A citation-based method for searching scientific literature

Harrison W Gabel, Benyam Kinde, Hume Stroud, Caitlin S Gilbert, David A Harmin, Nathaniel R Kastan, Martin Hemberg, Daniel H Ebert, Michael E Greenberg. Nature 2015
Times Cited: 318







List of co-cited articles
1090 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2.
R E Amir, I B Van den Veyver, M Wan, C Q Tran, U Francke, H Y Zoghbi. Nat Genet 1999
42

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
30

MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome.
Lin Chen, Kaifu Chen, Laura A Lavery, Steven Andrew Baker, Chad A Shaw, Wei Li, Huda Y Zoghbi. Proc Natl Acad Sci U S A 2015
158
27

MeCP2, a key contributor to neurological disease, activates and represses transcription.
Maria Chahrour, Sung Yun Jung, Chad Shaw, Xiaobo Zhou, Stephen T C Wong, Jun Qin, Huda Y Zoghbi. Science 2008
27

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.
Junjie U Guo, Yijing Su, Joo Heon Shin, Jaehoon Shin, Hongda Li, Bin Xie, Chun Zhong, Shaohui Hu, Thuc Le, Guoping Fan,[...]. Nat Neurosci 2014
439
26

Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor.
Matthew J Lyst, Robert Ekiert, Daniel H Ebert, Cara Merusi, Jakub Nowak, Jim Selfridge, Jacky Guy, Nathaniel R Kastan, Nathaniel D Robinson, Flavia de Lima Alves,[...]. Nat Neurosci 2013
221
24

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain.
Sabine Lagger, John C Connelly, Gabriele Schweikert, Shaun Webb, Jim Selfridge, Bernard H Ramsahoye, Miao Yu, Chuan He, Guido Sanguinetti, Lawrence C Sowers,[...]. PLoS Genet 2017
68
33

Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA.
J D Lewis, R R Meehan, W J Henzel, I Maurer-Fogy, P Jeppesen, F Klein, A Bird. Cell 1992
22

Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state.
Peter J Skene, Robert S Illingworth, Shaun Webb, Alastair R W Kerr, Keith D James, Daniel J Turner, Rob Andrews, Adrian P Bird. Mol Cell 2010
446
21

A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome.
J Guy, B Hendrich, M Holmes, J E Martin, A Bird. Nat Genet 2001
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
18

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
18

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
18

DNA methylation in the gene body influences MeCP2-mediated gene repression.
Benyam Kinde, Dennis Y Wu, Michael E Greenberg, Harrison W Gabel. Proc Natl Acad Sci U S A 2016
54
31

Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States.
Hume Stroud, Susan C Su, Sinisa Hrvatin, Alexander W Greben, William Renthal, Lisa D Boxer, M Aurel Nagy, Daniel R Hochbaum, Benyam Kinde, Harrison W Gabel,[...]. Cell 2017
96
17

Rett syndrome: a complex disorder with simple roots.
Matthew J Lyst, Adrian Bird. Nat Rev Genet 2015
190
17

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome.
Brian S Johnson, Ying-Tao Zhao, Maria Fasolino, Janine M Lamonica, Yoon Jung Kim, George Georgakilas, Kathleen H Wood, Daniel Bu, Yue Cui, Darren Goffin,[...]. Nat Med 2017
58
29

Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.
X Nan, H H Ng, C A Johnson, C D Laherty, B M Turner, R N Eisenman, A Bird. Nature 1998
16



MeCP2 Represses the Rate of Transcriptional Initiation of Highly Methylated Long Genes.
Lisa D Boxer, William Renthal, Alexander W Greben, Tess Whitwam, Andrew Silberfeld, Hume Stroud, Emmy Li, Marty G Yang, Benyam Kinde, Eric C Griffith,[...]. Mol Cell 2020
25
60

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2.
Benyam Kinde, Harrison W Gabel, Caitlin S Gilbert, Eric C Griffith, Michael E Greenberg. Proc Natl Acad Sci U S A 2015
134
14

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
14

Reversal of neurological defects in a mouse model of Rett syndrome.
Jacky Guy, Jian Gan, Jim Selfridge, Stuart Cobb, Adrian Bird. Science 2007
763
14

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.
Alisa Mo, Eran A Mukamel, Fred P Davis, Chongyuan Luo, Gilbert L Henry, Serge Picard, Mark A Urich, Joseph R Nery, Terrence J Sejnowski, Ryan Lister,[...]. Neuron 2015
341
13

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system.
Marian Mellén, Pinar Ayata, Scott Dewell, Skirmantas Kriaucionis, Nathaniel Heintz. Cell 2012
623
13

Topoisomerases facilitate transcription of long genes linked to autism.
Ian F King, Chandri N Yandava, Angela M Mabb, Jack S Hsiao, Hsien-Sung Huang, Brandon L Pearson, J Mauro Calabrese, Joshua Starmer, Joel S Parker, Terry Magnuson,[...]. Nature 2013
238
13

Dysfunction in GABA signalling mediates autism-like stereotypies and Rett syndrome phenotypes.
Hsiao-Tuan Chao, Hongmei Chen, Rodney C Samaco, Mingshan Xue, Maria Chahrour, Jong Yoo, Jeffrey L Neul, Shiaoching Gong, Hui-Chen Lu, Nathaniel Heintz,[...]. Nature 2010
770
13

The story of Rett syndrome: from clinic to neurobiology.
Maria Chahrour, Huda Y Zoghbi. Neuron 2007
823
13

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
322
13

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing.
William Renthal, Lisa D Boxer, Sinisa Hrvatin, Emmy Li, Andrew Silberfeld, M Aurel Nagy, Eric C Griffith, Thomas Vierbuchen, Michael E Greenberg. Nat Neurosci 2018
49
26


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

Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.
Ken Sugino, Chris M Hempel, Benjamin W Okaty, Hannah A Arnson, Saori Kato, Vardhan S Dani, Sacha B Nelson. J Neurosci 2014
85
14

Non-CG Methylation in the Human Genome.
Yupeng He, Joseph R Ecker. Annu Rev Genomics Hum Genet 2015
116
12

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
11

Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons.
Yun Li, Haoyi Wang, Julien Muffat, Albert W Cheng, David A Orlando, Jakob Lovén, Show-Ming Kwok, Danielle A Feldman, Helen S Bateup, Qing Gao,[...]. Cell Stem Cell 2013
196
11

Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.
Ayush T Raman, Amy E Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E Lowry, Huda Y Zoghbi, Zhandong Liu. Nat Commun 2018
23
47


Radically truncated MeCP2 rescues Rett syndrome-like neurological defects.
Rebekah Tillotson, Jim Selfridge, Martha V Koerner, Kamal K E Gadalla, Jacky Guy, Dina De Sousa, Ralph D Hector, Stuart R Cobb, Adrian Bird. Nature 2017
72
13


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
10

MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation.
Adam W Clemens, Dennis Y Wu, J Russell Moore, Diana L Christian, Guoyan Zhao, Harrison W Gabel. Mol Cell 2020
22
45

An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders.
Steven Andrew Baker, Lin Chen, Angela Dawn Wilkins, Peng Yu, Olivier Lichtarge, Huda Yahya Zoghbi. Cell 2013
146
10

Gene length matters in neurons.
Mark J Zylka, Jeremy M Simon, Benjamin D Philpot. Neuron 2015
54
16

The contribution of de novo coding mutations to autism spectrum disorder.
Ivan Iossifov, Brian J O'Roak, Stephan J Sanders, Michael Ronemus, Niklas Krumm, Dan Levy, Holly A Stessman, Kali T Witherspoon, Laura Vives, Karynne E Patterson,[...]. Nature 2014
9



edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells.
Maria C N Marchetto, Cassiano Carromeu, Allan Acab, Diana Yu, Gene W Yeo, Yangling Mu, Gong Chen, Fred H Gage, Alysson R Muotri. Cell 2010
885
9


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.