A citation-based method for searching scientific literature

Tassa Saldi, Nova Fong, David L Bentley. Genes Dev 2018
Times Cited: 36







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



Times Cited
  Times     Co-cited
Similarity



Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Vahid Aslanzadeh, Yuanhua Huang, Guido Sanguinetti, Jean D Beggs. Genome Res 2018
53
25

How slow RNA polymerase II elongation favors alternative exon skipping.
Gwendal Dujardin, Celina Lafaille, Manuel de la Mata, Luciano E Marasco, Manuel J Muñoz, Catherine Le Jossic-Corcos, Laurent Corcos, Alberto R Kornblihtt. Mol Cell 2014
135
25

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
169
22

Nascent transcript sequencing visualizes transcription at nucleotide resolution.
L Stirling Churchman, Jonathan S Weissman. Nature 2011
545
22

Birth and Death of Histone mRNAs.
William F Marzluff, Kaitlin P Koreski. Trends Genet 2017
88
19

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.
Artur Veloso, Killeen S Kirkconnell, Brian Magnuson, Benjamin Biewen, Michelle T Paulsen, Thomas E Wilson, Mats Ljungman. Genome Res 2014
158
19

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate.
Nova Fong, Hyunmin Kim, Yu Zhou, Xiong Ji, Jinsong Qiu, Tassa Saldi, Katrina Diener, Ken Jones, Xiang-Dong Fu, David L Bentley. Genes Dev 2014
164
19


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
19

RNA folding during transcription.
Tao Pan, Tobin Sosnick. Annu Rev Biophys Biomol Struct 2006
167
16

A slow RNA polymerase II affects alternative splicing in vivo.
Manuel de la Mata, Claudio R Alonso, Sebastián Kadener, Juan P Fededa, Matías Blaustein, Federico Pelisch, Paula Cramer, David Bentley, Alberto R Kornblihtt. Mol Cell 2003
497
16

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
16

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
216
16



Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.
William F Marzluff, Eric J Wagner, Robert J Duronio. Nat Rev Genet 2008
484
13

FLASH, a proapoptotic protein involved in activation of caspase-8, is essential for 3' end processing of histone pre-mRNAs.
Xiao-Cui Yang, Brandon D Burch, Yan Yan, William F Marzluff, Zbigniew Dominski. Mol Cell 2009
99
13


RNA structure maps across mammalian cellular compartments.
Lei Sun, Furqan M Fazal, Pan Li, James P Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T Kool, Howard Y Chang, Qiangfeng Cliff Zhang. Nat Struct Mol Biol 2019
99
13

Influence of RNA secondary structure on the pre-mRNA splicing process.
Emanuele Buratti, Francisco E Baralle. Mol Cell Biol 2004
298
13

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation.
Joanna Y Ip, Dominic Schmidt, Qun Pan, Arun K Ramani, Andrew G Fraser, Duncan T Odom, Benjamin J Blencowe. Genome Res 2011
177
13

DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation.
Manuel J Muñoz, M Soledad Pérez Santangelo, Maria P Paronetto, Manuel de la Mata, Federico Pelisch, Stéphanie Boireau, Kira Glover-Cutter, Claudia Ben-Dov, Matías Blaustein, Juan J Lozano,[...]. Cell 2009
227
13

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.
Laura Williamson, Marco Saponaro, Stefan Boeing, Philip East, Richard Mitter, Theodoros Kantidakis, Gavin P Kelly, Anna Lobley, Jane Walker, Bradley Spencer-Dene,[...]. Cell 2017
108
13

The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.
J Kenneth Wickiser, Wade C Winkler, Ronald R Breaker, Donald M Crothers. Mol Cell 2005
336
13

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
Hagen Tilgner, David G Knowles, Rory Johnson, Carrie A Davis, Sudipto Chakrabortty, Sarah Djebali, João Curado, Michael Snyder, Thomas R Gingeras, Roderic Guigó. Genome Res 2012
296
13

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.
Yevgenia L Khodor, Joseph Rodriguez, Katharine C Abruzzi, Chih-Hang Anthony Tang, Michael T Marr, Michael Rosbash. Genes Dev 2011
181
13

Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Fernando Carrillo Oesterreich, Stephan Preibisch, Karla M Neugebauer. Mol Cell 2010
185
13

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.
Fernando Carrillo Oesterreich, Lydia Herzel, Korinna Straube, Katja Hujer, Jonathon Howard, Karla M Neugebauer. Cell 2016
122
13

Splicing-dependent RNA polymerase pausing in yeast.
Ross D Alexander, Steven A Innocente, J David Barrass, Jean D Beggs. Mol Cell 2010
194
13

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
Hannes Braberg, Huiyan Jin, Erica A Moehle, Yujia A Chan, Shuyi Wang, Michael Shales, Joris J Benschop, John H Morris, Chenxi Qiu, Fuqu Hu,[...]. Cell 2013
101
13

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
Adam Ameur, Ammar Zaghlool, Jonatan Halvardson, Anna Wetterbom, Ulf Gyllensten, Lucia Cavelier, Lars Feuk. Nat Struct Mol Biol 2011
204
13

Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.
T Pan, I Artsimovitch, X W Fang, R Landick, T R Sosnick. Proc Natl Acad Sci U S A 1999
111
13

Cotranscriptional folding of a riboswitch at nucleotide resolution.
Kyle E Watters, Eric J Strobel, Angela M Yu, John T Lis, Julius B Lucks. Nat Struct Mol Biol 2016
92
11

NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs.
Takashi Narita, Tetsu M C Yung, Junichi Yamamoto, Yasunori Tsuboi, Hideyuki Tanabe, Kiyoji Tanaka, Yuki Yamaguchi, Hiroshi Handa. Mol Cell 2007
166
11

Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex.
Dazhi Tan, William F Marzluff, Zbigniew Dominski, Liang Tong. Science 2013
80
11

Knockdown of SLBP results in nuclear retention of histone mRNA.
Kelly D Sullivan, Thomas E Mullen, William F Marzluff, Eric J Wagner. RNA 2009
68
11


Getting up to speed with transcription elongation by RNA polymerase II.
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
480
11

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells.
Gilad Fuchs, Yoav Voichek, Sima Benjamin, Shlomit Gilad, Ido Amit, Moshe Oren. Genome Biol 2014
96
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

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
11

A decade of riboswitches.
Alexander Serganov, Evgeny Nudler. Cell 2013
641
11

Mimicking Co-Transcriptional RNA Folding Using a Superhelicase.
Boyang Hua, Subrata Panja, Yanbo Wang, Sarah A Woodson, Taekjip Ha. J Am Chem Soc 2018
28
14

Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing.
Robert J Sims, Scott Millhouse, Chi-Fu Chen, Brian A Lewis, Hediye Erdjument-Bromage, Paul Tempst, James L Manley, Danny Reinberg. Mol Cell 2007
414
11



Nucleosome positioning as a determinant of exon recognition.
Hagen Tilgner, Christoforos Nikolaou, Sonja Althammer, Michael Sammeth, Miguel Beato, Juan Valcárcel, Roderic Guigó. Nat Struct Mol Biol 2009
324
11

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing.
Tassa Saldi, Michael A Cortazar, Ryan M Sheridan, David L Bentley. J Mol Biol 2016
143
11

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue.
Kevin M Harlen, Kristine L Trotta, Erin E Smith, Mohammad M Mosaheb, Stephen M Fuchs, L Stirling Churchman. Cell Rep 2016
79
11


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.