A citation-based method for searching scientific literature

Congyao Xu, Zhe Wu, Hong-Chao Duan, Xiaofeng Fang, Guifang Jia, Caroline Dean. Nat Commun 2021
Times Cited: 24







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



Times Cited
  Times     Co-cited
Similarity


R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus.
Qianwen Sun, Tibor Csorba, Konstantina Skourti-Stathaki, Nicholas J Proudfoot, Caroline Dean. Science 2013
237
54

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA.
Federico Ariel, Leandro Lucero, Aurelie Christ, Maria Florencia Mammarella, Teddy Jegu, Alaguraj Veluchamy, Kiruthiga Mariappan, David Latrasse, Thomas Blein, Chang Liu,[...]. Mol Cell 2020
85
29

The R-loop is a common chromatin feature of the Arabidopsis genome.
Wei Xu, Hui Xu, Kuan Li, Yingxu Fan, Yang Liu, Xuerui Yang, Qianwen Sun. Nat Plants 2017
96
29

Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription.
Sebastian Marquardt, Oleg Raitskin, Zhe Wu, Fuquan Liu, Qianwen Sun, Caroline Dean. Mol Cell 2014
165
25


R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.
Paul A Ginno, Paul L Lott, Holly C Christensen, Ian Korf, Frédéric Chédin. Mol Cell 2012
491
25

Quantitative regulation of FLC via coordinated transcriptional initiation and elongation.
Zhe Wu, Robert Ietswaart, Fuquan Liu, Hongchun Yang, Martin Howard, Caroline Dean. Proc Natl Acad Sci U S A 2016
52
25

Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes.
Xiaofeng Fang, Liang Wang, Ryo Ishikawa, Yaoxi Li, Marc Fiedler, Fuquan Liu, Grant Calder, Beth Rowan, Detlef Weigel, Pilong Li,[...]. Nature 2019
94
25

Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing.
Fuquan Liu, Sebastian Marquardt, Clare Lister, Szymon Swiezewski, Caroline Dean. Science 2010
291
25


Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization.
Tibor Csorba, Julia I Questa, Qianwen Sun, Caroline Dean. Proc Natl Acad Sci U S A 2014
232
20

R-Loops as Cellular Regulators and Genomic Threats.
Madzia P Crossley, Michael Bocek, Karlene A Cimprich. Mol Cell 2019
287
20

The R-Loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli.
Wei Xu, Kuan Li, Shuai Li, Quancan Hou, Yushun Zhang, Kunpeng Liu, Qianwen Sun. Plant Cell 2020
32
20

The 3' processing of antisense RNAs physically links to chromatin-based transcriptional control.
Xiaofeng Fang, Zhe Wu, Oleg Raitskin, Kimberly Webb, Philipp Voigt, Tiancong Lu, Martin Howard, Caroline Dean. Proc Natl Acad Sci U S A 2020
21
23

The spen family protein FPA controls alternative cleavage and polyadenylation of RNA.
Csaba Hornyik, Lionel C Terzi, Gordon G Simpson. Dev Cell 2010
159
20


Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.
Federico Ariel, Teddy Jegu, David Latrasse, Natali Romero-Barrios, Aurélie Christ, Moussa Benhamed, Martin Crespi. Mol Cell 2014
209
16

PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR.
Yongke Tian, Han Zheng, Fei Zhang, Shiliang Wang, Xiaoru Ji, Chao Xu, Yuehui He, Yong Ding. Sci Adv 2019
52
16


ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis.
Wei Yuan, Jincong Zhou, Jinjin Tong, Wanqing Zhuo, Lishuan Wang, Yan Li, Qianwen Sun, Weiqiang Qian. Sci Adv 2019
23
17

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals.
Lionel A Sanz, Stella R Hartono, Yoong Wearn Lim, Sandra Steyaert, Aparna Rajpurkar, Paul A Ginno, Xiaoqin Xu, Frédéric Chédin. Mol Cell 2016
279
16

The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC.
Fuquan Liu, Victor Quesada, Pedro Crevillén, Isabel Bäurle, Szymon Swiezewski, Caroline Dean. Mol Cell 2007
219
16

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target.
Szymon Swiezewski, Fuquan Liu, Andreas Magusin, Caroline Dean. Nature 2009
540
16


A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization.
Pedro Crevillén, Cagla Sonmez, Zhe Wu, Caroline Dean. EMBO J 2013
110
16

mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana.
Susheel Sagar Bhat, Dawid Bielewicz, Tomasz Gulanicz, Zsuzsanna Bodi, Xiang Yu, Stephen J Anderson, Lukasz Szewc, Mateusz Bajczyk, Jakub Dolata, Natalia Grzelak,[...]. Proc Natl Acad Sci U S A 2020
36
16

N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis.
Lisha Shen, Zhe Liang, Xiaofeng Gu, Ying Chen, Zhi Wei Norman Teo, Xingliang Hou, Weiling Maggie Cai, Peter C Dedon, Lu Liu, Hao Yu. Dev Cell 2016
165
16

Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
528
12

A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves.
Hui-Wen Wu, Shulin Deng, Haiying Xu, Hui-Zhu Mao, Jun Liu, Qi-Wen Niu, Huan Wang, Nam-Hai Chua. New Phytol 2018
36
12

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation.
Peter Kindgren, Ryan Ard, Maxim Ivanov, Sebastian Marquardt. Nat Commun 2018
79
12

Modular function of long noncoding RNA, COLDAIR, in the vernalization response.
Dong-Hwan Kim, Yanpeng Xi, Sibum Sung. PLoS Genet 2017
64
12

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice.
Yuan Fang, Lifen Chen, Kande Lin, Yilong Feng, Pengyue Zhang, Xiucai Pan, Jennifer Sanders, Yufeng Wu, Xiu-E Wang, Zhen Su,[...]. Genome Res 2019
21
14

Regulatory R-loops as facilitators of gene expression and genome stability.
Christof Niehrs, Brian Luke. Nat Rev Mol Cell Biol 2020
139
12

RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts.
Zhuo Yang, Quancan Hou, Lingling Cheng, Wei Xu, Yantao Hong, Shuai Li, Qianwen Sun. Plant Cell 2017
41
12


R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells.
Kefei Yu, Frederic Chedin, Chih-Lin Hsieh, Thomas E Wilson, Michael R Lieber. Nat Immunol 2003
532
12

R loops: new modulators of genome dynamics and function.
José M Santos-Pereira, Andrés Aguilera. Nat Rev Genet 2015
432
12

R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes.
Konstantina Skourti-Stathaki, Elena Torlai Triglia, Marie Warburton, Philipp Voigt, Adrian Bird, Ana Pombo. Mol Cell 2019
49
12

R Loops: From Physiological to Pathological Roles.
Tatiana García-Muse, Andrés Aguilera. Cell 2019
209
12

DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice.
Sarfraz Shafiq, Chunli Chen, Jing Yang, Lingling Cheng, Fei Ma, Emilie Widemann, Qianwen Sun. Mol Plant 2017
28
12

GADD45A binds R-loops and recruits TET1 to CpG island promoters.
Khelifa Arab, Emil Karaulanov, Michael Musheev, Philipp Trnka, Andrea Schäfer, Ingrid Grummt, Christof Niehrs. Nat Genet 2019
99
12

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition.
Gordon G Simpson, Paul P Dijkwel, Victor Quesada, Ian Henderson, Caroline Dean. Cell 2003
274
12

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
12

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
12

Arabidopsis ARGONAUTE 1 Binds Chromatin to Promote Gene Transcription in Response to Hormones and Stresses.
Chang Liu, Ying Xin, Le Xu, Zhaokui Cai, Yuanchao Xue, Yong Liu, Daoxin Xie, Yule Liu, Yijun Qi. Dev Cell 2018
80
12

Antagonistic cotranscriptional regulation through ARGONAUTE1 and the THO/TREX complex orchestrates FLC transcriptional output.
Congyao Xu, Xiaofeng Fang, Tiancong Lu, Caroline Dean. Proc Natl Acad Sci U S A 2021
6
50

Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis.
Suhua Feng, Shawn J Cokus, Veit Schubert, Jixian Zhai, Matteo Pellegrini, Steven E Jacobsen. Mol Cell 2014
207
12

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.
Lejon E M Kralemann, Shujing Liu, Minerva S Trejo-Arellano, Rafael Muñoz-Viana, Claudia Köhler, Lars Hennig. Genome Biol 2020
14
21



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.