Literature DB >> 24636835

Navigating and mining modENCODE data.

Nathan Boley1, Kenneth H Wan2, Peter J Bickel3, Susan E Celniker4.   

Abstract

modENCODE was a 5year NHGRI funded project (2007-2012) to map the function of every base in the genomes of worms and flies characterizing positions of modified histones and other chromatin marks, origins of DNA replication, RNA transcripts and the transcription factor binding sites that control gene expression. Here we describe the Drosophila modENCODE datasets and how best to access and use them for genome wide and individual gene studies.
Copyright © 2014 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Chromatin; Drosophila; Mining; Transcription; modENCODE

Mesh：

Substances：

Year:  2014        PMID： 24636835      PMCID： PMC4857704          DOI： 10.1016/j.ymeth.2014.03.007

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  57 in total

1.  A sequencing method based on real-time pyrophosphate.

Authors:  M Ronaghi; M Uhlén; P Nyrén
Journal:  Science       Date:  1998-07-17       Impact factor: 47.728

2.  Synthetic spike-in standards for RNA-seq experiments.

Authors:  Lichun Jiang; Felix Schlesinger; Carrie A Davis; Yu Zhang; Renhua Li; Marc Salit; Thomas R Gingeras; Brian Oliver
Journal:  Genome Res       Date:  2011-08-04       Impact factor: 9.043

Review 3.  Exploiting Drosophila genetics to understand microRNA function and regulation.

Authors:  Qi Dai; Peter Smibert; Eric C Lai
Journal:  Curr Top Dev Biol       Date:  2012       Impact factor: 4.897

Review 4.  Next-generation sequencing platforms.

Authors:  Elaine R Mardis
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2013       Impact factor: 10.745

5.  Sequence finishing and mapping of Drosophila melanogaster heterochromatin.

Authors:  Roger A Hoskins; Joseph W Carlson; Cameron Kennedy; David Acevedo; Martha Evans-Holm; Erwin Frise; Kenneth H Wan; Soo Park; Maria Mendez-Lago; Fabrizio Rossi; Alfredo Villasante; Patrizio Dimitri; Gary H Karpen; Susan E Celniker
Journal:  Science       Date:  2007-06-15       Impact factor: 47.728

Review 6.  Lessons from microRNA mutants in worms, flies and mice.

Authors:  Peter Smibert; Eric C Lai
Journal:  Cell Cycle       Date:  2008-08-17       Impact factor: 4.534

7.  The developmental transcriptome of Drosophila melanogaster.

Authors:  Brenton R Graveley; Angela N Brooks; Joseph W Carlson; Michael O Duff; Jane M Landolin; Li Yang; Carlo G Artieri; Marijke J van Baren; Nathan Boley; Benjamin W Booth; James B Brown; Lucy Cherbas; Carrie A Davis; Alex Dobin; Renhua Li; Wei Lin; John H Malone; Nicolas R Mattiuzzo; David Miller; David Sturgill; Brian B Tuch; Chris Zaleski; Dayu Zhang; Marco Blanchette; Sandrine Dudoit; Brian Eads; Richard E Green; Ann Hammonds; Lichun Jiang; Phil Kapranov; Laura Langton; Norbert Perrimon; Jeremy E Sandler; Kenneth H Wan; Aarron Willingham; Yu Zhang; Yi Zou; Justen Andrews; Peter J Bickel; Steven E Brenner; Michael R Brent; Peter Cherbas; Thomas R Gingeras; Roger A Hoskins; Thomas C Kaufman; Brian Oliver; Susan E Celniker
Journal:  Nature       Date:  2010-12-22       Impact factor: 49.962

8.  FlyBase 101--the basics of navigating FlyBase.

Authors:  Peter McQuilton; Susan E St Pierre; Jim Thurmond
Journal:  Nucleic Acids Res       Date:  2011-11-29       Impact factor: 16.971

9.  Using GBrowse 2.0 to visualize and share next-generation sequence data.

Authors:  Lincoln D Stein
Journal:  Brief Bioinform       Date:  2013-02-01       Impact factor: 11.622

10.  Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Authors:  Peter V Kharchenko; Michael Y Tolstorukov; Peter J Park
Journal:  Nat Biotechnol       Date:  2008-11-16       Impact factor: 54.908
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  8 in total

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Journal:  Dev Cell       Date:  2022-04-11       Impact factor: 13.417

2.  Genetics on the Fly: A Primer on the Drosophila Model System.

Authors:  Karen G Hales; Christopher A Korey; Amanda M Larracuente; David M Roberts
Journal:  Genetics       Date:  2015-11       Impact factor: 4.562

3.  Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach.

Authors:  Flavio Pazos Obregón; Cecilia Papalardo; Sebastián Castro; Gustavo Guerberoff; Rafael Cantera
Journal:  BMC Genomics       Date:  2015-09-15       Impact factor: 3.969

4.  Survival of the fittest tools.

Authors:  Hugo J Bellen
Journal:  Genetics       Date:  2014-10       Impact factor: 4.562

5.  The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation.

Authors:  Neha P Paranjape; Brian R Calvi
Journal:  G3 (Bethesda)       Date:  2016-06-01       Impact factor: 3.154

6.  Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury.

Authors:  Gerald A Higgins; Patrick Georgoff; Vahagn Nikolian; Ari Allyn-Feuer; Brian Pauls; Richard Higgins; Brian D Athey; Hasan E Alam
Journal:  Pharm Res       Date:  2017-03-07       Impact factor: 4.200

7.  The Drosophila Gene Expression Tool (DGET) for expression analyses.

Authors:  Yanhui Hu; Aram Comjean; Norbert Perrimon; Stephanie E Mohr
Journal:  BMC Bioinformatics       Date:  2017-02-10       Impact factor: 3.169

8.  SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

Authors:  Benjamin C Hitz; Laurence D Rowe; Nikhil R Podduturi; David I Glick; Ulugbek K Baymuradov; Venkat S Malladi; Esther T Chan; Jean M Davidson; Idan Gabdank; Aditi K Narayana; Kathrina C Onate; Jason Hilton; Marcus C Ho; Brian T Lee; Stuart R Miyasato; Timothy R Dreszer; Cricket A Sloan; J Seth Strattan; Forrest Y Tanaka; Eurie L Hong; J Michael Cherry
Journal:  PLoS One       Date:  2017-04-12       Impact factor: 3.240
  8 in total

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