A citation-based method for searching scientific literature

Zhibin Wang, Chongzhi Zang, Jeffrey A Rosenfeld, Dustin E Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q Zhang, Keji Zhao. Nat Genet 2008
Times Cited: 1544







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



Times Cited
  Times     Co-cited
Similarity


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
32

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
24

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
22

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
19

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
17

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

Translating the histone code.
T Jenuwein, C D Allis. Science 2001
15


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
13

The language of covalent histone modifications.
B D Strahl, C D Allis. Nature 2000
11

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
11

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
11

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
9


Mapping and analysis of chromatin state dynamics in nine human cell types.
Jason Ernst, Pouya Kheradpour, Tarjei S Mikkelsen, Noam Shoresh, Lucas D Ward, Charles B Epstein, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael Coyne,[...]. Nature 2011
8

Writing, erasing and reading histone lysine methylations.
Kwangbeom Hyun, Jongcheol Jeon, Kihyun Park, Jaehoon Kim. Exp Mol Med 2017
381
8

The role of chromatin during transcription.
Bing Li, Michael Carey, Jerry L Workman. Cell 2007
8

Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.
Zhibin Wang, Chongzhi Zang, Kairong Cui, Dustin E Schones, Artem Barski, Weiqun Peng, Keji Zhao. Cell 2009
912
8

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
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
7

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

Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain.
Qin Feng, Hengbin Wang, Huck Hui Ng, Hediye Erdjument-Bromage, Paul Tempst, Kevin Struhl, Yi Zhang. Curr Biol 2002
569
7

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing.
Feng Tie, Rakhee Banerjee, Carl A Stratton, Jayashree Prasad-Sinha, Vincent Stepanik, Andrei Zlobin, Manuel O Diaz, Peter C Scacheri, Peter J Harte. Development 2009
334
7

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
7


Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
7

A unique chromatin signature uncovers early developmental enhancers in humans.
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
6

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
6

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
6

Genomic maps and comparative analysis of histone modifications in human and mouse.
Bradley E Bernstein, Michael Kamal, Kerstin Lindblad-Toh, Stefan Bekiranov, Dione K Bailey, Dana J Huebert, Scott McMahon, Elinor K Karlsson, Edward J Kulbokas, Thomas R Gingeras,[...]. Cell 2005
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

Histone lysine methyltransferases in biology and disease.
Dylan Husmann, Or Gozani. Nat Struct Mol Biol 2019
86
6

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
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

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

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
6

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
6


Understanding the language of Lys36 methylation at histone H3.
Eric J Wagner, Phillip B Carpenter. Nat Rev Mol Cell Biol 2012
540
6

Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
6

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
6


Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.
Kairong Cui, Chongzhi Zang, Tae-Young Roh, Dustin E Schones, Richard W Childs, Weiqun Peng, Keji Zhao. Cell Stem Cell 2009
453
5

A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin.
Gunnar Schotta, Monika Lachner, Kavitha Sarma, Anja Ebert, Roopsha Sengupta, Gunter Reuter, Danny Reinberg, Thomas Jenuwein. Genes Dev 2004
768
5

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
5

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
5

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
504
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.