A citation-based method for searching scientific literature

J Omar Yáñez-Cuna, Cosmas D Arnold, Gerald Stampfel, Lukasz M Boryń, Daniel Gerlach, Martina Rath, Alexander Stark. Genome Res 2014
Times Cited: 84







List of co-cited articles
869 articles co-cited >1



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
507
42

Transcriptional enhancers: from properties to genome-wide predictions.
Daria Shlyueva, Gerald Stampfel, Alexander Stark. Nat Rev Genet 2014
718
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
25



Transcription factors: from enhancer binding to developmental control.
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
133
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
231
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
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
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
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
169
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
312
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
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
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
354
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
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
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
13

Modification of enhancer chromatin: what, how, and why?
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
779
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
376
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
135
11

Genome-wide mapping of in vivo protein-DNA interactions.
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
242
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
11

FIMO: scanning for occurrences of a given motif.
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
261
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
998
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
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
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
62
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
842
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
75
12


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
10

DEEP: a general computational framework for predicting enhancers.
Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B Bajic. Nucleic Acids Res 2015
64
14

VISTA Enhancer Browser--a database of tissue-specific human enhancers.
Axel Visel, Simon Minovitsky, Inna Dubchak, Len A Pennacchio. Nucleic Acids Res 2007
636
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
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
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
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
686
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
861
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
171
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
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
81
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
68
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
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
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
332
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.