A citation-based method for searching scientific literature

E Wingender, P Dietze, H Karas, R Knüppel. Nucleic Acids Res 1996
Times Cited: 616







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



Times Cited
  Times     Co-cited
Similarity


JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
Anthony Mathelier, Oriol Fornes, David J Arenillas, Chih-Yu Chen, Grégoire Denay, Jessica Lee, Wenqiang Shi, Casper Shyr, Ge Tan, Rebecca Worsley-Hunt,[...]. Nucleic Acids Res 2016
600
14

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
Albin Sandelin, Wynand Alkema, Pär Engström, Wyeth W Wasserman, Boris Lenhard. Nucleic Acids Res 2004
990
12


MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
10

MATCH: A tool for searching transcription factor binding sites in DNA sequences.
A E Kel, E Gössling, I Reuter, E Cheremushkin, O V Kel-Margoulis, E Wingender. Nucleic Acids Res 2003
737
9

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
9

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
V Matys, O V Kel-Margoulis, E Fricke, I Liebich, S Land, A Barre-Dirrie, I Reuter, D Chekmenev, M Krull, K Hornischer,[...]. Nucleic Acids Res 2006
8

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
8

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
7

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
7

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan,[...]. Nucleic Acids Res 2018
521
7


Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
6

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
6

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Anthony Mathelier, Xiaobei Zhao, Allen W Zhang, François Parcy, Rebecca Worsley-Hunt, David J Arenillas, Sorana Buchman, Chih-yu Chen, Alice Chou, Hans Ienasescu,[...]. Nucleic Acids Res 2014
719
5

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
5

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
5

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.
Elodie Portales-Casamar, Supat Thongjuea, Andrew T Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W Wasserman, Albin Sandelin. Nucleic Acids Res 2010
443
5

MatInspector and beyond: promoter analysis based on transcription factor binding sites.
K Cartharius, K Frech, K Grote, B Klocke, M Haltmeier, A Klingenhoff, M Frisch, M Bayerlein, T Werner. Bioinformatics 2005
5

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
5

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey. Nat Biotechnol 2015
649
5


STRING v10: protein-protein interaction networks, integrated over the tree of life.
Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi P Tsafou,[...]. Nucleic Acids Res 2015
5

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
5

Sequence logos: a new way to display consensus sequences.
T D Schneider, R M Stephens. Nucleic Acids Res 1990
5


High-resolution profiling of histone methylations in the human genome.
Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao. Cell 2007
4

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.
Maxwell A Hume, Luis A Barrera, Stephen S Gisselbrecht, Martha L Bulyk. Nucleic Acids Res 2015
138
4

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
4

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
4

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
Roger Pique-Regi, Jacob F Degner, Athma A Pai, Daniel J Gaffney, Yoav Gilad, Jonathan K Pritchard. Genome Res 2011
332
4



GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
4

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
4

Genome-wide mapping of in vivo protein-DNA interactions.
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
4

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
4

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
4

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
4

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
297
4

Expression-based monitoring of transcription factor activity: the TELiS database.
Steve W Cole, Weihong Yan, Zoran Galic, Jesusa Arevalo, Jerome A Zack. Bioinformatics 2005
112
4

Annotation of functional variation in personal genomes using RegulomeDB.
Alan P Boyle, Eurie L Hong, Manoj Hariharan, Yong Cheng, Marc A Schaub, Maya Kasowski, Konrad J Karczewski, Julie Park, Benjamin C Hitz, Shuai Weng,[...]. Genome Res 2012
4


Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
C E Lawrence, S F Altschul, M S Boguski, J S Liu, A F Neuwald, J C Wootton. Science 1993
800
4

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
4

Determination and inference of eukaryotic transcription factor sequence specificity.
Matthew T Weirauch, Ally Yang, Mihai Albu, Atina G Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S Najafabadi, Samuel A Lambert, Ishminder Mann, Kate Cook,[...]. Cell 2014
600
4

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin. Nucleic Acids Res 2008
502
4

TRANSFAC: transcriptional regulation, from patterns to profiles.
V Matys, E Fricke, R Geffers, E Gössling, M Haubrock, R Hehl, K Hornischer, D Karas, A E Kel, O V Kel-Margoulis,[...]. Nucleic Acids Res 2003
4

PROMO: detection of known transcription regulatory elements using species-tailored searches.
Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M Mar Albà. Bioinformatics 2002
736
4

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
3


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.