Dereje Jima
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  • Experience
    • Creation and validation of the first infinium DNA methylation array for the human imprintome
    • Developmental regulation of cellular metabolism is required for intestinal elongation and rotation
    • DNA methylation of imprint control regions associated with Alzheimer’s disease in non-Hispanic Blacks and non-Hispanic Whites
    • Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits
    • Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence
    • Mutant Nrf2E79Q enhances the promotion and progression of a subset of oncogenic Ras keratinocytes and skin tumors
    • Profiling the cancer-prone microenvironment in a zebrafish model for MPNST
    • AHRR Hypomethylation mediates the association between maternal smoking and metabolic profiles in children
    • An epigenome-wide association study of child appetitive traits and DNA methylation
    • Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude
    • C/EBP$β$ deficiency enhances the keratinocyte innate immune response to direct activators of cytosolic pattern recognition receptors
    • DNA methylation of candidate imprint control regions associated with Alzheimer’s disease in Non-Hispanic Blacks and Non-Hispanic Whites
    • LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response
    • Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure
    • Proteomic approach reveals salinity-induced osmoregulatory changes in the gill of themayfly, Neocloeon triangulifer
    • Salinity-induced ionoregulatory changes in the gill proteome of the mayfly, Neocloeon triangulifer
    • TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells
    • The imprinted gene Zac1 regulates steatosis in developmental cadmium-induced nonalcoholic fatty liver disease
    • A resource for integrated genomic analysis of the human liver
    • Abstract PR011: Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model
    • AHRR METHYLATION MEDIATES THE EFFECTS OF MATERNAL SMOKING ON LIVER FAT CONTENT AND METABOLIC HEALTH IN CHILDREN
    • Alterations in DNA methylation associate with fatty liver and metabolic abnormalities in a multi-ethnic cohort of pre-teenage children
    • Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model.
    • Compositions and methods related to differentially methylated dna sequences associated with monoallelic gene expression and disease
    • Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress
    • Genomic map of candidate human imprint control regions: the imprintome
    • Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies
    • Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation
    • PRE-TEENS EXPOSED PRENATALLY TO MATERNAL OBESITY EXHIBIT PERSISTENT DNA METHYLATION CHANGES THAT ASSOCIATE WITH METABOLIC ABNORMALITIES, INCLUDING HIGH LIVER FAT
    • Zac1 and the I mprinted G ene N etwork program juvenile NAFLD in response to maternal metabolic syndrome
    • ZAC1 AND THE IMPRINTED GENE NETWORK CONNECT THE EARLY LIFE ENVIRONMENT TO NAFLD IN YOUNG MICE
    • Association between PEG3 DNA methylation and high-grade cervical intraepithelial neoplasia
    • Expression of UDP Glucuronosyltransferases 2B15 and 2B17 is associated with methylation status in prostate cancer cells
    • Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior
    • A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex-Biased Phenotypes
    • Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis
    • DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies
    • Effects of prenatal exposure to a mixture of organophosphate flame retardants on placental gene expression and serotonergic innervation in the fetal rat brain
    • NONALCOHOLIC FATTY LIVER AND ITS RISK FACTORS ASSOCIATE WITH DIFFERENTIAL DNA METHYLATION IN THE PERIPHERAL BLOOD OF PRE-TEENAGE CHILDREN
    • Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge
    • Vitamin D deficiency serves as a precursor to stunted growth and central adiposity in zebrafish
    • C/EBP$β$ suppresses keratinocyte autonomous type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer
    • Epigenome-wide meta-analysis of DNA methylation and childhood asthma
    • Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study
    • Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    • Transcriptome of the canine macular RPE/choroid and retina: parallels with human macular gene expression
    • A common allele in FGF21 associated with sugar intake is associated with body shape, lower total body-fat percentage, and higher blood pressure
    • C/EBP$β$ deletion in oncogenic Ras skin tumors is a synthetic lethal event
    • Cohort profile: pregnancy and childhood epigenetics (PACE) consortium
    • EDC IMPACT: Molecular effects of developmental FM 550 exposure in Wistar rat placenta and fetal forebrain
    • Effects of cadmium exposure on DNA methylation at imprinting control regions and genome-wide in mothers and newborn children
    • HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues
    • Obesity and Nonalcoholic Fatty Liver Disease in Childhood Associate with Altered DNA Methylation in Early Life
    • Prenatal bisphenol A (BPA) exposure alters the transcriptome of the neonate rat amygdala in a sex-specific manner: a CLARITY-BPA consortium study
    • The Daily Scorcher: Life History and Transcriptomic Responses of the Mayfly Neocloeon triangulifer to Chronic Daily Forays into Uncomfortably Warm Temperatures
    • The good, the bad, and the lethal: gene expression and metabolomics reveal physiological mechanisms underlying chronic thermal effects in mayfly larvae (Neocloeon triangulifer)
    • A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics
    • Disruption of Trim9 function abrogates macrophage motility in vivo
    • Editor’s highlight: Comparative dose-response analysis of liver and kidney transcriptomic effects of trichloroethylene and tetrachloroethylene in B6C3F1 mouse
    • Epstein-Barr virus induces adhesion receptor CD226 (DNAM-1) expression during primary B-cell transformation into lymphoblastoid cell lines
    • Genome sequences of Listeria monocytogenes strains with resistance to arsenic
    • Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic
    • Nuclear localized LSR: a novel regulator of breast cancer behavior and tumorigenesis
    • The arsenic resistance-associated Listeria genomic island LGI2 exhibits sequence and integration site diversity and a propensity for three Listeria monocytogenes clones with enhanced virulence
    • Draft genome sequences of two historical Listeria monocytogenes strains from human listeriosis cases in 1933
    • Draft genome sequences of two historical Listeria monocytogenes strains from human listeriosis cases in 1933.
    • Genome sequences of five arboviruses in field-captured mosquitoes in a unique rural environment of South Korea
    • Isolation and characterization of a novel Rickettsia species (Rickettsia asembonensis sp. nov.) obtained from cat fleas (Ctenocephalides felis)
    • Maternal blood lead concentrations, DNA methylation of MEG3 DMR regulating the DLK1/MEG3 imprinted domain and early growth in a multiethnic cohort
    • A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes
    • Pathosphere. org: pathogen detection and characterization through a web-based, open source informatics platform
    • Whole-genome sequence of “Candidatus Rickettsia asemboensis” strain NMRCii, isolated from fleas of western Kenya
    • Chemical genomics reveals JAK STAT activation as a mechanism of resistance to HDAC inhibitors in B cell lymphomas
    • Deletion of both Id2 and Id3 in developing T cell promotes NKT lymphoma formation in mice (TUM2P. 887)
    • Strand-specific total RNA sequencing establishes the complete transcriptome and alternative splicing repertoire in diffuse large B cell lymphoma
    • The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells
    • Genetic heterogeneity of diffuse large B-cell lymphoma
    • PAK1 mediates resistance to PI3K inhibition in lymphomas
    • ID3 Is a Novel Tumor Suppressor Gene in Burkitt Lymphom
    • The Epstein-Barr virus (EBV)-induced tumor suppressor microRNA MiR-34a is growth promoting in EBV-infected B cells
    • The genetic landscape of immune-competent and HIV lymphoma
    • The genetic landscape of mutations in Burkitt lymphoma
    • Using High-Throughput Sequencing of Red Blood Cells and Platelets to Identify Micrornas Associated with Hematopoiesis.
    • Identification of MicroRNAs Associated with Erythropoiesis Through Deep Sequencing of Red Blood Cells
    • Whole genome and exome sequencing reveals the genetic landscape of burkitt lymphoma
    • Alternative splicing is a major mechanism of gene regulation in diffuse large B cell lymphoma
    • Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs
    • Hematologic Malignancies Research Consortium: Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs
    • A Comprehensive Identification of the Microrna Transcriptome and Its Application in B Cell Malignancies.
    • Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting
    • Enhanced transcription of complement and coagulation genes in the absence of adaptive immunity
    • Patterns of microRNA expression characterize stages of human B-cell differentiation
    • Concomitant gene expression profiling and microRNA profiling reveal a role for microRNAs in B cell development and lymphomas at every stage
    • Massively Parallel High Throughput Sequencing Identifies Novel Micrornas in Normal and Malignant B Cells.
    • MicroRNAs Regulate Mature B Cell Differentiation
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  • Recent Publications
    • Creation and validation of the first infinium DNA methylation array for the human imprintome
    • Developmental regulation of cellular metabolism is required for intestinal elongation and rotation
    • DNA methylation of imprint control regions associated with Alzheimer’s disease in non-Hispanic Blacks and non-Hispanic Whites
    • Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits
    • Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence
    • Mutant Nrf2E79Q enhances the promotion and progression of a subset of oncogenic Ras keratinocytes and skin tumors
    • Profiling the cancer-prone microenvironment in a zebrafish model for MPNST
    • AHRR Hypomethylation mediates the association between maternal smoking and metabolic profiles in children
    • An epigenome-wide association study of child appetitive traits and DNA methylation
    • Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude
    • C/EBP$β$ deficiency enhances the keratinocyte innate immune response to direct activators of cytosolic pattern recognition receptors
    • DNA methylation of candidate imprint control regions associated with Alzheimer’s disease in Non-Hispanic Blacks and Non-Hispanic Whites
    • LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response
    • Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure
    • Proteomic approach reveals salinity-induced osmoregulatory changes in the gill of themayfly, Neocloeon triangulifer
    • Salinity-induced ionoregulatory changes in the gill proteome of the mayfly, Neocloeon triangulifer
    • TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells
    • The imprinted gene Zac1 regulates steatosis in developmental cadmium-induced nonalcoholic fatty liver disease
    • Genomic map of candidate human imprint control regions: the imprintome
    • A resource for integrated genomic analysis of the human liver
    • Abstract PR011: Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model
    • AHRR METHYLATION MEDIATES THE EFFECTS OF MATERNAL SMOKING ON LIVER FAT CONTENT AND METABOLIC HEALTH IN CHILDREN
    • Alterations in DNA methylation associate with fatty liver and metabolic abnormalities in a multi-ethnic cohort of pre-teenage children
    • Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model.
    • Compositions and methods related to differentially methylated dna sequences associated with monoallelic gene expression and disease
    • Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress
    • Genomic map of candidate human imprint control regions: the imprintome
    • Genomic map of candidate human imprint control regions: the imprintome
    • Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies
    • Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation
    • PRE-TEENS EXPOSED PRENATALLY TO MATERNAL OBESITY EXHIBIT PERSISTENT DNA METHYLATION CHANGES THAT ASSOCIATE WITH METABOLIC ABNORMALITIES, INCLUDING HIGH LIVER FAT
    • Zac1 and the I mprinted G ene N etwork program juvenile NAFLD in response to maternal metabolic syndrome
    • ZAC1 AND THE IMPRINTED GENE NETWORK CONNECT THE EARLY LIFE ENVIRONMENT TO NAFLD IN YOUNG MICE
    • Association between PEG3 DNA methylation and high-grade cervical intraepithelial neoplasia
    • Expression of UDP Glucuronosyltransferases 2B15 and 2B17 is associated with methylation status in prostate cancer cells
    • Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior
    • A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex-Biased Phenotypes
    • Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis
    • DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies
    • Effects of prenatal exposure to a mixture of organophosphate flame retardants on placental gene expression and serotonergic innervation in the fetal rat brain
    • NONALCOHOLIC FATTY LIVER AND ITS RISK FACTORS ASSOCIATE WITH DIFFERENTIAL DNA METHYLATION IN THE PERIPHERAL BLOOD OF PRE-TEENAGE CHILDREN
    • Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge
    • Vitamin D deficiency serves as a precursor to stunted growth and central adiposity in zebrafish
    • C/EBP$β$ suppresses keratinocyte autonomous type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer
    • Epigenome-wide meta-analysis of DNA methylation and childhood asthma
    • Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study
    • Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    • Transcriptome of the canine macular RPE/choroid and retina: parallels with human macular gene expression
    • A common allele in FGF21 associated with sugar intake is associated with body shape, lower total body-fat percentage, and higher blood pressure
    • C/EBP$β$ deletion in oncogenic Ras skin tumors is a synthetic lethal event
    • Cohort profile: pregnancy and childhood epigenetics (PACE) consortium
    • EDC IMPACT: Molecular effects of developmental FM 550 exposure in Wistar rat placenta and fetal forebrain
    • Effects of cadmium exposure on DNA methylation at imprinting control regions and genome-wide in mothers and newborn children
    • HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues
    • Obesity and Nonalcoholic Fatty Liver Disease in Childhood Associate with Altered DNA Methylation in Early Life
    • Prenatal bisphenol A (BPA) exposure alters the transcriptome of the neonate rat amygdala in a sex-specific manner: a CLARITY-BPA consortium study
    • The Daily Scorcher: Life History and Transcriptomic Responses of the Mayfly Neocloeon triangulifer to Chronic Daily Forays into Uncomfortably Warm Temperatures
    • The good, the bad, and the lethal: gene expression and metabolomics reveal physiological mechanisms underlying chronic thermal effects in mayfly larvae (Neocloeon triangulifer)
    • A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics
    • Disruption of Trim9 function abrogates macrophage motility in vivo
    • Editor’s highlight: Comparative dose-response analysis of liver and kidney transcriptomic effects of trichloroethylene and tetrachloroethylene in B6C3F1 mouse
    • Epstein-Barr virus induces adhesion receptor CD226 (DNAM-1) expression during primary B-cell transformation into lymphoblastoid cell lines
    • Genome sequences of Listeria monocytogenes strains with resistance to arsenic
    • Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic
    • Nuclear localized LSR: a novel regulator of breast cancer behavior and tumorigenesis
    • The arsenic resistance-associated Listeria genomic island LGI2 exhibits sequence and integration site diversity and a propensity for three Listeria monocytogenes clones with enhanced virulence
    • Draft genome sequences of two historical Listeria monocytogenes strains from human listeriosis cases in 1933
    • Draft genome sequences of two historical Listeria monocytogenes strains from human listeriosis cases in 1933.
    • Genome sequences of five arboviruses in field-captured mosquitoes in a unique rural environment of South Korea
    • Isolation and characterization of a novel Rickettsia species (Rickettsia asembonensis sp. nov.) obtained from cat fleas (Ctenocephalides felis)
    • Maternal blood lead concentrations, DNA methylation of MEG3 DMR regulating the DLK1/MEG3 imprinted domain and early growth in a multiethnic cohort
    • A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes
    • Pathosphere. org: pathogen detection and characterization through a web-based, open source informatics platform
    • Whole-genome sequence of “Candidatus Rickettsia asemboensis” strain NMRCii, isolated from fleas of western Kenya
    • Chemical genomics reveals JAK STAT activation as a mechanism of resistance to HDAC inhibitors in B cell lymphomas
    • Deletion of both Id2 and Id3 in developing T cell promotes NKT lymphoma formation in mice (TUM2P. 887)
    • Strand-specific total RNA sequencing establishes the complete transcriptome and alternative splicing repertoire in diffuse large B cell lymphoma
    • The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells
    • Genetic heterogeneity of diffuse large B-cell lymphoma
    • PAK1 mediates resistance to PI3K inhibition in lymphomas
    • The genetic landscape of mutations in Burkitt lymphoma
    • ID3 Is a Novel Tumor Suppressor Gene in Burkitt Lymphom
    • The Epstein-Barr virus (EBV)-induced tumor suppressor microRNA MiR-34a is growth promoting in EBV-infected B cells
    • The genetic landscape of immune-competent and HIV lymphoma
    • The genetic landscape of mutations in Burkitt lymphoma
    • Using High-Throughput Sequencing of Red Blood Cells and Platelets to Identify Micrornas Associated with Hematopoiesis.
    • Identification of MicroRNAs Associated with Erythropoiesis Through Deep Sequencing of Red Blood Cells
    • Whole genome and exome sequencing reveals the genetic landscape of burkitt lymphoma
    • Alternative splicing is a major mechanism of gene regulation in diffuse large B cell lymphoma
    • Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs
    • Hematologic Malignancies Research Consortium: Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs
    • A Comprehensive Identification of the Microrna Transcriptome and Its Application in B Cell Malignancies.
    • Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting
    • Enhanced transcription of complement and coagulation genes in the absence of adaptive immunity
    • Patterns of microRNA expression characterize stages of human B-cell differentiation
    • Concomitant gene expression profiling and microRNA profiling reveal a role for microRNAs in B cell development and lymphomas at every stage
    • Massively Parallel High Throughput Sequencing Identifies Novel Micrornas in Normal and Malignant B Cells.
    • MicroRNAs Regulate Mature B Cell Differentiation
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My first blog post

Jan 16, 2025 · 1 min read

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Last updated on Jan 16, 2025
Dereje D. Jima
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Dereje D. Jima
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