A citation-based method for searching scientific literature

Gary Dixon, Heng Pan, Dapeng Yang, Bess P Rosen, Therande Jashari, Nipun Verma, Julian Pulecio, Inbal Caspi, Kihyun Lee, Stephanie Stransky, Abigail Glezer, Chang Liu, Marco Rivas, Ritu Kumar, Yahui Lan, Ingrid Torregroza, Chuan He, Simone Sidoli, Todd Evans, Olivier Elemento, Danwei Huangfu. Science 2021
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


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
50

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
37

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape.
Daniel N Weinberg, Simon Papillon-Cavanagh, Haifen Chen, Yuan Yue, Xiao Chen, Kartik N Rajagopalan, Cynthia Horth, John T McGuire, Xinjing Xu, Hamid Nikbakht,[...]. Nature 2019
123
25

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.
Xiaotian Zhang, Mira Jeong, Xingfan Huang, Xue Qing Wang, Xinyu Wang, Wanding Zhou, Muhammad S Shamim, Haley Gore, Pamela Himadewi, Yushuai Liu,[...]. Mol Cell 2020
18
25

Paradoxical association of TET loss of function with genome-wide DNA hypomethylation.
Isaac F López-Moyado, Ageliki Tsagaratou, Hiroshi Yuita, Hyungseok Seo, Benjamin Delatte, Sven Heinz, Christopher Benner, Anjana Rao. Proc Natl Acad Sci U S A 2019
31
25

Dynamic DNA methylation across diverse human cell lines and tissues.
Katherine E Varley, Jason Gertz, Kevin M Bowling, Stephanie L Parker, Timothy E Reddy, Florencia Pauli-Behn, Marie K Cross, Brian A Williams, John A Stamatoyannopoulos, Gregory E Crawford,[...]. Genome Res 2013
443
25


TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers.
Jocelyn Charlton, Eunmi J Jung, Alexandra L Mattei, Nina Bailly, Jing Liao, Eric J Martin, Pay Giesselmann, Björn Brändl, Elena K Stamenova, Franz-Josef Müller,[...]. Nat Genet 2020
24
25

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
725
25

DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells.
Tianpeng Gu, Xueqiu Lin, Sean M Cullen, Min Luo, Mira Jeong, Marcos Estecio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su,[...]. Genome Biol 2018
60
12

Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation.
Delphine Douillet, Christie C Sze, Caila Ryan, Andrea Piunti, Avani P Shah, Michal Ugarenko, Stacy A Marshall, Emily J Rendleman, Didi Zha, Kathryn A Helmin,[...]. Nat Genet 2020
28
12

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice.
Gintarė Sendžikaitė, Courtney W Hanna, Kathleen R Stewart-Morgan, Elena Ivanova, Gavin Kelsey. Nat Commun 2019
36
12

Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.
Ting-Hai Xu, Minmin Liu, X Edward Zhou, Gangning Liang, Gongpu Zhao, H Eric Xu, Karsten Melcher, Peter A Jones. Nature 2020
17
12

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
Wei Xie, Matthew D Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W Whitaker, Shulan Tian, R David Hawkins, Danny Leung,[...]. Cell 2013
471
12

Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands.
Massimiliano Manzo, Joël Wirz, Christina Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki, Tuncay Baubec. EMBO J 2017
54
12

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.
Nipun Verma, Heng Pan, Louis C Doré, Abhijit Shukla, Qing V Li, Bobbie Pelham-Webb, Virginia Teijeiro, Federico González, Andrei Krivtsov, Chan-Jung Chang,[...]. Nat Genet 2018
88
12

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency.
Yael Costa, Junjun Ding, Thorold W Theunissen, Francesco Faiola, Timothy A Hore, Pavel V Shliaha, Miguel Fidalgo, Arven Saunders, Moyra Lawrence, Sabine Dietmann,[...]. Nature 2013
272
12

Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions.
Patricia Heyn, Clare V Logan, Adeline Fluteau, Rachel C Challis, Tatsiana Auchynnikava, Carol-Anne Martin, Joseph A Marsh, Francesca Taglini, Fiona Kilanowski, David A Parry,[...]. Nat Genet 2019
50
12

Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes.
Hao Wu, Volkan Coskun, Jifang Tao, Wei Xie, Weihong Ge, Kazuaki Yoshikawa, En Li, Yi Zhang, Yi Eve Sun. Science 2010
417
12

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
Tuncay Baubec, Daniele F Colombo, Christiane Wirbelauer, Juliane Schmidt, Lukas Burger, Arnaud R Krebs, Altuna Akalin, Dirk Schübeler. Nature 2015
344
12

Large conserved domains of low DNA methylation maintained by Dnmt3a.
Mira Jeong, Deqiang Sun, Min Luo, Yun Huang, Grant A Challen, Benjamin Rodriguez, Xiaotian Zhang, Lukas Chavez, Hui Wang, Rebecca Hannah,[...]. Nat Genet 2014
206
12

A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.
Qiang Song, Benjamin Decato, Elizabeth E Hong, Meng Zhou, Fang Fang, Jianghan Qu, Tyler Garvin, Michael Kessler, Jun Zhou, Andrew D Smith. PLoS One 2013
182
12

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate.
Jose Luis Sardina, Samuel Collombet, Tian V Tian, Antonio Gómez, Bruno Di Stefano, Clara Berenguer, Justin Brumbaugh, Ralph Stadhouders, Carolina Segura-Morales, Marta Gut,[...]. Cell Stem Cell 2018
28
12

Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming.
Inês Milagre, Thomas M Stubbs, Michelle R King, Julia Spindel, Fátima Santos, Felix Krueger, Martin Bachman, Anne Segonds-Pichon, Shankar Balasubramanian, Simon R Andrews,[...]. Cell Rep 2017
30
12

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.
Joseph M Zullo, Ignacio A Demarco, Roger Piqué-Regi, Daniel J Gaffney, Charles B Epstein, Chauncey J Spooner, Teresa R Luperchio, Bradley E Bernstein, Jonathan K Pritchard, Karen L Reddy,[...]. Cell 2012
288
12

Kaiso-deficient mice show resistance to intestinal cancer.
Anna Prokhortchouk, Owen Sansom, Jim Selfridge, Isabel M Caballero, Sergey Salozhin, Dana Aithozhina, Leandro Cerchietti, Fan Guo Meng, Leonard H Augenlicht, John M Mariadason,[...]. Mol Cell Biol 2006
120
12

Kaiso Gene Knockout Promotes Somatic Cell Reprogramming.
D S Kaplun, R E Fok, V S Korostina, E B Prokhortchouk, S V Zhenilo. Biochemistry (Mosc) 2019
2
50

Genome engineering using the CRISPR-Cas9 system.
F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
12

The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides.
Juliet M Daniel, Christopher M Spring, Howard C Crawford, Albert B Reynolds, Akeel Baig. Nucleic Acids Res 2002
176
12

DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation.
Jaqueline Loaeza-Loaeza, Adriana S Beltran, Daniel Hernández-Sotelo. Genes (Basel) 2020
4
25


VHL inactivation without hypoxia is sufficient to achieve genome hypermethylation.
Artem V Artemov, Nadezhda Zhigalova, Svetlana Zhenilo, Alexander M Mazur, Egor B Prokhortchouk. Sci Rep 2018
6
16

Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain.
Xiaopan Zuo, Jipo Sheng, Ho-Tak Lau, Carol M McDonald, Monica Andrade, Dana E Cullen, Fong T Bell, Michelina Iacovino, Michael Kyba, Guoliang Xu,[...]. J Biol Chem 2012
115
12

Dnmt1/Transcription factor interactions: an alternative mechanism of DNA methylation inheritance.
Eric Hervouet, François M Vallette, Pierre-François Cartron. Genes Cancer 2010
45
12

DNA Methylation in Memory Formation: Emerging Insights.
Frankie D Heyward, J David Sweatt. Neuroscientist 2015
44
12

Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding.
Sofia Gkountela, Francesc Castro-Giner, Barbara Maria Szczerba, Marcus Vetter, Julia Landin, Ramona Scherrer, Ilona Krol, Manuel C Scheidmann, Christian Beisel, Christian U Stirnimann,[...]. Cell 2019
291
12

Structural basis for Klf4 recognition of methylated DNA.
Yiwei Liu, Yusuf Olatunde Olanrewaju, Yu Zheng, Hideharu Hashimoto, Robert M Blumenthal, Xing Zhang, Xiaodong Cheng. Nucleic Acids Res 2014
60
12

[S100A3 is a new target gene of Kaiso in mouse skin].
N A Zhigalova, A S Sokolov, E B Prokhortchouk, S V Zhenilo. Mol Biol (Mosk) 2015
2
50

Kaiso mediates human ICR1 methylation maintenance and H19 transcriptional fine regulation.
Florian Bohne, David Langer, Ursula Martiné, Claudia S Eider, Regina Cencic, Matthias Begemann, Miriam Elbracht, Luzie Bülow, Thomas Eggermann, Ulrich Zechner,[...]. Clin Epigenetics 2016
8
12

DeSUMOylation switches Kaiso from activator to repressor upon hyperosmotic stress.
Svetlana Zhenilo, Igor Deyev, Ekaterina Litvinova, Nadezhda Zhigalova, Daria Kaplun, Alexey Sokolov, Alexander Mazur, Egor Prokhortchouk. Cell Death Differ 2018
8
12


Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women.
Blessing I Bassey-Archibong, Shawn M Hercules, Lyndsay G A Rayner, Desiree H A Skeete, Suzanne P Smith Connell, Ian Brain, Adetola Daramola, Adekunbiola A F Banjo, Jung S Byun, Kevin Gardner,[...]. Cancer Causes Control 2017
10
12

The dimeric ectodomain of the alkali-sensing insulin receptor-related receptor (ectoIRR) has a droplike shape.
Eleonora V Shtykova, Maxim V Petoukhov, Andrey A Mozhaev, Igor E Deyev, Liubov A Dadinova, Nikita A Loshkarev, Alexander S Goryashchenko, Eduard V Bocharov, Cy M Jeffries, Dmitri I Svergun,[...]. J Biol Chem 2019
4
25

Comparative transcriptomics of primary cells in vertebrates.
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S Young, Robin Andersson, Erik Arner, Akira Hasegawa, Marina Lizio, Jordan A Ramilowski, Imad Abugessaisa,[...]. Genome Res 2020
6
16



Importance of epigenetic mechanisms in visceral pain induced by chronic water avoidance stress.
L Tran, A Chaloner, A H Sawalha, B Greenwood Van-Meerveld. Psychoneuroendocrinology 2013
79
12

Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation.
Eric Hervouet, François M Vallette, Pierre-François Cartron. Epigenetics 2009
143
12

A family of human zinc finger proteins that bind methylated DNA and repress transcription.
Guillaume J P Filion, Svetlana Zhenilo, Sergey Salozhin, Daisuke Yamada, Egor Prokhortchouk, Pierre-Antoine Defossez. Mol Cell Biol 2006
200
12

The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso.
Pierre-Antoine Defossez, Kevin F Kelly, Guillaume J P Filion, Roberto Pérez-Torrado, Frédérique Magdinier, Hervé Menoni, Curtis L Nordgaard, Juliet M Daniel, Eric Gilson. J Biol Chem 2005
63
12


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.