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Ensembl regulation resources

author

Steven P Wilder

Ewan Birney

Ian Dunham

Paul Flicek

Damian Keefe

Rhoda Kinsella

Michael Nuhn

Dan Sheppard

Daniel Sobral

Emily Pritchard

Ikhlak Ahmed

Daniel R Zerbino

Stefan Gräf

Nathan Johnson

Bethan Pritchard

M Ridwan Amode

Ilias Lavidas

published in: Database

date of publication: 2016-02-17

Cites articles 61

Date

Title

Authors

2016-02-20

Ensembl comparative genomics resources

Javier Herrero, Matthieu Muffato, Eugene Kulesha, Paul Flicek, Andrew D Yates, Albert J. Vilella, M Ridwan Amode, Miguel Pignatelli
2015-03-24

The ensembl regulatory build

Steven P Wilder, Paul Flicek, Thomas Juettemann, Daniel R Zerbino, Nathan Johnson
2015-03-09

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Mayra Furlan-Magaril, Borbala Mifsud, Filipe Tavares-Cadete, Biola M. Javierre, Steven W Wingett, Andrew Dimond, Cameron S. Osborne, Peter Fraser
2015-02-12

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Michael M. Hoffman, Maxwell W Libbrecht, Ferhat Ay, William S. Noble
2015-01-01

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts

Wilfried Haerty, Chris Ponting, Yang I Li, Luis Sanchez Pulido
2014-10-28

Ensembl 2015

Fiona Cunningham, Konstantinos Billis, Denise Carvalho Silva, Guy Coates, Laurent Gil, Thibaut Hourlier, Sarah E. Hunt, Sophie H Janacek, Thomas Juettemann, Andreas K Kähäri, Stephen Keenan, Fergal J Martin, Thomas Maurel, William M McLaren, Daniel N Murphy, Rishi Nag, Mateus Patricio, Emily Pritchard, Dan Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P Wilder, Bronwen Aken, Ewan Birney, Matthieu Muffato, Magali Ruffier, Stephen Trevanion, Andrew D Yates, Daniel R Zerbino, Paul Flicek, Jennifer Harrow, Carlos García Girón, M Ridwan Amode, Harpreet Singh Riat, Daniel Barrell, Miguel Pignatelli, Giulietta Spudich, Bert Overduin, Rhoda Kinsella
2014-09-17

The Ensembl REST API: Ensembl Data for Any Language

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2014-03-01

A promoter-level mammalian expression atlas

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2014-03-01

An atlas of active enhancers across human cell types and tissues

Christopher J. Mungall, Evgenia Ntini, Irene Miguel-Escalada, Takahiro Suzuki, Andreas Lennartsson, Owen Rackham, Frederik Otzen Bagger, Nicolas Rapin, Terrence F Meehan, Eivind Valen, Nicolas Bertin, Carsten O Daub, Robin Andersson, Albin Sandelin, Timo Lassmann, Hideya Kawaji, Masayoshi Itoh, Torben Heick Jensen, David A Hume, Piero Carninci, Maxwell Burroughs, Yoshihide Hayashizaki, Peter Heutink, John Kenneth Baillie, Alan Knox, Juha Kere, Emiliano Dalla, Jeroen Laros, Alistair Forrest, Harukazu Suzuki, Michael Rehli, Yuri Ishizu, Ilka Hoof, Naoto Kondo, Berit Lilje, Xiaobei Zhao, Claudia Gebhard, Jette Bornholdt, Mette Boyd, Yutaka Negishi, A Maxwell Burroughs
2013-11-04

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Albin Sandelin, Casper Shyr, Chih-Yu Chen, Ge Tan, Anthony Mathelier, Boris Lenhard, Wyeth Wasserman
2013-10-06

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

William Greenleaf, Jason D. Buenrostro
2013-01-17

DNA-binding specificities of human transcription factors

Jarkko Toivonen, Martin Enge, Mikko Taipale, Arttu Jolma, Jian Yan, Kimmo Palin, Ekaterina Morgunova, Juan M. Vaquerizas, Patrick Lemaire, Esko Ukkonen, Gonghong Wei
2012-12-05

Integrative annotation of chromatin elements from ENCODE data

Michael M. Hoffman, Steven P Wilder, Ewan Birney, Ian Dunham, Ross Hardison, Anshul Kundaje, Manolis Kellis, William S. Noble
2012-09-06

The accessible chromatin landscape of the human genome

Eric D Nguyen, Jeff Vierstra, Amartya Sanyal, Nathan C. Sheffield, Richard Sandstrom, Eric Haugen, Terrence S. Furey, Boris Lenhard, Darin London, Alexias Safi, John Stamatoyannopoulos, Gregory E. Crawford, Lingyun Song, Tristan Frum, Rajinder K Kaul, Jason D Lieb, Vishwanath R Iyer, Job Dekker, Benjamin Vernot, Joshua M. Akey
2012-09-06

An integrated encyclopedia of DNA elements in the human genome

Alvis Brazma, Laurens G Wilming, Toby Hunt, Andrew Berry
2012-03-18

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Michael M. Hoffman, William S. Noble, Orion J Buske
2012-02-28

ChromHMM: automating chromatin-state discovery and characterization

Manolis Kellis
2012-03-07

BLUEPRINT to decode the epigenetic signature written in blood.

Stilianos Antonarakis, Christoph Bock, Manel Esteller, Xavier Estivill i Pallejà, Paul Flicek, Thomas Graf, Kristian Helin, Ralf Küppers, Antonello Mai, Willem H. Ouwehand, Bo Torben Porse, Wolf Reik, Nicole Soranzo, David Torrents, Salvatore Spicuglia, Lucia Altucci, Elías Campo, Thomas Lengauer, Hans Lehrach, Jude Fitzgibbon, Åke Lernmark, Roderic Guigó i Serra, Tariq Enver, Martin Schrappe, Martin Vingron, Michael Stratton, Reiner Siebert, Amos Tanay, Hendrik Gerard Stunnenberg, Jörn Walter, Dirk Schübeler, Saverio Minucci, Emmanouil Dermitzakis
2011-12-01

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Manolis Maragkakis, Panagiotis Alexiou, Martin Reczko, Ioannis S. Vlachos
2011-07-23

Ensembl BioMarts: a hub for data retrieval across taxonomic space

Paul J. Kersey, Paul Flicek, Jeff Almeida-King, Andreas K Kähäri, Daniel M Staines, Arnaud Kerhornou, Giulietta Spudich, Rhoda Kinsella, Glenn Proctor, Paul F. Derwent
2011-06-01

Principles for the post-GWAS functional characterization of cancer risk loci

Angela Risch, Alvaro Monteiro, Michael A James, Gerhard A. Coetzee, Simon A Gayther
2011-05-05

Mapping and analysis of chromatin state dynamics in nine human cell types
2011-03-10

Human-specific loss of regulatory DNA and the evolution of human-specific traits

Cory Y McLean, Philip L. Reno, Alex A Pollen, Gill Bejerano, Douglas B Menke
2011-01

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

Martha L Bulyk
2011-01

The European Nucleotide Archive

Ewan Birney, Rajesh Radhakrishnan, Nima Pakseresht, Neil Goodgame, Sheila Plaister, Iain Cleland, Robert Vaughan, Richard Gibson, Vadim Zalunin, Petra Ten Hoopen, Rasko Leinonen, Ana M. Cerdeño-Tárraga, Guy R. Cochrane
2011-04-14

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Felix Krueger
2011-12-14

DNA-binding factors shape the mouse methylome at distal regulatory regions

Erik van Nimwegen, Rabih Murr, Robert Ivánek, Dirk Schübeler, Dimos Gaidatzis, Anne Schöler, Lukas Burger, Florian Lienert, Christiane Wirbelauer
2010-10-01

The NIH Roadmap Epigenomics Mapping Consortium

Joseph R. Ecker, Peggy Farnham, Eric Lander, Tarjei S Mikkelsen, Manolis Kellis, Bradley Bernstein, Aleksandar Milosavljevic
2010-06-18

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

William M McLaren, Paul Flicek, Fiona Cunningham, Bethan Pritchard
2010-05-11

Using caching and optimization techniques to improve performance of the Ensembl website

Stephen Trevanion, James Smith, Bethan Pritchard
2010-05-11

Consistent annotation of gene expression arrays

Paul Flicek, Benoit Ballester, Nathan Johnson
2010

Ensembl variation resources

Ewan Birney, Paul Flicek, Eugene Kulesha, Bethan Pritchard, James Smith, Fiona Cunningham, William M McLaren, Pablo Marin-Garcia, Damian Smedley, Giulietta Spudich

Article - wd:Q35926900

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