A citation-based method for searching scientific literature

Sarfraz Shafiq, Chunli Chen, Jing Yang, Lingling Cheng, Fei Ma, Emilie Widemann, Qianwen Sun. Mol Plant 2017
Times Cited: 28







List of co-cited articles
174 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
57

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
57

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
46

R loops: new modulators of genome dynamics and function.
José M Santos-Pereira, Andrés Aguilera. Nat Rev Genet 2015
432
42

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
42

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
39

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
39

Nascent Connections: R-Loops and Chromatin Patterning.
Frédéric Chédin. Trends Genet 2016
119
28

A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation.
Vanessa M Conn, Véronique Hugouvieux, Aditya Nayak, Stephanie A Conos, Giovanna Capovilla, Gökhan Cildir, Agnès Jourdain, Vinay Tergaonkar, Markus Schmid, Chloe Zubieta,[...]. Nat Plants 2017
272
28

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
38


Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.
Yujia A Chan, Maria J Aristizabal, Phoebe Y T Lu, Zongli Luo, Akil Hamza, Michael S Kobor, Peter C Stirling, Philip Hieter. PLoS Genet 2014
155
25

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation.
Lamia Wahba, Lorenzo Costantino, Frederick J Tan, Anjali Zimmer, Douglas Koshland. Genes Dev 2016
155
25


GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination.
Paul A Ginno, Yoong Wearn Lim, Paul L Lott, Ian Korf, Frédéric Chédin. Genome Res 2013
222
21

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
21

R loops: from transcription byproducts to threats to genome stability.
Andrés Aguilera, Tatiana García-Muse. Mol Cell 2012
617
21

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
21

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
21

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships.
Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey Jeddeloh, Cristina Montagna, Aaron Golden,[...]. Epigenetics Chromatin 2015
92
17

R-loops induce repressive chromatin marks over mammalian gene terminators.
Konstantina Skourti-Stathaki, Kinga Kamieniarz-Gdula, Nicholas J Proudfoot. Nature 2014
231
17

Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination.
Konstantina Skourti-Stathaki, Nicholas J Proudfoot, Natalia Gromak. Mol Cell 2011
480
17

Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids.
S J Boguslawski, D E Smith, M A Michalak, K E Mickelson, C O Yehle, W L Patterson, R J Carrico. J Immunol Methods 1986
270
17

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
17


R-Loops as Cellular Regulators and Genomic Threats.
Madzia P Crossley, Michael Bocek, Karlene A Cimprich. Mol Cell 2019
287
17

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
14

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
14

Transcription as a Threat to Genome Integrity.
Hélène Gaillard, Andrés Aguilera. Annu Rev Biochem 2016
110
14

Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.
Stephan Hamperl, Michael J Bocek, Joshua C Saldivar, Tomek Swigut, Karlene A Cimprich. Cell 2017
274
14

R-loop: an emerging regulator of chromatin dynamics.
Qais Al-Hadid, Yanzhong Yang. Acta Biochim Biophys Sin (Shanghai) 2016
18
22

R Loops: From Physiological to Pathological Roles.
Tatiana García-Muse, Andrés Aguilera. Cell 2019
209
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

R loops regulate promoter-proximal chromatin architecture and cellular differentiation.
Poshen B Chen, Hsiuyi V Chen, Diwash Acharya, Oliver J Rando, Thomas G Fazzio. Nat Struct Mol Biol 2015
93
14


Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
10


Breaking bad: R-loops and genome integrity.
Julie Sollier, Karlene A Cimprich. Trends Cell Biol 2015
209
10

Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation.
Zhi-Ping Wang, Hui-Li Xing, Li Dong, Hai-Yan Zhang, Chun-Yan Han, Xue-Chen Wang, Qi-Jun Chen. Genome Biol 2015
483
10

The Yin and Yang of R-loop biology.
Lorenzo Costantino, Douglas Koshland. Curr Opin Cell Biol 2015
86
10

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
10

Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair.
Corina Ohle, Rafael Tesorero, Géza Schermann, Nikolay Dobrev, Irmgard Sinning, Tamás Fischer. Cell 2016
233
10

Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.
Christopher Grunseich, Isabel X Wang, Jason A Watts, Joshua T Burdick, Robert D Guber, Zhengwei Zhu, Alan Bruzel, Tyler Lanman, Kelian Chen, Alice B Schindler,[...]. Mol Cell 2018
89
10

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.
Liang Chen, Jia-Yu Chen, Xuan Zhang, Ying Gu, Rui Xiao, Changwei Shao, Peng Tang, Hao Qian, Daji Luo, Hairi Li,[...]. Mol Cell 2017
164
10

Hybridization of RNA to double-stranded DNA: formation of R-loops.
M Thomas, R L White, R W Davis. Proc Natl Acad Sci U S A 1976
364
10

Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
10


Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis.
Kevin S Lang, Ashley N Hall, Christopher N Merrikh, Mark Ragheb, Hannah Tabakh, Alex J Pollock, Joshua J Woodward, Julia E Dreifus, Houra Merrikh. Cell 2017
123
10

m6A promotes R-loop formation to facilitate transcription termination.
Xin Yang, Qian-Lan Liu, Wei Xu, Yi-Chang Zhang, Ying Yang, Lin-Fang Ju, Jing Chen, Yu-Sheng Chen, Kuan Li, Jie Ren,[...]. Cell Res 2019
57
10

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
10


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.