A citation-based method for searching scientific literature

Tarjei S Mikkelsen, Manching Ku, David B Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, Pablo Alvarez, William Brockman, Tae-Kyung Kim, Richard P Koche, William Lee, Eric Mendenhall, Aisling O'Donovan, Aviva Presser, Carsten Russ, Xiaohui Xie, Alexander Meissner, Marius Wernig, Rudolf Jaenisch, Chad Nusbaum, Eric S Lander, Bradley E Bernstein. Nature 2007
Times Cited: 2916







List of co-cited articles
989 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
37

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
32

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
18

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

Genome-wide mapping of in vivo protein-DNA interactions.
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
15

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
14

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
14

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
14


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
13

A double take on bivalent promoters.
Philipp Voigt, Wee-Wei Tee, Danny Reinberg. Genes Dev 2013
491
13


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

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
11

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
11

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
11

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
341
10


Translating the histone code.
T Jenuwein, C D Allis. Science 2001
10


Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Alexander Meissner, Tarjei S Mikkelsen, Hongcang Gu, Marius Wernig, Jacob Hanna, Andrey Sivachenko, Xiaolan Zhang, Bradley E Bernstein, Chad Nusbaum, David B Jaffe,[...]. Nature 2008
10

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
Manching Ku, Richard P Koche, Esther Rheinbay, Eric M Mendenhall, Mitsuhiro Endoh, Tarjei S Mikkelsen, Aviva Presser, Chad Nusbaum, Xiaohui Xie, Andrew S Chi,[...]. PLoS Genet 2008
723
9


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
937
9

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
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Genome Regulation by Polycomb and Trithorax: 70 Years and Counting.
Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli. Cell 2017
412
9

Chromatin signatures of pluripotent cell lines.
Véronique Azuara, Pascale Perry, Stephan Sauer, Mikhail Spivakov, Helle F Jørgensen, Rosalind M John, Mina Gouti, Miguel Casanova, Gary Warnes, Matthias Merkenschlager,[...]. Nat Cell Biol 2006
958
9

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
9

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
8

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
8

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

The Bivalent Genome: Characterization, Structure, and Regulation.
Enrique Blanco, Mar González-Ramírez, Anna Alcaine-Colet, Sergi Aranda, Luciano Di Croce. Trends Genet 2020
44
18

Role of the polycomb protein EED in the propagation of repressive histone marks.
Raphael Margueron, Neil Justin, Katsuhito Ohno, Miriam L Sharpe, Jinsook Son, William J Drury, Philipp Voigt, Stephen R Martin, William R Taylor, Valeria De Marco,[...]. Nature 2009
753
8

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8

PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes.
Zhonghua Gao, Jin Zhang, Roberto Bonasio, Francesco Strino, Ayana Sawai, Fabio Parisi, Yuval Kluger, Danny Reinberg. Mol Cell 2012
526
7


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
7

The Polycomb complex PRC2 and its mark in life.
Raphaël Margueron, Danny Reinberg. Nature 2011
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
7

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
7

Asymmetrically modified nucleosomes.
Philipp Voigt, Gary LeRoy, William J Drury, Barry M Zee, Jinsook Son, David B Beck, Nicolas L Young, Benjamin A Garcia, Danny Reinberg. Cell 2012
265
7

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.
Emily Brookes, Inês de Santiago, Daniel Hebenstreit, Kelly J Morris, Tom Carroll, Sheila Q Xie, Julie K Stock, Martin Heidemann, Dirk Eick, Naohito Nozaki,[...]. Cell Stem Cell 2012
200
7

Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide.
Eva Madi Riising, Itys Comet, Benjamin Leblanc, Xudong Wu, Jens Vilstrup Johansen, Kristian Helin. Mol Cell 2014
263
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

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A Sperling, Alon Goren, David A Weitz, Bradley E Bernstein. Nat Biotechnol 2015
457
6

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
76
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
669
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


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.