A citation-based method for searching scientific literature

Sarah A Peck, Katlyn D Hughes, Jose F Victorino, Amber L Mosley. Wiley Interdiscip Rev RNA 2019
Times Cited: 15







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



Times Cited
  Times     Co-cited
Similarity


The RNA polymerase II carboxy-terminal domain (CTD) code.
Dirk Eick, Matthias Geyer. Chem Rev 2013
251
33

The CTD code.
Stephen Buratowski. Nat Struct Biol 2003
251
26

Transcriptome surveillance by selective termination of noncoding RNA synthesis.
Daniel Schulz, Bjoern Schwalb, Anja Kiesel, Carlo Baejen, Phillipp Torkler, Julien Gagneur, Johannes Soeding, Patrick Cramer. Cell 2013
135
26


The pol II CTD: new twists in the tail.
Justyna Zaborowska, Sylvain Egloff, Shona Murphy. Nat Struct Mol Biol 2016
106
26


The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain.
Kevin M Harlen, L Stirling Churchman. Nat Rev Mol Cell Biol 2017
180
26

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition.
Nova Fong, Kristopher Brannan, Benjamin Erickson, Hyunmin Kim, Michael A Cortazar, Ryan M Sheridan, Tram Nguyen, Shai Karp, David L Bentley. Mol Cell 2015
104
20

Extensive degradation of RNA precursors by the exosome in wild-type cells.
Rajani Kanth Gudipati, Zhenyu Xu, Alice Lebreton, Bertrand Séraphin, Lars M Steinmetz, Alain Jacquier, Domenico Libri. Mol Cell 2012
166
20

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function.
Lydia Herzel, Diana S M Ottoz, Tara Alpert, Karla M Neugebauer. Nat Rev Mol Cell Biol 2017
140
20

The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.
Lidia Vasiljeva, Minkyu Kim, Hannes Mutschler, Stephen Buratowski, Anton Meinhart. Nat Struct Mol Biol 2008
205
20


Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3.
John T Arigo, Daniel E Eyler, Kristina L Carroll, Jeffry L Corden. Mol Cell 2006
204
20


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
125
20

Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.
Amber L Mosley, Samantha G Pattenden, Michael Carey, Swaminathan Venkatesh, Joshua M Gilmore, Laurence Florens, Jerry L Workman, Michael P Washburn. Mol Cell 2009
105
20

Uniform transitions of the general RNA polymerase II transcription complex.
Andreas Mayer, Michael Lidschreiber, Matthias Siebert, Kristin Leike, Johannes Söding, Patrick Cramer. Nat Struct Mol Biol 2010
326
20

The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome.
Dong-hyuk Heo, Inhea Yoo, Jiwon Kong, Michael Lidschreiber, Andreas Mayer, Byung-Yi Choi, Yoonsoo Hahn, Patrick Cramer, Stephen Buratowski, Minkyu Kim. J Biol Chem 2013
17
20



Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.
Bradley M Lunde, Steve L Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani. Nat Struct Mol Biol 2010
102
20

Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase.
Françoise Wyers, Mathieu Rougemaille, Gwenaël Badis, Jean-Claude Rousselle, Marie-Elisabeth Dufour, Jocelyne Boulay, Béatrice Régnault, Frédéric Devaux, Abdelkader Namane, Bertrand Séraphin,[...]. Cell 2005
653
20

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.
Minkyu Kim, Nevan J Krogan, Lidia Vasiljeva, Oliver J Rando, Eduard Nedea, Jack F Greenblatt, Stephen Buratowski. Nature 2004
358
20

CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II.
Andreas Mayer, Martin Heidemann, Michael Lidschreiber, Amelie Schreieck, Mai Sun, Corinna Hintermair, Elisabeth Kremmer, Dirk Eick, Patrick Cramer. Science 2012
171
20

RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7.
Amelie Schreieck, Ashley D Easter, Stefanie Etzold, Katrin Wiederhold, Michael Lidschreiber, Patrick Cramer, Lori A Passmore. Nat Struct Mol Biol 2014
50
20

Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity.
Karyn Schmidt, J Scott Butler. Wiley Interdiscip Rev RNA 2013
64
20


Molecular basis for coordinating transcription termination with noncoding RNA degradation.
Agnieszka Tudek, Odil Porrua, Tomasz Kabzinski, Michael Lidschreiber, Karel Kubicek, Andrea Fortova, François Lacroute, Stepanka Vanacova, Patrick Cramer, Richard Stefl,[...]. Mol Cell 2014
70
20


A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes.
Alain R Bataille, Célia Jeronimo, Pierre-Étienne Jacques, Louise Laramée, Marie-Ève Fortin, Audrey Forest, Maxime Bergeron, Steven D Hanes, François Robert. Mol Cell 2012
158
20

RNA degradation by the exosome is promoted by a nuclear polyadenylation complex.
John LaCava, Jonathan Houseley, Cosmin Saveanu, Elisabeth Petfalski, Elizabeth Thompson, Alain Jacquier, David Tollervey. Cell 2005
669
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20



Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts.
Romy Honorine, Christine Mosrin-Huaman, Nadège Hervouet-Coste, Domenico Libri, A Rachid Rahmouni. Nucleic Acids Res 2011
23
13

Pcf11 orchestrates transcription termination pathways in yeast.
Pawel Grzechnik, Michal Ryszard Gdula, Nick J Proudfoot. Genes Dev 2015
43
13

Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination.
Dane Z Hazelbaker, Sebastian Marquardt, Wiebke Wlotzka, Stephen Buratowski. Mol Cell 2013
76
13

Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest.
Baggavalli P Somesh, James Reid, Wei-Feng Liu, T Max M Søgaard, Hediye Erdjument-Bromage, Paul Tempst, Jesper Q Svejstrup. Cell 2005
174
13

Interaction profiling identifies the human nuclear exosome targeting complex.
Michal Lubas, Marianne S Christensen, Maiken S Kristiansen, Michal Domanski, Lasse G Falkenby, Søren Lykke-Andersen, Jens S Andersen, Andrzej Dziembowski, Torben Heick Jensen. Mol Cell 2011
260
13

Architecture of eukaryotic mRNA 3'-end processing machinery.
Ana Casañal, Ananthanarayanan Kumar, Chris H Hill, Ashley D Easter, Paul Emsley, Gianluca Degliesposti, Yuliya Gordiyenko, Balaji Santhanam, Jana Wolf, Katrin Wiederhold,[...]. Science 2017
68
13

Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin.
Lidia Vasiljeva, Minkyu Kim, Nihal Terzi, Luis M Soares, Stephen Buratowski. Mol Cell 2008
109
13


Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing.
Nuttara Jamonnak, Tyler J Creamer, Miranda M Darby, Paul Schaughency, Sarah J Wheelan, Jeffry L Corden. RNA 2011
71
13

Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1.
Karel Kubicek, Hana Cerna, Peter Holub, Josef Pasulka, Dominika Hrossova, Frank Loehr, Ctirad Hofr, Stepanka Vanacova, Richard Stefl. Genes Dev 2012
75
13

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
50
13

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice.
Rajani Kanth Gudipati, Tommaso Villa, Jocelyne Boulay, Domenico Libri. Nat Struct Mol Biol 2008
118
13

Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII.
Alexandre Wagschal, Emilie Rousset, Poornima Basavarajaiah, Xavier Contreras, Alex Harwig, Sabine Laurent-Chabalier, Mirai Nakamura, Xin Chen, Ke Zhang, Oussama Meziane,[...]. Cell 2012
124
13

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
198
13

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity.
Joshua D Eaton, Lee Davidson, David L V Bauer, Toyoaki Natsume, Masato T Kanemaki, Steven West. Genes Dev 2018
48
13

Dynamic turnover of paused Pol II complexes at human promoters.
Benjamin Erickson, Ryan M Sheridan, Michael Cortazar, David L Bentley. Genes Dev 2018
32
13


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.