A citation-based method for searching scientific literature

Steven West, Natalia Gromak, Nick J Proudfoot. Nature 2004
Times Cited: 308







List of co-cited articles
1304 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
357
54

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
103
37


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
273
25

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
430
21

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
41


mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription.
Kris Brannan, Hyunmin Kim, Benjamin Erickson, Kira Glover-Cutter, Soojin Kim, Nova Fong, Lauren Kiemele, Kirk Hansen, Richard Davis, Jens Lykke-Andersen,[...]. Mol Cell 2012
139
19



Transcription termination by nuclear RNA polymerases.
Patricia Richard, James L Manley. Genes Dev 2009
226
15

Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.
Song Xiang, Amalene Cooper-Morgan, Xinfu Jiao, Megerditch Kiledjian, James L Manley, Liang Tong. Nature 2009
133
15



Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
Corey R Mandel, Syuzo Kaneko, Hailong Zhang, Damara Gebauer, Vasupradha Vethantham, James L Manley, Liang Tong. Nature 2006
288
15

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes.
Carlo Baejen, Jessica Andreani, Phillipp Torkler, Sofia Battaglia, Bjoern Schwalb, Michael Lidschreiber, Kerstin C Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger,[...]. Mol Cell 2017
59
25

RNA exosome depletion reveals transcription upstream of active human promoters.
Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen, Marianne S Christensen, Christophe K Mapendano, Mikkel H Schierup, Torben Heick Jensen. Science 2008
519
14

XRN2 Links Transcription Termination to DNA Damage and Replication Stress.
Julio C Morales, Patricia Richard, Praveen L Patidar, Edward A Motea, Tuyen T Dang, James L Manley, David A Boothman. PLoS Genet 2016
54
25

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13

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
177
13

Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II.
David Baillat, Mohamed-Ali Hakimi, Anders M Näär, Ali Shilatifard, Neil Cooch, Ramin Shiekhattar. Cell 2005
299
12


Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.
Evgenia Ntini, Aino I Järvelin, Jette Bornholdt, Yun Chen, Mette Boyd, Mette Jørgensen, Robin Andersson, Ilka Hoof, Aleks Schein, Peter R Andersen,[...]. Nat Struct Mol Biol 2013
178
12

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
12

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
652
12

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes.
Kira Glover-Cutter, Soojin Kim, Joaquin Espinosa, David L Bentley. Nat Struct Mol Biol 2008
235
12

Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.
Minkyu Kim, Seong-Hoon Ahn, Nevan J Krogan, Jack F Greenblatt, Stephen Buratowski. EMBO J 2004
243
12

XRN 5'→3' exoribonucleases: structure, mechanisms and functions.
Vinay K Nagarajan, Christopher I Jones, Sarah F Newbury, Pamela J Green. Biochim Biophys Acta 2013
185
12

Widespread Inducible Transcription Downstream of Human Genes.
Anna Vilborg, Maria C Passarelli, Therese A Yario, Kazimierz T Tycowski, Joan A Steitz. Mol Cell 2015
79
15

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
12

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
47
25

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
11

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
204
11

Promoter directionality is controlled by U1 snRNP and polyadenylation signals.
Albert E Almada, Xuebing Wu, Andrea J Kriz, Christopher B Burge, Phillip A Sharp. Nature 2013
267
11

Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae.
Ana G Rondón, Hannah E Mischo, Junya Kawauchi, Nick J Proudfoot. Mol Cell 2009
87
12

The RNA exosome promotes transcription termination of backtracked RNA polymerase II.
Jean-François Lemay, Marc Larochelle, Samuel Marguerat, Sophie Atkinson, Jürg Bähler, François Bachand. Nat Struct Mol Biol 2014
59
18

Co-transcriptional degradation of aberrant pre-mRNA by Xrn2.
Lee Davidson, Alastair Kerr, Steven West. EMBO J 2012
66
16


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

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
11

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot. Mol Cell 2017
108
11

Molecular architecture of the human pre-mRNA 3' processing complex.
Yongsheng Shi, Dafne Campigli Di Giammartino, Derek Taylor, Ali Sarkeshik, William J Rice, John R Yates, Joachim Frank, James L Manley. Mol Cell 2009
353
11


Bidirectional promoters generate pervasive transcription in yeast.
Zhenyu Xu, Wu Wei, Julien Gagneur, Fabiana Perocchi, Sandra Clauder-Münster, Jurgi Camblong, Elisa Guffanti, Françoise Stutz, Wolfgang Huber, Lars M Steinmetz. Nature 2009
656
10

R loops: from transcription byproducts to threats to genome stability.
Andrés Aguilera, Tatiana García-Muse. Mol Cell 2012
569
10

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.
Elodie Hatchi, Konstantina Skourti-Stathaki, Steffen Ventz, Luca Pinello, Angela Yen, Kinga Kamieniarz-Gdula, Stoil Dimitrov, Shailja Pathania, Kristine M McKinney, Matthew L Eaton,[...]. Mol Cell 2015
217
10

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
258
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.