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modENCODE

The National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements

The modENCODE Project will try to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes.

Publications of the modENCODE project

This is a collection of publications connected to the project. If you note any omission or mistake please contact us at help@modencode.org.

Title Citation PMID
Salt fractionation of nucleosomes for genome-wide profiling Teves et al, Methods Mol Biol. 2012;833:421-32 22183608
Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling Steiner et al., Genome Res. 2012 Apr;22(4):766-77 22219512
Developmental control of gene copy number by repression of replication initiation and fork progression. Sher et al., Genome Res. 2012 Jan;22(1):64-75 22090375
Epigenome characterization at single base-pair resolution Henikoff et al., Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318-23 22025700
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. Cheng et al, PLoS Comput Biol. 2011 Nov;7(11):e1002190 22125477
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Deng et al., Nat Genet. 2011 Oct 23;43(12):1179-85 22019781
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Jungreis et al, Genome Res. 2011 Dec;21(12):2096-113 21994247
Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. Brooks et al., RNA. 2011 Oct;17(10):1884-94 21865603
Synthetic spike-in standards for RNA-seq experiments Jiang et al, Genome Res. 2011 Sep;21(9):1543-51 21816910
Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. Kato et al, RNA. 2011 Oct;17(10):1804-20 21810936
Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression Kim et al, Genes Dev. 2011 Jul 1;25(13):1384-98. 21724831
Determinants of antigenicity and specificity in immune response for protein sequences Wang et al, BMC Bioinformatics. 2011 Jun 21;12:251 21693021
PeakRanger: a cloud-enabled peak caller for ChIP-seq data Feng et al, BMC Bioinformatics. 2011 May 9;12:139. 21554709
A cis-regulatory map of the Drosophila genome Negre et al., Nature. 2011 March 24; 471(7339): 527-531. 21430782
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. Ho et al, BMC Genomics. 2011 Feb 28;12:134. 21356108
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets Cheng et al, Genome Biol. 2011;12(2):R15 21324173
Developmental control of the DNA replication and transcription programs Nordman et al, Genome Res. 2011 Feb;21(2):175-81. 21177957
Genome-wide analysis of promoter architecture in Drosophila melanogaster Hoskins et al, Genome Res. 2011 Feb;21(2):182-92 21177961
The transcriptional diversity of 25 Drosophila cell lines Cherbas et al, Genome Res. 2011. 21: 301-314 21177962
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence Berezikov et al, Genome Res. 2011 Feb;21(2):203-15 21177969
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin Riddle et al, Genome Res. 2011 Feb;21(2):147-63 21177972
Chromatin signatures of the Drosophila replication program Eaton et al, Genome Res. 2011 Feb;21(2):164-74 21177973
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE modENCODE Consortium et al., Science 24 December 2010:
Vol. 330 no. 6012 pp. 1787-1797
21177974
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster Kharchenko et al, Nature. 2011 Mar 24;471(7339):480-5 21179089
The developmental transcriptome of Drosophila melanogaster Graveley et al, Nature. 2011 Mar 24;471(7339):473-9 21179090
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans Chung et al, Genome Res. 2011. 21: 286-300 21177960
A global analysis of C. elegans trans-splicing Allen et al, Genome Res. 2011. 21: 255-264 21177958
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans Niu et al, Genome Res. 2011. 21: 245-254 21177963
Broad chromosomal domains of histone modification patterns in C. elegans Liu et al, Genome Res. 2011. 21: 227-236 21177964
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans Ercan et al, Genome Res. 2011. 21: 237-244 21177966
A spatial and temporal map of C. elegans gene expression Spencer et al; Genome Res. 2010 21177967
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data Lu et al, Genome Res. 2011. 21: 276-285 21177971
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project Gerstein et al; Science 24 December 2010:Vol. 330 no. 6012 pp. 1775-1787 21177976
An assessment of histone-modification antibody quality Egelhofer et al, Nat Struct Mol Biol. 2011 Jan;18(1):91-3 21131980
Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2 Ikegami et al., Genome Biology 2010;11:R120. 21176223
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays Agarwal et al, BMC Genomics. 2010 Jun 17;11:383. 20565764
The landscape of C. elegans 3'UTRs. Mangone et al, Science. 2010 July 23; 329(5990): 432-435. 20522740
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Zhong et al, PLoS Genet. 2010 Feb 19;6(2):e1000848 20174564
Conservation of an RNA regulatory map between Drosophila and mammals Brooks et al, Genome Res. 2011 Feb;21(2):193-202 20921232
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. MacAlpine et al., Genome Res. 2010 Feb;20(2):201-11 19996087
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans Hillier et al., Genome Res. 2009. 19: 657-666 19181841
Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. Ooi et al, PLoS Genet. 2006 Jun;2(6):e97 16846252