List of works - Feixiong Cheng

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data

article

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

scientific article

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

scientific article published on 19 February 2019

A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules

scientific article

A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19

scientific article published on 06 November 2020

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.

scientific article published on 28 March 2016

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

scientific article published on 24 August 2015

Adverse drug events: database construction and in silico prediction

scientific article published on 8 April 2013

AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery

scientific article published on 13 January 2021

Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer's disease

scientific article published on 10 January 2022

Autoimmune Cardiotoxicity of Cancer Immunotherapy

scientific article published on 2 December 2016

Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science

scientific article

Cardiac risk stratification in cancer patients: A longitudinal patient-patient network analysis

scientific article published on 02 August 2021

Classification of cytochrome P450 inhibitors and noninhibitors using combined classifiers

scientific article published on 14 April 2011

Computational Insights into Ligand Selectivity of Estrogen Receptors from Pharmacophore Modeling.

scientific article

Computational models to predict endocrine-disrupting chemical binding with androgen or oestrogen receptors.

scientific article published on 3 October 2014

Computational prediction of microRNA networks incorporating environmental toxicity and disease etiology

scientific article

Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer

scientific article published on 18 April 2019

Correction: Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations.

scientific article published on 5 September 2012

Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity

scientific article published on 15 February 2019

Drug Repurposing of Histone Deacetylase Inhibitors That Alleviate Neutrophilic Inflammation in Acute Lung Injury and Idiopathic Pulmonary Fibrosis via Inhibiting Leukotriene A4 Hydrolase and Blocking LTB4 Biosynthesis.

scientific article published on 20 February 2017

Drug Repurposing: New Treatments for Zika Virus Infection?

scientific article published on 27 September 2016

Entropy-based Consensus Clustering for Patient Stratification

scientific article

Estimation of ADME properties with substructure pattern recognition.

scientific article published in June 2010

Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer

scientific article published on 10 April 2017

FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach

scientific article

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

scientific article

Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing

scientific article published on 13 July 2020

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

scientific article published on 19 November 2014

In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex

scientific article published on 25 February 2020

In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers.

scientific article

In silico ADMET prediction: recent advances, current challenges and future trends

scientific article published on January 2013

In silico Prediction of Drug Induced Liver Toxicity Using Substructure Pattern Recognition Method

scientific article published on 3 February 2016

In silico assessment of chemical biodegradability

scientific article published on 29 February 2012

In silico polypharmacology of natural products

scientific article published on 27 April 2017

In silico prediction of chemical Ames mutagenicity.

scientific article published on 17 October 2012

In silico prediction of chemical acute oral toxicity using multi-classification methods.

scientific article published on 16 April 2014

In silico prediction of chemical mechanism of action via an improved network-based inference method

scientific article published on 20 September 2016

In silico prediction of chemical toxicity on avian species using chemical category approaches.

scientific article published on 19 December 2014

Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes

scientific article published on 26 February 2020

Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era.

scientific article published on 12 June 2016

Insights into binding modes of adenosine A(2B) antagonists with ligand-based and receptor-based methods.

scientific article published on 7 May 2010

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

scientific article

Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

scientific article

Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner

scientific article published on 16 April 2020

Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

scientific article published on 09 June 2021

Network-based Prediction of Drug-Target Interactions using an Arbitrary-Order Proximity Embedded Deep Forest

scientific article published on 23 January 2020

Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs

scientific article published on 14 June 2016

Network-based prediction of drug combinations

article

PTEN Mutations Trigger Resistance to Immunotherapy

scientific article published on 27 March 2019

Pharmacophore modeling of human adenosine receptor A(₂A) antagonists.

scientific article published on 12 March 2010

Phosphorylation of PLCγ1 by EphA2 receptor tyrosine kinase promotes tumor growth in lung cancer

scientific article published on 04 August 2020

Prediction of chemical-protein interactions network with weighted network-based inference method

scientific article

Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods.

scientific article published on 2 July 2012

Prediction of drug-target interactions and drug repositioning via network-based inference

scientific article

Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs).

scientific article published in March 2013

Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space

scientific article

Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes

scientific article

Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy

scientific article published on 28 September 2017

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

scientific article

Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from non-coding genome findings

scientific article published in 2022

Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers

scientific article published on 9 July 2015

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

article

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning

scientific article

SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations.

scientific article published on 23 October 2015

Selective targeting p53WT lung cancer cells harboring homozygous p53 Arg72 by an inhibitor of CypA.

scientific article published on 10 April 2017

SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents

scientific article published on May 2015

Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome

scientific article

Suppression of KRas-mutant cancer through the combined inhibition of KRAS with PLK1 and ROCK

scientific article (publication date: 19 May 2016)

Suppression of the SLC7A11/glutathione axis causes synthetic lethality in KRAS-mutant lung adenocarcinoma

scientific article published on 01 April 2020

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

scientific article published on 9 December 2015

Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types

scientific article published on 09 December 2015

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

scientific article

Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes.

scientific article published on 14 March 2017

Target identification among known drugs by deep learning from heterogeneous networks

scientific article published on 13 January 2020

Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery

scientific article published on 31 March 2017

Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer

scientific article

Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations.

scientific article published on 5 November 2012

admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties

scientific article published on November 2012

ccmGDB: a database for cancer cell metabolism genes

scientific article

deepDR: a network-based deep learning approach to in silico drug repositioning

scientific article published on 01 December 2019

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

scientific article published on 15 July 2020

List of works by Feixiong Cheng

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data

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

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules

A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

Adverse drug events: database construction and in silico prediction

AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery

Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer's disease

Autoimmune Cardiotoxicity of Cancer Immunotherapy

Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science

Cardiac risk stratification in cancer patients: A longitudinal patient-patient network analysis

Classification of cytochrome P450 inhibitors and noninhibitors using combined classifiers

Computational Insights into Ligand Selectivity of Estrogen Receptors from Pharmacophore Modeling.

Computational models to predict endocrine-disrupting chemical binding with androgen or oestrogen receptors.

Computational prediction of microRNA networks incorporating environmental toxicity and disease etiology

Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer

Correction: Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations.

Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity

Drug Repurposing of Histone Deacetylase Inhibitors That Alleviate Neutrophilic Inflammation in Acute Lung Injury and Idiopathic Pulmonary Fibrosis via Inhibiting Leukotriene A4 Hydrolase and Blocking LTB4 Biosynthesis.

Drug Repurposing: New Treatments for Zika Virus Infection?

Entropy-based Consensus Clustering for Patient Stratification

Estimation of ADME properties with substructure pattern recognition.

Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer

FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex

In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers.

In silico ADMET prediction: recent advances, current challenges and future trends

In silico Prediction of Drug Induced Liver Toxicity Using Substructure Pattern Recognition Method

In silico assessment of chemical biodegradability

In silico polypharmacology of natural products

In silico prediction of chemical Ames mutagenicity.

In silico prediction of chemical acute oral toxicity using multi-classification methods.

In silico prediction of chemical mechanism of action via an improved network-based inference method

In silico prediction of chemical toxicity on avian species using chemical category approaches.

Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes

Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era.

Insights into binding modes of adenosine A(2B) antagonists with ligand-based and receptor-based methods.

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner

Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

Network-based Prediction of Drug-Target Interactions using an Arbitrary-Order Proximity Embedded Deep Forest

Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs

Network-based prediction of drug combinations

PTEN Mutations Trigger Resistance to Immunotherapy

Pharmacophore modeling of human adenosine receptor A(₂A) antagonists.

Phosphorylation of PLCγ1 by EphA2 receptor tyrosine kinase promotes tumor growth in lung cancer

Prediction of chemical-protein interactions network with weighted network-based inference method

Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods.

Prediction of drug-target interactions and drug repositioning via network-based inference

Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs).

Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space

Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes

Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from non-coding genome findings

Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning

SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations.

Selective targeting p53WT lung cancer cells harboring homozygous p53 Arg72 by an inhibitor of CypA.

SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents

Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome

Suppression of KRas-mutant cancer through the combined inhibition of KRAS with PLK1 and ROCK

Suppression of the SLC7A11/glutathione axis causes synthetic lethality in KRAS-mutant lung adenocarcinoma

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes.

Target identification among known drugs by deep learning from heterogeneous networks

Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery

Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer

Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations.

admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties