List of works - Mehdi Pirooznia

A comparative study of different machine learning methods on microarray gene expression data

scientific article

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

scientific article

A genome-wide association study of attempted suicide.

scientific article

A hybrid likelihood model for sequence-based disease association studies

scientific article

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

scientific article published on 16 April 2021

Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses

scientific article published on 30 November 2020

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

article

Apolipoprotein E Signals via TLR4 to Induce CXCL5 Secretion by Asthmatic Airway Epithelial Cells

scientific article published on 01 August 2020

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

scientific article published on 03 January 2022

Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.

scientific article published on 18 January 2017

Batch Blast Extractor: an automated blastx parser application

scientific article

Boosting NAD+ blunts TLR4-induced type I IFN in control and systemic lupus erythematosus monocytes

scientific article published on 01 March 2022

Circulating Lymphangioleiomyomatosis Tumor Cells With Loss of Heterozygosity in the TSC2 Gene Show Increased Aldehyde Dehydrogenase Activity

scientific article published on 26 April 2019

Circulating cell-free DNA as a biomarker of tissue injury: Assessment in a cardiac xenotransplantation model

scientific article published on 26 April 2018

Circulating mitochondrial DNA is a proinflammatory DAMP in sickle cell disease

scientific article published on 01 June 2021

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

scientific article

Complement receptor CD46 co-stimulates optimal human CD8 T cell effector function via fatty acid metabolism

scientific article published in Nature Communications

Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics

scientific article published on 29 March 2011

Converging Evidence for Epistasis between ANK3 and Potassium Channel Gene KCNQ2 in Bipolar Disorder

scientific article published on 17 May 2013

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

scientific article published on 16 April 2021

DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling.

scientific article

Data mining approaches for genome-wide association of mood disorders

scientific article

De novo variation in bipolar disorder

scientific article published on 27 November 2019

Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida

scientific article (publication date: 8 December 2010)

Discriminating bipolar depression from major depressive disorder with polygenic risk scores

scientific article published on 17 February 2020

Distinguishing bipolar from unipolar depression: the importance of clinical symptoms and illness features

scientific article published on 8 April 2015

Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in

scientific article published on 15 October 2019

Erratum to “Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder”, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics”, April 1; 156(3):370-378

article

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

scientific article published on 09 September 2021

Exome Sequencing of Familial Bipolar Disorder

scientific article

Fasting-induced FOXO4 blunts human CD4<sup>+</sup> T helper cell responsiveness

scientific article published on 15 March 2021

Functional Genomics, Genetics, and Bioinformatics 2016

scientific article

GATA-2-deficient mast cells limit IgE-mediated immediate hypersensitivity reactions in human subjects

scientific article published on 15 May 2019

GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking

scientific article published on 20 November 2018

GOfetcher: a database with complex searching facility for gene ontology.

scientific article published on 26 August 2008

Gene expression analysis of CL-20-induced reversible neurotoxicity reveals GABA(A) receptors as potential targets in the earthworm Eisenia fetida

scientific article published on 6 January 2012

GeneVenn - A web application for comparing gene lists using Venn diagrams

scientific article published on 10 April 2007

Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus).

scientific article

Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones

scientific article published on 13 December 2020

Genome-wide DNA hydroxymethylation identifies potassium channels in the nucleus accumbens as discriminators of methamphetamine addiction and abstinence.

scientific article published on 5 April 2016

Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure.

scientific article published on 30 May 2017

Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder

scientific article

Genome-wide association of mood-incongruent psychotic bipolar disorder

scientific article

Genome-wide association study of schizophrenia in Ashkenazi Jews.

scientific article published on 21 July 2015

Genomic signatures and gene networking: challenges and promises ⬇️

scientific article published on December 23, 2011

High density lipoprotein proteome is associated with cardiovascular risk factors and atherosclerosis burden as evaluated by coronary CT angiography

scientific article published on 25 September 2018

High-throughput sequencing of the synaptome in major depressive disorder

scientific article published on 28 July 2015

Human retinoic acid-regulated CD161 regulatory T cells support wound repair in intestinal mucosa

scholarly article by Giovanni A. M. Povoleri et al published 5 November 2018 in Nature Immunology

IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis

scientific article published on 01 October 2019

ILOOP--a web application for two-channel microarray interwoven loop design

scientific article

Identification of Genes Contributing to a Long Circadian Period in <i>Drosophila Melanogaster</i>

scientific article published on 04 December 2020

In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits

scientific article published on 02 January 2020

Late manifestation of alloantibody-associated injury and clinical pulmonary antibody-mediated rejection: Evidence from cell-free DNA analysis

scientific article published on 31 January 2018

Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz.

scientific article

Metamoodics: meta-analysis and bioinformatics resource for mood disorders.

scientific article published on 10 September 2013

Misregulation of ELK1, AP1, and E12 Transcription Factor Networks Is Associated with Melanoma Progression

scientific article published on 17 February 2020

Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer.

scientific article published on 18 April 2018

NOTCH-mediated ex vivo expansion of human hematopoietic stem and progenitor cells by culture under hypoxia

scientific article published on 26 August 2021

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

scientific article published on 15 May 2020

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

scientific article published on 16 March 2021

Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus).

scientific article published on 5 May 2009

Neutrophil Subsets, Platelets, and Vascular Disease in Psoriasis

scientific article published on 25 February 2019

Pathogenic TERT promoter variants in telomere diseases

scientific article published on 07 December 2018

Polygenic Risk of Schizophrenia and Cognition in a Population-Based Survey of Older Adults.

scientific article published on 12 February 2016

Polygenic risk, stressful life events and depressive symptoms in older adults: a polygenic score analysis.

scientific article published on 9 December 2014

Reconstructing Druze population history.

scientific article

Reducing fatty acid oxidation improves cancer-free survival in a mouse model of Li-Fraumeni syndrome

scientific article published on 21 September 2020

RiboaptDB: a comprehensive database of ribozymes and aptamers

scientific article published on 6 September 2006

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

scientific article published on 11 March 2013

SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data

scientific article

Search for common targets of lithium and valproic acid identifies novel epigenetic effects of lithium on the rat leptin receptor gene.

scientific article published on 14 July 2015

SynaptomeDB: an ontology-based knowledgebase for synaptic genes ⬇️

scientific article published on January 27, 2012

Systematic review of genome-wide gene expression studies of bipolar disorder

scientific article

Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia

scientific article published on 31 August 2018

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.

scientific article

The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish.

scientific article

The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage

scientific article published on 06 December 2018

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

scientific article published on 09 September 2021

Toxicogenomic analysis provides new insights into molecular mechanisms of the sublethal toxicity of 2,4,6-trinitrotoluene in Eisenia fetida

scientific article

Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida

scientific article

Validation and assessment of variant calling pipelines for next-generation sequencing

scientific article

Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer

scientific article published on 9 December 2015

Whole genome sequence-based haplotypes reveal a single origin of the 1393 bp HBB deletion

scientific article published on 30 January 2020

Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families

scientific article published on 04 February 2020

Whole-genome CNV analysis: advances in computational approaches

scientific article published on 13 April 2015

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

scientific article published on 21 June 2017

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA

scientific article published on 05 October 2020

List of works by Mehdi Pirooznia

A comparative study of different machine learning methods on microarray gene expression data

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

A genome-wide association study of attempted suicide.

A hybrid likelihood model for sequence-based disease association studies

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

Apolipoprotein E Signals via TLR4 to Induce CXCL5 Secretion by Asthmatic Airway Epithelial Cells

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.

Batch Blast Extractor: an automated blastx parser application

Boosting NAD+ blunts TLR4-induced type I IFN in control and systemic lupus erythematosus monocytes

Circulating Lymphangioleiomyomatosis Tumor Cells With Loss of Heterozygosity in the TSC2 Gene Show Increased Aldehyde Dehydrogenase Activity

Circulating cell-free DNA as a biomarker of tissue injury: Assessment in a cardiac xenotransplantation model

Circulating mitochondrial DNA is a proinflammatory DAMP in sickle cell disease

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

Complement receptor CD46 co-stimulates optimal human CD8 T cell effector function via fatty acid metabolism

Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics

Converging Evidence for Epistasis between ANK3 and Potassium Channel Gene KCNQ2 in Bipolar Disorder

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling.

Data mining approaches for genome-wide association of mood disorders

De novo variation in bipolar disorder

Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida

Discriminating bipolar depression from major depressive disorder with polygenic risk scores

Distinguishing bipolar from unipolar depression: the importance of clinical symptoms and illness features

Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in

Erratum to “Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder”, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics”, April 1; 156(3):370-378

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Exome Sequencing of Familial Bipolar Disorder

Fasting-induced FOXO4 blunts human CD4<sup>+</sup> T helper cell responsiveness

Functional Genomics, Genetics, and Bioinformatics 2016

GATA-2-deficient mast cells limit IgE-mediated immediate hypersensitivity reactions in human subjects

GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking

GOfetcher: a database with complex searching facility for gene ontology.

Gene expression analysis of CL-20-induced reversible neurotoxicity reveals GABA(A) receptors as potential targets in the earthworm Eisenia fetida

GeneVenn - A web application for comparing gene lists using Venn diagrams

Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus).

Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones

Genome-wide DNA hydroxymethylation identifies potassium channels in the nucleus accumbens as discriminators of methamphetamine addiction and abstinence.

Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure.

Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder

Genome-wide association of mood-incongruent psychotic bipolar disorder

Genome-wide association study of schizophrenia in Ashkenazi Jews.

Genomic signatures and gene networking: challenges and promises ⬇️

High density lipoprotein proteome is associated with cardiovascular risk factors and atherosclerosis burden as evaluated by coronary CT angiography

High-throughput sequencing of the synaptome in major depressive disorder

Human retinoic acid-regulated CD161 regulatory T cells support wound repair in intestinal mucosa

IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis

ILOOP--a web application for two-channel microarray interwoven loop design

Identification of Genes Contributing to a Long Circadian Period in <i>Drosophila Melanogaster</i>

In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits

Late manifestation of alloantibody-associated injury and clinical pulmonary antibody-mediated rejection: Evidence from cell-free DNA analysis

Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz.

Metamoodics: meta-analysis and bioinformatics resource for mood disorders.

Misregulation of ELK1, AP1, and E12 Transcription Factor Networks Is Associated with Melanoma Progression

Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer.

NOTCH-mediated ex vivo expansion of human hematopoietic stem and progenitor cells by culture under hypoxia

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus).

Neutrophil Subsets, Platelets, and Vascular Disease in Psoriasis

Pathogenic TERT promoter variants in telomere diseases

Polygenic Risk of Schizophrenia and Cognition in a Population-Based Survey of Older Adults.

Polygenic risk, stressful life events and depressive symptoms in older adults: a polygenic score analysis.

Reconstructing Druze population history.

Reducing fatty acid oxidation improves cancer-free survival in a mouse model of Li-Fraumeni syndrome

RiboaptDB: a comprehensive database of ribozymes and aptamers

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data

Search for common targets of lithium and valproic acid identifies novel epigenetic effects of lithium on the rat leptin receptor gene.

SynaptomeDB: an ontology-based knowledgebase for synaptic genes ⬇️

Systematic review of genome-wide gene expression studies of bipolar disorder

Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.

The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish.

The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Toxicogenomic analysis provides new insights into molecular mechanisms of the sublethal toxicity of 2,4,6-trinitrotoluene in Eisenia fetida