A citation-based method for searching scientific literature

Leah S VandenBosch, Kelsey Luu, Andrew E Timms, Shriya Challam, Yue Wu, Aaron Y Lee, Timothy J Cherry. Transl Vis Sci Technol 2022
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


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
100

A novel multi-alignment pipeline for high-throughput sequencing data.
Shunping Huang, James Holt, Chia-Yu Kao, Leonard McMillan, Wei Wang. Database (Oxford) 2014
26
100

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function.
Verena M Link, Sascha H Duttke, Hyun B Chun, Inge R Holtman, Emma Westin, Marten A Hoeksema, Yohei Abe, Dylan Skola, Casey E Romanoski, Jenhan Tao,[...]. Cell 2018
90
100


Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Zhihao Ding, Yunyun Ni, Sander W Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, Ian Dunham, Gregory E Crawford, Jason D Lieb,[...]. PLoS Genet 2014
34
100

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.
Qian Zhu, Nan Liu, Stuart H Orkin, Guo-Cheng Yuan. Genome Biol 2019
45
100

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
David N Arnosti, Meghana M Kulkarni. J Cell Biochem 2005
186
100

Genetic and epigenetic fine mapping of causal autoimmune disease variants.
Kyle Kai-How Farh, Alexander Marson, Jiang Zhu, Markus Kleinewietfeld, William J Housley, Samantha Beik, Noam Shoresh, Holly Whitton, Russell J H Ryan, Alexander A Shishkin,[...]. Nature 2015
100

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding.
Simon C Biddie, Sam John, Pete J Sabo, Robert E Thurman, Thomas A Johnson, R Louis Schiltz, Tina B Miranda, Myong-Hee Sung, Saskia Trump, Stafford L Lightman,[...]. Mol Cell 2011
326
100

AP-1: a double-edged sword in tumorigenesis.
Robert Eferl, Erwin F Wagner. Nat Rev Cancer 2003
100

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
100

A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.
Bei Wei, Arttu Jolma, Biswajyoti Sahu, Lukas M Orre, Fan Zhong, Fangjie Zhu, Teemu Kivioja, Inderpreet Sur, Janne Lehtiö, Minna Taipale,[...]. Nat Biotechnol 2018
13
100

Genome-wide identification and characterization of functional neuronal activity-dependent enhancers.
Athar N Malik, Thomas Vierbuchen, Martin Hemberg, Alex A Rubin, Emi Ling, Cameron H Couch, Hume Stroud, Ivo Spiegel, Kyle Kai-How Farh, David A Harmin,[...]. Nat Neurosci 2014
159
100

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot. Genome Biol 2015
842
100

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
100

The Genetics of Transcription Factor DNA Binding Variation.
Bart Deplancke, Daniel Alpern, Vincent Gardeux. Cell 2016
186
100

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.
Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R Kazane,[...]. Nat Genet 2017
248
100



Structural and functional insights into the TEAD-YAP complex in the Hippo signaling pathway.
Liming Chen, Portia Gloria Loh, Haiwei Song. Protein Cell 2010
43
100

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
100

M-CAT binding factor is related to the SV40 enhancer binding factor, TEF-1.
I K Farrance, J H Mar, C P Ordahl. J Biol Chem 1992
135
100

In pursuit of design principles of regulatory sequences.
Michal Levo, Eran Segal. Nat Rev Genet 2014
142
100

Origins of specificity in protein-DNA recognition.
Remo Rohs, Xiangshu Jin, Sean M West, Rohit Joshi, Barry Honig, Richard S Mann. Annu Rev Biochem 2010
569
100

Local sequence features that influence AP-1 cis-regulatory activity.
Hemangi G Chaudhari, Barak A Cohen. Genome Res 2018
11
100

The effect of micrococcal nuclease digestion on nucleosome positioning data.
Ho-Ryun Chung, Ilona Dunkel, Franziska Heise, Christian Linke, Sylvia Krobitsch, Ann E Ehrenhofer-Murray, Silke R Sperling, Martin Vingron. PLoS One 2010
89
100

Index and biological spectrum of human DNase I hypersensitive sites.
Wouter Meuleman, Alexander Muratov, Eric Rynes, Jessica Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Neri, Athanasios Teodosiadis,[...]. Nature 2020
71
100

Latent enhancers activated by stimulation in differentiated cells.
Renato Ostuni, Viviana Piccolo, Iros Barozzi, Sara Polletti, Alberto Termanini, Silvia Bonifacio, Alessia Curina, Elena Prosperini, Serena Ghisletti, Gioacchino Natoli. Cell 2013
519
100

Structural constraints in collaborative competition of transcription factors against the nucleosome.
Georgette Moyle-Heyrman, Hannah S Tims, Jonathan Widom. J Mol Biol 2011
44
100

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
100

The role of regulatory variation in complex traits and disease.
Frank W Albert, Leonid Kruglyak. Nat Rev Genet 2015
532
100

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.
Abdenour Soufi, Meilin Fernandez Garcia, Artur Jaroszewicz, Nebiyu Osman, Matteo Pellegrini, Kenneth S Zaret. Cell 2015
414
100

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
100

Single-molecule analysis of steroid receptor and cofactor action in living cells.
Ville Paakinaho, Diego M Presman, David A Ball, Thomas A Johnson, R Louis Schiltz, Peter Levitt, Davide Mazza, Tatsuya Morisaki, Tatiana S Karpova, Gordon L Hager. Nat Commun 2017
79
100

gkmSVM: an R package for gapped-kmer SVM.
Mahmoud Ghandi, Morteza Mohammad-Noori, Narges Ghareghani, Dongwon Lee, Levi Garraway, Michael A Beer. Bioinformatics 2016
73
100

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Emily S Wong, Bianca M Schmitt, Anastasiya Kazachenka, David Thybert, Aisling Redmond, Frances Connor, Tim F Rayner, Christine Feig, Anne C Ferguson-Smith, John C Marioni,[...]. Nat Commun 2017
33
100

Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.
Iros Barozzi, Marta Simonatto, Silvia Bonifacio, Lin Yang, Remo Rohs, Serena Ghisletti, Gioacchino Natoli. Mol Cell 2014
137
100

Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity.
Jelena Erceg, Timothy E Saunders, Charles Girardot, Damien P Devos, Lars Hufnagel, Eileen E M Furlong. PLoS Genet 2014
34
100

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
100

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.
Ozren Bogdanovic, Ana Fernandez-Miñán, Juan J Tena, Elisa de la Calle-Mustienes, Carmen Hidalgo, Ila van Kruysbergen, Simon J van Heeringen, Gert Jan C Veenstra, José Luis Gómez-Skarmeta. Genome Res 2012
156
100

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.
Shujun Ou, Weija Su, Yi Liao, Kapeel Chougule, Jireh R A Agda, Adam J Hellinga, Carlos Santiago Blanco Lugo, Tyler A Elliott, Doreen Ware, Thomas Peterson,[...]. Genome Biol 2019
172
100


Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Helena Kilpinen, Sebastian M Waszak, Andreas R Gschwind, Sunil K Raghav, Robert M Witwicki, Andrea Orioli, Eugenia Migliavacca, Michaël Wiederkehr, Maria Gutierrez-Arcelus, Nikolaos I Panousis,[...]. Science 2013
260
100

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability.
Ryan Rickels, Hans-Martin Herz, Christie C Sze, Kaixiang Cao, Marc A Morgan, Clayton K Collings, Maria Gause, Yoh-Hei Takahashi, Lu Wang, Emily J Rendleman,[...]. Nat Genet 2017
102
100


Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation.
Kristel M Dorighi, Tomek Swigut, Telmo Henriques, Natarajan V Bhanu, Benjamin S Scruggs, Nataliya Nady, Christopher D Still, Benjamin A Garcia, Karen Adelman, Joanna Wysocka. Mol Cell 2017
195
100

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.
Emma K Farley, Katrina M Olson, Wei Zhang, Daniel S Rokhsar, Michael S Levine. Proc Natl Acad Sci U S A 2016
80
100

Inducible chromatin priming is associated with the establishment of immunological memory in T cells.
Sarah L Bevington, Pierre Cauchy, Jason Piper, Elisabeth Bertrand, Naveen Lalli, Rebecca C Jarvis, Liam Niall Gilding, Sascha Ott, Constanze Bonifer, Peter N Cockerill. EMBO J 2016
68
100

Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.
Venkata Rajesh Yella, Devesh Bhimsaria, Debostuti Ghoshdastidar, José A Rodríguez-Martínez, Aseem Z Ansari, Manju Bansal. Nucleic Acids Res 2018
24
100

Accurate prediction of cell type-specific transcription factor binding.
Jens Keilwagen, Stefan Posch, Jan Grau. Genome Biol 2019
44
100


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.