Frontiers in Cell and Developmental Biology.

[2]  A. Wu,et al.  Identification of a novel immune-inflammatory signature of COVID-19 infections, and evaluation of pharmacokinetics and therapeutic potential of RXn-02, a novel small-molecule derivative of quinolone , 2022, Computers in Biology and Medicine.

[3]  A. Wu,et al.  Preclinical anti-inflammatory and antioxidant effects of Azanza garckeana in STZ-induced glycemic-impaired rats, and pharmacoinformatics of it major phytoconstituents. , 2022, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[4]  A. Wu,et al.  Leveraging Bulk and Single-Cell RNA Sequencing Data of NSCLC Tumor Microenvironment and Therapeutic Potential of NLOC-15A, A Novel Multi-Target Small Molecule , 2022, Frontiers in Immunology.

[5]  Yang An,et al.  OShnscc: a novel user-friendly online survival analysis tool for head and neck squamous cell carcinoma based on RNA expression profiles and long-term survival information , 2022, Journal of Zhejiang University-SCIENCE B.

[6]  T. Salo,et al.  Oral Microbiota—A New Frontier in the Pathogenesis and Management of Head and Neck Cancers , 2021, Cancers.

[7]  A. Wu,et al.  MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types , 2021, Computational and structural biotechnology journal.

[8]  A. Wu,et al.  In vivo Pharmacokinetic and Anticancer Studies of HH-N25, a Selective Inhibitor of Topoisomerase I, and Hormonal Signaling for Treating Breast Cancer , 2021, Journal of inflammation research.

[9]  Yang Liu,et al.  A review on the advances and challenges of immunotherapy for head and neck cancer , 2021, Cancer Cell International.

[10]  David T. W. Tzeng,et al.  Identification of Cancer Hub Gene Signatures Associated with Immune-Suppressive Tumor Microenvironment and Ovatodiolide as a Potential Cancer Immunotherapeutic Agent , 2021, Cancers.

[11]  Aiping Lu,et al.  ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties , 2021, Nucleic Acids Res..

[12]  Feng Zhu,et al.  Pharmacometabonomics: data processing and statistical analysis , 2021, Briefings Bioinform..

[13]  A. Wu,et al.  mTOR/EGFR/iNOS/MAP2K1/FGFR/TGFB1 Are Druggable Candidates for N-(2,4-Difluorophenyl)-2′,4′-Difluoro-4-Hydroxybiphenyl-3-Carboxamide (NSC765598), With Consequent Anticancer Implications , 2021, Frontiers in Oncology.

[14]  T. Bekaii-Saab,et al.  Multi-Omics Data Analysis of Gene Expressions and Alterations, Cancer-Associated Fibroblast and Immune Infiltrations, Reveals the Onco-Immune Prognostic Relevance of STAT3/CDK2/4/6 in Human Malignancies , 2021, Cancers.

[15]  A. Jemal,et al.  Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries , 2021, CA: a cancer journal for clinicians.

[16]  A. Wu,et al.  Pharmacoinformatics and Preclinical Studies of NSC765690 and NSC765599, Potential STAT3/CDK2/4/6 Inhibitors with Antitumor Activities against NCI60 Human Tumor Cell Lines , 2021, Biomedicines.

[17]  Su-jin Yang,et al.  An Integrative Pan-Cancer Analysis Revealing LCN2 as an Oncogenic Immune Protein in Tumor Microenvironment , 2020, Frontiers in Oncology.

[18]  Qun Wang,et al.  The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers , 2020, Frontiers in Molecular Biosciences.

[19]  B. Győrffy,et al.  TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues , 2020, bioRxiv.

[20]  Li Bo,et al.  MMEASE: Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis. , 2020, Journal of proteomics.

[21]  Yunxia Wang,et al.  MetaFS: Performance assessment of biomarker discovery in metaproteomics , 2020, Briefings Bioinform..

[22]  Xiaole Shirley Liu,et al.  TIMER2.0 for analysis of tumor-infiltrating immune cells , 2020, Nucleic Acids Res..

[23]  H. Zayed,et al.  Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients – A Bioinformatics Approach , 2020, Frontiers in Bioengineering and Biotechnology.

[24]  Y. Qiu,et al.  NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data , 2020, Nucleic Acids Res..

[25]  Yang Zhang,et al.  SSizer: Determining the Sample Sufficiency for Comparative Biological Study. , 2020, Journal of molecular biology.

[26]  H. Zayed,et al.  Integrative Bioinformatics Approaches to Map Potential Novel Genes and Pathways Involved in Ovarian Cancer , 2019, Front. Bioeng. Biotechnol..

[27]  Ke Wang,et al.  Identification of differentially expressed genes in non-small cell lung cancer , 2019, Aging.

[28]  Feng Zhu,et al.  A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies , 2019, Briefings Bioinform..

[29]  Luca Pinzi,et al.  Molecular Docking: Shifting Paradigms in Drug Discovery , 2019, International journal of molecular sciences.

[30]  Yu Jin,et al.  Identification and analysis of genes associated with head and neck squamous cell carcinoma by integrated bioinformatics methods , 2019, Molecular genetics & genomic medicine.

[31]  Feng Zhu,et al.  Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains* , 2019, Molecular & Cellular Proteomics.

[32]  E. Genden,et al.  Head and neck cancer prevention: from primary prevention to impact of clinicians on reducing burden. , 2019, Annals of oncology : official journal of the European Society for Medical Oncology.

[33]  Feng Zhu,et al.  How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics. , 2019, ACS chemical neuroscience.

[34]  Y. Tzeng,et al.  Antrocin, a bioactive component from Antrodia cinnamomea, suppresses breast carcinogenesis and stemness via downregulation of β-catenin/Notch1/Akt signaling. , 2019, Phytomedicine : international journal of phytotherapy and phytopharmacology.

[35]  David T. W. Tzeng,et al.  Antrocin Sensitizes Prostate Cancer Cells to Radiotherapy through Inhibiting PI3K/AKT and MAPK Signaling Pathways , 2018, Cancers.

[36]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[37]  Qiong Zhang,et al.  GSCALite: a web server for gene set cancer analysis , 2018, Bioinform..

[38]  Daniel Toro-Domínguez,et al.  ImaGEO: integrative gene expression meta-analysis from GEO database , 2018, Bioinform..

[39]  Feng Zhu,et al.  Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification , 2018, Front. Pharmacol..

[40]  M. Pawlita,et al.  Tobacco smoking and alcohol drinking at diagnosis of head and neck cancer and all‐cause mortality: Results from head and neck 5000, a prospective observational cohort of people with head and neck cancer , 2018, International journal of cancer.

[41]  Jun S. Liu,et al.  Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies. , 2018, Cell systems.

[42]  B. Zeng,et al.  SPP1 promotes ovarian cancer progression via Integrin β1/FAK/AKT signaling pathway , 2018, OncoTargets and therapy.

[43]  Feng Zhu,et al.  Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations. , 2018, ACS chemical neuroscience.

[44]  Yuzong Chen,et al.  What Contributes to Serotonin-Norepinephrine Reuptake Inhibitors' Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation. , 2018, ACS chemical neuroscience.

[45]  Hong Zhou,et al.  SPP1, analyzed by bioinformatics methods, promotes the metastasis in colorectal cancer by activating EMT pathway. , 2017, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[46]  Bo Li,et al.  NOREVA: normalization and evaluation of MS-based metabolomics data , 2017, Nucleic Acids Res..

[47]  Aiqing Li,et al.  Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer , 2016, World Journal of Surgical Oncology.

[48]  Bin Zhang,et al.  DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database , 2016, Nucleic Acids Res..

[49]  C. Ivan,et al.  NFAT1 Directly Regulates IL8 and MMP3 to Promote Melanoma Tumor Growth and Metastasis. , 2016, Cancer research.

[50]  E. Diamandis,et al.  Cancer immunotherapy: the beginning of the end of cancer? , 2016, BMC Medicine.

[51]  Y. Tzeng,et al.  Inhibition of growth, migration and invasion of human bladder cancer cells by antrocin, a sesquiterpene lactone isolated from Antrodia cinnamomea, and its molecular mechanisms. , 2016, Cancer letters.

[52]  Leonardo L. G. Ferreira,et al.  Molecular Docking and Structure-Based Drug Design Strategies , 2015, Molecules.

[53]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[54]  Scott M Langevin,et al.  High‐risk HPV types and head and neck cancer , 2014, International journal of cancer.

[55]  Haibin Liu,et al.  AlzPlatform: An Alzheimer’s Disease Domain-Specific Chemogenomics Knowledgebase for Polypharmacology and Target Identification Research , 2014, J. Chem. Inf. Model..

[56]  Chi-Ying F. Huang,et al.  A sesquiterpene lactone antrocin from Antrodia camphorata negatively modulates JAK2/STAT3 signaling via microRNA let-7c and induces apoptosis in lung cancer cells. , 2013, Carcinogenesis.

[57]  Z. Trajanoski,et al.  Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. , 2013, Immunity.

[58]  Md. Lutful Amin.  P-glycoprotein Inhibition for Optimal Drug Delivery , 2013, Drug target insights.

[59]  Gail M. Sullivan,et al.  Using Effect Size-or Why the P Value Is Not Enough. , 2012, Journal of graduate medical education.

[60]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[61]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[62]  Zhen Yang,et al.  Total syntheses of drimane-type sesquiterpenoids enabled by a gold-catalyzed tandem reaction. , 2011, Journal of the American Chemical Society.

[63]  Jacob J. Kennedy,et al.  Tumor microenvironment-derived proteins dominate the plasma proteome response during breast cancer induction and progression. , 2011, Cancer research.

[64]  P. Delvenne,et al.  Immune Suppression in Head and Neck Cancers: A Review , 2011, Clinical & developmental immunology.

[65]  Y. Tzeng,et al.  Identification of antrocin from Antrodia camphorata as a selective and novel class of small molecule inhibitor of Akt/mTOR signaling in metastatic breast cancer MDA-MB-231 cells. , 2011, Chemical research in toxicology.

[66]  Y. Tzeng,et al.  Review of Pharmacological Effects of Antrodia camphorata and Its Bioactive Compounds , 2011, Evidence-based complementary and alternative medicine : eCAM.

[67]  J. Luong,et al.  Cytotoxic triterpenes from Antrodia camphorata and their mode of action in HT-29 human colon cancer cells. , 2009, Cancer letters.

[68]  Jean-Louis Foulley,et al.  Gene expression Moderated effect size and P-value combinations for microarray meta-analyses , 2009 .

[69]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[70]  P. Angel,et al.  The receptor RAGE: Bridging inflammation and cancer , 2009, Cell Communication and Signaling.

[71]  Herbert J Zeh,et al.  Journal of Translational Medicine BioMed Central Review , 2009 .

[72]  J. Luong,et al.  Probing inhibitory effects of Antrodia camphorata isolates using insect cell-based impedance spectroscopy: inhibition vs chemical structure. , 2008, Chemical research in toxicology.

[73]  David Warde-Farley,et al.  GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function , 2008, Genome Biology.

[74]  Jih-Jung Chen,et al.  Anti-inflammatory benzenoids from Antrodia camphorata. , 2007, Journal of natural products.

[75]  B. Fingleton,et al.  Matrix Metalloproteinase Inhibitors and Cancer—Trials and Tribulations , 2002, Science.

[76]  Constance E. Brinckerhoff,et al.  Matrix metalloproteinases: a tail of a frog that became a prince , 2002, Nature Reviews Molecular Cell Biology.

[77]  Z. Werb,et al.  New functions for the matrix metalloproteinases in cancer progression , 2002, Nature Reviews Cancer.

[78]  Z. Werb,et al.  The matrix metalloproteinase stromelysin-1 acts as a natural mammary tumor promoter , 2000, Oncogene.

[79]  W. Pardridge,et al.  CNS Drug Design Based on Principles of Blood‐Brain Barrier Transport , 1998, Journal of neurochemistry.

[80]  Z. Werb,et al.  Matrix Metalloproteinase Stromelysin-1 Triggers a Cascade of Molecular Alterations That Leads to Stable Epithelial-to-Mesenchymal Conversion and a Premalignant Phenotype in Mammary Epithelial Cells , 1997, The Journal of cell biology.

[81]  C. George Priya Doss,et al.  A computational model revealing the immune-related hub genes and key pathways involved in rheumatoid arthritis (RA). , 2022, Advances in protein chemistry and structural biology.

[82]  OUP accepted manuscript , 2022, Briefings In Bioinformatics.

[83]  H. Zayed,et al.  A review of bioinformatics tools and web servers in different microarray platforms used in cancer research. , 2022, Advances in protein chemistry and structural biology.

[84]  B. Fingleton.  Matrix metalloproteinases: roles in cancer and metastasis. , 2006, Frontiers in bioscience : a journal and virtual library.