(Q31033184)

18 August 2017

Providing data science support for systems pharmacology and its implications to drug discovery (English)

1 reference

18 August 2017

1 reference

1 reference

1 reference

Thomas Hart

1

1 reference

PMCID

4988863

18 August 2017

Lei Xie

series ordinal

2

1 reference

PMCID

4988863

18 August 2017

language of work or name

English

0 references

publication date

22 December 2015

1 reference

Expert Opinion on Drug Discovery

18 August 2017

1 reference

18 August 2017

11

1 reference

18 August 2017

3

1 reference

18 August 2017

241-256

1 reference

Data Science and its Relationship to Big Data and Data-Driven Decision Making

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Unmasking determinants of specificity in the human kinome.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Identifying compound efficacy targets in phenotypic drug discovery

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Elucidating Compound Mechanism of Action by Network Perturbation Analysis.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Pathway and network analysis of cancer genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Improving compound-protein interaction prediction by building up highly credible negative samples

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Data-driven integration of genome-scale regulatory and metabolic network models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Trans-species learning of cellular signaling systems with bimodal deep belief networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Understanding multicellular function and disease with human tissue-specific networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A new method to improve network topological similarity search: applied to fold recognition

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Deep neural nets as a method for quantitative structure-activity relationships

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Overcome support vector machine diagnosis overfitting

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Resampling-based similarity measures for high-dimensional data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Identifying predictive features in drug response using machine learning: opportunities and challenges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A community computational challenge to predict the activity of pairs of compounds

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

An argument for mechanism-based statistical inference in cancer.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

HDL and cardiovascular disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

e-Driver: a novel method to identify protein regions driving cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A community effort to assess and improve drug sensitivity prediction algorithms.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Towards structural systems pharmacology to study complex diseases and personalized medicine

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Computational target fishing: what should chemogenomics researchers expect for the future of in silico drug design and discovery?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Constraint-based models predict metabolic and associated cellular functions.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Systems pharmacology modeling: an approach to improving drug safety

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Methods and approaches in the topology-based analysis of biological pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Network-based stratification of tumor mutations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Representation learning: a review and new perspectives

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A pharmacological organization of G protein-coupled receptors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Random forest-based similarity measures for multi-modal classification of Alzheimer's disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

EnrichNet: network-based gene set enrichment analysis.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Novel computational approaches to polypharmacology as a means to define responses to individual drugs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Gene set enrichment analysis: performance evaluation and usage guidelines.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Structure-based systems biology for analyzing off-target binding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Drug off-target effects predicted using structural analysis in the context of a metabolic network model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

ABC-SysBio--approximate Bayesian computation in Python with GPU support

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Simulation-based model selection for dynamical systems in systems and population biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A novel signaling pathway impact analysis.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

A ligand-based approach to mining the chemogenomic space of drugs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Context-specific metabolic networks are consistent with experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Universally sloppy parameter sensitivities in systems biology models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

qPIPSA: relating enzymatic kinetic parameters and interaction fields.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Relating protein pharmacology by ligand chemistry

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Toxicogenomics and systems toxicology: aims and prospects

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4988863

Anton, a special-purpose machine for molecular dynamics simulation

14 July 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

AceCloud: Molecular Dynamics Simulations in the Cloud

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

Closing the scientific loop: bridging correlation and causality in the petaflop age.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

Gaussian interaction profile kernels for predicting drug-target interaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

Toward more realistic drug-target interaction predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

Machine learning for quantum mechanics in a nutshell

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

A Survey of Collaborative Filtering Techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2016.1135126

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/26689499

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Network-based prediction of human tissue-specific metabolism

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26689499

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26689499

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1517/17460441.2016.1135126

1 reference

18 August 2017

1 reference

18 August 2017

1 reference

PMCID

4988863