Jeremy R. Ash

Works (11)

Updated: July 15th, 2023 21:19

2022 journal article

Confidence bands and hypothesis tests for hit enrichment curves

JOURNAL OF CHEMINFORMATICS, 14(1).

By: J. Ash n & J. Hughes-Oliver n

author keywords: Virtual screening; Enrichment factor; Lift curve; Early enrichment; Ranking algorithm; Empirical process
TL;DR: In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment, and inferential procedures are developed to address both the needs of those interested in a few testing fractions, as well as the entire curve. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 8, 2022

2021 journal article

Race and smoking status associated with paclitaxel drug response in patient-derived lymphoblastoid cell lines

PHARMACOGENETICS AND GENOMICS, 31(2), 48–52.

By: F. Akhtari n, T. Havener *, D. Hertz *, J. Ash n, A. Larson n, L. Carey *, H. McLeod *, A. Motsinger-Reif*

author keywords: dose-response; lymphoblastoid cell lines; paclitaxel; patient-derived cell lines; pharmacogenomics; smoking
MeSH headings : Breast Neoplasms / drug therapy; Breast Neoplasms / genetics; Breast Neoplasms / pathology; Cell Line, Tumor; Cell Survival / drug effects; Dose-Response Relationship, Drug; Drug Resistance, Neoplasm / genetics; Female; Humans; Middle Aged; Paclitaxel / adverse effects; Paclitaxel / pharmacology; Pharmacogenetics; Racial Groups / genetics; Smoking / adverse effects; Smoking / genetics
TL;DR: It is indicated that in-vivo smoking status can influence ex- vivo dose-response in LCLs, and more precise measures of covariates may allow for more precise forecasting of clinical effect. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: May 10, 2021

2020 journal article

Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

ANALYST, 145(22), 7197–7209.

By: M. Odenkirk n, P. Zin n , J. Ash n, D. Reif n , D. Fourches n & E. Baker n 

MeSH headings : Cheminformatics; Lipidomics; Lipids; Mass Spectrometry; Phenotype
TL;DR: A Structural-based Connectivity and Omic Phenotype Evaluations (SCOPE) cheminformatics toolbox to aid in these evaluations of lipid species and their respective biological roles is developed. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: November 24, 2020

2020 journal article

Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools

MOLECULAR OMICS, 16(6).

By: M. Odenkirk n, K. Stratton *, M. Gritsenko *, L. Bramer *, B. Webb-Robertson *, K. Bloodsworth *, K. Weitz *, A. Lipton* ...

MeSH headings : Case-Control Studies; Diabetes, Gestational / genetics; Female; Genomics; Humans; Lipidomics; Metabolic Networks and Pathways; Pre-Eclampsia / genetics; Pregnancy
TL;DR: The multi-omic evaluations performed here provide new insight into the end-stage molecular profiles of each disease, thereby supplying information potentially crucial for earlier diagnosis and treatments. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
5. Gender Equality (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 4, 2021

2019 review

4D-quantitative structure-activity relationship modeling: making a comeback

[Review of ]. EXPERT OPINION ON DRUG DISCOVERY, 14(12), 1227–1235.

By: D. Fourches n & J. Ash n

author keywords: 4D descriptors; cheminformatics; QSAR; molecular dynamics
MeSH headings : Drug Design; Drug Discovery / methods; Humans; Ligands; Models, Molecular; Molecular Dynamics Simulation; Pharmaceutical Preparations / chemistry; Quantitative Structure-Activity Relationship
TL;DR: There has never been a better time and relevance for molecular modeling teams to engage in hyper-predictive MD-QSAR modeling, which could represent a disruptive technology for analyzing, understanding, and optimizing dynamic protein-ligand interactions with countless applications for drug discovery and chemical toxicity assessment. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: September 30, 2019

2019 journal article

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles

JOURNAL OF CHEMINFORMATICS, 11.

By: J. Ash n, M. Kuenemann n, D. Rotroff n, A. Motsinger-Reif n & D. Fourches n

author keywords: Metabolomics; Data mining; Cheminformatics; Molecular fragmentation; Statistics; Visualization; Chemical structure
TL;DR: A novel cheminformatics-based approach capable of identifying predictive, interpretable, and reproducible trait-metabolite relationships that could ultimately facilitate biological understanding and advance research based on metabolomics data, especially with respect to the identification of novel biomarkers. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: July 15, 2019

2019 journal article

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

NATURE COMMUNICATIONS, 10.

By: D. Fourches, M. Kuenemann, A. Motsinger-Reif, Y. Shen, W. Zhang, J. Ash, F. Akhtari (7 connected NC State authors and many others, 354 authors in total )

MeSH headings : ADAM17 Protein / antagonists & inhibitors; Antineoplastic Combined Chemotherapy Protocols / pharmacology; Antineoplastic Combined Chemotherapy Protocols / therapeutic use; Benchmarking; Biomarkers, Tumor / genetics; Cell Line, Tumor; Computational Biology / methods; Computational Biology / standards; Datasets as Topic; Drug Antagonism; Drug Resistance, Neoplasm / drug effects; Drug Resistance, Neoplasm / genetics; Drug Synergism; Genomics / methods; Humans; Molecular Targeted Therapy / methods; Mutation; Neoplasms / drug therapy; Neoplasms / genetics; Pharmacogenetics / methods; Pharmacogenetics / standards; Phosphatidylinositol 3-Kinases / genetics; Phosphoinositide-3 Kinase Inhibitors; Treatment Outcome
TL;DR: A large drug combination screen across cancer cell lines is provided to benchmark crowdsourced methods and to computationally predict drug synergies, and genomic rationale for synergy predictions are identified. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: July 1, 2019

2019 review

Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples

[Review of ]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299.

By: K. Burnum-Johnson *, X. Zheng *, J. Dodds n, J. Ash n, D. Fourches n, C. Nicora *, J. Wendler *, T. Metz * ...

Contributors: K. Burnum-Johnson *, X. Zheng *, J. Dodds n, J. Ash n, D. Fourches n, C. Nicora *, J. Wendler *, T. Metz * ...

author keywords: Ion mobility spectrometry; Mass spectrometry; Omics; Proteomics; Lipidomics; Metabolomics; Glycomics; Exposomics
TL;DR: Ion mobility spectrometry has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 1, 2019

2018 journal article

chemmodlab: a cheminformatics modeling laboratoryR package for fitting and assessing machine learning models

JOURNAL OF CHEMINFORMATICS, 10.

By: J. Ash n & J. Hughes-Oliver n

author keywords: Machine learning; QSAR; R package; Initial enhancement; Enrichment factor; Accumulation curve; Hit enrichment curve; Repeated cross-validation
TL;DR: The goal of chemmodlab is to streamline the fitting and assessment pipeline for many machine learning models in R, making it easy for researchers to compare the utility of these models. (via Semantic Scholar)
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Source: Web Of Science
Added: December 10, 2018

2017 journal article

Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(6), 1286–1299.

By: J. Ash n & D. Fourches n

MeSH headings : Ligands; Mitogen-Activated Protein Kinase 1 / antagonists & inhibitors; Mitogen-Activated Protein Kinase 1 / chemistry; Mitogen-Activated Protein Kinase 1 / metabolism; Molecular Dynamics Simulation; Protein Conformation; Protein Kinase Inhibitors / chemistry; Protein Kinase Inhibitors / metabolism; Protein Kinase Inhibitors / pharmacology; Quantitative Structure-Activity Relationship; Solvents / chemistry; Temperature
TL;DR: This study represents the largest attempt to utilize MD-extracted chemical descriptors to characterize and model a series of bioactive molecules and showed that MD descriptors had little correlation with conventionally used 2D/3D descriptors, and were able to distinguish the most active ERK2 inhibitors from the moderate/weak actives and inactives. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2016 journal article

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees

MOLECULAR BIOLOGY AND EVOLUTION, 33(12), 3314–3316.

By: W. Huang *, G. Zhou*, M. Marchand*, J. Ash n, D. Morris*, P. Van Dooren *, J. Brown *, K. Gallivan *, J. Wilgenbusch *

author keywords: TreeScaper; visualization; community detection; phylogenetic trees
MeSH headings : Computer Simulation; Databases, Nucleic Acid; Evolution, Molecular; Phylogeny; Sequence Analysis, DNA / methods; Software
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UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

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