Articles with public access mandates - Peggy J. FarnhamLearn more
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Perspectives on ENCODE
F Abascal, R Acosta, NJ Addleman, J Adrian, V Afzal, B Aken, JA Akiyama
Nature 583 (7818), 693-699, 2020
Mandates: US National Institutes of Health
Available somewhere: 89
Integrative analysis of 111 reference human epigenomes
A Kundaje, W Meuleman, J Ernst, M Bilenky, A Yen, A Heravi-Moussavi, ...
Nature 518 (7539), 317-330, 2015
Mandates: US National Institutes of Health, Howard Hughes Medical Institute, National …
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...
nature 447 (7146), 799-816, 2007
Mandates: German Research Foundation
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ...
Genome research 22 (9), 1813-1831, 2012
Mandates: US National Institutes of Health
The NIH roadmap epigenomics mapping consortium
BE Bernstein, JA Stamatoyannopoulos, JF Costello, B Ren, ...
Nature biotechnology 28 (10), 1045-1048, 2010
Mandates: US National Institutes of Health
Architecture of the human regulatory network derived from ENCODE data
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, ...
Nature 489 (7414), 91-100, 2012
Mandates: US National Institutes of Health
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
Mandates: US Department of Energy, US National Institutes of Health, UK Biotechnology …
Defining functional DNA elements in the human genome
M Kellis, B Wold, MP Snyder, BE Bernstein, A Kundaje, GK Marinov, ...
Proceedings of the National Academy of Sciences 111 (17), 6131-6138, 2014
Mandates: US National Institutes of Health
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
RA Harris, T Wang, C Coarfa, RP Nagarajan, C Hong, SL Downey, ...
Nature biotechnology 28 (10), 1097-1105, 2010
Mandates: US National Institutes of Health
A user's guide to the encyclopedia of DNA elements (ENCODE)
RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ...
PLoS biology 9 (4), 2011
Mandates: US National Institutes of Health
Insights from genomic profiling of transcription factors
PJ Farnham
Nature Reviews Genetics 10 (9), 605-616, 2009
Mandates: US National Institutes of Health
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy
T Fujiwara, H O'Geen, S Keles, K Blahnik, AK Linnemann, YA Kang, ...
Molecular cell 36 (4), 667-681, 2009
Mandates: US National Institutes of Health
KAP1 protein: an enigmatic master regulator of the genome
S Iyengar, PJ Farnham
Journal of Biological Chemistry 286 (30), 26267-26276, 2011
Mandates: US National Institutes of Health
Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome
YG Tak, PJ Farnham
Epigenetics & chromatin 8, 1-18, 2015
Mandates: US National Institutes of Health
The psychencode project
S Akbarian, C Liu, JA Knowles, FM Vaccarino, PJ Farnham, GE Crawford, ...
Nature neuroscience 18 (12), 1707-1712, 2015
Mandates: US National Institutes of Health, US Department of Veterans Affairs
The human epigenome browser at Washington University
X Zhou, B Maricque, M Xie, D Li, V Sundaram, EA Martin, BC Koebbe, ...
Nature methods 8 (12), 989-990, 2011
Mandates: US National Institutes of Health
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
M Xie, C Hong, B Zhang, RF Lowdon, X Xing, D Li, X Zhou, HJ Lee, ...
Nature genetics 45 (7), 836-841, 2013
Mandates: US National Institutes of Health, Howard Hughes Medical Institute
dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression
H O’Geen, C Ren, CM Nicolet, AA Perez, J Halmai, VM Le, JP Mackay, ...
Nucleic acids research 45 (17), 9901-9916, 2017
Mandates: US National Institutes of Health, Australian Research Council
Cross-talk between site-specific transcription factors and DNA methylation states
A Blattler, PJ Farnham
Journal of Biological Chemistry 288 (48), 34287-34294, 2013
Mandates: US National Institutes of Health
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages
X Lan, H Witt, K Katsumura, Z Ye, Q Wang, EH Bresnick, PJ Farnham, ...
Nucleic acids research 40 (16), 7690-7704, 2012
Mandates: US National Institutes of Health, Howard Hughes Medical Institute
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