List of works - Erik K Flemington

A comprehensive approach to expression of L1 loci

scientific article

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association

scientific article published on 11 July 2016

A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks

scientific article published on 19 May 2017

Analysis of EBV Transcription Using High-Throughput RNA Sequencing

scientific article published on January 2017

Androgen Receptor Splice Variants Dimerize to Transactivate Target Genes

scientific article

Arsenic mediated disruption of promyelocytic leukemia protein nuclear bodies induces ganciclovir susceptibility in Epstein-Barr positive epithelial cells

scientific article published on 24 May 2011

Arsenic trioxide inhibits EBV reactivation and promotes cell death in EBV-positive lymphoma cells

scientific article

B-cell receptor activation induces BIC/miR-155 expression through a conserved AP-1 element

scientific article

Co-treatment with arsenic trioxide and ganciclovir reduces tumor volume in a murine xenograft model of nasopharyngeal carcinoma

scientific article published on 16 May 2013

Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

scientific article published on 02 October 2012

Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis

scientific article published on 10 October 2018

Correction for Strong et al., Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing

scientific article published on 30 December 2015

Defining the dynamic chromatin landscape of nephron progenitors

article published in 2019

Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.

scientific article published on 11 January 2012

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy

scientific article

Differential expression of the miR-200 family microRNAs in epithelial and B cells and regulation of Epstein-Barr virus reactivation by the miR-200 family member miR-429

scientific article

Differential regulation of microRNA-146a and microRNA-146b-5p in human retinal pigment epithelial cells by interleukin-1β, tumor necrosis factor-α, and interferon-γ.

scientific article published on 3 April 2013

Driver gene mutations based clustering of tumors: methods and applications.

scientific article published in July 2018

E2F1 expression is deregulated and plays an oncogenic role in sporadic Burkitt's lymphoma

scientific article published on May 2009

Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells

scientific article

Elevated expression of long intergenic non-coding RNA HOTAIR in a basal-like variant of MCF-7 breast cancer cells

scientific article

Epstein - Barr virus Latent Membrane Protein 1 suppresses reporter activity through modulation of promyelocytic leukemia protein-nuclear bodies

scientific article published on 5 October 2011

Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing

scientific article published on 18 September 2013

Epstein-Barr virus growth/latency III program alters cellular microRNA expression

scientific article

Epstein-Barr virus latent membrane protein 1 induces cellular MicroRNA miR-146a, a modulator of lymphocyte signaling pathways

scientific article

Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources

scientific article published on 28 October 2014

Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress.

scientific article published in December 2016

Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma

scientific article published on 23 June 2016

Global bidirectional transcription of the Epstein-Barr virus genome during reactivation

scientific article

Global transcript structure resolution of high gene density genomes through multi-platform data integration

scientific article

High-fat diet induced leptin and Wnt expression: RNA-sequencing and pathway analysis of mouse colonic tissue and tumors

scientific article published on March 2017

High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project

scientific article

Histone deacetylase inhibitors prevent oxidative neuronal death independent of expanded polyglutamine repeats via an Sp1-dependent pathway

scholarly article

Identification of a negative regulatory element in the Epstein-Barr virus Zta transactivation domain that is regulated by the cell cycle control factors c-Myc and E2F1.

scientific article

Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq

scientific article published on 16 November 2011

In colonic ρ0 (rho0) cells reduced mitochondrial function mediates transcriptomic alterations associated with cancer

scientific article published in November 2017

Induction of a novel isoform of the lncRNA HOTAIR in Claudin-low breast cancer cells attached to extracellular matrix

scientific article published on 28 August 2017

Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen

scientific article

Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets

scientific article

Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas

scientific article published on 25 April 2016

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome

scientific article published on 21 March 2017

Interleukin-17A in the Pathogenesis of Lung Adenocarcinoma.

scientific article published in April 2018

Interplay between Cytoplasmic and Nuclear Androgen Receptor Splice Variants Mediates Castration Resistance

scientific article published on 26 September 2016

Isoform-level microRNA-155 target prediction using RNA-seq ⬇️

scientific article

Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas

scientific article

Maintenance of AP-2 Dependent Functional Activities of Nef Restricts Pathways of Immune Escape from CD8 T Lymphocyte Responses

scientific article

Methylation status and AP1 elements are involved in EBV-mediated miR-155 expression in EBV positive lymphoma cells

scientific article published on 22 April 2016

MicroRNA miR-155 inhibits bone morphogenetic protein (BMP) signaling and BMP-mediated Epstein-Barr virus reactivation

scientific article

MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways

scientific article

Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples

scientific article

Modulation of lung inflammation by the Epstein-Barr virus protein Zta ⬇️

scientific article published on September 3, 2010

Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types

scientific article published on 9 July 2016

Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator

scientific article published on 10 June 2016

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

scientific article published on 29 April 2015

OncomiR addiction is generated by a miR-155 feedback loop in Theileria-transformed leukocytes

scientific article

Post-transcriptional up-regulation of miR-21 by type I collagen

scientific article published on 11 February 2011

Preferential star strand biogenesis of pre-miR-24-2 targets PKC-alpha and suppresses cell survival in MCF-7 breast cancer cells

scientific article

Quantitative and Qualitative RNA-Seq-Based Evaluation of Epstein-Barr Virus Transcription in Type I Latency Burkitt's Lymphoma Cells ⬇️

scientific article published on October 13, 2010

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets

scientific article

RNA-sequencing study of peripheral blood monocytes in chronic periodontitis

scientific article

Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate

scientific article

Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation

scientific article published on 9 February 2017

S100P/RAGE signaling regulates microRNA-155 expression via AP-1 activation in colon cancer

scientific article published on 18 May 2013

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

scientific article

Significant Prognostic Features and Patterns of Somatic TP53 Mutations in Human Cancers

scientific article

Small interfering RNA effectively inhibits protein expression and negative strand RNA synthesis from a full-length hepatitis C virus clone

scientific article

Somatic mutations favorable to patient survival are predominant in ovarian carcinomas

scientific article

SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.: Supplemental File 1

TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene

scientific article published on 23 March 2016

The Epstein-Barr virus transactivator Zta binds to its own promoter and is required for full promoter activity during anti-Ig and TGF-beta1 mediated reactivation

scientific article published on September 2004

The impact of oil spill to lung health - insights from an RNA-seq study of human airway epithelial cells

journal article published in 2016

The microRNA expression associated with morphogenesis of breast cancer cells in three-dimensional organotypic culture

scientific article published on 19 April 2012

The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication

scientific article published on 27 February 2016

The sequence structures of human microRNA molecules and their implications

scientific article

Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development.

scientific article

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

scientific article

Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus

scientific article published on 30 May 2016

Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.

scientific article

Use of gene overexpression to assess function in cell cycle control

scientific article published in January 2004

Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains

scientific article published on 14 November 2012

miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling

scientific article

miRNA-mRNA correlation-network modules in human prostate cancer and the differences between primary and metastatic tumor subtypes

scientific article (publication date: 2012)

miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines

scientific article

miRNAs in the pathogenesis of oncogenic human viruses ⬇️

scientific article published on October 12, 2010

microRNA regulation of mammalian target of rapamycin expression and activity controls estrogen receptor function and RAD001 sensitivity

scientific article

siRNAs against the Epstein Barr virus latency replication factor, EBNA1, inhibit its function and growth of EBV-dependent tumor cells

scientific article published on 15 December 2005

List of works by Erik K Flemington

A comprehensive approach to expression of L1 loci

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association

A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks

Analysis of EBV Transcription Using High-Throughput RNA Sequencing

Androgen Receptor Splice Variants Dimerize to Transactivate Target Genes

Arsenic mediated disruption of promyelocytic leukemia protein nuclear bodies induces ganciclovir susceptibility in Epstein-Barr positive epithelial cells

Arsenic trioxide inhibits EBV reactivation and promotes cell death in EBV-positive lymphoma cells

B-cell receptor activation induces BIC/miR-155 expression through a conserved AP-1 element

Co-treatment with arsenic trioxide and ganciclovir reduces tumor volume in a murine xenograft model of nasopharyngeal carcinoma

Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis

Correction for Strong et al., Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing

Defining the dynamic chromatin landscape of nephron progenitors

Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy

Differential expression of the miR-200 family microRNAs in epithelial and B cells and regulation of Epstein-Barr virus reactivation by the miR-200 family member miR-429

Differential regulation of microRNA-146a and microRNA-146b-5p in human retinal pigment epithelial cells by interleukin-1β, tumor necrosis factor-α, and interferon-γ.

Driver gene mutations based clustering of tumors: methods and applications.

E2F1 expression is deregulated and plays an oncogenic role in sporadic Burkitt's lymphoma

Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells

Elevated expression of long intergenic non-coding RNA HOTAIR in a basal-like variant of MCF-7 breast cancer cells

Epstein - Barr virus Latent Membrane Protein 1 suppresses reporter activity through modulation of promyelocytic leukemia protein-nuclear bodies

Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing

Epstein-Barr virus growth/latency III program alters cellular microRNA expression

Epstein-Barr virus latent membrane protein 1 induces cellular MicroRNA miR-146a, a modulator of lymphocyte signaling pathways

Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources

Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress.

Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma

Global bidirectional transcription of the Epstein-Barr virus genome during reactivation

Global transcript structure resolution of high gene density genomes through multi-platform data integration

High-fat diet induced leptin and Wnt expression: RNA-sequencing and pathway analysis of mouse colonic tissue and tumors

High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project

Histone deacetylase inhibitors prevent oxidative neuronal death independent of expanded polyglutamine repeats via an Sp1-dependent pathway

Identification of a negative regulatory element in the Epstein-Barr virus Zta transactivation domain that is regulated by the cell cycle control factors c-Myc and E2F1.

Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq

In colonic ρ0 (rho0) cells reduced mitochondrial function mediates transcriptomic alterations associated with cancer

Induction of a novel isoform of the lncRNA HOTAIR in Claudin-low breast cancer cells attached to extracellular matrix

Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen

Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets

Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome

Interleukin-17A in the Pathogenesis of Lung Adenocarcinoma.

Interplay between Cytoplasmic and Nuclear Androgen Receptor Splice Variants Mediates Castration Resistance

Isoform-level microRNA-155 target prediction using RNA-seq ⬇️

Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas

Maintenance of AP-2 Dependent Functional Activities of Nef Restricts Pathways of Immune Escape from CD8 T Lymphocyte Responses

Methylation status and AP1 elements are involved in EBV-mediated miR-155 expression in EBV positive lymphoma cells

MicroRNA miR-155 inhibits bone morphogenetic protein (BMP) signaling and BMP-mediated Epstein-Barr virus reactivation

MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways

Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples

Modulation of lung inflammation by the Epstein-Barr virus protein Zta ⬇️

Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types

Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

OncomiR addiction is generated by a miR-155 feedback loop in Theileria-transformed leukocytes

Post-transcriptional up-regulation of miR-21 by type I collagen

Preferential star strand biogenesis of pre-miR-24-2 targets PKC-alpha and suppresses cell survival in MCF-7 breast cancer cells

Quantitative and Qualitative RNA-Seq-Based Evaluation of Epstein-Barr Virus Transcription in Type I Latency Burkitt's Lymphoma Cells ⬇️

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets

RNA-sequencing study of peripheral blood monocytes in chronic periodontitis

Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate

Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation

S100P/RAGE signaling regulates microRNA-155 expression via AP-1 activation in colon cancer

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

Significant Prognostic Features and Patterns of Somatic TP53 Mutations in Human Cancers

Small interfering RNA effectively inhibits protein expression and negative strand RNA synthesis from a full-length hepatitis C virus clone

Somatic mutations favorable to patient survival are predominant in ovarian carcinomas

SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.: Supplemental File 1

TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene

The Epstein-Barr virus transactivator Zta binds to its own promoter and is required for full promoter activity during anti-Ig and TGF-beta1 mediated reactivation

The impact of oil spill to lung health - insights from an RNA-seq study of human airway epithelial cells

The microRNA expression associated with morphogenesis of breast cancer cells in three-dimensional organotypic culture

The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication

The sequence structures of human microRNA molecules and their implications

Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development.

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus

Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.

Use of gene overexpression to assess function in cell cycle control