Jeremy R. Ash

Works (11)

Updated: July 15th, 2023 21:19

2022 article

Confidence bands and hypothesis tests for hit enrichment curves

Ash, J. R., & Hughes-Oliver, J. M. (2022, July 28). Journal of Cheminformatics.

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

author keywords: Virtual screening; Enrichment factor; Lift curve; Early enrichment; Ranking algorithm; Empirical process
topics (OpenAlex): Computational Drug Discovery Methods; Statistical Methods in Clinical Trials; Machine Learning and Data Classification
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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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 8, 2022

2020 article

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

Akhtari, F. S., Havener, T. M., Hertz, D. L., Ash, J., Larson, A., Carey, L. A., … Motsinger-Reif, A. A. (2020, September 15). Pharmacogenetics and Genomics.

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
topics (OpenAlex): Cancer Genomics and Diagnostics; Statistical Methods in Clinical Trials; Breast Cancer Treatment Studies
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)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: May 10, 2021

2020 article

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

Odenkirk, M. T., Zin, P. P. K., Ash, J. R., Reif, D. M., Fourches, D., & Baker, E. S. (2020, January 1). The Analyst, Vol. 145, pp. 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
topics (OpenAlex): Metabolomics and Mass Spectrometry Studies; Computational Drug Discovery Methods; Bioinformatics and Genomic Networks
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 article

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

Odenkirk, M. T., Stratton, K. G., Gritsenko, M. A., Bramer, L. M., Webb-Robertson, B.-J. M., Bloodsworth, K. J., … Baker, E. S. (2020, September 8). Molecular Omics, Vol. 16.

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
topics (OpenAlex): Pregnancy and preeclampsia studies; Birth, Development, and Health; Gestational Diabetes Research and Management
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 article

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

Fourches, D., & Ash, J. (2019, September 12). Expert Opinion on Drug Discovery.

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
topics (OpenAlex): Computational Drug Discovery Methods; Protein Structure and Dynamics; Machine Learning in Materials Science
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 article

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles

Ash, J. R., Kuenemann, M. A., Rotroff, D., Motsinger-Reif, A., & Fourches, D. (2019, June 24). Journal of Cheminformatics.

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
topics (OpenAlex): Metabolomics and Mass Spectrometry Studies; Computational Drug Discovery Methods; Bioinformatics and Genomic Networks
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 article

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

Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., … Fourches, D. (2019, June 17). Nature Communications.

By: M. Menden *, D. Wang *, M. Mason *, B. Szalai *, K. Bulusu *, Y. Guan *, T. Yu *, J. Kang * ...

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
topics (OpenAlex): Computational Drug Discovery Methods; Bioinformatics and Genomic Networks; Protein Degradation and Inhibitors
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)
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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 1, 2019

2019 article

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

Burnum-Johnson, K. E., Zheng, X., Dodds, J. N., Ash, J., Fourches, D., Nicora, C. D., … Baker, E. S. (2019, April 29). TrAC Trends in Analytical Chemistry, Vol. 116, pp. 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
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Analytical Chemistry and Chromatography; Metabolomics and Mass Spectrometry Studies
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 article

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

Ash, J. R., & Hughes-Oliver, J. M. (2018, November 28). Journal of Cheminformatics.

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
topics (OpenAlex): Data Analysis with R; Explainable Artificial Intelligence (XAI); Machine Learning and Data Classification
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 article

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

Ash, J., & Fourches, D. (2017, May 4). Journal of Chemical Information and Modeling.

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
topics (OpenAlex): Computational Drug Discovery Methods; Synthesis and biological activity; Melanoma and MAPK Pathways
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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UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2016 article

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees

Huang, W., Zhou, G., Marchand, M., Ash, J. R., Morris, D., Dooren, P. V., … Wilgenbusch, J. C. (2016, September 15). Molecular Biology and Evolution.

By: W. Huang *, G. Zhou*, M. Marchand*, J. Ash n, D. Morris*, P. 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
topics (OpenAlex): Genomics and Phylogenetic Studies; Bioinformatics and Genomic Networks; Genetic diversity and population structure
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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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