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List of works by Peggy Farnham

5-azacytidine treatment reorganizes genomic histone modification patterns

scientific article published on April 2010

A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

scientific article

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1

scientific article

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

scientific article published on 12 September 2019

A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs

scientific article published in July 1980

A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter

scientific article published on March 1993

A re-examination of the distributions of octopamine and phenylethanolamine in the aplysia nervous system

scientific article

Activation of the murine dihydrofolate reductase promoter by E2F1. A requirement for CBP recruitment

scientific article published on May 1999

Altering cancer transcriptomes using epigenomic inhibitors

scientific article published on 24 February 2015

An E-box-mediated increase in cad transcription at the G1/S-phase boundary is suppressed by inhibitory c-Myc mutants

scientific article published on May 1995

An inhibitory Raf-1 mutant suppresses expression of a subset of v-raf-activated genes

scientific article published on July 1993

Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression

scientific article

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

scientific article

Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors

scientific article published on April 2008

Applying whole-genome studies of epigenetic regulation to study human disease

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Autophagy driven by a master regulator of hematopoiesis

scientific article

CAD, a c-Myc target gene, is not deregulated in Burkitt's lymphoma cell lines

scientific article published on February 2000

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

article

Can genome engineering be used to target cancer-associated enhancers?

scientific article

Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts

scientific article published on September 1991

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

scientific article

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Characterization of the 3' untranslated region of mouse E2F1 mRNA.

scientific article published on November 1998

Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene

scientific article published in April 1990

Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

scientific article published on 14 May 2020

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes

scientific article

Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation

scientific article

Cloning, chromosomal location, and characterization of mouse E2F1 ⬇️

scientific article published on March 1994

Coexamination of site-specific transcription factor binding and promoter activity in living cells

scientific article

Comparison of sample preparation methods for ChIP-chip assays

scientific article

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation

scientific article

Comprehensive functional annotation of 77 prostate cancer risk loci

scientific article published on 30 January 2014

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors

article

Conclusions and future directions

article

Context-dependent transcriptional regulation

scientific article

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

scientific article

Cross-talk between site-specific transcription factors and DNA methylation states

scientific article

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

scientific article published on 26 May 2013

De novo identification of in vivo binding sites from ChIP-chip data

scientific article published on 8 July 2008

Defining functional DNA elements in the human genome

scientific article

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

scientific article published on 08 October 2015

Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation

scientific article published on October 2000

Direct recruitment of N-myc to target gene promoters

scientific article published on October 2000

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy

scientific article

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites

scientific article

E2F-mediated growth regulation requires transcription factor cooperation

scientific article published on July 1997

E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9.

scientific article

Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of EScherichia coli

scientific article

Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli

scientific article published on 01 July 1982

Effects of gentamicin on trypsin, chymotrypsin, and collagenase

scientific article published on August 1978

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells

scientific article published on 6 January 2016

Epigenetic and transcriptional determinants of the human breast

scientific article

Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation

scientific article

Exogenous E2F expression is growth inhibitory before, during, and after cellular transformation

scientific article published on April 2000

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties ⬇️

scientific article (publication date: 24 July 1992)

Expression patterns of the E2F family of transcription factors during mouse nervous system development

scientific article published on August 1997

Expression patterns of the E2F family of transcription factors during murine epithelial development

scientific article published on May 1997

Expression profiling and identification of novel genes in hepatocellular carcinomas

scientific article published in May 2001

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

scientific article published on 26 June 2013

Functional analysis of KAP1 genomic recruitment

scientific article

Functional annotation of colon cancer risk SNPs

scientific article

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

scientific article

Genetic framework for GATA factor function in vascular biology

scientific article

Genome-scale ChIP-chip analysis using 10,000 human cells

scientific article

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

scientific article published on 03 February 2020

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs

scientific article

Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome

scientific article published on 10 February 2011

Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

scientific article

Genomic approaches that aid in the identification of transcription factor target genes.

scientific article published in September 2004

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263

scientific article

Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha

scientific article

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

scientific article

Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions

scientific article published in February 1985

High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays

scientific article published on January 2004

Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ tumor suppressor signaling pathways

scientific article published on 23 May 2012

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and characterization of CRG-L2, a new marker for liver tumor development

article

Identification of a new promoter upstream of the murine dihydrofolate reductase gene

scientific article published on October 1989

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

scientific article published on June 2007

Identification of cis-acting elements that can obviate a requirement for the C-terminal domain of RNA polymerase II.

scientific article

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays

scientific article published on 26 January 2007

Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase

scientific article

Identification of target genes of oncogenic transcription factors

scientific article

Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy

scientific article

Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20.

scientific article published on July 1990

Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation

scientific article

In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene

scientific article published on July 1986

In vivo assays to examine transcription factor localization and target gene specificity

article

Inappropriate transcription from the 5' end of the murine dihydrofolate reductase gene masks transcriptional regulation

scientific article

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

scientific article published on 21 May 2015

Insights from genomic profiling of transcription factors

scientific article

Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes

scientific article

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

scientific article

Intermediate DNA methylation is a conserved signature of genome regulation

scientific article

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

scientific article

KAP1 protein: an enigmatic master regulator of the genome

scientific article published on 07 June 2011

L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure

scientific article

LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data

scientific article

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

scientific article

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

scientific article

Mre11 complex and DNA replication: linkage to E2F and sites of DNA synthesis

scientific article

Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter

scientific article published on July 1994

Murine dihydrofolate reductase transcripts through the cell cycle

scientific article published on February 1986

Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter

scientific article

Myc versus USF: discrimination at the cad gene is determined by core promoter elements

scientific article published on May 1997

N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor

scientific article

No effect of loss of E2F1 on liver regeneration or hepatocarcinogenesis in C57BL/6J or C3H/HeJ mice

scientific article published in August 1999

Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene

scientific article published on June 1985

Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain

scientific article published on April 1997

Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins

scientific article published on January 2003

Recombinant antibodies to histone post-translational modifications

scientific article

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types

scientific article

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Review of the 1998 Keystone Symposium on Transcriptional Mechanisms Taos, NM, USA, February 21–26, 19981

scientific article published on 01 November 1998

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros

scientific article

Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter

scientific article published on April 1990

Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27.

scientific article

Site-specific initiation of transcription by RNA polymerase II.

scientific article

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

scientific article

Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component.

scientific article

Spark: a navigational paradigm for genomic data exploration

scientific article

Start site selection at the TATA-less carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter.

scientific article published on January 1994

Steps toward understanding the inheritance of repressive methyl-lysine marks in histones.

scientific article

Strain-dependent differences in DNA synthesis and gene expression in the regenerating livers of C57BL/6J and C3H/HeJ mice

article

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

scientific article

Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro

scientific article

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

scientific article published on 7 February 2008

T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells

scientific article

TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

scientific article published on 14 September 2020

Target gene specificity of E2F and pocket protein family members in living cells

scientific article

The Enigmatic HOX Genes: Can We Crack Their Code?

article

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter

scientific article published on March 1992

The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II.

scientific article published on May 1992

The Human Epigenome Browser at Washington University

scientific article

The NIH Roadmap Epigenomics Mapping Consortium

scientific article (publication date: October 2010)

The PsychENCODE project

scientific article

The bidirectionally transcribed dihydrofolate reductase and rep-3a promoters are growth regulated by distinct mechanisms.

scientific article published on May 1995

The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements

scientific article published on 20 February 2001

The identification of E2F1-specific target genes

scientific article

The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression

scientific article published on 17 July 2019

The role of DNA methylation in directing the functional organization of the cancer epigenome

scientific article

The role of E2F in the mammalian cell cycle

scientific article

The transcription factor encyclopedia

scientific article (publication date: 2012)

The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation

scientific article published on 24 August 2004

Thematic Minireview Series on Results from the ENCODE Project: Integrative Global Analyses of Regulatory Regions in the Human Genome ⬇️

scientific article published on September 5, 2012

Transcription factor effector domains

scientific article

Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site

scientific article published on February 1990

Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle.

scientific article published in June 1985

Transcriptional regulation of the dihydrofolate reductase gene

scientific article

Transcriptional regulation of the dihydrofolate reductase/rep-3 locus

scientific article published on January 1994

Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line

scientific article published on February 1985

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

scientific article published on 10 April 2006

Uncovering Transcription Factor Modules Using One- and Three-dimensional Analyses ⬇️

scientific article published on September 5, 2012

Use of chromatin immunoprecipitation to clone novel E2F target promoters

scientific article

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

article

Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

scientific article published on 17 March 2008

Using ChIP-seq technology to generate high-resolution profiles of histone modifications

scientific article

Using ChIP-seq technology to identify targets of zinc finger transcription factors

scientific article

Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments

scientific article published on January 2012

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data

scientific article

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

scientific article published on 21 May 2013

ZNF217, a candidate breast cancer oncogene amplified at 20q13, regulates expression of the ErbB3 receptor tyrosine kinase in breast cancer cells

scientific article

ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes

scientific article

c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism

scientific article published on 22 October 2001

c-Myc target gene specificity is determined by a post-DNAbinding mechanism

scientific article published on November 1998

krox 20 messenger RNA and protein expression in the adult central nervous system

scientific article published in June 1992

v-Raf activates transcription of growth-responsive promoters via GC-rich sequences that bind the transcription factor Sp1.

scientific article published on May 1995

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