A citation-based method for searching scientific literature

Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao. Cell 2007
Times Cited: 4475







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



Times Cited
  Times     Co-cited
Similarity


Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Tarjei S Mikkelsen, Manching Ku, David B Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, Pablo Alvarez, William Brockman, Tae-Kyung Kim, Richard P Koche,[...]. Nature 2007
24

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
17

Combinatorial patterns of histone acetylations and methylations in the human genome.
Zhibin Wang, Chongzhi Zang, Jeffrey A Rosenfeld, Dustin E Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q Zhang,[...]. Nat Genet 2008
17

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bradley E Bernstein, Tarjei S Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J Huebert, James Cuff, Ben Fry, Alex Meissner, Marius Wernig, Kathrin Plath,[...]. Cell 2006
16

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
15


Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
13

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
13

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
13

Genome-wide mapping of in vivo protein-DNA interactions.
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
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
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
11

The language of covalent histone modifications.
B D Strahl, C D Allis. Nature 2000
10


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

Active genes are tri-methylated at K4 of histone H3.
Helena Santos-Rosa, Robert Schneider, Andrew J Bannister, Julia Sherriff, Bradley E Bernstein, N C Tolga Emre, Stuart L Schreiber, Jane Mellor, Tony Kouzarides. Nature 2002
8

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
8

Writing, erasing and reading histone lysine methylations.
Kwangbeom Hyun, Jongcheol Jeon, Kihyun Park, Jaehoon Kim. Exp Mol Med 2017
333
8

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
8

Translating the histone code.
T Jenuwein, C D Allis. Science 2001
7

Histone demethylation mediated by the nuclear amine oxidase homolog LSD1.
Yujiang Shi, Fei Lan, Caitlin Matson, Peter Mulligan, Johnathan R Whetstine, Philip A Cole, Robert A Casero, Yang Shi. Cell 2004
7



The Encyclopedia of DNA elements (ENCODE): data portal update.
Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan,[...]. Nucleic Acids Res 2018
557
7

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
7

CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
264
7

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
7

A chromatin landmark and transcription initiation at most promoters in human cells.
Matthew G Guenther, Stuart S Levine, Laurie A Boyer, Rudolf Jaenisch, Richard A Young. Cell 2007
6

Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.
M Lachner, D O'Carroll, S Rea, K Mechtler, T Jenuwein. Nature 2001
6

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.
John L Rinn, Michael Kertesz, Jordon K Wang, Sharon L Squazzo, Xiao Xu, Samantha A Brugmann, L Henry Goodnough, Jill A Helms, Peggy J Farnham, Eran Segal,[...]. Cell 2007
6

The Polycomb complex PRC2 and its mark in life.
Raphaël Margueron, Danny Reinberg. Nature 2011
6

Role of histone H3 lysine 27 methylation in Polycomb-group silencing.
Ru Cao, Liangjun Wang, Hengbin Wang, Li Xia, Hediye Erdjument-Bromage, Paul Tempst, Richard S Jones, Yi Zhang. Science 2002
6

Dynamic regulation of nucleosome positioning in the human genome.
Dustin E Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao. Cell 2008
912
6



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
6


Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.
Kaifu Chen, Zhong Chen, Dayong Wu, Lili Zhang, Xueqiu Lin, Jianzhong Su, Benjamin Rodriguez, Yuanxin Xi, Zheng Xia, Xi Chen,[...]. Nat Genet 2015
151
5

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney,[...]. Nat Methods 2007
928
5


Histone modifications at human enhancers reflect global cell-type-specific gene expression.
Nathaniel D Heintzman, Gary C Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F Harp, Zhen Ye, Leonard K Lee, Rhona K Stuart, Christina W Ching,[...]. Nature 2009
5

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Joshua C Black, Capucine Van Rechem, Johnathan R Whetstine. Mol Cell 2012
609
5


ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Stephen G Landt, Georgi K Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E Bernstein, Peter Bickel, James B Brown, Philip Cayting,[...]. Genome Res 2012
5

Histone modification levels are predictive for gene expression.
Rosa Karlić, Ho-Ryun Chung, Julia Lasserre, Kristian Vlahovicek, Martin Vingron. Proc Natl Acad Sci U S A 2010
434
5

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification.
Wai Lim Ku, Kosuke Nakamura, Weiwu Gao, Kairong Cui, Gangqing Hu, Qingsong Tang, Bing Ni, Keji Zhao. Nat Methods 2019
68
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.