A citation-based method for searching scientific literature

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, Miao Yu, Julian Tonti-Filippini, Holger Heyn, Shijun Hu, Joseph C Wu, Anjana Rao, Manel Esteller, Chuan He, Fatemeh G Haghighi, Terrence J Sejnowski, M Margarita Behrens, Joseph R Ecker. Science 2013
Times Cited: 1066







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



Times Cited
  Times     Co-cited
Similarity


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
423
22


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
20

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval,[...]. Science 2017
186
18

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
17

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
16

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
13

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
315
13


The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
378
12

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
91
13

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
Shinsuke Ito, Li Shen, Qing Dai, Susan C Wu, Leonard B Collins, James A Swenberg, Chuan He, Yi Zhang. Science 2011
11


DNA-binding factors shape the mouse methylome at distal regulatory regions.
Michael B Stadler, Rabih Murr, Lukas Burger, Robert Ivanek, Florian Lienert, Anne Schöler, Erik van Nimwegen, Christiane Wirbelauer, Edward J Oakeley, Dimos Gaidatzis,[...]. Nature 2011
863
10



Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10


CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
10

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

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome.
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
299
10

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
66
15

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
10

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
10

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
10


Non-CG Methylation in the Human Genome.
Yupeng He, Joseph R Ecker. Annu Rev Genomics Hum Genet 2015
111
9

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
9

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
608
9

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
9

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
128
9

5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging.
Keith E Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Hao Wu, Qing Dai, Hasan Irier, Anup K Upadhyay, Marla Gearing, Allan I Levey,[...]. Nat Neurosci 2011
528
9

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation.
Amanda J Price, Leonardo Collado-Torres, Nikolay A Ivanov, Wei Xia, Emily E Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M Hyde,[...]. Genome Biol 2019
24
33

Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
8

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

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
149
8

Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Danny Leung, Nisha Rajagopal, Joseph R Nery, Mark A Urich, Huaming Chen,[...]. Nature 2015
338
8




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
8

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
7

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.
Lindsay F Rizzardi, Peter F Hickey, Varenka Rodriguez DiBlasi, Rakel Tryggvadóttir, Colin M Callahan, Adrian Idrizi, Kasper D Hansen, Andrew P Feinberg. Nat Neurosci 2019
50
14

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex.
Andrew E Jaffe, Yuan Gao, Amy Deep-Soboslay, Ran Tao, Thomas M Hyde, Daniel R Weinberger, Joel E Kleinman. Nat Neurosci 2016
239
7

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Qin, Peng Jin, Karen N Conneely. Nucleic Acids Res 2015
121
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

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
Wei Xie, Cathy L Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L Dempster, Bing Ren. Cell 2012
332
7

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA.
Yu-Fei He, Bin-Zhong Li, Zheng Li, Peng Liu, Yang Wang, Qingyu Tang, Jianping Ding, Yingying Jia, Zhangcheng Chen, Lin Li,[...]. Science 2011
7




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.