List of works - Paul Pavlidis

A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse.

scientific article

A critical assessment of single-cell transcriptomes sampled following patch-clamp electrophysiology

A cross-laboratory comparison of expression profiling data from normal human postmortem brain

scientific article

A high-throughput study of gene expression in preterm labor with a subtractive microarray approach

article

A low affinity cis-regulatory BMP response element restricts target gene activation to subsets of Drosophila neurons

scientific article published on 30 October 2020

A methodology for the analysis of differential coexpression across the human lifespan

scientific article

Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophy

scientific article

Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy

scientific article

Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning

scholarly article

Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model

scientific article

Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice

scientific article

An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse

scientific article published on 14 June 2006

Analysis of strain and regional variation in gene expression in mouse brain

scientific article

Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text

scientific article

Application and evaluation of automated semantic annotation of gene expression experiments

scientific article published on 17 April 2009

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

scientific article published on 06 January 2013

Automated recognition of brain region mentions in neuroscience literature

scientific article published on September 2009

Bias tradeoffs in the creation and analysis of protein-protein interaction networks

scientific article published on 27 January 2014

Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction

scientific article published in October 2003

Book Review

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA) ⬇️

scientific article published on January 1, 2013

Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling

scientific article published in May 2003

Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH.

scientific article published in February 2004

Coexpression analysis of human genes across many microarray data sets

scientific article

Comparison of techniques for correlating survival and gene expression data from wild salmon

article

Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka).

scientific article

Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID).

scientific article

Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355–1363]

scholarly article published in NeuroImage

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing

scientific article

Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

scientific article published on 30 November 2017

Curation of over 10 000 transcriptomic studies to enable data reuse

scientific article published on 28 January 2021

DNA methylation signature of human fetal alcohol spectrum disorder.

scientific article published on 29 June 2016

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability

scientific article

Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity

scientific article

Diverse epigenetic strategies interact to control epidermal differentiation

scientific article

EGAD: Ultra-fast functional analysis of gene networks

article

ErmineJ: tool for functional analysis of gene expression data sets

scientific article

Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities

scientific article published on 30 November 2014

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms

scientific article

FTO, obesity and the adolescent brain

scientific article published on 30 November 2012

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

scientific article

Gene Ontology term overlap as a measure of gene functional similarity

scientific article

Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis.

scientific article published on 18 May 2004

Gene expression profiling of depression and suicide in human prefrontal cortex

scientific article published in February 2004

Gene expression signatures in chronic and aggressive periodontitis: a pilot study

article

Gene expression signatures in polyarticular juvenile idiopathic arthritis demonstrate disease heterogeneity and offer a molecular classification of disease subsets

scientific article published on July 2009

Gene function analysis in complex data sets using ErmineJ.

scientific article

Genome-wide expression profiling of schizophrenia using a large combined cohort

scientific article published on 3 January 2012

Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon

scientific article published in Science

Gingival tissue transcriptomes identify distinct periodontitis phenotypes.

scientific article

Granulocyte chemotactic protein 2 (gcp-2/cxcl6) complements interleukin-8 in periodontal disease

scientific article published on 07 October 2008

Hierarchical model of gene regulation by transforming growth factor beta

scientific article published on 20 August 2003

Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells

scientific article published on April 2009

Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins

scientific article

Informatics in neuroscience

scientific article published on 10 October 2007

Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb

scientific article published on 9 May 2016

KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study.

scientific article

Learning gene functional classifications from multiple data types

scientific article

Matrix2png: a utility for visualizing matrix data

scientific article

Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease

scientific article published on 01 November 2019

Meta-Analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling

scientific article published on 20 March 2016

Meta-Analysis of Gene Expression in Autism Spectrum Disorder

scientific article published on 26 February 2015

Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls

scientific article

Meta-analysis of kindling-induced gene expression changes in the rat hippocampus

scientific article published on 15 September 2009

Metaanalysis of flawed expression profiling data leading to erroneous Parkinson's biomarker identification

scientific article published on 23 June 2015

Microarray analysis of gene expression following the formalin test in the infant rat.

scientific article published in September 2005

Molecular aging in human prefrontal cortex is selective and continuous throughout adult life

scientific article published in March 2005

Monitoring changes in the Gene Ontology and their impact on genomic data analysis

article

Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction

scientific article published on 29 April 2020

Network analyses reveal pervasive functional regulation between proteases in the human protease web

scientific article (publication date: May 2014)

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences

scientific article published on 26 February 2013

Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain

scientific article published on 4 February 2013

Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics

scientific article published on 29 May 2010

Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation

scientific article (publication date: March 2001)

Periodontal therapy alters gene expression of peripheral blood monocytes

scientific article published on September 2007

Pitfalls in the application of gene-set analysis to genetics studies

scientific article published on December 2014

Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain.

scientific article published on February 2015

Profiling placental and fetal DNA methylation in human neural tube defects

scientific article published on 16 February 2016

Progress and challenges in the computational prediction of gene function using networks

scientific article published on 7 September 2012

Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update

scientific article published on 31 October 2013

Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions

scientific article

Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.

scientific article

Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain ⬇️

scientific article published on January 6, 2011

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?

scientific article published on 17 November 2015

Sharing and reusing gene expression profiling data in neuroscience

scientific article (publication date: 2007)

Subgingival bacterial colonization profiles correlate with gingival tissue gene expression

scientific article

Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis

scientific article published on July 2009

Support vector machine classification on the web.

scientific article

Systematic evaluation of isoform function in literature reports of alternative splicing

Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application

scientific article published on 21 May 2015

The Drosophila easily shocked gene: a mutation in a phospholipid synthetic pathway causes seizure, neuronal failure, and paralysis.

scientific article published in October 1994

The Impact of Multifunctional Genes on "Guilt by Association" Analysis ⬇️

scientific article published on February 18, 2011

The NeuroDevNet Neuroinformatics Core

scientific article published on March 2011

The effect of replication on gene expression microarray experiments

scientific article published in September 2003

The path of no return--Truncated protein N-termini and current ignorance of their genesis

scientific article

The role of indirect connections in gene networks in predicting function ⬇️

scientific article published on May 6, 2011

Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice

scientific article published on 23 October 2005

Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis

scientific article

Transcriptome sequencing of the anterior cingulate in bipolar disorder: dysregulation of G protein-coupled receptors

scientific article published on 04 August 2015

Transcriptomes in healthy and diseased gingival tissues.

scientific article published in November 2008

Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia

article

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes

scientific article published on 18 June 2019

Transcriptomic responses to high water temperature in two species of Pacific salmon

scientific article

Understanding the impact of 1q21.1 copy number variant

scientific article

Untangling the effects of cellular composition on coexpression analysis

scientific article published on 24 June 2020

Using ANOVA for gene selection from microarray studies of the nervous system ⬇️

scientific article published on December 1, 2003

Using predictive specificity to determine when gene set analysis is biologically meaningful

article

Using text mining to link journal articles to neuroanatomical databases ⬇️

scientific article (publication date: June 2012)

Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex

scientific article published in June 2004

VariCarta: A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies

scientific article published on 09 November 2019

Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies

Wikidata as a semantic framework for the Gene Wiki initiative ⬇️

scientific article

Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth

scientific article published on November 2006

beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors

scientific article published on September 2007

miR-1202 is a primate-specific and brain-enriched microRNA involved in major depression and antidepressant treatment

scientific article

miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability

scientific article

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks ⬇️

scientific article published on March 29, 2012

List of works by Paul Pavlidis

A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse.

A critical assessment of single-cell transcriptomes sampled following patch-clamp electrophysiology

A cross-laboratory comparison of expression profiling data from normal human postmortem brain

A high-throughput study of gene expression in preterm labor with a subtractive microarray approach

A low affinity cis-regulatory BMP response element restricts target gene activation to subsets of Drosophila neurons

A methodology for the analysis of differential coexpression across the human lifespan

Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophy

Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy

Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning

Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model

Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice

An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse

Analysis of strain and regional variation in gene expression in mouse brain

Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text

Application and evaluation of automated semantic annotation of gene expression experiments

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

Automated recognition of brain region mentions in neuroscience literature

Bias tradeoffs in the creation and analysis of protein-protein interaction networks

Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction

Book Review

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA) ⬇️

Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling

Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH.

Coexpression analysis of human genes across many microarray data sets

Comparison of techniques for correlating survival and gene expression data from wild salmon

Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka).

Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID).

Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355–1363]

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing

Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

Curation of over 10 000 transcriptomic studies to enable data reuse

DNA methylation signature of human fetal alcohol spectrum disorder.

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability

Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity

Diverse epigenetic strategies interact to control epidermal differentiation

EGAD: Ultra-fast functional analysis of gene networks

ErmineJ: tool for functional analysis of gene expression data sets

Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms

FTO, obesity and the adolescent brain

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

Gene Ontology term overlap as a measure of gene functional similarity

Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis.

Gene expression profiling of depression and suicide in human prefrontal cortex

Gene expression signatures in chronic and aggressive periodontitis: a pilot study

Gene expression signatures in polyarticular juvenile idiopathic arthritis demonstrate disease heterogeneity and offer a molecular classification of disease subsets

Gene function analysis in complex data sets using ErmineJ.

Genome-wide expression profiling of schizophrenia using a large combined cohort

Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon

Gingival tissue transcriptomes identify distinct periodontitis phenotypes.

Granulocyte chemotactic protein 2 (gcp-2/cxcl6) complements interleukin-8 in periodontal disease

Hierarchical model of gene regulation by transforming growth factor beta

Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells

Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins

Informatics in neuroscience

Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb

KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study.

Learning gene functional classifications from multiple data types

Matrix2png: a utility for visualizing matrix data

Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease

Meta-Analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling

Meta-Analysis of Gene Expression in Autism Spectrum Disorder

Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls

Meta-analysis of kindling-induced gene expression changes in the rat hippocampus

Metaanalysis of flawed expression profiling data leading to erroneous Parkinson's biomarker identification

Microarray analysis of gene expression following the formalin test in the infant rat.

Molecular aging in human prefrontal cortex is selective and continuous throughout adult life

Monitoring changes in the Gene Ontology and their impact on genomic data analysis

Monitoring changes in the Gene Ontology and their impact on genomic data analysis

Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction

Network analyses reveal pervasive functional regulation between proteases in the human protease web

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences

Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain

Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics

Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation

Periodontal therapy alters gene expression of peripheral blood monocytes

Pitfalls in the application of gene-set analysis to genetics studies

Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain.

Profiling placental and fetal DNA methylation in human neural tube defects