A citation-based method for searching scientific literature

Peter Kindgren, Maxim Ivanov, Sebastian Marquardt. Nucleic Acids Res 2020
Times Cited: 40







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



Times Cited
  Times     Co-cited
Similarity


RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis.
Jiafu Zhu, Min Liu, Xiaobin Liu, Zhicheng Dong. Nat Plants 2018
74
55

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
35

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing.
Takayuki Nojima, Tomás Gomes, Ana Rita Fialho Grosso, Hiroshi Kimura, Michael J Dye, Somdutta Dhir, Maria Carmo-Fonseca, Nicholas J Proudfoot. Cell 2015
316
32

Organismal benefits of transcription speed control at gene boundaries.
Xueyuan Leng, Maxim Ivanov, Peter Kindgren, Indranil Malik, Axel Thieffry, Peter Brodersen, Albin Sandelin, Craig D Kaplan, Sebastian Marquardt. EMBO Rep 2020
17
76

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.
Quentin Angelo Thomas, Ryan Ard, Jinghan Liu, Bingnan Li, Jingwen Wang, Vicent Pelechano, Sebastian Marquardt. Nat Commun 2020
21
57


Transcription-driven chromatin repression of Intragenic transcription start sites.
Mathias Nielsen, Ryan Ard, Xueyuan Leng, Maxim Ivanov, Peter Kindgren, Vicent Pelechano, Sebastian Marquardt. PLoS Genet 2019
41
27

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target.
Szymon Swiezewski, Fuquan Liu, Andreas Magusin, Caroline Dean. Nature 2009
540
27

Nascent RNA sequencing reveals distinct features in plant transcription.
Jonathan Hetzel, Sascha H Duttke, Christopher Benner, Joanne Chory. Proc Natl Acad Sci U S A 2016
91
27

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.
Matthew T Parker, Katarzyna Knop, Anna V Sherwood, Nicholas J Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Jw Hall, Geoffrey J Barton, Gordon G Simpson. Elife 2020
147
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
22

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
22

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.
Andreas Mayer, Julia di Iulio, Seth Maleri, Umut Eser, Jeff Vierstra, Alex Reynolds, Richard Sandstrom, John A Stamatoyannopoulos, L Stirling Churchman. Cell 2015
218
20

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores.
Heather L Drexler, Karine Choquet, L Stirling Churchman. Mol Cell 2020
75
20

TT-seq maps the human transient transcriptome.
Björn Schwalb, Margaux Michel, Benedikt Zacher, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur, Patrick Cramer. Science 2016
227
20

Nascent transcript sequencing visualizes transcription at nucleotide resolution.
L Stirling Churchman, Jonathan S Weissman. Nature 2011
545
20

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation.
Micaela A Godoy Herz, M Guillermina Kubaczka, Grzegorz Brzyżek, Lucas Servi, Michal Krzyszton, Craig Simpson, John Brown, Szymon Swiezewski, Ezequiel Petrillo, Alberto R Kornblihtt. Mol Cell 2019
51
17

A chromatin-based mechanism for limiting divergent noncoding transcription.
Sebastian Marquardt, Renan Escalante-Chong, Nam Pho, Jue Wang, L Stirling Churchman, Michael Springer, Stephen Buratowski. Cell 2014
75
17

Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
Hojoong Kwak, Nicholas J Fuda, Leighton J Core, John T Lis. Science 2013
443
17

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
17


Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA.
Xinyue Zhao, Jingrui Li, Bi Lian, Hanqing Gu, Yan Li, Yijun Qi. Nat Commun 2018
121
17


Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants.
Jinbu Jia, Yanping Long, Hong Zhang, Zhuowen Li, Zhijian Liu, Yan Zhao, Dongdong Lu, Xianhao Jin, Xian Deng, Rui Xia,[...]. Nat Plants 2020
35
20

Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways.
Axel Thieffry, Maria Louisa Vigh, Jette Bornholdt, Maxim Ivanov, Peter Brodersen, Albin Sandelin. Plant Cell 2020
24
29


Getting up to speed with transcription elongation by RNA polymerase II.
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
480
15

Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor.
Zhi-Wei Wang, Zhe Wu, Oleg Raitskin, Qianwen Sun, Caroline Dean. Proc Natl Acad Sci U S A 2014
67
15

Dealing with pervasive transcription.
Torben Heick Jensen, Alain Jacquier, Domenico Libri. Mol Cell 2013
186
15

Born to run: control of transcription elongation by RNA polymerase II.
Fei Xavier Chen, Edwin R Smith, Ali Shilatifard. Nat Rev Mol Cell Biol 2018
179
15


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
15

Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs.
Shaofang Li, Yuan Wang, Yonghui Zhao, Xinjie Zhao, Xuemei Chen, Zhizhong Gong. Mol Plant 2020
18
33

The Features and Regulation of Co-transcriptional Splicing in Arabidopsis.
Danling Zhu, Fei Mao, Yuanchun Tian, Xiaoya Lin, Lianfeng Gu, Hongya Gu, Li-Jia Qu, Yufeng Wu, Zhe Wu. Mol Plant 2020
29
20

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.
Takayuki Nojima, Kenny Rebelo, Tomás Gomes, Ana Rita Grosso, Nicholas J Proudfoot, Maria Carmo-Fonseca. Mol Cell 2018
68
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

Pause & go: from the discovery of RNA polymerase pausing to its functional implications.
Andreas Mayer, Heather M Landry, L Stirling Churchman. Curr Opin Cell Biol 2017
68
12

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
12

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
12

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors.
Wojciech Antosz, Alexander Pfab, Hans F Ehrnsberger, Philipp Holzinger, Karin Köllen, Simon A Mortensen, Astrid Bruckmann, Thomas Schubert, Gernot Längst, Joachim Griesenbeck,[...]. Plant Cell 2017
69
12



A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription.
Xueyuan Leng, Quentin Thomas, Simon Horskjær Rasmussen, Sebastian Marquardt. Trends Plant Sci 2020
14
35

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome.
Cristiane P G Calixto, Wenbin Guo, Allan B James, Nikoleta A Tzioutziou, Juan Carlos Entizne, Paige E Panter, Heather Knight, Hugh G Nimmo, Runxuan Zhang, John W S Brown. Plant Cell 2018
129
12


RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis.
Wanlu Liu, Sascha H Duttke, Jonathan Hetzel, Martin Groth, Suhua Feng, Javier Gallego-Bartolome, Zhenhui Zhong, Hsuan Yu Kuo, Zonghua Wang, Jixian Zhai,[...]. Nat Plants 2018
57
12


Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.
Jules Deforges, Rodrigo S Reis, Philippe Jacquet, Shaoline Sheppard, Veerendra P Gadekar, Gene Hart-Smith, Andrea Tanzer, Ivo L Hofacker, Christian Iseli, Ioannis Xenarios,[...]. Plant Physiol 2019
24
20

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis.
Huan Wang, Pil Joong Chung, Jun Liu, In-Cheol Jang, Michelle J Kean, Jun Xu, Nam-Hai Chua. Genome Res 2014
221
12

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


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.