Topic 112

bioinformatics drug cancer drugs network based approach data methods omics predict method networks clinical biological discovery disease targets computational prediction genes multi datasets predictive predicting profiles combinations models patients interaction systems machine gene diseases approaches novel learning patient precision pathways interactions therapeutic identifying identify applied effective medicine identification algorithm validation existing predictions validated graph integration developed knowledge biomarkers treatment breast framework therapy information using relationships random new predicted problem tcga associations proposed similarity oncology silico available database relevant personalized used candidate can databases potential integrative tumor terms combination repositioning classification experimental develop therapies screening types algorithms various better build analysis

220 items. Top items listed below.

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer 112 13 4

Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology 112 26 4

A novel single-cell based method for breast cancer prognosis 43 26 4

Multi-Objective Approach for Identifying Cancer Subnetwork Markers 112 26 4

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers 112 38 26 4

Predicting drug sensitivity of cancer cells based on DNA methylation levels 112 26 4

Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivity 112 26 4

PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse 112 13 4

CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer 112 14 4

Investigate the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model 112 26 9 4

A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response 112 4

NOGEA: Network-Oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning 112 13 4

A deep learning framework for high-throughput mechanism-driven phenotype compound screening 26 4

Patient-tailored design of AML cell subpopulation-selective drug combinations 112 14 4

Cluster Analysis of Medicinal Plants and Targets Based on Multipartite Network 112 4

TranSynergy: Mechanism-Driven Interpretable Deep Neural Network for the Synergistic Prediction and Pathway Deconvolution of Drug Combinations 105 13 4

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples 112 4

A Deep Learning Framework for Predicting Human Essential Genes by Integrating Sequence and Functional data 105 26 4

Highly Accurate Cancer Phenotype Prediction with AKLIMATE, a Stacked Kernel Learner Integrating Multimodal Genomic Data and Pathway Knowledge 112 26 4

Network reconstruction for trans acting genetic loci using multi-omics data and prior information 112 4

Multiobjective optimization identifies cancer-selective combination therapies 112 14 4

Interpretable Machine Learning for Perturbation Biology 112 26 4

ECMarker: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages 105 26 13 4

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

A Systems Pharmacology Approach based on Oncogenic Signalling Pathways to Determine the Mechanisms of Action of Natural Products in Breast Cancer from Transcriptome Data 112 9

Personalized anti-cancer drug combination prediction by an Integrated Multi-level Network 112 105 26 4

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

Discovery of disease treatment mechanisms through the multiscale interactome 112

Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model 112 105 26 4

A comparative study of supervised machine learning algorithms for the prediction of long-range chromatin interactions 105 26 4

Imputing missing RNA-seq data from DNA methylation by using transfer learning based-deep neural network 105 26 4

Small Molecule Modulation of Microbiome Ecosystem: A Systems Pharmacology Perspective 112 4

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites 112 45 4

comboFM: leveraging multi-way interactions for systematic prediction of drug combination effects 112 26 4

An Ensemble Learning Approach for Cancer Drug Prediction 112 26 4

Multi-tissue transcriptome-wide association studies 19 4

Integration of Biodynamic Imaging and RNA-seq predicts chemotherapy response in canine diffuse large B-cell lymphoma 112 14 9 4

GraphGR: A graph neural network to predict the effect of pharmacotherapy on the cancer cell growth 112 13 4

TimeTeller: a New Tool for Precision Circadian Medicine and Cancer Prognosis 112 14 4

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions 139 112 9

pDriver: A novel method for unravelling personalised coding and miRNA cancer drivers 13 4

Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways 112 4

Multiscale virtual screening optimization for shotgun drug repurposing using the CANDO platform 112 4

Identification of the associated expression patterns as potential predictive markers for cancer prognosis 112 9

Finding human gene-disease associations using a Network Enhanced Similarity Search (NESS) of multi-species heterogeneous functional genomics data 13 4

ERWR: Predicting Efficacious Drug Combinations in Cancer Based on Random Walk with Restart 112 26 4

Integrative omics data analysis uncovers biomarker genes and potential candidate drugs for G3 medulloblastoma 112 14 9

Personalized in-silico drug response prediction based on the genetic landscape of muscle-invasive bladder cancer 112 14 4

Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance 112 14 4

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Drug2ways: Reasoning over causal paths in biological networks for drug discovery 112 4

K-means Based Unsupervised Feature Selection to Prioritize Biomarkers of Different Disease Clinical Phases 112 9 4

DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning 105 26 13 4

PRER: A Patient Representation with Pairwise Relative Expression of Proteins on Biological Networks 184 7 4

Novel analysis of drug-drug interactions reveals the appearance of non-linear dose dependence under the single drug treatment 112 105 26 4

Integrative computational approach identifies new targets in CD4+ T cell-mediated immune disorders 112 9

Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines 7 4

Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators and co-option of cellular pathways 112 1

iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm 105 26 4

"3G" Trial: An RNA Editing Signature for Guiding Gastric Cancer Chemotherapy 112 9 4

DeepPheno: Predicting single gene loss of function phenotypes 105 26 13 4

Diversity-based enumeration of optimal context-specific metabolic networks 112 4

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments 158 112 4

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method 112 9 4

Learning epistatic gene interactions from perturbation screens 112 4

CEN-tools: An integrative platform to identify the contexts of essential genes 139 112 9 4 3

Artificial intelligence based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease 112 26 4

Computational genomics of brain tumors: identification and characterization of glioma candidate biomarkers through multi-omics integrative molecular profiling 112 14 9 4

Two-step multi-omics modelling of drug sensitivity in cancer cell lines to identify driving mechanisms 112 4

Combination Treatment Optimization Using aPan-Cancer Pathway Model 112 38 4

Multi-BIRW:a network-based algorithm for drug repurposing 112 4

SPRDA: a matrix completion approach based on the structural perturbation to infer disease-associated Piwi-Interacting RNAs 7 4

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data 112 4

Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer 112 45 4

A composite method to infer drug resistance with mixed genomic data 26 4

e-MutPath: Computational modelling reveals the functional landscape of genetic mutations rewiring interactome networks 112 13 9 4

Geographic heterogeneity impacts drug resistance predictions in Mycobacterium tuberculosis 112 26 4

Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes 97 9 4

Genetic program activity delineates risk, relapse, and therapy responsiveness in Multiple Myeloma 112 9

Identifying digenic disease genes using machine learning in the undiagnosed diseases network 112 26 4

Using Single Protein/Ligand Binding Models to Predict Active Ligands for Unseen Proteins 105 26 4

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets 26 4

A deep learning framework for characterization of genotype data 26 4

Ranking Cancer Drivers via Betweenness-based Outlier Detection and Random Walks 112 4

Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity 105 26 4

MatchMaker: A Deep Learning Framework for Drug Synergy Prediction 105 13 4

A meta-learning approach for genomic survival analysis 26 4

Massive-scale biological activity-based modeling identifies novel antiviral leads against SARS-CoV-2 44 1

A computational network approach to identify predictive biomarkers and therapeutic combinations for anti-PD-1 immunotherapy in cancer 126 112 14 9

Extended Application of Genomic Selection to Screen Multi-Omics Data for Prognostic Signatures of Prostate Cancer 112 4

Detection of pre-microRNA with Convolutional Neural Networks 105 26 4

A validated strategy to infer protein biomarkers from RNA-Seq by combining multiple mRNA splice variants and time-delay 45 9 4

Cell type-specific proteogenomic signal diffusion for integrating multi-omics data predicts novel schizophrenia risk genes 112 9

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

A network Based method to predict cancer causal genes in GR Network. 112 105 26 4

Precision combination therapies based on recurrent oncogenic co-alterations 112 14 4

Optimizing the use of gene expression data to predict plant metabolic pathway memberships 105 26 4

Finding associations in a heterogeneous setting: Statistical test for aberration enrichment 123 112 4

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules 175 112 4

Knowledge guided multi-level network inference 13 4