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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.