Works Published in 2015
Displaying works 1 - 20 of 53 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2015 journal article
Comprehensive characterization of the Published Kinase Inhibitor Set
Nature Biotechnology, 34(1), 95–103.
MeSH headings : Glycosylation; Phosphotransferases / antagonists & inhibitors; Protein Kinase Inhibitors / pharmacology
TL;DR:
A thorough characterization of the Published Kinase Inhibitor Set is provided and chemical starting points for designing new chemical probes of orphan kinases are identified and the utility of these leads are illustrated by developing a selective inhibitor for the previously untargeted kinases LOK and SLK.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: January 21, 2021
2015 journal article
Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
Scientific Reports, 5(1), 15145.
MeSH headings : Adult; Aged; Aging / genetics; Animals; Cluster Analysis; Computational Biology / methods; Female; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genetic Association Studies; Humans; Male; Mice; Middle Aged; Molecular Sequence Annotation; Mutation; Organ Specificity / genetics; Young Adult
TL;DR:
This work catalogueed age-related gene expression changes in nine tissues from nearly two hundred individuals collected by the Genotype-Tissue Expression (GTEx) project, finding the aging gene expression signatures are very tissue specific and enrichment for some well-known aging components such as mitochondria biology is observed in many tissues.
(via Semantic Scholar)
www.nature.com (publisher PDF)
Source: Crossref
Added: January 4, 2021
2015 journal article
Erratum: Gene expression in major depressive disorder
Molecular Psychiatry, 21(3), 444–444.
TL;DR:
The authors noticed that the Supplementary Figure legends were not published with the paper, and the legends accompany this erratum.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2015 journal article
Gene expression in major depressive disorder
Molecular Psychiatry, 21(3), 339–347.
MeSH headings : Adult; Anxiety Disorders / genetics; Cross-Sectional Studies; Depressive Disorder, Major / diagnosis; Depressive Disorder, Major / genetics; Female; Gene Expression / genetics; Gene Expression Regulation / genetics; Genetic Predisposition to Disease / genetics; Genome-Wide Association Study; Humans; Interleukin-6 / genetics; Interleukin-6 / metabolism; Killer Cells, Natural / metabolism; Longitudinal Studies; Male; Middle Aged; Polymorphism, Single Nucleotide / genetics; Signal Transduction / genetics
TL;DR:
Multiple gene expression associations with MDD were identified and a measurable impact of current MDD state on gene expression is suggested, in line with the immune suppression and immune activation hypothesis of MDD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: August 28, 2020
2015 journal article
Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds
Toxicology and Applied Pharmacology, 284(2), 262–272.
author keywords: Skin sensitization; QSAR; Virtual screening; Skin toxicants
MeSH headings : Databases, Factual; Dermatitis, Allergic Contact / etiology; Dermatitis, Allergic Contact / immunology; Hazardous Substances / poisoning; Humans; Models, Chemical; Models, Immunological; Quantitative Structure-Activity Relationship; Skin / drug effects; Skin / immunology; Software
TL;DR:
This study aims to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitized individuals, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints
Chemistry of Materials, 27(3), 735–743.
TL;DR:
The issue of scientific discovery in materials databases is addressed by introducing novel analytical approaches based on structural and electronic materials fingerprints, which contribute to the emerging field of materials informati...
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization
Toxicology and Applied Pharmacology, 284(2), 273–280.
author keywords: Skin sensitization; Skin permeability; QSAR; Virtual screening; Skin toxicants
MeSH headings : Computer Simulation; Databases, Factual; Dermatitis, Allergic Contact / etiology; Dermatitis, Allergic Contact / immunology; Dermatitis, Allergic Contact / metabolism; Hazardous Substances / poisoning; Humans; Models, Theoretical; Permeability; Quantitative Structure-Activity Relationship; Skin / drug effects; Skin / immunology; Skin / metabolism; Skin Absorption / physiology; Software
TL;DR:
The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity
Molecular Informatics, 34(2-3), 160–170.
author keywords: Side effects; Machine learning; QSAR; Drug repurposing
MeSH headings : Animals; Data Mining / methods; Dopamine Antagonists / adverse effects; Humans; MEDLINE; Models, Biological; Serotonin Antagonists / adverse effects
TL;DR:
The results demonstrate that side effect profiles can be utilized to predict a drug’s unknown molecular activity, thus representing a valuable opportunity in repositioning the drug for a new indications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis
Nature Communications, 6(1).
MeSH headings : Adolescent; Adult; Amino Acid Transport Systems; Amino Acid Transport Systems, Neutral / genetics; Child; Cystic Fibrosis / genetics; Cystic Fibrosis / metabolism; Cystic Fibrosis / pathology; Female; Genome-Wide Association Study; Humans; Lung / metabolism; Lung / pathology; Male; Middle Aged; Mucin-4 / genetics; Mucins / genetics; Severity of Illness Index; Transcription Factors / genetics; Young Adult
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology, 33(9), 933–940.
MeSH headings : Computer Simulation; Dose-Response Relationship, Drug; Genetic Predisposition to Disease / genetics; Genetics, Population; Hazardous Substances / toxicity; High-Throughput Screening Assays / methods; Humans; Incidence; Lymphocytes / cytology; Lymphocytes / drug effects; Lymphocytes / physiology; Models, Genetic; Risk Assessment / methods; Toxicity Tests / methods
TL;DR:
The results from a community-based DREAM challenge to predict toxicities of environmental compounds with potential adverse health effects for human populations highlight the possibility of predicting health risks associated with unknown compounds, although risk estimation accuracy remains suboptimal.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Crossref
Added: February 24, 2020
2015 journal article
Erratum: Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology, 33(10), 1109–1109.
TL;DR:
The authors have added 12 additional authors to the list of “Other participants in the NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration,” including Alok Jaiswal, Antti Poso, Himanshu Chheda, Ismeet Kaur, Jing Tang, John-Patrick Mpindi, Krister Wennerberg, Natalio Krasnogor, Samuel Kaski and Tero Aittokallio.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Identification of Novel Gene Targets and Putative Regulators of Arsenic-Associated DNA Methylation in Human Urothelial Cells and Bladder Cancer
Chemical Research in Toxicology, 28(6), 1144–1155.
MeSH headings : Adult; Aged; Arsenic / metabolism; Arsenic / toxicity; Cell Transformation, Neoplastic / chemically induced; DNA Methylation / drug effects; DNA Methylation / genetics; Female; Humans; Middle Aged; Urinary Bladder Neoplasms / chemically induced; Urinary Bladder Neoplasms / genetics; Urinary Bladder Neoplasms / pathology; Urothelium / cytology; Urothelium / drug effects; Young Adult
TL;DR:
Both the arsenic- and cancer-associated genes are enriched for the binding sites of common transcription factors known to play roles in carcinogenesis, demonstrating a novel potential mechanistic link between iAs exposure and bladder cancer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
6. Clean Water and Sanitation
(Web of Science)
Source: Crossref
Added: February 24, 2020
2015 journal article
Pharmacometabolomic Assessments of Atenolol and Hydrochlorothiazide Treatment Reveal Novel Drug Response Phenotypes
CPT: Pharmacometrics & Systems Pharmacology, 4(11), 669–679.
TL;DR:
The metabolites identified herein may serve as biomarkers for improving treatment decisions and elucidating mechanisms driving HTN treatment responses as part of a quantitative systems pharmacology approach.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
Erratum: Corrigendum: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
Nature Genetics, 47(6), 690–690.
Source: Crossref
Added: February 24, 2020
2015 journal article
Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
Nature Genetics, 47(4), 353–360.
MeSH headings : Alleles; Allelic Imbalance / genetics; Animals; Crosses, Genetic; Dosage Compensation, Genetic; Female; Gene Expression; Genetic Speciation; Humans; Male; Mice / genetics; Mice, Knockout; Phylogeny; Polymorphism, Single Nucleotide
TL;DR:
It is concluded that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 book
Exploiting solved genomes of plant-parasitic nematodes to understand parasitism
In Advances in Botanical Research (Vol. 73, pp. 241–258).
Contributors: D. Bird n , V. Williamson * & C. Opperman n
TL;DR:
Comparative genomics has confirmed much of what had been deduced from expressed sequence tag sequencing, and expanded the understanding of the extent of horizontal gene transfer as a source of novelty during the evolution of parasitism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: January 30, 2020
2015 journal article
Molecular cloning, functional characterization, and evolutionary analysis of vitamin D receptors isolated from basal vertebrates
PLoS ONE, 10(4).
Contributors: E. Kollitz n, G. Zhang n, M. Hawkins n, G. Whitfield*, D. Reif n & S. Kullman n
MeSH headings : Animals; Base Sequence; Cloning, Molecular; Computational Biology; Electrophoretic Mobility Shift Assay; Evolution, Molecular; Fishes / genetics; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Petromyzon / genetics; Phylogeny; Protein Binding; Protein Interaction Mapping; Receptors, Calcitriol / genetics; Sequence Analysis, DNA; Skates, Fish / genetics; Species Specificity; Two-Hybrid System Techniques
TL;DR:
This study compares molecular activities of vitamin D receptors (VDR) from basal species that diverged at key points in vertebrate evolution in order to infer derived and ancestral VDR functions of teleost paralogs and suggests that 1, 25D3 acts as a partial agonist in basal species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2015 journal article
Food for Thought...: Toxicity testing in the 21st century beyond environmental chemicals
Altex, 32(3), 171–181.
Contributors: C. Rovida*, S. Asakura*, M. Daneshian*, H. Hofman-Huether*, M. Leist *, L. Meunier *, D. Reif n , A. Rossi*
author keywords: food ingredients; drugs; Tox21c; safety assessment
MeSH headings : Animal Testing Alternatives / methods; Animals; Drug Approval; Drug Evaluation / methods; Drug Industry; Humans; In Vitro Techniques; Risk Assessment; Safety / standards; Toxicity Tests / methods; United States; United States Environmental Protection Agency
TL;DR:
The question is whether the latest paradigm shift proposed by the Tox21c report for chemicals may provide a useful tool to improve the risk assessment approach also for drugs and food ingredients.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: ORCID
Added: May 14, 2019
2015 book
Embracing complexity: Searching for gene-gene and gene environment interactions in genetic epidemiology
In Genomics and Proteomics: Principles, Technologies, and Applications (pp. 19–58).
Contributors: A. Motsinger & D. Reif
TL;DR:
Mango (Mangifera indica L.) is an important tropical fruit crop that is thought to be an allotetraploid species with an estimated genome size of 439 mega base pairs.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2015 journal article
Data-driven asthma endotypes defined from blood biomarker and gene expression data
PLoS ONE, 10(2).
Contributors: B. George *, D. Reif* , J. Gallagher*, C. Williams-DeVane *, B. Heidenfelder*, E. Hudgens*, W. Jones *, L. Neas *, E. Cohen Hubal *, S. Edwards*
MeSH headings : Adaptive Immunity; Anti-Asthmatic Agents / therapeutic use; Asthma / blood; Asthma / classification; Asthma / genetics; Asthma / immunology; Biomarkers / blood; Decision Trees; Eosinophilia / complications; Humans; Immunity, Innate; Medical Informatics / methods; Metabolic Syndrome / complications; Transcriptome
TL;DR:
This study describes four distinct asthma endotypes identified via a purely data-driven method, specifically designed to integrate blood gene expression and clinical biomarkers in a way that provides new mechanistic insights regarding the different asthma endotype.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
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