A citation-based method for searching scientific literature

Seychelle M Vos, Lucas Farnung, Marc Boehning, Christoph Wigge, Andreas Linden, Henning Urlaub, Patrick Cramer. Nature 2018
Times Cited: 185







List of co-cited articles
1566 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Structure of paused transcription complex Pol II-DSIF-NELF.
Seychelle M Vos, Lucas Farnung, Henning Urlaub, Patrick Cramer. Nature 2018
158
48


Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
Seychelle M Vos, Lucas Farnung, Andreas Linden, Henning Urlaub, Patrick Cramer. Nat Struct Mol Biol 2020
45
71

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
186
28

Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Carrie Bernecky, Jürgen M Plitzko, Patrick Cramer. Nat Struct Mol Biol 2017
83
28

RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II.
Ming Yu, Wenjing Yang, Ting Ni, Zhanyun Tang, Tomoyoshi Nakadai, Jun Zhu, Robert G Roeder. Science 2015
134
23

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release.
Yuki Aoi, Edwin R Smith, Avani P Shah, Emily J Rendleman, Stacy A Marshall, Ashley R Woodfin, Fei X Chen, Ramin Shiekhattar, Ali Shilatifard. Mol Cell 2020
56
41


CDK9-dependent RNA polymerase II pausing controls transcription initiation.
Saskia Gressel, Björn Schwalb, Tim Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer. Elife 2017
114
22

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II.
Fei Xavier Chen, Ashley R Woodfin, Alessandro Gardini, Ryan A Rickels, Stacy A Marshall, Edwin R Smith, Ramin Shiekhattar, Ali Shilatifard. Cell 2015
128
20

P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation.
Tomoko Yamada, Yuki Yamaguchi, Naoto Inukai, Sachiko Okamoto, Takashi Mura, Hiroshi Handa. Mol Cell 2006
260
20


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
20

Paf1C regulates RNA polymerase II progression by modulating elongation rate.
Liming Hou, Yating Wang, Yu Liu, Nan Zhang, Ilya Shamovsky, Evgeny Nudler, Bin Tian, Brian David Dynlacht. Proc Natl Acad Sci U S A 2019
44
43

c-Myc regulates transcriptional pause release.
Peter B Rahl, Charles Y Lin, Amy C Seila, Ryan A Flynn, Scott McCuine, Christopher B Burge, Phillip A Sharp, Richard A Young. Cell 2010
918
18

DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.
T Wada, T Takagi, Y Yamaguchi, A Ferdous, T Imai, S Hirose, S Sugimoto, K Yano, G A Hartzog, F Winston,[...]. Genes Dev 1998
566
18

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism.
Michael A Cortazar, Ryan M Sheridan, Benjamin Erickson, Nova Fong, Kira Glover-Cutter, Kristopher Brannan, David L Bentley. Mol Cell 2019
68
26

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence.
Takayuki Nojima, Michael Tellier, Jonathan Foxwell, Claudia Ribeiro de Almeida, Sue Mei Tan-Wong, Somdutta Dhir, Gwendal Dujardin, Ashish Dhir, Shona Murphy, Nick J Proudfoot. Mol Cell 2018
94
19

A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II.
Pabitra K Parua, Gregory T Booth, Miriam Sansó, Bradley Benjamin, Jason C Tanny, John T Lis, Robert P Fisher. Nature 2018
67
25


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
325
17


Getting up to speed with transcription elongation by RNA polymerase II.
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
489
17

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
232
17

NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.
Y Yamaguchi, T Takagi, T Wada, K Yano, A Furuya, S Sugimoto, J Hasegawa, H Handa. Cell 1999
608
16

Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination.
Kai-Lieh Huang, David Jee, Chad B Stein, Nathan D Elrod, Telmo Henriques, Lauren G Mascibroda, David Baillat, William K Russell, Karen Adelman, Eric J Wagner. Mol Cell 2020
51
31

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II.
Pabitra K Parua, Sampada Kalan, Bradley Benjamin, Miriam Sansó, Robert P Fisher. Nat Commun 2020
24
66

Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase.
Hai Zheng, Yilun Qi, Shibin Hu, Xuan Cao, Congling Xu, Zhinang Yin, Xizi Chen, Yan Li, Weida Liu, Jie Li,[...]. Science 2020
42
38

Paused RNA polymerase II inhibits new transcriptional initiation.
Wanqing Shao, Julia Zeitlinger. Nat Genet 2017
122
15


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
15

PAF1 regulation of promoter-proximal pause release via enhancer activation.
Fei Xavier Chen, Peng Xie, Clayton K Collings, Kaixiang Cao, Yuki Aoi, Stacy A Marshall, Emily J Rendleman, Michal Ugarenko, Patrick A Ozark, Anda Zhang,[...]. Science 2017
61
22


The RNA polymerase II carboxy-terminal domain (CTD) code.
Dirk Eick, Matthias Geyer. Chem Rev 2013
275
14

Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals.
Telmo Henriques, Daniel A Gilchrist, Sergei Nechaev, Michael Bern, Ginger W Muse, Adam Burkholder, David C Fargo, Karen Adelman. Mol Cell 2013
147
14

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
451
14

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
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

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
14

Structure of transcribing RNA polymerase II-nucleosome complex.
Lucas Farnung, Seychelle M Vos, Patrick Cramer. Nat Commun 2018
51
25

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Haruhiko Ehara, Tomoya Kujirai, Yuka Fujino, Mikako Shirouzu, Hitoshi Kurumizaka, Shun-Ichi Sekine. Science 2019
81
16

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates.
Miriam Sansó, Rebecca S Levin, Jesse J Lipp, Vivien Ya-Fan Wang, Ann Katrin Greifenberg, Elizabeth M Quezada, Akbar Ali, Animesh Ghosh, Stéphane Larochelle, Tariq M Rana,[...]. Genes Dev 2016
79
16

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.
Arnaud R Krebs, Dilek Imanci, Leslie Hoerner, Dimos Gaidatzis, Lukas Burger, Dirk Schübeler. Mol Cell 2017
96
13

Structure and mechanism of the RNA polymerase II transcription machinery.
Allison C Schier, Dylan J Taatjes. Genes Dev 2020
93
13

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes.
Nathan D Elrod, Telmo Henriques, Kai-Lieh Huang, Deirdre C Tatomer, Jeremy E Wilusz, Eric J Wagner, Karen Adelman. Mol Cell 2019
77
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
13

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer.
Stephin J Vervoort, Sarah A Welsh, Jennifer R Devlin, Elisa Barbieri, Deborah A Knight, Sarah Offley, Stefan Bjelosevic, Matteo Costacurta, Izabela Todorovski, Conor J Kearney,[...]. Cell 2021
33
39

Structure of the complete elongation complex of RNA polymerase II with basal factors.
Haruhiko Ehara, Takeshi Yokoyama, Hideki Shigematsu, Shigeyuki Yokoyama, Mikako Shirouzu, Shun-Ichi Sekine. Science 2017
100
12

Widespread transcriptional pausing and elongation control at enhancers.
Telmo Henriques, Benjamin S Scruggs, Michiko O Inouye, Ginger W Muse, Lucy H Williams, Adam B Burkholder, Christopher A Lavender, David C Fargo, Karen Adelman. Genes Dev 2018
181
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.