PubRank

Peggy J Farnham

Author PubWeight™ 286.76‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
2 Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007 30.22
3 The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 2010 13.99
4 ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2012 9.13
5 Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010 7.00
6 Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 2006 6.75
7 Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 2002 6.74
8 Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 2006 6.54
9 T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity 2004 6.43
10 Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev 2004 6.19
11 Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 2008 4.08
12 Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A 2007 4.00
13 Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell 2009 3.96
14 High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol 2004 3.76
15 Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet 2007 3.75
16 Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 2002 3.37
17 Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 2014 3.35
18 ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One 2010 3.15
19 Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 2002 2.99
20 A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 2007 2.97
21 Comparison of sample preparation methods for ChIP-chip assays. Biotechniques 2006 2.89
22 Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 2006 2.82
23 Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 2009 2.74
24 Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem 2002 2.68
25 Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol 2003 2.47
26 Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 2007 2.28
27 Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 2003 2.22
28 Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol 2012 2.19
29 KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem 2011 2.15
30 Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol 2003 2.12
31 E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res 2008 2.07
32 E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem 2003 2.02
33 CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 2005 1.89
34 Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem 2007 1.88
35 Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol 2013 1.88
36 Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther 2003 1.84
37 A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res 2006 1.74
38 Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem 2009 1.71
39 DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet 2013 1.64
40 The identification of E2F1-specific target genes. Proc Natl Acad Sci U S A 2002 1.63
41 N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res 2008 1.52
42 Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res 2007 1.50
43 Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res 2008 1.45
44 W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics 2009 1.42
45 Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med (Maywood) 2004 1.41
46 Functional analysis of KAP1 genomic recruitment. Mol Cell Biol 2011 1.39
47 Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol 2011 1.37
48 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 2010 1.34
49 Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One 2011 1.34
50 Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res 2013 1.33
51 L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell 2011 1.32
52 Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res 2012 1.32
53 Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A 2011 1.29
54 The transcription factor encyclopedia. Genome Biol 2012 1.28
55 Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem 2013 1.24
56 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. J Biol Chem 2011 1.18
57 Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 2008 1.13
58 Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol 2011 1.13
59 Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol 2014 1.12
60 Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation. PLoS One 2011 1.11
61 Spark: a navigational paradigm for genomic data exploration. Genome Res 2012 1.10
62 Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol 2010 1.06
63 Recombinant antibodies to histone post-translational modifications. Nat Methods 2013 1.05
64 The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem 2004 1.05
65 Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics 2010 1.01
66 ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics Chromatin 2013 0.93
67 LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data. PLoS One 2013 0.87
68 In vivo assays to examine transcription factor localization and target gene specificity. Methods 2002 0.84
69 Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics 2014 0.82
70 Can genome engineering be used to target cancer-associated enhancers? Epigenomics 2014 0.81
71 Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene 2003 0.81
72 Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ tumor suppressor signaling pathways. Mol Cancer Res 2012 0.81
73 Transcription factor effector domains. Subcell Biochem 2011 0.81
74 Uncovering transcription factor modules using one- and three-dimensional analyses. J Biol Chem 2012 0.78
75 Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A 2014 0.76
76 Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. Methods Mol Biol 2012 0.75