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1. Full Text Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells
by Godini, Rasoul and Fallahi, Hossein and Ebrahimie, Esmaeil
PLoS ONE, ISSN 1932-6203, 08/2018, Volume 13, Issue 8, p. e0201674
Sepsis is a life-threatening syndrome causing thousands of deaths yearly worldwide. Sepsis is a result of infection and could lead to systemic inflammatory... 
GENE | EXPRESSION | MULTIDISCIPLINARY SCIENCES | Sepsis | Care and treatment | Research | Gene expression | Risk factors | Neutrophils | Disease | Modules | Genes | Erythrocytes | Critical care | Leukocytes (mononuclear) | Infections | Blood | Proteins | Signal transduction | Immunology | Pathways | Network analysis | Interleukin 1 | Peripheral blood mononuclear cells | Tumor necrosis factor-TNF | Stat1 protein | Bioinformatics | Immune system | Cytokines | Dendritic cells | Blood cells | Leukocytes (neutrophilic) | Inflammation | RNA polymerase | Metabolism | Information technology | Biological activity | White blood cells | CD83 antigen | Diagnostic software | Signal processing | Transduction | Diagnostic systems | Protein interaction | Methods | Apoptosis
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2. Full Text Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process
by Alanazi, Ibrahim O and Ebrahimie, Esmaeil
Molecular Biotechnology, ISSN 1073-6085, 7/2016, Volume 58, Issue 7, pp. 460 - 479
Novel computational systems biology tools such as common targets analysis, common regulators analysis, pathway discovery, and transcriptomic-based hotspot... 
Biochemistry, general | Protein Science | Human Genetics | Biotechnology | Apoptosi | Chemistry | Transcription factors | MicroRNA | Network analysis | Hotspots | Biological Techniques | Cell Biology | PATHWAYS | CANCER CELLS | BIOCHEMISTRY & MOLECULAR BIOLOGY | RECEPTOR | DEATH | FUNCTIONAL GENOMICS | FEEDBACK LOOP | P53 | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GROWTH | EXPRESSION | Cell Line | Apoptosis - drug effects | Humans | Repressor Proteins - genetics | Transcriptome - drug effects | Transcription Factors - genetics | Systems Biology | Algorithms | MicroRNAs - genetics | Epidermal Growth Factor - pharmacology | Proteomics - methods | Genomics - methods | Positive Regulatory Domain I-Binding Factor 1 | Genetic research | Genetic transcription | DNA binding proteins | Analysis | Apoptosis | MicroRNAs | Genomics
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3. Full Text Using the zebrafish model for Alzheimer's disease research
by Newman, Morgan and Ebrahimie, Esmaeil and Lardelli, Michael
Frontiers in Genetics, ISSN 1664-8021, 2014, Volume 5, p. 189
Rodent models have been extensively used to investigate the cause and mechanisms behind Alzheimer's disease. Despite many years of intensive research using... 
Gamma-secretase | Zebrafish | MAPT | Alzheimer disease | Presenilins | Amyloid beta-protein precursor
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4. Full Text A novel hypothesis-unbiased method for gene ontology enrichment based on transcriptome data
by Fruzangohar, Mario and Ebrahimie, Esmaeil and Adelson, David L
PLoS ONE, ISSN 1932-6203, 02/2017, Volume 12, Issue 2, p. e0170486
Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of... 
SYSTEM | INTERLEUKIN-1 | ALZHEIMERS-DISEASE | MULTIDISCIPLINARY SCIENCES | INJURY | CEREBROSPINAL-FLUID | VIRULENCE | DEFICITS | MOTILITY | TOOL | Humans | Alzheimer Disease - metabolism | Transcriptome | Salmonella enteritidis - metabolism | Alzheimer Disease - genetics | Gene Expression Regulation, Bacterial | Databases, Nucleic Acid | Salmonella enteritidis - genetics | Gene Ontology | Genomics | Genetic research | Genotype | Models | Research | Gene expression | Properties | Enrichment | Brain | Salmonella | Motility | Ontology | Genes | Interleukin | Genomes | Statistical methods | Data bases | Case studies | Genotype & phenotype | Mitochondria | E coli | Granulocyte colony-stimulating factor | Classification | Bacteria | Colony-stimulating factor | Molybdopterin | Alzheimer's disease | Binding | Statistical analysis | Genomic analysis | Cytokines | Neurodegenerative diseases | Time series | Information technology | Studies | Pathology | Brain research | Leukocytes (granulocytic) | Alzheimers disease | Functional groups | Neuromedin
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5. Full Text Correction to: Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis
by Alanazi, Ibrahim and Alanazi, Ibrahim and Ebrahimie, Esmaeil and Ebrahimie, Esmaeil and Hoffmann, Peter and Hoffmann, Peter and Adelson, David L and Adelson, David L
Apoptosis, ISSN 1360-8185, 1/2018, Volume 23, Issue 1, pp. 92 - 92
The original version of this article unfortunately contained a mistake. The affiliation of first author Dr. Ibrahim Alanazi was incorrect. 
Biochemistry, general | Cancer Research | Oncology | Biomedicine | Cell Biology | Virology | Gene expression | Analysis | Epidermal growth factor | Apoptosis
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6. Full Text Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development
by Shiri, Yasoub and Solouki, Mahmood and Ebrahimie, Esmaeil and Emamjomeh, Abbasali and Zahiri, Javad
Genomics, ISSN 0888-7543, 2019
Yaghooti grape of Sistan is seedless, early ripening but has compact clusters. To study gibberellin effect on cluster compactness of Yaghooti grape, it has... 
Gene ontology | RNA seq | Gene co-expression network | Vitis vinifera | Transcriptome
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7. Full Text Prediction of potential cancer-risk regions based on transcriptome data: Towards a comprehensive view
by Alisoltani, Arghavan and Fallahi, Hossein and Ebrahimi, Mahdi and Ebrahimi, Mansour and Ebrahimie, Esmaeil
PLoS ONE, ISSN 1932-6203, 05/2014, Volume 9, Issue 5, p. e96320
A novel integrative pipeline is presented for discovery of potential cancer-susceptibility regions (PCSRs) by calculating the number of altered genes at each... 
SUBTYPE | 8Q24 | GENE | MULTIDISCIPLINARY SCIENCES | PANCREATIC-CANCER | SUSCEPTIBILITY REGION | LOCI | SCAN | EXPRESSION | GENOME-WIDE ASSOCIATION | Promoter Regions, Genetic | Genetic Predisposition to Disease | Neoplasms - genetics | Humans | MicroRNAs | Risk Factors | Chromosomes, Human | Gene Expression Profiling | Gene Regulatory Networks | Somatotropin | MicroRNA | Health aspects | Risk factors | Cancer | Regulators | Genes | Genomics | MiRNA | Health risks | Gene expression | Risk analysis | Sox10 protein | Ovarian cancer | Studies | DNA microarrays | KLF4 protein | Predictions | Glyceraldehyde-3-phosphate dehydrogenase | Chromosomes
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8. Full Text Efficient and simple production of insulin-producing cells from embryonal carcinoma stem cells using mouse neonate pancreas extract, as a natural inducer
by Ebrahimie, Marzieh and Esmaeili, Fariba and Cheraghi, Somayeh and Houshmand, Fariba and Shabani, Leila and Ebrahimie, Esmaeil
PLoS ONE, ISSN 1932-6203, 03/2014, Volume 9, Issue 3, p. e90885
An attractive approach to replace the destroyed insulin-producing cells (IPCs) is the generation of functional beta cells from stem cells. Embryonal carcinoma... 
IN-VITRO | RAT PANCREAS | ISLETS | NUTRITIONAL-STATUS | MULTIDISCIPLINARY SCIENCES | TISSUE | REGENERATING PANCREAS | GENE COEXPRESSION | PLURIPOTENCY | VITRO TRANS-DIFFERENTIATION | EXPRESSION | Neoplastic Stem Cells - drug effects | Tissue Extracts - pharmacology | Gene Regulatory Networks - drug effects | Cell Culture Techniques - methods | Cell Differentiation - genetics | Insulin-Secreting Cells - metabolism | Neoplastic Stem Cells - metabolism | Neoplastic Stem Cells - pathology | Female | Insulin Secretion | Real-Time Polymerase Chain Reaction | Animals, Newborn | Biomarkers - metabolism | Signal Transduction - genetics | Transcription Factors - genetics | Cell Shape - drug effects | Gene Expression Regulation - drug effects | Pluripotent Stem Cells - metabolism | Transcription Factors - metabolism | Insulin - metabolism | Animals | Insulin-Secreting Cells - drug effects | Signal Transduction - drug effects | Cell Differentiation - drug effects | Pluripotent Stem Cells - drug effects | Staining and Labeling | Embryonal Carcinoma Stem Cells - pathology | Cell Line, Tumor | Mice, Inbred BALB C | Infants (Newborn) | Carcinoma | Analysis | Genes | Stem cells | DNA binding proteins | Gene expression | Insulin | Cancer | Biotechnology | Transcription factors | Biology | Insulin-like growth factors | Embryos | Studies | Rodents | Diabetes | Pancreas | Pluripotency | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid | DNA
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9. Full Text Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments
by Kargarfard, Fatemeh and Sami, Ashkan and Mohammadi-Dehcheshmeh, Manijeh and Ebrahimie, Esmaeil
BMC Genomics, ISSN 1471-2164, 11/2016, Volume 17, Issue 1, p. 925
Background: Recent (2013 and 2009) zoonotic transmission of avian or porcine influenza to humans highlights an increase in host range by evading species... 
Association rule mining | Host range of influenza | Detecting hot spots | PANDEMICS | SWINE | CLASSIFICATION | ALGORITHMS | EMERGENCE | PREDICTION | ALIGNMENT | EUROPEAN PIGS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | A VIRUSES | GENETICS & HEREDITY | PROTEINS | Genome, Viral | Humans | Influenza A virus - genetics | Orthomyxoviridae Infections - pathology | Viral Proteins - genetics | Birds | Host Specificity | Influenza in Birds - transmission | Influenza A virus - isolation & purification | Hemagglutinin Glycoproteins, Influenza Virus - metabolism | Viral Proteins - metabolism | Virus Internalization | Hemagglutinin Glycoproteins, Influenza Virus - genetics | Zoonoses - transmission | Influenza in Birds - pathology | Algorithms | Animals | Influenza in Birds - genetics | Orthomyxoviridae Infections - transmission | Swine | Orthomyxoviridae Infections - virology | Influenza viruses | Viral proteins | Analysis | Genetic aspects | Research | Decision tree | Identification and classification
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10. Full Text Minimizing the cost of translocation failure with decision‐tree models that predict species’ behavioral response in translocation sites
by Ebrahimi, Mehregan and Ebrahimie, Esmaeil and Bull, C. Michael
Conservation Biology, ISSN 0888-8892, 08/2015, Volume 29, Issue 4, pp. 1208 - 1216
The high number of failures is one reason why translocation is often not recommended. Considering how behavior changes during translocations may improve... 
decision tree | species management | animal behavior | the pygmy bluetongue lizard | lagartija pigmea de lengua azul | comportamiento animal | manejo de especies | árbol de decisión | Species management | The pygmy bluetongue lizard | Animal behavior | Decision tree | arbol de decision | CLIMATE-CHANGE | PYGMY BLUETONGUE LIZARDS | ANIMAL TRANSLOCATION | DISPERSAL | LIZARD TILIQUA-ADELAIDENSIS | ENVIRONMENTAL SCIENCES | CONSERVATION | MANAGED RELOCATION | MOVEMENT | BLUE-TONGUE LIZARD | ECOLOGY | SCINCIDAE | BIODIVERSITY CONSERVATION | Conservation of Natural Resources - methods | Lizards - physiology | Animals | Movement | Models, Biological | Female | Male | Animal Distribution | Decision Trees | Endangered Species | Conservation of Natural Resources - economics | South Australia | Models | Algorithms | Analysis | Endangered & extinct species | Trees | Wildlife conservation | Reptiles & amphibians | Biological diversity
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11. Full Text Genomic analysis reveals variant association with high altitude adaptation in native chickens
by Kharrati-Koopaee, Hamed and Ebrahimie, Esmaeil and Dadpasand, Mohammad and Niazi, Ali and Esmailizadeh, Ali
Scientific Reports, ISSN 2045-2322, 12/2019, Volume 9, Issue 1, pp. 9224 - 22
Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes,... 
HEAT-SHOCK PROTEINS | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | SKIN | MUTATIONS | ULTRAVIOLET-RADIATION | HYPOXIA | IDENTIFICATION | CANCER | SIGNATURE | LRP6 | Adaptations | Genomic analysis | Immune response | Poultry | Genetic resources | Hypoxia | Genomes | Mitochondrial DNA | DNA repair | Altitude | Adaptation
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12. Full Text Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle
by Sharifi, S and Pakdel, A and Ebrahimi, M and Reecy, JM and Farsani, SF and Ebrahimie, E
PLOS ONE, ISSN 1932-6203, 02/2018, Volume 13, Issue 2, p. e0191227
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in... 
ESCHERICHIA-COLI MASTITIS | DAIRY-COWS | MILK-YIELD | INFLAMMATORY-BOWEL-DISEASE | ACUTE-PHASE PROTEINS | CLINICAL MASTITIS | MULTIDISCIPLINARY SCIENCES | INDUCIBLE NUCLEAR-PROTEIN | LARGE GENE LISTS | KAPPA-B-ZETA | REPRODUCTIVE-PERFORMANCE | Mastitis | Usage | Disease transmission | Analysis | Escherichia coli | Dairy cattle | Machine learning | Causes of | Genetic aspects | Health aspects | Meta-analysis | Repositories | Transcription | Disease | Zoology | Genes | Gene regulation | Medical services | Data mining | DNA-directed RNA polymerase | Datasets | Proteins | E coli | Cattle | CCL20 protein | Bioindicators | Gram-negative bacteria | Diagnosis | Mammary gland | Decision trees | Interleukin 8 | Milk | Immune system | Immune response | Cytokines | Medical treatment | Animal sciences | Data processing | Antimicrobial agents | Gene expression | Ribonucleic acid--RNA | Information technology | Studies | Polymerase | Learning algorithms | Weighting | Algorithms | DNA microarrays | Antibiotics | Biomarkers | Hypoxia | Artificial intelligence | RNA polymerase II | Apoptosis | RNA | Ribonucleic acid
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13. Full Text Minimizing the cost of translocation failure with decision-tree models that predict species’ behavioral response in translocation sites
: Species Behavior and Decision-Tree Models
by Ebrahimi, Mehregan and Ebrahimie, Esmaeil and Bull, C. Michael
Conservation Biology, ISSN 0888-8892, 08/2015, Volume 29, Issue 4, pp. 1208 - 1216
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14. Full Text Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis
by Pashaiasl, Maryam and Ebrahimi, Mansour and Ebrahimie, Esmaeil
Molecular Biology Reports, ISSN 0301-4851, 9/2016, Volume 43, Issue 9, pp. 923 - 937
Diminished ovarian reserve (DOR) is one of the reasons for infertility that not only affects both older and young women. Ovarian reserve assessment can be used... 
Life Sciences | Molecular functions | Animal Biochemistry | Diminished ovarian reserve | Biological processes | Interaction network | Granulosa cells | Animal Anatomy / Morphology / Histology | OOCYTE | CELLS | CUMULUS | BIOCHEMISTRY & MOLECULAR BIOLOGY | MOUSE | MICRORNAS | MICE LACKING | FOLLICLE DEVELOPMENT | GROWTH | YOUNG-WOMEN | EXPRESSION | Ovarian Reserve - genetics | Gene Expression | Humans | Female | Gene Regulatory Networks | Infertility, Female - genetics | Gene Ontology | Infertility, Female - metabolism | Protein Interaction Maps | Genetic research | Bone morphogenetic proteins | Genetic transcription | Analysis | Genes | Cells | Ontology | Ovarian cancer
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15. Full Text Determining the most important physiological and agronomic traits contributing to maize grain yield through machine learning algorithms: A new avenue in intelligent agriculture
by Shekoofa, Avat and Emam, Yahya and Shekoufa, Navid and Ebrahimi, Mansour and Ebrahimie, Esmaeil
PLoS ONE, ISSN 1932-6203, 05/2014, Volume 9, Issue 5, p. e97288
Prediction is an attempt to accurately forecast the outcome of a specific situation while using input information obtained from a set of variables that... 
SYSTEM | TEMPERATE HYBRIDS | MULTIDISCIPLINARY SCIENCES | CORN | NITROGEN | KERNEL WATER RELATIONS | WEIGHT | PLANT-GROWTH | ARTIFICIAL NEURAL-NETWORKS | Zea mays - genetics | Algorithms | Seeds - physiology | Genes, Plant | Artificial Intelligence | Agriculture - methods | Decision Trees | Data Mining - methods | Cluster Analysis | Corn | Crop yields | Data mining | Analysis | Machine learning | Performance evaluation | Physiological effects | Grain | Maize | Information systems | Variables | Moisture content | Agricultural production | Agronomy | Water content | Physiology | Agriculture | Mathematical models | Decision trees | Crop yield | Filtration | Breeding | Crops | Linear programming | Clustering | Soils | Learning algorithms | Teaching methods | Plant breeding |