List of works - Esmaeil Ebrahimie

A comparative system-level analysis of the neurodegenerative diseases

scientific article published on 10 September 2018

A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease.

scientific article

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

scientific article published on 17 August 2017

A large-scale study of indicators of sub-clinical mastitis in dairy cattle by attribute weighting analysis of milk composition features: highlighting the predictive power of lactose and electrical conductivity

scientific article published on 01 May 2018

A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

scientific article

A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis.

scientific article published on 7 October 2014

A transcription factor contributes to pathogenesis and virulence in Streptococcus pneumoniae

scientific article

Alzheimer's disease-related peptide PS2V plays ancient, conserved roles in suppression of the unfolded protein response under hypoxia and stimulation of γ-secretase activity.

scientific article published on 26 March 2015

Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution

scientific article (publication date: 17 April 2011)

Analysis of nicastrin gene phylogeny and expression in zebrafish.

scientific article published on 5 May 2015

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

scientific article published on 21 May 2012

Characterization of Pneumococcal Genes Involved in Bloodstream Invasion in a Mouse Model ⬇️

scientific article published on 5 November 2015

Combined direct regeneration protocols in tissue culture of different cumin genotypes based on pre-existing meristems

scientific article

Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis.

scientific article published on November 2013

Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

scientific article

Comparison of hematopoietic cancer stem cells with normal stem cells leads to discovery of novel differentially expressed SSRs.

scientific article

Comprehensive analysis of machine learning models for prediction of sub-clinical mastitis: Deep Learning and Gradient-Boosted Trees outperform other models

scientific article published on 18 September 2019

Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process

scientific article published on 13 May 2016

Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates

scientific article published on 16 March 2018

Correction to: Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis.

scientific article published on 12 December 2017

Correction: Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

scientific article published on 17 April 2015

Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process

scientific article published on 12 July 2018

De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress

scientific article

Determining the most important physiological and agronomic traits contributing to maize grain yield through machine learning algorithms: a new avenue in intelligent agriculture.

scientific article

Development of an improved Streptococcus uberis experimental mastitis challenge model using different doses and strains in lactating dairy cows

scientific article published on 20 July 2015

Differential expression of TLP, ERF1, and R2R3MYB in annual Medicago species under salinity conditions

scientific article published on 21 August 2015

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus

scientific article published on 17 September 2015

Differentiation of P19 embryonal carcinoma stem cells into insulin-producing cells promoted by pancreas-conditioned medium

scientific article published on 06 July 2014

Discovery of EST-SSRs in lung cancer: tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues

scientific article

DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins.

scientific article published on 25 January 2016

Enhancement of anticancer activity by silibinin and paclitaxel combination on the ovarian cancer

scientific article published on 8 September 2017

Epitope Mapping of Avian Influenza M2e Protein: Different Species Recognise Various Epitopes

scientific article

Expression analyses of salinity stress- associated ESTs in Aeluropus littoralis.

scientific article published on 15 June 2017

Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia

scientific article published on 10 January 2018

Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses.

scientific article published on 5 October 2012

Functional Analysis of a Pomegranate (Punica granatum L.) MYB Transcription Factor Involved in the Regulation of Anthocyanin Biosynthesis

scientific article published on March 2015

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

scientific article published on 5 September 2017

Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

scientific article published on 05 May 2018

Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis.

scientific article published on 07 October 2015

Genome-wide survey of Alternative Splicing in Sorghum Bicolor.

scientific article

Genomic analysis reveals variant association with high altitude adaptation in native chickens

scientific article published on 25 June 2019

Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development

scientific article published on 25 May 2019

How the nucleus and mitochondria communicate in energy production during stress: nuclear MtATP6, an early-stress responsive gene, regulates the mitochondrial F₁F₀-ATP synthase complex.

scientific article published in July 2013

Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis

scientific article published on 20 June 2016

Identifying mutation positions in all segments of influenza genome enables better differentiation between pandemic and seasonal strains

scientific article published on 12 February 2019

In vitro comparison of the dermal penetration of three different topical formulations containing lasalocid.

scientific article published on 3 May 2017

Induction of pancreatic β cell gene expression in mesenchymal stem cells.

scientific article published on 4 December 2015

Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle.

scientific article published on 22 February 2018

Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

article

Interaction between Bovine leukemia virus (BLV) infection and age on telomerase misregulation

scientific article published on 11 February 2015

Isolation and in silico functional analysis of MtATP6, a 6-kDa subunit of mitochondrial F₁F0-ATP synthase, in response to abiotic stress.

scientific article published on 4 October 2012

Knowledge discovery and sequence-based prediction of pandemic influenza using an integrated classification and association rule mining (CBA) algorithm.

scientific article

Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations

scientific article published on 24 November 2015

MicroRNA-194 Promotes Prostate Cancer Metastasis by Inhibiting SOCS2.

scientific article published on 23 December 2016

Minimizing the cost of translocation failure with decision-tree models that predict species' behavioral response in translocation sites

scientific article published on 3 March 2015

Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network.

scientific article published on 2 July 2015

Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes

scientific article published on 23 July 2018

Multimeric recombinant M2e protein-based ELISA: a significant improvement in differentiating avian influenza infected chickens from vaccinated ones.

scientific article

Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells

scientific article published in PLoS ONE

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

scientific article published on 10 May 2014

New Opportunities for Targeting the Androgen Receptor in Prostate Cancer.

scientific article published on 12 March 2018

New insights into the expression profile of MicroRNA-34c and P53 in infertile men spermatozoa and testicular tissue.

scientific article published on 30 August 2017

New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase.

scientific article published on 26 August 2014

Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other

scientific article published on 31 January 2019

Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments

scientific article

Oxalate-degrading bacteria, including Oxalobacter formigenes, colonise the gastrointestinal tract of healthy koalas (Phascolarctos cinereus) and those with oxalate nephrosis

scientific article published on 01 May 2019

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

scientific article published on 13 September 2013

Prediction of key regulators and downstream targets of E. coli induced mastitis

scientific article published on 11 June 2019

Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view

scientific article

Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: a new vista in engineering enzymes.

scientific article

Protein attributes contribute to halo-stability, bioinformatics approach.

scientific article published on 18 May 2011

Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations

scientific article

Recombinant M2e protein-based ELISA: a novel and inexpensive approach for differentiating avian influenza infected chickens from vaccinated ones

scientific article

Root and shoot parts of strawberry: factories for production of functional human pro-insulin

scientific article published on 18 November 2014

SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs.

scientific article

The Inhibitory Effect of Ginger Extract on Ovarian Cancer Cell Line; Application of Systems Biology

scientific article

The Magnitude of Androgen Receptor Positivity in Breast Cancer Is Critical for Reliable Prediction of Disease Outcome

scientific article published on 7 March 2018

The Zebrafish Equivalent of Alzheimer's Disease-Associated PRESENILIN Isoform PS2V Regulates Inflammatory and Other Responses to Hypoxic Stress.

scientific article published on 31 March 2016

The combined effects of three-dimensional cell culture and natural tissue extract on neural differentiation of P19 embryonal carcinoma stem cells

scientific article published on 13 August 2018

Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology

scientific article published on 05 January 2019

Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys

scientific article published on 11 May 2022

Underlying functional genomics of fat deposition in adipose tissue ⬇️

scientific article published on March 20, 2013

Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein

scientific article (publication date: 2014)

Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

scientific article published on 12 November 2018

Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders.

scientific article

Unraveling the transcriptional complexity of compactness in sistan grape cluster.

scientific article published on 14 February 2018

Unravelling evolution of Nanog, the key transcription factor involved in self-renewal of undifferentiated embryonic stem cells, by pattern recognition in nucleotide and tandem repeats characteristics

scientific article

Using the zebrafish model for Alzheimer's disease research

scientific article published on 30 June 2014

List of works by Esmaeil Ebrahimie

A comparative system-level analysis of the neurodegenerative diseases

A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease.

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

A large-scale study of indicators of sub-clinical mastitis in dairy cattle by attribute weighting analysis of milk composition features: highlighting the predictive power of lactose and electrical conductivity

A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis.

A transcription factor contributes to pathogenesis and virulence in Streptococcus pneumoniae

Alzheimer's disease-related peptide PS2V plays ancient, conserved roles in suppression of the unfolded protein response under hypoxia and stimulation of γ-secretase activity.

Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution

Analysis of nicastrin gene phylogeny and expression in zebrafish.

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Characterization of Pneumococcal Genes Involved in Bloodstream Invasion in a Mouse Model ⬇️

Combined direct regeneration protocols in tissue culture of different cumin genotypes based on pre-existing meristems

Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis.

Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

Comparison of hematopoietic cancer stem cells with normal stem cells leads to discovery of novel differentially expressed SSRs.

Comprehensive analysis of machine learning models for prediction of sub-clinical mastitis: Deep Learning and Gradient-Boosted Trees outperform other models

Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process

Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates

Correction to: Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis.

Correction: Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process

De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress

Determining the most important physiological and agronomic traits contributing to maize grain yield through machine learning algorithms: a new avenue in intelligent agriculture.

Development of an improved Streptococcus uberis experimental mastitis challenge model using different doses and strains in lactating dairy cows

Differential expression of TLP, ERF1, and R2R3MYB in annual Medicago species under salinity conditions

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus

Differentiation of P19 embryonal carcinoma stem cells into insulin-producing cells promoted by pancreas-conditioned medium

Discovery of EST-SSRs in lung cancer: tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues

DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins.

Enhancement of anticancer activity by silibinin and paclitaxel combination on the ovarian cancer

Epitope Mapping of Avian Influenza M2e Protein: Different Species Recognise Various Epitopes

Expression analyses of salinity stress- associated ESTs in Aeluropus littoralis.

Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia

Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses.

Functional Analysis of a Pomegranate (Punica granatum L.) MYB Transcription Factor Involved in the Regulation of Anthocyanin Biosynthesis

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis.

Genome-wide survey of Alternative Splicing in Sorghum Bicolor.

Genomic analysis reveals variant association with high altitude adaptation in native chickens

Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development

How the nucleus and mitochondria communicate in energy production during stress: nuclear MtATP6, an early-stress responsive gene, regulates the mitochondrial F₁F₀-ATP synthase complex.

Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis

Identifying mutation positions in all segments of influenza genome enables better differentiation between pandemic and seasonal strains

In vitro comparison of the dermal penetration of three different topical formulations containing lasalocid.

Induction of pancreatic β cell gene expression in mesenchymal stem cells.

Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle.

Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

Interaction between Bovine leukemia virus (BLV) infection and age on telomerase misregulation

Isolation and in silico functional analysis of MtATP6, a 6-kDa subunit of mitochondrial F₁F0-ATP synthase, in response to abiotic stress.

Knowledge discovery and sequence-based prediction of pandemic influenza using an integrated classification and association rule mining (CBA) algorithm.

Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations

MicroRNA-194 Promotes Prostate Cancer Metastasis by Inhibiting SOCS2.

Minimizing the cost of translocation failure with decision-tree models that predict species' behavioral response in translocation sites

Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network.

Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes

Multimeric recombinant M2e protein-based ELISA: a significant improvement in differentiating avian influenza infected chickens from vaccinated ones.

Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

New Opportunities for Targeting the Androgen Receptor in Prostate Cancer.

New insights into the expression profile of MicroRNA-34c and P53 in infertile men spermatozoa and testicular tissue.

New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase.

Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other

Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments

Oxalate-degrading bacteria, including Oxalobacter formigenes, colonise the gastrointestinal tract of healthy koalas (Phascolarctos cinereus) and those with oxalate nephrosis

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Prediction of key regulators and downstream targets of E. coli induced mastitis

Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view

Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: a new vista in engineering enzymes.

Protein attributes contribute to halo-stability, bioinformatics approach.

Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations

Recombinant M2e protein-based ELISA: a novel and inexpensive approach for differentiating avian influenza infected chickens from vaccinated ones

Root and shoot parts of strawberry: factories for production of functional human pro-insulin

SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs.

The Inhibitory Effect of Ginger Extract on Ovarian Cancer Cell Line; Application of Systems Biology

The Magnitude of Androgen Receptor Positivity in Breast Cancer Is Critical for Reliable Prediction of Disease Outcome

The Zebrafish Equivalent of Alzheimer's Disease-Associated PRESENILIN Isoform PS2V Regulates Inflammatory and Other Responses to Hypoxic Stress.

The combined effects of three-dimensional cell culture and natural tissue extract on neural differentiation of P19 embryonal carcinoma stem cells