A citation-based method for searching scientific literature

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
Times Cited: 170







List of co-cited articles
1414 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
499
46

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
137
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
325
26

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
149
25

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
24

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Vahid Aslanzadeh, Yuanhua Huang, Guido Sanguinetti, Jean D Beggs. Genome Res 2018
53
43

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
126
23



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
178
19


Alternative isoform regulation in human tissue transcriptomes.
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
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
161
18

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
172
17

Splicing-dependent RNA polymerase pausing in yeast.
Ross D Alexander, Steven A Innocente, J David Barrass, Jean D Beggs. Mol Cell 2010
194
17


Regulation of alternative splicing through coupling with transcription and chromatin structure.
Shiran Naftelberg, Ignacio E Schor, Gil Ast, Alberto R Kornblihtt. Annu Rev Biochem 2015
271
16

Chromatin organization marks exon-intron structure.
Schraga Schwartz, Eran Meshorer, Gil Ast. Nat Struct Mol Biol 2009
437
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
224
16

Getting up to speed with transcription elongation by RNA polymerase II.
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
489
15

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
182
15

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
Qun Pan, Ofer Shai, Leo J Lee, Brendan J Frey, Benjamin J Blencowe. Nat Genet 2008
15

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sanjeev Shukla, Ersen Kavak, Melissa Gregory, Masahiko Imashimizu, Bojan Shutinoski, Mikhail Kashlev, Philipp Oberdoerffer, Rickard Sandberg, Shalini Oberdoerffer. Nature 2011
676
14

Spliceosome structure and function.
Cindy L Will, Reinhard Lührmann. Cold Spring Harb Perspect Biol 2011
966
14

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
103
14

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

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
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
301
13




Rates of in situ transcription and splicing in large human genes.
Jarnail Singh, Richard A Padgett. Nat Struct Mol Biol 2009
309
12

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
328
12

Regulation of alternative splicing by histone modifications.
Reini F Luco, Qun Pan, Kaoru Tominaga, Benjamin J Blencowe, Olivia M Pereira-Smith, Tom Misteli. Science 2010
736
12

Epigenetics in alternative pre-mRNA splicing.
Reini F Luco, Mariano Allo, Ignacio E Schor, Alberto R Kornblihtt, Tom Misteli. Cell 2011
545
12

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
70
17

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes.
Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F Cáceres. EMBO J 2019
27
44

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
228
11

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing.
Ignacio E Schor, Nicolás Rascovan, Federico Pelisch, Mariano Alló, Alberto R Kornblihtt. Proc Natl Acad Sci U S A 2009
204
11

A splicing-dependent transcriptional checkpoint associated with prespliceosome formation.
Keerthi T Chathoth, J David Barrass, Shaun Webb, Jean D Beggs. Mol Cell 2014
67
16

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
11

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
52
21

The spliceosome: design principles of a dynamic RNP machine.
Markus C Wahl, Cindy L Will, Reinhard Lührmann. Cell 2009
11

The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing.
Yehuda Brody, Noa Neufeld, Nicole Bieberstein, Sebastien Z Causse, Eva-Maria Böhnlein, Karla M Neugebauer, Xavier Darzacq, Yaron Shav-Tal. PLoS Biol 2011
151
11

Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Fernando Carrillo Oesterreich, Stephan Preibisch, Karla M Neugebauer. Mol Cell 2010
185
11

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription.
S McCracken, N Fong, K Yankulov, S Ballantyne, G Pan, J Greenblatt, S D Patterson, M Wickens, D L Bentley. Nature 1997
736
11

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
207
11

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
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.