A citation-based method for searching scientific literature

Pengze Yan, Zunpeng Liu, Moshi Song, Zeming Wu, Wei Xu, Kuan Li, Qianzhao Ji, Si Wang, Xiaoqian Liu, Kaowen Yan, Concepcion Rodriguez Esteban, Weimin Ci, Juan Carlos Izpisua Belmonte, Wei Xie, Jie Ren, Weiqi Zhang, Qianwen Sun, Jing Qu, Guang-Hui Liu. Cell Rep 2020
Times Cited: 12







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



Times Cited
  Times     Co-cited
Similarity


R-Loops as Cellular Regulators and Genomic Threats.
Madzia P Crossley, Michael Bocek, Karlene A Cimprich. Mol Cell 2019
194
33

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
33

Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach.
Qingqing Yan, Emily J Shields, Roberto Bonasio, Kavitha Sarma. Cell Rep 2019
22
25

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
74
25

Regulatory R-loops as facilitators of gene expression and genome stability.
Christof Niehrs, Brian Luke. Nat Rev Mol Cell Biol 2020
71
25



R Loops: From Physiological to Pathological Roles.
Tatiana García-Muse, Andrés Aguilera. Cell 2019
130
25

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast.
Stella R Hartono, Amélie Malapert, Pénélope Legros, Pascal Bernard, Frédéric Chédin, Vincent Vanoosthuyse. J Mol Biol 2018
57
25

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
118
25

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
230
25

Human proteins that interact with RNA/DNA hybrids.
Isabel X Wang, Christopher Grunseich, Jennifer Fox, Joshua Burdick, Zhengwei Zhu, Niema Ravazian, Markus Hafner, Vivian G Cheung. Genome Res 2018
55
25

Single-cell omics in ageing: a young and growing field.
Xiaojuan He, Sebastian Memczak, Jing Qu, Juan Carlos Izpisua Belmonte, Guang-Hui Liu. Nat Metab 2020
16
16

Histone modifications at human enhancers reflect global cell-type-specific gene expression.
Nathaniel D Heintzman, Gary C Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F Harp, Zhen Ye, Leonard K Lee, Rhona K Stuart, Christina W Ching,[...]. Nature 2009
16


R-Loops Promote Antisense Transcription across the Mammalian Genome.
Sue Mei Tan-Wong, Somdutta Dhir, Nick J Proudfoot. Mol Cell 2019
44
16


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
432
16

RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases.
László Halász, Zsolt Karányi, Beáta Boros-Oláh, Tímea Kuik-Rózsa, Éva Sipos, Éva Nagy, Ágnes Mosolygó-L, Anett Mázló, Éva Rajnavölgyi, Gábor Halmos,[...]. Genome Res 2017
43
16

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2.
Vaibhav Bhatia, Sonia I Barroso, María L García-Rubio, Emanuela Tumini, Emilia Herrera-Moyano, Andrés Aguilera. Nature 2014
286
16

R loops: from transcription byproducts to threats to genome stability.
Andrés Aguilera, Tatiana García-Muse. Mol Cell 2012
574
16

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
436
16

R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1.
Jia-Yu Chen, Xuan Zhang, Xiang-Dong Fu, Liang Chen. Nat Protoc 2019
17
16

DNA Topoisomerase I differentially modulates R-loops across the human genome.
Stefano G Manzo, Stella R Hartono, Lionel A Sanz, Jessica Marinello, Sara De Biasi, Andrea Cossarizza, Giovanni Capranico, Frederic Chedin. Genome Biol 2018
58
16

qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide.
Magdalena P Crossley, Michael J Bocek, Stephan Hamperl, Tomek Swigut, Karlene A Cimprich. Nucleic Acids Res 2020
12
16

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
132
16


Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death.
Hui Jiang, Xiaoyu Xue, Swarupa Panda, Ajinkya Kawale, Richard M Hooy, Fengshan Liang, Jungsan Sohn, Patrick Sung, Nelson O Gekara. EMBO J 2019
75
16

Breaking bad: R-loops and genome integrity.
Julie Sollier, Karlene A Cimprich. Trends Cell Biol 2015
189
16

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
16

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome.
Yoong Wearn Lim, Lionel A Sanz, Xiaoqin Xu, Stella R Hartono, Frédéric Chédin. Elife 2015
92
16

Tight nuclear tethering of cGAS is essential for preventing autoreactivity.
Hannah E Volkman, Stephanie Cambier, Elizabeth E Gray, Daniel B Stetson. Elife 2019
78
16

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
240
16

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
16

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
16

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation.
Wenbo Li, Dimple Notani, Qi Ma, Bogdan Tanasa, Esperanza Nunez, Aaron Yun Chen, Daria Merkurjev, Jie Zhang, Kenneth Ohgi, Xiaoyuan Song,[...]. Nature 2013
586
16

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation.
Chen-Lin Hsieh, Teng Fei, Yiwen Chen, Tiantian Li, Yanfei Gao, Xiaodong Wang, Tong Sun, Christopher J Sweeney, Gwo-Shu Mary Lee, Shaoyong Chen,[...]. Proc Natl Acad Sci U S A 2014
207
16

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
16

The role of transcription in shaping the spatial organization of the genome.
Bas van Steensel, Eileen E M Furlong. Nat Rev Mol Cell Biol 2019
101
16

DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells.
Alessio De Magis, Stefano G Manzo, Marco Russo, Jessica Marinello, Rita Morigi, Olivier Sordet, Giovanni Capranico. Proc Natl Acad Sci U S A 2019
96
16

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites.
Alexy Promonet, Ismaël Padioleau, Yaqun Liu, Lionel Sanz, Anna Biernacka, Anne-Lyne Schmitz, Magdalena Skrzypczak, Amélie Sarrazin, Clément Mettling, Maga Rowicka,[...]. Nat Commun 2020
28
16

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
Leighton J Core, André L Martins, Charles G Danko, Colin T Waters, Adam Siepel, John T Lis. Nat Genet 2014
339
16

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
43
16

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
78
16

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor.
Kang Wang, Honghong Wang, Conghui Li, Zhinang Yin, Ruijing Xiao, Qiuzi Li, Ying Xiang, Wen Wang, Jian Huang, Liang Chen,[...]. Sci Adv 2021
7
28

G-quadruplex structures are stable and detectable in human genomic DNA.
Enid Yi Ni Lam, Dario Beraldi, David Tannahill, Shankar Balasubramanian. Nat Commun 2013
280
16

R Loops and Links to Human Disease.
Patricia Richard, James L Manley. J Mol Biol 2017
74
16

DNA double strand break repair, aging and the chromatin connection.
Vera Gorbunova, Andrei Seluanov. Mutat Res 2016
37
8

Artificial intelligence for aging and longevity research: Recent advances and perspectives.
Alex Zhavoronkov, Polina Mamoshina, Quentin Vanhaelen, Morten Scheibye-Knudsen, Alexey Moskalev, Alex Aliper. Ageing Res Rev 2019
42
8

Deciphering primate retinal aging at single-cell resolution.
Si Wang, Yuxuan Zheng, Qingqing Li, Xiaojuan He, Ruotong Ren, Weiqi Zhang, Moshi Song, Huifang Hu, Feifei Liu, Guoqiang Sun,[...]. Protein Cell 2021
4
25


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.