A citation-based method for searching scientific literature

Michael-Christopher Keogh, Siavash K Kurdistani, Stephanie A Morris, Seong Hoon Ahn, Vladimir Podolny, Sean R Collins, Maya Schuldiner, Kayu Chin, Thanuja Punna, Natalie J Thompson, Charles Boone, Andrew Emili, Jonathan S Weissman, Timothy R Hughes, Brian D Strahl, Michael Grunstein, Jack F Greenblatt, Stephen Buratowski, Nevan J Krogan. Cell 2005
Times Cited: 597







List of co-cited articles
1483 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.
Michael J Carrozza, Bing Li, Laurence Florens, Tamaki Suganuma, Selene K Swanson, Kenneth K Lee, Wei-Jong Shia, Scott Anderson, John Yates, Michael P Washburn,[...]. Cell 2005
945
76


Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes.
Swaminathan Venkatesh, Michaela Smolle, Hua Li, Madelaine M Gogol, Malika Saint, Shambhu Kumar, Krishnamurthy Natarajan, Jerry L Workman. Nature 2012
220
30

A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation.
Kelby O Kizer, Hemali P Phatnani, Yoichiro Shibata, Hana Hall, Arno L Greenleaf, Brian D Strahl. Mol Cell Biol 2005
339
29

Understanding the language of Lys36 methylation at histone H3.
Eric J Wagner, Phillip B Carpenter. Nat Rev Mol Cell Biol 2012
597
24

Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression.
Brian D Strahl, Patrick A Grant, Scott D Briggs, Zu-Wen Sun, James R Bone, Jennifer A Caldwell, Sahana Mollah, Richard G Cook, Jeffrey Shabanowitz, Donald F Hunt,[...]. Mol Cell Biol 2002
419
24

The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II.
Bing Li, LeAnn Howe, Scott Anderson, John R Yates, Jerry L Workman. J Biol Chem 2003
278
22

Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway.
Ji Hyun Kim, Bo Bae Lee, Young Mi Oh, Chenchen Zhu, Lars M Steinmetz, Yookyeong Lee, Wan Kyu Kim, Sung Bae Lee, Stephen Buratowski, TaeSoo Kim. Nat Commun 2016
62
35

Genome-wide map of nucleosome acetylation and methylation in yeast.
Dmitry K Pokholok, Christopher T Harbison, Stuart Levine, Megan Cole, Nancy M Hannett, Tong Ihn Lee, George W Bell, Kimberly Walker, P Alex Rolfe, Elizabeth Herbolsheimer,[...]. Cell 2005
20

Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast.
Tiaojiang Xiao, Hana Hall, Kelby O Kizer, Yoichiro Shibata, Mark C Hall, Christoph H Borchers, Brian D Strahl. Genes Dev 2003
330
20

Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin.
Bing Li, Madelaine Gogol, Mike Carey, Daeyoup Lee, Chris Seidel, Jerry L Workman. Science 2007
244
20


Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes.
Chhabi K Govind, Hongfang Qiu, Daniel S Ginsburg, Chun Ruan, Kimberly Hofmeyer, Cuihua Hu, Venkatesh Swaminathan, Jerry L Workman, Bing Li, Alan G Hinnebusch. Mol Cell 2010
171
19

Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Nevan J Krogan, Minkyu Kim, Amy Tong, Ashkan Golshani, Gerard Cagney, Veronica Canadien, Dawn P Richards, Bryan K Beattie, Andrew Emili, Charles Boone,[...]. Mol Cell Biol 2003
504
19

Intragenic DNA methylation prevents spurious transcription initiation.
Francesco Neri, Stefania Rapelli, Anna Krepelova, Danny Incarnato, Caterina Parlato, Giulia Basile, Mara Maldotti, Francesca Anselmi, Salvatore Oliviero. Nature 2017
360
18



Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange.
Michaela Smolle, Swaminathan Venkatesh, Madelaine M Gogol, Hua Li, Ying Zhang, Laurence Florens, Michael P Washburn, Jerry L Workman. Nat Struct Mol Biol 2012
207
17



Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics.
TaeSoo Kim, Zhenyu Xu, Sandra Clauder-Münster, Lars M Steinmetz, Stephen Buratowski. Cell 2012
140
16

Shaping the cellular landscape with Set2/SETD2 methylation.
Stephen L McDaniel, Brian D Strahl. Cell Mol Life Sci 2017
74
20

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
15

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
15

Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription.
Bing Li, Madelaine Gogol, Mike Carey, Samantha G Pattenden, Chris Seidel, Jerry L Workman. Genes Dev 2007
147
15

Selective suppression of antisense transcription by Set2-mediated H3K36 methylation.
Swaminathan Venkatesh, Hua Li, Madelaine M Gogol, Jerry L Workman. Nat Commun 2016
44
34

Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome.
Vanessa Cheung, Gordon Chua, Nizar N Batada, Christian R Landry, Stephen W Michnick, Timothy R Hughes, Fred Winston. PLoS Biol 2008
216
14

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription.
Sílvia Carvalho, Ana Cláudia Raposo, Filipa Batalha Martins, Ana Rita Grosso, Sreerama Chaitanya Sridhara, José Rino, Maria Carmo-Fonseca, Sérgio Fernandes de Almeida. Nucleic Acids Res 2013
109
14

The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα.
Feng Li, Guogen Mao, Dan Tong, Jian Huang, Liya Gu, Wei Yang, Guo-Min Li. Cell 2013
388
14

The role of chromatin during transcription.
Bing Li, Michael Carey, Jerry L Workman. Cell 2007
14

High-resolution chromatin dynamics during a yeast stress response.
Assaf Weiner, Tsung-Han S Hsieh, Alon Appleboim, Hsiuyi V Chen, Ayelet Rahat, Ido Amit, Oliver J Rando, Nir Friedman. Mol Cell 2015
125
14

Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36.
Michael L Youdell, Kelby O Kizer, Elena Kisseleva-Romanova, Stephen M Fuchs, Eris Duro, Brian D Strahl, Jane Mellor. Mol Cell Biol 2008
117
13

Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes.
Andrew J Bannister, Robert Schneider, Fiona A Myers, Alan W Thorne, Colyn Crane-Robinson, Tony Kouzarides. J Biol Chem 2005
299
13

The language of covalent histone modifications.
B D Strahl, C D Allis. Nature 2000
13

Crystal structure of the nucleosome core particle at 2.8 A resolution.
K Luger, A W Mäder, R K Richmond, D F Sargent, T J Richmond. Nature 1997
13

Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription.
Bing Li, Jessica Jackson, Matthew D Simon, Brian Fleharty, Madelaine Gogol, Chris Seidel, Jerry L Workman, Ali Shilatifard. J Biol Chem 2009
118
12

High-resolution profiling of histone methylations in the human genome.
Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao. Cell 2007
12

DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes.
Simon Drouin, Louise Laramée, Pierre-Étienne Jacques, Audrey Forest, Maxime Bergeron, François Robert. PLoS Genet 2010
101
12

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
12

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
690
11



Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
11

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


H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity.
Stephen L McDaniel, Austin J Hepperla, Jie Huang, Raghuvar Dronamraju, Alexander T Adams, Vidyadhar G Kulkarni, Ian J Davis, Brian D Strahl. Cell Rep 2017
44
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
11


The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation.
Daniel Schaft, Assen Roguev, Kimberly M Kotovic, Anna Shevchenko, Mihail Sarov, Andrej Shevchenko, Karla M Neugebauer, A Francis Stewart. Nucleic Acids Res 2003
123
11

A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation.
Rajaraman Gopalakrishnan, Sharon K Marr, Robert E Kingston, Fred Winston. Nucleic Acids Res 2019
19
57


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.