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List of works by Jonathan Wren

404 not found: the stability and persistence of URLs published in MEDLINE.

scientific article published on 22 January 2004

A TMEFF2-regulated cell cycle derived gene signature is prognostic of recurrence risk in prostate cancer

article

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide

scientific article

A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools

scientific article published on 15 July 2005

A scalable machine-learning approach to recognize chemical names within large text databases

scientific article

A system-wide analysis of differentially expressed genes in ectopic and eutopic endometrium

article

ALE: automated label extraction from GEO metadata

scientific article published on 28 December 2017

APache Is an AP2-Interacting Protein Involved in Synaptic Vesicle Trafficking and Neuronal Development

scientific article published in December 2017

ARID3a gene profiles are strongly associated with human interferon alpha production

article

ARROGANT: an application to manipulate large gene collections

scientific article

ASTRAL, a hyperspectral imaging DNA sequencer

Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice

scientific article published on 13 July 2016

Activated signature of antiphospholipid syndrome neutrophils reveals potential therapeutic target

scientific article published on 21 September 2017

Aging exacerbates hypertension-induced cerebral microhemorrhages in mice: role of resveratrol treatment in vasoprotection.

scientific article published on 9 February 2015

Aging exacerbates obesity-induced cerebromicrovascular rarefaction, neurovascular uncoupling, and cognitive decline in mice

scientific article

Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and p-values

scientific article published on 22 December 2017

Algorithmically outsourcing the detection of statistical errors and other problems

scientific article published on 24 May 2018

Analysis of TMEFF2 allografts and transgenic mouse models reveals roles in prostate regeneration and cancer

scientific article

Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage

scientific article published on 18 December 2020

Automating Literature-Based Lead Discovery

Automating genomic data mining via a sequence-based matrix format and associative rule set

scientific article

Bioimage informatics: a new category in Bioinformatics ⬇️

scientific article

Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades

scientific article published on 5 May 2016

Biomedical term mapping databases

scientific article

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

scientific article published on 18 April 2016

CAGm: a repository of germline microsatellite variations in the 1000 genomes project

scientific article published on 01 January 2019

CD4+CD28+KIR+CD11ahi T cells correlate with disease activity and are characterized by a pro-inflammatory epigenetic and transcriptional profile in lupus patients

scientific article published on 20 October 2017

CD82 restrains pathological angiogenesis by altering lipid raft clustering and CD44 trafficking in endothelial cells

scientific article published on 22 August 2014

CNS-wide Sexually Dimorphic Induction of the Major Histocompatibility Complex 1 Pathway With Aging

scientific article published on 18 January 2016

Caloric restriction confers persistent anti-oxidative, pro-angiogenic, and anti-inflammatory effects and promotes anti-aging miRNA expression profile in cerebromicrovascular endothelial cells of aged rats

scientific article

Characterization of cxorf21 Provides Molecular Insight Into Female-Bias Immune Response in SLE Pathogenesis

scientific article published on 21 October 2019

ChemDistiller: an engine for metabolite annotation in mass spectrometry

scientific article published on 12 February 2018

Chondrosarcoma-associated gene 1 (CSAG1) maintains the integrity of the mitotic centrosome in cells with defective p53

scientific article published on 15 April 2020

Circulating IGF-1 deficiency exacerbates hypertension-induced microvascular rarefaction in the mouse hippocampus and retrosplenial cortex: implications for cerebromicrovascular and brain aging.

scientific article published on 9 September 2016

Circulating anti-geronic factors from heterochonic parabionts promote vascular rejuvenation in aged mice: transcriptional footprint of mitochondrial protection, attenuation of oxidative stress, and rescue of endothelial function by young blood

scientific article published on 15 March 2020

Clinical trial IDs need to be validated prior to publication because hundreds of invalid National Clinical Trial Identifications are regularly entering MEDLINE.

scientific article

Clustering microarray-derived gene lists through implicit literature relationships

scientific article published on 30 May 2007

Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog

scientific article

Correction to: Tetraspanin-enriched microdomains regulate digitation junctions

scientific article published on 01 November 2018

Cross-hybridization on PCR-spotted microarrays

scientific article

DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks

scientific article

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

scientific article published on 16 May 2017

Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes

scientific article

Databases, data tombs and dust in the wind

scientific article published on October 2008

DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier

scientific article published on 28 September 2017

Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation

scientific article published in 2022

Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.

scientific article

Differential Activation Profiles of Multiple Transcription Factors During Dendritic Cell Maturation

scientific article published on 01 April 2005

Differential effects of selective frankincense (Ru Xiang) essential oil versus non-selective sandalwood (Tan Xiang) essential oil on cultured bladder cancer cells: a microarray and bioinformatics study

scientific article

Déjà vu--a study of duplicate citations in Medline

scientific article

E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells

scientific article published on 19 August 2020

E-mail decay rates among corresponding authors in MEDLINE.

scientific article published in April 2006

E-mail decay rates among corresponding authors in MEDLINE. The ability to communicate with and request materials from authors is being eroded by the expiration of e-mail addresses

scientific article

ELTD1, a potential new biomarker for gliomas

scientific article published on January 2013

ELTD1, an effective anti-angiogenic target for gliomas: preclinical assessment in mouse GL261 and human G55 xenograft glioma models

scientific article published on 14 July 2016

Effects of transgenic methionine sulfoxide reductase A (MsrA) expression on lifespan and age-dependent changes in metabolic function in mice

scientific article

Elevated AKR1C3 expression promotes prostate cancer cell survival and prostate cell-mediated endothelial cell tube formation: implications for prostate cancer progression

scientific article

Endothelial dysfunction and angiogenesis impairment in the ageing vasculature

scientific article published on 01 September 2018

Epigenetic Reprogramming in Naive CD4+ T Cells Favoring T Cell Activation and Non-Th1 Effector T Cell Immune Response as an Early Event in Lupus Flares

scientific article published on 25 April 2016

Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils

scientific article

Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes

scientific article

Erratum to: The Development of Translational Biomarkers as a Tool for Improving the Understanding, Diagnosis and Treatment of Chronic Neuropathic Pain

scientific article published on 01 March 2018

Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity

scientific article

Evolving research trends in bioinformatics

scientific article published on 31 October 2006

Examination of CIs in health and medical journals from 1976 to 2019: an observational study

scientific article published on 21 November 2019

Experimental validation of 5 in-silico predicted glioma biomarkers

scientific article published on 24 October 2013

Expression profiling of the ubiquitin conjugating enzyme UbcM2 in murine brain reveals modest age-dependent decreases in specific neurons.

scientific article published on 13 November 2015

Extending the mutual information measure to rank inferred literature relationships

scientific article

Fibroblast-specific Stat1 deletion enhances the myofibroblast phenotype during tissue repair

scientific article published on 16 March 2020

Fine mapping and conditional analysis identify a new mutation in the autoimmunity susceptibility gene BLK that leads to reduced half-life of the BLK protein

scientific article published on July 2012

Functional characterization of the MECP2/IRAK1 lupus risk haplotype in human T cells and a human MECP2 transgenic mouse

scientific article published on 18 February 2013

GFP Affects Human T Cell Activation and Cytokine Production following In Vitro Stimulation ⬇️

scientific article published on April 5, 2013

GTSE1 regulates spindle microtubule dynamics to control Aurora B kinase and Kif4A chromokinesin on chromosome arms

scientific article published on 18 August 2017

Genetic Variation in the Platelet Endothelial Aggregation Receptor 1 Gene Results in Endothelial Dysfunction

scientific article published on 25 September 2015

Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus

scientific article

Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients

scientific article published on 24 April 2013

GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets

scientific article published on April 2016

GenomeRunner: automating genome exploration

scientific article published on 6 December 2011

High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry

scientific article

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses ⬇️

scientific article published on October 18, 2011

Hippocampal subregions exhibit both distinct and shared transcriptomic responses to aging and nonneurodegenerative cognitive decline.

scientific article

Histone Deacetylase 5 Is Overexpressed in Scleroderma Endothelial Cells and Impairs Angiogenesis via Repression of Proangiogenic Factors

scientific article published on 2 August 2016

Histone demethylase JMJD2A drives prostate tumorigenesis through transcription factor ETV1.

scientific article published on 5 January 2016

Homozygous Expression of Mutant ELOVL4 Leads to Seizures and Death in a Novel Animal Model of Very Long-Chain Fatty Acid Deficiency.

scientific article published on 22 November 2017

Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

scientific article published on 25 July 2016

IGF-1 deficiency in a critical period early in life influences the vascular aging phenotype in mice by altering miRNA-mediated post-transcriptional gene regulation: implications for the developmental origins of health and disease hypothesis.

scientific article published on 26 August 2016

IL-18 acts in synergy with IL-7 to promote ex vivo expansion of T lymphoid progenitor cells.

scientific article

Identification and characterization of zebrafish ocular formation genes

scientific article

Identification of Susceptibility Loci in IL6, RPS9/LILRB3, and an Intergenic Locus on Chromosome 21q22 in Takayasu Arteritis in a Genome-Wide Association Study

scientific article published on May 2015

Identification of a novel senolytic agent, navitoclax, targeting the Bcl-2 family of anti-apoptotic factors

scientific article

Identification of susceptibility loci for Takayasu arteritis through a large multi-ancestral genome-wide association study

scientific article published on 03 December 2020

Identifying duplicate content using statistically improbable phrases

scientific article

Insights From Analysis of Human Antigen-Specific Memory B Cell Repertoires

Insulin-like growth factor 1 deficiency exacerbates hypertension-induced cerebral microhemorrhages in mice, mimicking the aging phenotype

scientific article

KRCC1: A potential therapeutic target in ovarian cancer

scientific article published on 23 December 2019

Knowledge discovery by automated identification and ranking of implicit relationships

scientific article published on 22 January 2004

Large-scale directional relationship extraction and resolution

scientific article (publication date: 12 August 2008)

Letter to the Editor

scientific article published on 01 July 2004

Lifelong reduction in complex IV induces tissue-specific metabolic effects but does not reduce lifespan or healthspan in mice

scientific article published on 25 April 2018

Loss of Nrf2 exacerbates the visual deficits and optic neuritis elicited by experimental autoimmune encephalomyelitis

scientific article published on 30 December 2016

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations

Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging

scientific article published on 16 October 2021

Markov model recognition and classification of DNA/protein sequences within large text databases

scientific article published on 13 September 2005

Medline: the knowledge buried therein, its potential, and cost

scientific article published in May 2007

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

scientific article published on 16 July 2013

Melatonin administration does not affect isoproterenol-induced LVH

article

Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions

scientific article published in January 2006

MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer

scientific article published on 27 August 2020

Molecular changes in transcription and metabolic pathways underlying muscle atrophy in the CuZnSOD null mouse model of sarcopenia

scientific article published on 12 May 2020

Myelin-specific Th17 cells induce severe relapsing optic neuritis with irreversible loss of retinal ganglion cells in C57BL/6 mice

scientific article published on 11 April 2016

Neuroretinal-Derived Caveolin-1 Promotes Endotoxin-Induced Inflammation in the Murine Retina

scientific article published on 01 October 2020

Nicotinamide mononucleotide (NMN) supplementation promotes anti-aging miRNA expression profile in the aorta of aged mice, predicting epigenetic rejuvenation and anti-atherogenic effects

scientific article published on 28 August 2019

Nicotinamide mononucleotide (NMN) supplementation promotes neurovascular rejuvenation in aged mice: transcriptional footprint of SIRT1 activation, mitochondrial protection, anti-inflammatory, and anti-apoptotic effects

scientific article published on 13 February 2020

Novel protein ADTRP regulates TFPI expression and function in human endothelial cells in normal conditions and in response to androgen

scientific article

OKN-007 Increases temozolomide (TMZ) Sensitivity and Suppresses TMZ-Resistant Glioblastoma (GBM) Tumor Growth

scientific article published on 20 November 2018

Obesity in Aging Exacerbates Neuroinflammation, Dysregulating Synaptic Function-Related Genes and Altering Eicosanoid Synthesis in the Mouse Hippocampus: Potential Role in Impaired Synaptic Plasticity and Cognitive Decline.

scientific article published in February 2019

Olfactomedin 4 defines a subset of human neutrophils

scientific article published on 20 December 2011

Open access and openly accessible: a study of scientific publications shared via the internet

scientific article

Optimized monoclonal antibody treatment against ELTD1 for GBM in a G55 xenograft mouse model

scientific article published on 21 December 2019

PDGFRα signaling drives adipose tissue fibrosis by targeting progenitor cell plasticity

scientific article published on 27 May 2015

Plant virus biodiversity and ecology

scientific article

Predicting gene ontology from a global meta-analysis of 1-color microarray experiments

scientific article

Predictive bioinformatics identifies novel regulators of proliferation in a cancer stem cell model

scientific article

Prioritizing uncharacterized genes in the search for glioma biomarkers

scientific article published in March 2014

Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article

Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction

scientific article

Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference

scientific article

Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction

scientific article

Proceedings of the 2012 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.

scientific article

Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article published on 9 October 2013

Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article published on 21 October 2014

Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article published on 25 September 2015

Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

scientific article published on 6 October 2016

Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article published on 28 December 2017

Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

scientific article published on 06 July 2020

Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

scientific article

Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction

scientific article

Proceedings of the second annual conference of the MidSouth Computational Biology and Bioinformatics Society. 7-9 October 2004, Little Rock, Arkansas, USA

article

Profiling of m6A RNA modifications identified an age-associated regulation of AGO2 mRNA stability.

scientific article published on 23 March 2018

Question answering systems in biology and medicine--the time is now

scientific article published on 14 June 2011

ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction

scientific article published on 23 October 2017

Regional societies: fostering competitive research through virtual infrastructures

scientific article

Repeat polymorphisms within gene regions: phenotypic and evolutionary implications

scientific article

Restoration of Sarcoplasmic Reticulum Ca<sup>2+</sup> ATPase (SERCA) Activity Prevents Age-Related Muscle Atrophy and Weakness in Mice

scientific article published on 22 December 2020

Reviewer-coerced citation: Case report, update on journal policy, and suggestions for future prevention

scientific article published on 01 September 2019

Ribosomal and immune transcripts associate with relapse in acquired ADAMTS13-deficient thrombotic thrombocytopenic purpura

scientific article

Role of DNA methylation in the dietary restriction mediated cellular memory.

scientific article published on 5 May 2017

SIGNAL-Sequence Information and GeNomic AnaLysis

scientific article published in May 2002

Searching for microsatellite mutations in coding regions in lung, breast, ovarian and colorectal cancers

scientific article published in February 2001

Sex differences in changes of protein synthesis with rapamycin treatment are minimized when metformin is added to rapamycin

scientific article published on 05 August 2020

Sexually divergent DNA methylation patterns with hippocampal aging

scientific article published on 25 September 2017

Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network

scientific article published on January 2004

Simulated Annealing of Microarray Data Reduces Noise and Enables Cross-Experimental Comparisons

scholarly article by Jonathan Wren published in October 2004

Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons

scientific article

Sjögren's Syndrome Minor Salivary Gland CD4+ Memory T Cells Associate with Glandular Disease Features and have a Germinal Center T Follicular Helper Transcriptional Profile

scientific article published on 08 July 2020

Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis

scientific article

Suppression of ILC2 differentiation from committed T cell precursors by E protein transcription factors

scientific article published on 21 March 2019

Systematic classification of non-coding RNAs by epigenomic similarity

scientific article

Systemic lupus erythematosus biomarkers: the challenging quest

scientific article published on 24 December 2016

Targeting ELTD1, an angiogenesis marker for glioblastoma (GBM), also affects VEGFR2: molecular-targeted MRI assessment

Targeting cPLA2 derived lipid hydroperoxides as a potential intervention for sarcopenia

scientific article published on 18 August 2020

Temporal and spatial regulation of epsin abundance and VEGFR3 signaling are required for lymphatic valve formation and function

scientific article

Tetraspanin CD82: a suppressor of solid tumors and a modulator of membrane heterogeneity.

scientific article published on 03 September 2015

Tetraspanin-enriched microdomains regulate digitation junctions.

scientific article

The Achilles' heel of senescent cells: from transcriptome to senolytic drugs.

scientific article

The Development of Translational Biomarkers as a Tool for Improving the Understanding, Diagnosis and Treatment of Chronic Neuropathic Pain

scientific article published on 30 March 2017

The Need for Greater Rigor in Childhood Nutrition and Obesity Research

scientific article published on 01 April 2019

The Role of Neutrophil Proteins on the Amyloid Beta-RAGE Axis.

scientific article

The emerging in-silico scientist: how text-based bioinformatics is bridging biology and artificial intelligence

scientific article published in March 2004

The long noncoding RNA neuroLNC regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43

scientific article published on 18 December 2019

The role of DNA methylation in epigenetics of aging

The write position. A survey of perceived contributions to papers based on byline position and number of authors

scientific article published on November 2007

Theory and reality for software patents: good in concept, not so good in practice

scientific article published in July 2006

ThinkLab as a vetting system for traditional grants

Trends in the production of scientific data analysis resources

scientific article

Truth, probability, and frameworks

scientific article

URL decay in MEDLINE--a 4-year follow-up study

scientific article

Uniform resource locator decay in dermatology journals: author attitudes and preservation practices

scientific article published in September 2006

Upregulation of PSMD10 caused by the JMJD2A histone demethylase

scientific article published on 30 June 2016

Use it or lose it: citations predict the continued online availability of published bioinformatics resources

scientific article

Using fuzzy set theory and scale-free network properties to relate MEDLINE terms

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome

scientific article published on 6 October 2013

Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus

scientific article published on April 2009

ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data

scientific article published on 26 October 2017

eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications

scientific article

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis

scientific article

xMWAS: a data-driven integration and differential network analysis tool.

scientific article published on 23 October 2017

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