CHAO CHENG to Humans
This is a "connection" page, showing publications CHAO CHENG has written about Humans.
Connection Strength
1.012
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The prognostic effect of infiltrating immune cells is shaped by proximal M2 macrophages in lung adenocarcinoma. Mol Cancer. 2024 Sep 04; 23(1):185.
Score: 0.024
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Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. Blood Cancer J. 2024 03 06; 14(1):38.
Score: 0.023
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TimiGP: An R package to depict the tumor microenvironment from bulk transcriptomics. STAR Protoc. 2023 12 15; 4(4):102742.
Score: 0.023
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TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs. Cell Rep Med. 2023 07 18; 4(7):101121.
Score: 0.022
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A combination of intrinsic and extrinsic features improves prognostic prediction in malignant pleural mesothelioma. Br J Cancer. 2022 11; 127(9):1691-1700.
Score: 0.021
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A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction. Sci Rep. 2022 02 09; 12(1):2211.
Score: 0.020
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A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. Genome Med. 2022 01 12; 14(1):5.
Score: 0.020
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Computational modeling of chromatin accessibility identified important epigenomic regulators. BMC Genomics. 2022 Jan 08; 23(1):19.
Score: 0.020
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Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer Res. 2022 01 15; 82(2):199-209.
Score: 0.020
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Impact of Oncotype DX testing on ER+ breast cancer treatment and survival in the first decade of use. Breast Cancer Res. 2021 07 17; 23(1):74.
Score: 0.019
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Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy. Br J Cancer. 2021 08; 125(3):422-432.
Score: 0.019
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Chr20q Amplification Defines a Distinct Molecular Subtype of Microsatellite Stable Colorectal Cancer. Cancer Res. 2021 04 15; 81(8):1977-1987.
Score: 0.019
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MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers. Mol Cancer Res. 2021 03; 19(3):414-428.
Score: 0.019
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Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer. Lab Invest. 2020 10; 100(10):1356-1366.
Score: 0.018
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Systematic computational identification of prognostic cytogenetic markers in neuroblastoma. BMC Med Genomics. 2019 12 12; 12(1):192.
Score: 0.017
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Computational STAT3 activity inference reveals its roles in the pancreatic tumor microenvironment. Sci Rep. 2019 12 03; 9(1):18257.
Score: 0.017
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Statins associate with improved mortality among patients with certain histological subtypes of lung cancer. Lung Cancer. 2018 12; 126:89-96.
Score: 0.016
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Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs. Cancer Res. 2018 11 15; 78(22):6413-6423.
Score: 0.016
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A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis. Mol Cancer Res. 2019 01; 17(1):109-119.
Score: 0.016
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Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Sci Rep. 2017 Nov 16; 7(1):15742.
Score: 0.015
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A P53-Deficiency Gene Signature Predicts Recurrence Risk of Patients with Early-Stage Lung Adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2018 01; 27(1):86-95.
Score: 0.015
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The E2F4 prognostic signature predicts pathological response to neoadjuvant chemotherapy in breast cancer patients. BMC Cancer. 2017 05 02; 17(1):306.
Score: 0.014
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Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment. Cancer Res. 2017 03 15; 77(6):1271-1282.
Score: 0.014
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Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PLoS Comput Biol. 2017 01; 13(1):e1005340.
Score: 0.014
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Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis. Oncotarget. 2016 Dec 20; 7(51):84142-84154.
Score: 0.014
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Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer. Genome Med. 2016 10 27; 8(1):114.
Score: 0.014
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In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics. Expert Opin Drug Discov. 2016 Dec; 11(12):1213-1222.
Score: 0.014
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Adaptive immunity programmes in breast cancer. Immunology. 2017 Jan; 150(1):25-34.
Score: 0.014
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iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. BMC Genomics. 2016 08 12; 17(1):632.
Score: 0.014
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Integrative analysis of cancer genes in a functional interactome. Sci Rep. 2016 06 30; 6:29228.
Score: 0.014
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Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. Pharmacogenomics J. 2017 07; 17(4):351-359.
Score: 0.013
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Aberrant expression and hormonal regulation of Galectin-3 in endometriosis women with infertility. J Endocrinol Invest. 2016 Jul; 39(7):785-91.
Score: 0.013
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Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value. Mol Cancer Res. 2016 Apr; 14(4):332-43.
Score: 0.013
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Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Nat Commun. 2016 Jan 04; 7:10248.
Score: 0.013
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Systematic analysis of hematopoietic gene expression profiles for prognostic prediction in acute myeloid leukemia. Sci Rep. 2015 Nov 24; 5:16987.
Score: 0.013
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E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Mol Cancer Res. 2015 Sep; 13(9):1316-24.
Score: 0.013
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Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. PLoS Comput Biol. 2015 May; 11(5):e1004269.
Score: 0.013
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An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Genome Biol. 2015 Mar 31; 16:63.
Score: 0.013
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Integrative analysis of survival-associated gene sets in breast cancer. BMC Med Genomics. 2015 Mar 12; 8:11.
Score: 0.012
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E2F4 regulatory program predicts patient survival prognosis in breast cancer. Breast Cancer Res. 2014 Dec 02; 16(6):486.
Score: 0.012
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Big data bioinformatics. J Cell Physiol. 2014 Dec; 229(12):1896-900.
Score: 0.012
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Relating gene expression evolution with CpG content changes. BMC Genomics. 2014 Aug 20; 15:693.
Score: 0.012
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Effect of estrogen receptor a binding on functional DNA methylation in breast cancer. Epigenetics. 2014 Apr; 9(4):523-32.
Score: 0.012
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Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing. Pac Symp Biocomput. 2014; 412-6.
Score: 0.011
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DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D178-83.
Score: 0.011
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REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics. 2013 Jul 26; 14:504.
Score: 0.011
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Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PLoS Comput Biol. 2013; 9(7):e1003132.
Score: 0.011
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An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74.
Score: 0.010
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Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep; 22(9):1658-67.
Score: 0.010
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A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046.
Score: 0.010
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A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol. 2011; 12(2):R15.
Score: 0.009
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The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics. 2009 Sep 14; 10:431.
Score: 0.009
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mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Genome Biol. 2009; 10(9):R90.
Score: 0.008
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Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics. 2009 May 15; 10:225.
Score: 0.008
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Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One. 2008 Apr 23; 3(4):e1989.
Score: 0.008
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Sub-array normalization subject to differentiation. Nucleic Acids Res. 2005; 33(17):5565-73.
Score: 0.006
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Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nat Commun. 2024 Feb 08; 15(1):1199.
Score: 0.006
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Cloning, expression and characterization of a novel human VMP gene. Mol Biol Rep. 2002 Sep; 29(3):281-6.
Score: 0.005
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Predicting clinical outcomes of cancer patients with a p53 deficiency gene signature. Sci Rep. 2022 01 25; 12(1):1317.
Score: 0.005
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Cloning and characterization of a novel human transcription factor AP-2 beta like gene (TFAP2BL1). Int J Biochem Cell Biol. 2002 Jan; 34(1):78-86.
Score: 0.005
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Resident memory CD8+ T?cells in regional lymph nodes mediate immunity to metastatic melanoma. Immunity. 2021 09 14; 54(9):2117-2132.e7.
Score: 0.005
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Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy. Clin Cancer Res. 2020 06 15; 26(12):2908-2920.
Score: 0.004
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CD36-Mediated Metabolic Rewiring of Breast Cancer Cells Promotes Resistance to HER2-Targeted Therapies. Cell Rep. 2019 12 10; 29(11):3405-3420.e5.
Score: 0.004
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A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition. Clin Cancer Res. 2020 01 01; 26(1):159-170.
Score: 0.004
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Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. BMC Med Genomics. 2019 05 31; 12(1):79.
Score: 0.004
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Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. Cancer Immunol Res. 2019 07; 7(7):1079-1090.
Score: 0.004
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H22954, a novel long non-coding RNA down-regulated in AML, inhibits cancer growth in a BCL-2-dependent mechanism. Cancer Lett. 2019 07 10; 454:26-36.
Score: 0.004
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Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier. Breast Cancer Res. 2019 01 25; 21(1):14.
Score: 0.004
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Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. J Cell Biochem. 2019 04; 120(4):5459-5471.
Score: 0.004
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Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics. Melanoma Res. 2018 10; 28(5):380-389.
Score: 0.004
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Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer. FASEB J. 2019 02; 33(2):1644-1657.
Score: 0.004
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VISTA expression on tumor-infiltrating inflammatory cells in primary cutaneous melanoma correlates with poor disease-specific survival. Cancer Immunol Immunother. 2018 Jul; 67(7):1113-1121.
Score: 0.004
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A recombinant lentiviral PDGF-driven mouse model of proneural glioblastoma. Neuro Oncol. 2018 02 19; 20(3):332-342.
Score: 0.004
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Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. J Exp Med. 2018 03 05; 215(3):895-910.
Score: 0.004
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Decreased expression of FOXA2 promotes eutopic endometrial cell proliferation and migration in patients with endometriosis. Reprod Biomed Online. 2018 Feb; 36(2):181-187.
Score: 0.004
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Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Nat Genet. 2017 Oct; 49(10):1428-1436.
Score: 0.004
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Intestinal stem cell overproliferation resulting from inactivation of the APC tumor suppressor requires the transcription cofactors Earthbound and Erect wing. PLoS Genet. 2017 Jul; 13(7):e1006870.
Score: 0.004
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Population effect model identifies gene expression predictors of survival outcomes in lung adenocarcinoma for both Caucasian and Asian patients. PLoS One. 2017; 12(4):e0175850.
Score: 0.004
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Immunoregulatory functions of VISTA. Immunol Rev. 2017 03; 276(1):66-79.
Score: 0.004
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Insulin-Mediated Signaling Facilitates Resistance to PDGFR Inhibition in Proneural hPDGFB-Driven Gliomas. Mol Cancer Ther. 2017 04; 16(4):705-716.
Score: 0.004
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Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. BMC Genomics. 2017 01 10; 18(1):61.
Score: 0.004
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MYC Mediates mRNA Cap Methylation of Canonical Wnt/?-Catenin Signaling Transcripts By Recruiting CDK7 and RNA Methyltransferase. Mol Cancer Res. 2017 02; 15(2):213-224.
Score: 0.004
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Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution. Genome Biol Evol. 2016 10 23; 8(10):3159-3170.
Score: 0.003
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GLITTER: a web-based application for gene link inspection through tissue-specific coexpression. Sci Rep. 2016 09 14; 6:33460.
Score: 0.003
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Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics. Mol Cell Proteomics. 2016 07; 15(7):2448-61.
Score: 0.003
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PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells. Cancer Res. 2016 05 15; 76(10):2964-76.
Score: 0.003
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CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res. 2016 Jan 04; 44(D1):D209-15.
Score: 0.003
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Integrative Analysis Reveals Regulatory Programs in Endometriosis. Reprod Sci. 2015 Sep; 22(9):1060-72.
Score: 0.003
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Loregic: a method to characterize the cooperative logic of regulatory factors. PLoS Comput Biol. 2015 Apr; 11(4):e1004132.
Score: 0.003
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p53 and ?Np63a Coregulate the Transcriptional and Cellular Response to TGF? and BMP Signals. Mol Cancer Res. 2015 Apr; 13(4):732-42.
Score: 0.003
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Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput. 2015; 132-43.
Score: 0.003
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Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8.
Score: 0.003
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Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6.
Score: 0.003
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Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Epigenetics. 2014 Feb; 9(2):268-75.
Score: 0.003
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Association of gamma-aminobutyric acid A receptor a2 gene (GABRA2) with alcohol use disorder. Neuropsychopharmacology. 2014 Mar; 39(4):907-18.
Score: 0.003
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Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol Biol Cell. 2013 Dec; 24(23):3634-50.
Score: 0.003
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Paeonol induces apoptosis in human ovarian cancer cells. Acta Histochem. 2013 Oct; 115(8):835-9.
Score: 0.003
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An MLL-dependent network sustains hematopoiesis. Proc Natl Acad Sci U S A. 2013 Jul 16; 110(29):12000-5.
Score: 0.003
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Machine learning and genome annotation: a match meant to be? Genome Biol. 2013 May 29; 14(5):205.
Score: 0.003
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Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. BMC Genomics. 2013 May 08; 14:310.
Score: 0.003
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A comprehensive nuclear receptor network for breast cancer cells. Cell Rep. 2013 Feb 21; 3(2):538-51.
Score: 0.003
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Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 26; 13(9):R48.
Score: 0.003
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Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100.
Score: 0.003
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The antiapoptotic effect of galectin-3 in human endometrial cells under the regulation of estrogen and progesterone. Biol Reprod. 2012 Aug; 87(2):39.
Score: 0.003
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Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Jun 13; 13(9):R53.
Score: 0.003
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Average rank-based score to measure deregulation of molecular pathway gene sets. PLoS One. 2011; 6(11):e27579.
Score: 0.002
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Hormonal regulation of galectin 3 in trophoblasts and its effects on endometrium. Reprod Sci. 2011 Nov; 18(11):1118-27.
Score: 0.002
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Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. BMC Syst Biol. 2010 Dec 30; 4:179.
Score: 0.002
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Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res. 2010 Nov; 38(20):6997-7007.
Score: 0.002
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Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol. 2010 Apr 01; 6(4):e1000730.
Score: 0.002
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Isolation and characterization of a human putative receptor protein kinase cDNA STYK1. Mol Biol Rep. 2003 Jun; 30(2):91-6.
Score: 0.001
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Isolation and characterization of a novel human putative anemia-related gene homologous to mouse sideroflexin. Biochem Genet. 2003 Apr; 41(3-4):119-25.
Score: 0.001
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Identification and characterization of AGTRAP, a human homolog of murine Angiotensin II Receptor-Associated Protein (Agtrap). Int J Biochem Cell Biol. 2002 Jan; 34(1):93-102.
Score: 0.001
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Cloning, expression and characterization of a novel human REPS1 gene. Biochim Biophys Acta. 2001 Dec 03; 1522(2):118-21.
Score: 0.001
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Cloning and characterization of a novel human TEKTIN1 gene. Int J Biochem Cell Biol. 2001 Dec; 33(12):1172-82.
Score: 0.001
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Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain. Cytogenet Cell Genet. 2001; 95(1-2):43-7.
Score: 0.001
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A novel human hydroxysteroid dehydrogenase like 1 gene (HSDL1) is highly expressed in reproductive tissues. Mol Biol Rep. 2001; 28(4):185-91.
Score: 0.001
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Molecular cloning and characterization of a novel Dehydrogenase/reductase (SDR family) member 1 genea from human fetal brain. Mol Biol Rep. 2001; 28(4):193-8.
Score: 0.001