Dereje Jima
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    • Pandas
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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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Pandas

Oct 26, 2023 · 1 min read
Go to Project Site

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures.

Last updated on Dec 17, 2024
Hugo Wowchemy Markdown
Dereje D. Jima
Authors
Dereje D. Jima
Senior Research Scholar
PyTorch Oct 26, 2023 →

Created by Dereje Jima © 2025

Licensed under CC BY 4.0.