J Omar Yáñez-Cuna, Cosmas D Arnold, Gerald Stampfel, Lukasz M Boryń, Daniel Gerlach, Martina Rath, Alexander Stark. Genome Res 2014
Times Cited: 84
Times Cited: 84
Times Cited
Times Co-cited
Similarity
Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Cosmas D Arnold, Daniel Gerlach, Christoph Stelzer, Łukasz M Boryń, Martina Rath, Alexander Stark. Science 2013
Cosmas D Arnold, Daniel Gerlach, Christoph Stelzer, Łukasz M Boryń, Martina Rath, Alexander Stark. Science 2013
42
Transcriptional enhancers: from properties to genome-wide predictions.
Daria Shlyueva, Gerald Stampfel, Alexander Stark. Nat Rev Genet 2014
Daria Shlyueva, Gerald Stampfel, Alexander Stark. Nat Rev Genet 2014
26
An atlas of active enhancers across human cell types and tissues.
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
25
Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.
J Banerji, S Rusconi, W Schaffner. Cell 1981
J Banerji, S Rusconi, W Schaffner. Cell 1981
19
Transcription factors: from enhancer binding to developmental control.
François Spitz, Eileen E M Furlong. Nat Rev Genet 2012
François Spitz, Eileen E M Furlong. Nat Rev Genet 2012
16
High-throughput functional testing of ENCODE segmentation predictions.
Jamie C Kwasnieski, Christopher Fiore, Hemangi G Chaudhari, Barak A Cohen. Genome Res 2014
Jamie C Kwasnieski, Christopher Fiore, Hemangi G Chaudhari, Barak A Cohen. Genome Res 2014
16
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.
Muhammad A Zabidi, Cosmas D Arnold, Katharina Schernhuber, Michaela Pagani, Martina Rath, Olga Frank, Alexander Stark. Nature 2015
Muhammad A Zabidi, Cosmas D Arnold, Katharina Schernhuber, Michaela Pagani, Martina Rath, Olga Frank, Alexander Stark. Nature 2015
16
ChIP-seq accurately predicts tissue-specific activity of enhancers.
Axel Visel, Matthew J Blow, Zirong Li, Tao Zhang, Jennifer A Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen,[...]. Nature 2009
Axel Visel, Matthew J Blow, Zirong Li, Tao Zhang, Jennifer A Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen,[...]. Nature 2009
16
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
15
Histone modifications at human enhancers reflect global cell-type-specific gene expression.
Nathaniel D Heintzman, Gary C Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F Harp, Zhen Ye, Leonard K Lee, Rhona K Stuart, Christina W Ching,[...]. Nature 2009
Nathaniel D Heintzman, Gary C Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F Harp, Zhen Ye, Leonard K Lee, Rhona K Stuart, Christina W Ching,[...]. Nature 2009
15
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.
Pouya Kheradpour, Jason Ernst, Alexandre Melnikov, Peter Rogov, Li Wang, Xiaolan Zhang, Jessica Alston, Tarjei S Mikkelsen, Manolis Kellis. Genome Res 2013
Pouya Kheradpour, Jason Ernst, Alexandre Melnikov, Peter Rogov, Li Wang, Xiaolan Zhang, Jessica Alston, Tarjei S Mikkelsen, Manolis Kellis. Genome Res 2013
15
ChromHMM: automating chromatin-state discovery and characterization.
Jason Ernst, Manolis Kellis. Nat Methods 2012
Jason Ernst, Manolis Kellis. Nat Methods 2012
15
Massively parallel functional dissection of mammalian enhancers in vivo.
Rupali P Patwardhan, Joseph B Hiatt, Daniela M Witten, Mee J Kim, Robin P Smith, Dalit May, Choli Lee, Jennifer M Andrie, Su-In Lee, Gregory M Cooper,[...]. Nat Biotechnol 2012
Rupali P Patwardhan, Joseph B Hiatt, Daniela M Witten, Mee J Kim, Robin P Smith, Dalit May, Choli Lee, Jennifer M Andrie, Su-In Lee, Gregory M Cooper,[...]. Nat Biotechnol 2012
14
Mapping and analysis of chromatin state dynamics in nine human cell types.
Jason Ernst, Pouya Kheradpour, Tarjei S Mikkelsen, Noam Shoresh, Lucas D Ward, Charles B Epstein, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael Coyne,[...]. Nature 2011
Jason Ernst, Pouya Kheradpour, Tarjei S Mikkelsen, Noam Shoresh, Lucas D Ward, Charles B Epstein, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael Coyne,[...]. Nature 2011
14
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
14
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
Leighton J Core, André L Martins, Charles G Danko, Colin T Waters, Adam Siepel, John T Lis. Nat Genet 2014
Leighton J Core, André L Martins, Charles G Danko, Colin T Waters, Adam Siepel, John T Lis. Nat Genet 2014
14
Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
13
The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
13
Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
13
Modification of enhancer chromatin: what, how, and why?
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
13
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.
Alexandre Melnikov, Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov, Soheil Feizi, Andreas Gnirke, Curtis G Callan, Justin B Kinney,[...]. Nat Biotechnol 2012
Alexandre Melnikov, Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov, Soheil Feizi, Andreas Gnirke, Curtis G Callan, Justin B Kinney,[...]. Nat Biotechnol 2012
13
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
Robin P Smith, Leila Taher, Rupali P Patwardhan, Mee J Kim, Fumitaka Inoue, Jay Shendure, Ivan Ovcharenko, Nadav Ahituv. Nat Genet 2013
Robin P Smith, Leila Taher, Rupali P Patwardhan, Mee J Kim, Fumitaka Inoue, Jay Shendure, Ivan Ovcharenko, Nadav Ahituv. Nat Genet 2013
11
Genome-wide mapping of in vivo protein-DNA interactions.
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
11
Genome-scale functional characterization of Drosophila developmental enhancers in vivo.
Evgeny Z Kvon, Tomas Kazmar, Gerald Stampfel, J Omar Yáñez-Cuna, Michaela Pagani, Katharina Schernhuber, Barry J Dickson, Alexander Stark. Nature 2014
Evgeny Z Kvon, Tomas Kazmar, Gerald Stampfel, J Omar Yáñez-Cuna, Michaela Pagani, Katharina Schernhuber, Barry J Dickson, Alexander Stark. Nature 2014
11
Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
11
FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
11
Enhancers: five essential questions.
Len A Pennacchio, Wendy Bickmore, Ann Dean, Marcelo A Nobrega, Gill Bejerano. Nat Rev Genet 2013
Len A Pennacchio, Wendy Bickmore, Ann Dean, Marcelo A Nobrega, Gill Bejerano. Nat Rev Genet 2013
11
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.
Darío G Lupiáñez, Katerina Kraft, Verena Heinrich, Peter Krawitz, Francesco Brancati, Eva Klopocki, Denise Horn, Hülya Kayserili, John M Opitz, Renata Laxova,[...]. Cell 2015
Darío G Lupiáñez, Katerina Kraft, Verena Heinrich, Peter Krawitz, Francesco Brancati, Eva Klopocki, Denise Horn, Hülya Kayserili, John M Opitz, Renata Laxova,[...]. Cell 2015
11
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
11
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
11
Resolving systematic errors in widely used enhancer activity assays in human cells.
Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath, Muhammad A Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R Catarino,[...]. Nat Methods 2018
Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath, Muhammad A Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R Catarino,[...]. Nat Methods 2018
16
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Sushmita Roy, Jason Ernst, Peter V Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L Eaton, Jane M Landolin, Christopher A Bristow, Lijia Ma, Michael F Lin,[...]. Science 2010
Sushmita Roy, Jason Ernst, Peter V Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L Eaton, Jane M Landolin, Christopher A Bristow, Lijia Ma, Michael F Lin,[...]. Science 2010
10
Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.
Daria Shlyueva, Christoph Stelzer, Daniel Gerlach, J Omar Yáñez-Cuna, Martina Rath, Łukasz M Boryń, Cosmas D Arnold, Alexander Stark. Mol Cell 2014
Daria Shlyueva, Christoph Stelzer, Daniel Gerlach, J Omar Yáñez-Cuna, Martina Rath, Łukasz M Boryń, Cosmas D Arnold, Alexander Stark. Mol Cell 2014
12
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
10
Widespread transcription at neuronal activity-regulated enhancers.
Tae-Kyung Kim, Martin Hemberg, Jesse M Gray, Allen M Costa, Daniel M Bear, Jing Wu, David A Harmin, Mike Laptewicz, Kellie Barbara-Haley, Scott Kuersten,[...]. Nature 2010
Tae-Kyung Kim, Martin Hemberg, Jesse M Gray, Allen M Costa, Daniel M Bear, Jing Wu, David A Harmin, Mike Laptewicz, Kellie Barbara-Haley, Scott Kuersten,[...]. Nature 2010
10
DEEP: a general computational framework for predicting enhancers.
Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B Bajic. Nucleic Acids Res 2015
Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B Bajic. Nucleic Acids Res 2015
14
VISTA Enhancer Browser--a database of tissue-specific human enhancers.
Axel Visel, Simon Minovitsky, Inna Dubchak, Len A Pennacchio. Nucleic Acids Res 2007
Axel Visel, Simon Minovitsky, Inna Dubchak, Len A Pennacchio. Nucleic Acids Res 2007
10
Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
10
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
10
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
9
DNA-binding specificities of human transcription factors.
Arttu Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen, Kazuhiro R Nitta, Pasi Rastas, Ekaterina Morgunova, Martin Enge, Mikko Taipale, Gonghong Wei,[...]. Cell 2013
Arttu Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen, Kazuhiro R Nitta, Pasi Rastas, Ekaterina Morgunova, Martin Enge, Mikko Taipale, Gonghong Wei,[...]. Cell 2013
9
High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
9
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder,[...]. Genome Biol 2012
Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder,[...]. Genome Biol 2012
9
Selective inhibition of tumor oncogenes by disruption of super-enhancers.
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
9
High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
Laurent Vanhille, Aurélien Griffon, Muhammad Ahmad Maqbool, Joaquin Zacarias-Cabeza, Lan T M Dao, Nicolas Fernandez, Benoit Ballester, Jean Christophe Andrau, Salvatore Spicuglia. Nat Commun 2015
Laurent Vanhille, Aurélien Griffon, Muhammad Ahmad Maqbool, Joaquin Zacarias-Cabeza, Lan T M Dao, Nicolas Fernandez, Benoit Ballester, Jean Christophe Andrau, Salvatore Spicuglia. Nat Commun 2015
9
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells.
Matthew Murtha, Zeynep Tokcaer-Keskin, Zuojian Tang, Francesco Strino, Xi Chen, Yatong Wang, Xiangmei Xi, Claudio Basilico, Stuart Brown, Richard Bonneau,[...]. Nat Methods 2014
Matthew Murtha, Zeynep Tokcaer-Keskin, Zuojian Tang, Francesco Strino, Xi Chen, Yatong Wang, Xiangmei Xi, Claudio Basilico, Stuart Brown, Richard Bonneau,[...]. Nat Methods 2014
11
A unique chromatin signature uncovers early developmental enhancers in humans.
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
9
Systematic localization of common disease-associated variation in regulatory DNA.
Matthew T Maurano, Richard Humbert, Eric Rynes, Robert E Thurman, Eric Haugen, Hao Wang, Alex P Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody,[...]. Science 2012
Matthew T Maurano, Richard Humbert, Eric Rynes, Robert E Thurman, Eric Haugen, Hao Wang, Alex P Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody,[...]. Science 2012
9
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Michael M Hoffman, Orion J Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes, William Stafford Noble. Nat Methods 2012
Michael M Hoffman, Orion J Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes, William Stafford Noble. Nat Methods 2012
9
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.