A citation-based method for searching scientific literature

Karla M Neugebauer. Cold Spring Harb Perspect Biol 2019
Times Cited: 39







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



Times Cited
  Times     Co-cited
Similarity


Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores.
Heather L Drexler, Karine Choquet, L Stirling Churchman. Mol Cell 2020
81
33


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
170
23


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
23

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Vahid Aslanzadeh, Yuanhua Huang, Guido Sanguinetti, Jean D Beggs. Genome Res 2018
53
20

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
20

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
20

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
20

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
17

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
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

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

Co-transcriptional splicing and the CTD code.
Noélia Custódio, Maria Carmo-Fonseca. Crit Rev Biochem Mol Biol 2016
31
22

Linking transcription, RNA polymerase II elongation and alternative splicing.
Luciana E Giono, Alberto R Kornblihtt. Biochem J 2020
13
53

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
15

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
15

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
15


Recursive splicing in long vertebrate genes.
Christopher R Sibley, Warren Emmett, Lorea Blazquez, Ana Faro, Nejc Haberman, Michael Briese, Daniah Trabzuni, Mina Ryten, Michael E Weale, John Hardy,[...]. Nature 2015
89
15

Transcription and splicing: A two-way street.
Michael Tellier, Isabella Maudlin, Shona Murphy. Wiley Interdiscip Rev RNA 2020
31
19

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

Spliceosome structure and function.
Cindy L Will, Reinhard Lührmann. Cold Spring Harb Perspect Biol 2011
966
12

Global donor and acceptor splicing site kinetics in human cells.
Leonhard Wachutka, Livia Caizzi, Julien Gagneur, Patrick Cramer. Elife 2019
26
19

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
12

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
12

Nascent transcript sequencing visualizes transcription at nucleotide resolution.
L Stirling Churchman, Jonathan S Weissman. Nature 2011
550
12

Expansion of the eukaryotic proteome by alternative splicing.
Timothy W Nilsen, Brenton R Graveley. Nature 2010
12

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.
Hui Y Xiong, Babak Alipanahi, Leo J Lee, Hannes Bretschneider, Daniele Merico, Ryan K C Yuen, Yimin Hua, Serge Gueroussov, Hamed S Najafabadi, Timothy R Hughes,[...]. Science 2015
634
12

Alternative splicing as a regulator of development and tissue identity.
Francisco E Baralle, Jimena Giudice. Nat Rev Mol Cell Biol 2017
548
12


Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.
Yang Eric Guo, John C Manteiga, Jonathan E Henninger, Benjamin R Sabari, Alessandra Dall'Agnese, Nancy M Hannett, Jan-Hendrik Spille, Lena K Afeyan, Alicia V Zamudio, Krishna Shrinivas,[...]. Nature 2019
271
12

Exon-Mediated Activation of Transcription Starts.
Ana Fiszbein, Keegan S Krick, Bridget E Begg, Christopher B Burge. Cell 2019
40
12

A splicing-dependent transcriptional checkpoint associated with prespliceosome formation.
Keerthi T Chathoth, J David Barrass, Shaun Webb, Jean D Beggs. Mol Cell 2014
67
12


The spliceosome: design principles of a dynamic RNP machine.
Markus C Wahl, Cindy L Will, Reinhard Lührmann. Cell 2009
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
12

RNA Splicing by the Spliceosome.
Max E Wilkinson, Clément Charenton, Kiyoshi Nagai. Annu Rev Biochem 2020
180
12


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
12

Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.
Berthold Kastner, Cindy L Will, Holger Stark, Reinhard Lührmann. Cold Spring Harb Perspect Biol 2019
90
12

Long-read sequencing of nascent RNA reveals coupling among RNA processing events.
Lydia Herzel, Korinna Straube, Karla M Neugebauer. Genome Res 2018
50
12

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
12


Widespread intron retention in mammals functionally tunes transcriptomes.
Ulrich Braunschweig, Nuno L Barbosa-Morais, Qun Pan, Emil N Nachman, Babak Alipanahi, Thomas Gonatopoulos-Pournatzis, Brendan Frey, Manuel Irimia, Benjamin J Blencowe. Genome Res 2014
387
12

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency.
Annita Louloupi, Evgenia Ntini, Thomas Conrad, Ulf Andersson Vang Ørom. Cell Rep 2018
103
10

Thiol-linked alkylation of RNA to assess expression dynamics.
Veronika A Herzog, Brian Reichholf, Tobias Neumann, Philipp Rescheneder, Pooja Bhat, Thomas R Burkard, Wiebke Wlotzka, Arndt von Haeseler, Johannes Zuber, Stefan L Ameres. Nat Methods 2017
200
10

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development.
Seth D Kasowitz, Jun Ma, Stephen J Anderson, N Adrian Leu, Yang Xu, Brian D Gregory, Richard M Schultz, P Jeremy Wang. PLoS Genet 2018
257
10

Splicing-dependent RNA polymerase pausing in yeast.
Ross D Alexander, Steven A Innocente, J David Barrass, Jean D Beggs. Mol Cell 2010
194
10

Prespliceosome structure provides insights into spliceosome assembly and regulation.
Clemens Plaschka, Pei-Chun Lin, Clément Charenton, Kiyoshi Nagai. Nature 2018
74
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.