A citation-based method for searching scientific literature

Galit Lev Maor, Ahuvi Yearim, Gil Ast. Trends Genet 2015
Times Cited: 255







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



Times Cited
  Times     Co-cited
Similarity



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
626
17

HP1 is involved in regulating the global impact of DNA methylation on alternative splicing.
Ahuvi Yearim, Sahar Gelfman, Ronna Shayevitch, Shai Melcer, Ohad Glaich, Jan-Philipp Mallm, Malka Nissim-Rafinia, Ayelet-Hashahar S Cohen, Karsten Rippe, Eran Meshorer,[...]. Cell Rep 2015
120
16


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12



CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
9

Conserved role of intragenic DNA methylation in regulating alternative promoters.
Alika K Maunakea, Raman P Nagarajan, Mikhail Bilenky, Tracy J Ballinger, Cletus D'Souza, Shaun D Fouse, Brett E Johnson, Chibo Hong, Cydney Nielsen, Yongjun Zhao,[...]. Nature 2010
9

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
708
9

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
959
8

Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2.
Juan I Young, Eugene P Hong, John C Castle, Juan Crespo-Barreto, Aaron B Bowman, Matthew F Rose, Dongcheul Kang, Ron Richman, Jason M Johnson, Susan Berget,[...]. Proc Natl Acad Sci U S A 2005
313
8

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
8

Epigenetics in alternative pre-mRNA splicing.
Reini F Luco, Mariano Allo, Ignacio E Schor, Alberto R Kornblihtt, Tom Misteli. Cell 2011
510
8

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
8

The importance of DNA methylation of exons on alternative splicing.
Ronna Shayevitch, Dan Askayo, Ifat Keydar, Gil Ast. RNA 2018
41
19

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.
Shihao Shen, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D Henry, Ying Nian Wu, Qing Zhou, Yi Xing. Proc Natl Acad Sci U S A 2014
631
7

Global epigenomic reconfiguration during mammalian brain development.
Ryan Lister, Eran A Mukamel, Joseph R Nery, Mark Urich, Clare A Puddifoot, Nicholas D Johnson, Jacinta Lucero, Yun Huang, Andrew J Dwork, Matthew D Schultz,[...]. Science 2013
7

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
7

Gene body methylation can alter gene expression and is a therapeutic target in cancer.
Xiaojing Yang, Han Han, Daniel D De Carvalho, Fides D Lay, Peter A Jones, Gangning Liang. Cancer Cell 2014
575
7


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
7

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
6

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
683
6

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
6

Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
318
6

DNA Methylation Affects Gene Alternative Splicing in Plants: An Example from Rice.
Xutong Wang, Lanjuan Hu, Xiaofei Wang, Ning Li, Chunming Xu, Lei Gong, Bao Liu. Mol Plant 2016
37
16

Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Yimeng Yin, Ekaterina Morgunova, Arttu Jolma, Eevi Kaasinen, Biswajyoti Sahu, Syed Khund-Sayeed, Pratyush K Das, Teemu Kivioja, Kashyap Dave, Fan Zhong,[...]. Science 2017
388
6

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.
Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A Kibbe, Lifang Hou, Simon M Lin. BMC Bioinformatics 2010
997
6

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
6

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
6

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
965
6

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
6

DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
6

Transcription factors as readers and effectors of DNA methylation.
Heng Zhu, Guohua Wang, Jiang Qian. Nat Rev Genet 2016
231
6

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Martin J Aryee, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, Rafael A Irizarry. Bioinformatics 2014
6

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

The DNA methylation paradox.
P A Jones. Trends Genet 1999
458
6

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
236
6

Expansion of the eukaryotic proteome by alternative splicing.
Timothy W Nilsen, Brenton R Graveley. Nature 2010
5

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
5


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
273
5

Epigenetic programming by maternal behavior.
Ian C G Weaver, Nadia Cervoni, Frances A Champagne, Ana C D'Alessio, Shakti Sharma, Jonathan R Seckl, Sergiy Dymov, Moshe Szyf, Michael J Meaney. Nat Neurosci 2004
5


DNA methylation arrays as surrogate measures of cell mixture distribution.
Eugene Andres Houseman, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, Karl T Kelsey. BMC Bioinformatics 2012
5

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
5




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.