A citation-based method for searching scientific literature

Colette L Baxter, Saša Šviković, Julian E Sale, Caroline Dean, Silvia Costa. Proc Natl Acad Sci U S A 2021
Times Cited: 6







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



Times Cited
  Times     Co-cited
Similarity


Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution.
Chang Liu, Congmao Wang, George Wang, Claude Becker, Maricris Zaidem, Detlef Weigel. Genome Res 2016
129
16


Transposable element-derived sequences in vertebrate development.
Ema Etchegaray, Magali Naville, Jean-Nicolas Volff, Zofia Haftek-Terreau. Mob DNA 2021
27
16

psRNATarget: a plant small RNA target analysis server (2017 release).
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao. Nucleic Acids Res 2018
475
16

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
16

Control of female gamete formation by a small RNA pathway in Arabidopsis.
Vianey Olmedo-Monfil, Noé Durán-Figueroa, Mario Arteaga-Vázquez, Edgar Demesa-Arévalo, Daphné Autran, Daniel Grimanelli, R Keith Slotkin, Robert A Martienssen, Jean-Philippe Vielle-Calzada. Nature 2010
340
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
16

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
16

Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation.
Marcel Lafos, Phillip Kroll, Mareike L Hohenstatt, Frazer L Thorpe, Oliver Clarenz, Daniel Schubert. PLoS Genet 2011
225
16

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis.
Yu Zhang, C Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie,[...]. Proc Natl Acad Sci U S A 2018
36
16

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.
Hume Stroud, Truman Do, Jiamu Du, Xuehua Zhong, Suhua Feng, Lianna Johnson, Dinshaw J Patel, Steven E Jacobsen. Nat Struct Mol Biol 2014
469
16

Nuclear dynamics of the Set1C subunit Spp1 prepares meiotic recombination sites for break formation.
Zsolt Karányi, László Halász, Laurent Acquaviva, Dávid Jónás, Szabolcs Hetey, Beáta Boros-Oláh, Feng Peng, Doris Chen, Franz Klein, Vincent Géli,[...]. J Cell Biol 2018
10
16

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
16

RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA.
Gudrun Böhmdorfer, M Jordan Rowley, Jan Kuciński, Yongyou Zhu, Ivan Amies, Andrzej T Wierzbicki. Plant J 2014
58
16

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid.
Wangsheng Zhu, Bo Hu, Claude Becker, Ezgi Süheyla Doğan, Kenneth Wayne Berendzen, Detlef Weigel, Chang Liu. Genome Biol 2017
58
16

Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
A M Lindroth, X Cao, J P Jackson, D Zilberman, C M McCallum, S Henikoff, S E Jacobsen. Science 2001
599
16

The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation.
Yusheng Zhang, Tong Liu, Fenghua Yuan, Liliana Garcia-Martinez, Kyutae D Lee, Stephanie Stransky, Simone Sidoli, Ramiro E Verdun, Yanbin Zhang, Zheng Wang,[...]. Nucleic Acids Res 2021
8
16

HiGlass: web-based visual exploration and analysis of genome interaction maps.
Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M Luber, Scott B Ouellette, Alaleh Azhir, Nikhil Kumar,[...]. Genome Biol 2018
209
16


Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome.
Frédéric Pontvianne, Marie-Christine Carpentier, Nathalie Durut, Veronika Pavlištová, Karin Jaške, Šárka Schořová, Hugues Parrinello, Marine Rohmer, Craig S Pikaard, Miloslava Fojtová,[...]. Cell Rep 2016
84
16

Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.
Thomas J Hardcastle, Sebastian Y Müller, David C Baulcombe. Sci Rep 2018
6
16

The pause-initiation limit restricts transcription activation in human cells.
Saskia Gressel, Björn Schwalb, Patrick Cramer. Nat Commun 2019
28
16

DNA Topoisomerase Iα Affects the Floral Transition.
Ximing Gong, Lisha Shen, Ya Zhi Peng, Yinbo Gan, Hao Yu. Plant Physiol 2017
14
16

Distinguishing the roles of Topoisomerases I and II in relief of transcription-induced torsional stress in yeast rRNA genes.
Sarah L French, Martha L Sikes, Robert D Hontz, Yvonne N Osheim, Tashima E Lambert, Aziz El Hage, Mitchell M Smith, David Tollervey, Jeffrey S Smith, Ann L Beyer. Mol Cell Biol 2011
66
16

The transition to flowering
Levy, Dean. Plant Cell 1998
214
16

The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors.
Kyuha Choi, Juhyun Kim, Hyun-Ju Hwang, Sanghee Kim, Chulmin Park, Sang Yeol Kim, Ilha Lee. Plant Cell 2011
184
16

Born to run: control of transcription elongation by RNA polymerase II.
Fei Xavier Chen, Edwin R Smith, Ali Shilatifard. Nat Rev Mol Cell Biol 2018
186
16

Chromatin-based mechanisms to coordinate convergent overlapping transcription.
Soichi Inagaki, Mayumi Takahashi, Kazuya Takashima, Satoyo Oya, Tetsuji Kakutani. Nat Plants 2021
11
16

Alternative polyadenylation of mRNA precursors.
Bin Tian, James L Manley. Nat Rev Mol Cell Biol 2017
536
16

FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains.
R Macknight, I Bancroft, T Page, C Lister, R Schmidt, K Love, L Westphal, G Murphy, S Sherson, C Cobbett,[...]. Cell 1997
332
16

Chromatin architectural proteins regulate flowering time by precluding gene looping.
Bo Zhao, Yanpeng Xi, Junghyun Kim, Sibum Sung. Sci Adv 2021
7
16

The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis.
Fengyue Zhao, Huairen Zhang, Ting Zhao, Zicong Li, Danhua Jiang. Plant Physiol 2021
7
16

Three-dimensional chromatin organization in brain function and dysfunction.
Vishnu Dileep, Li-Huei Tsai. Curr Opin Neurobiol 2021
5
20

Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor.
Zhi-Wei Wang, Zhe Wu, Oleg Raitskin, Qianwen Sun, Caroline Dean. Proc Natl Acad Sci U S A 2014
68
16

Analysis of the molecular basis of flowering time variation in Arabidopsis accessions.
Silvia Gazzani, Anthony R Gendall, Clare Lister, Caroline Dean. Plant Physiol 2003
244
16

Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription.
Sebastian Marquardt, Oleg Raitskin, Zhe Wu, Fuquan Liu, Qianwen Sun, Caroline Dean. Mol Cell 2014
171
16

NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila.
Chwen-Huey Wu, Yuki Yamaguchi, Lawrence R Benjamin, Maria Horvat-Gordon, Jodi Washinsky, Espen Enerly, Jan Larsson, Andrew Lambertsson, Hiroshi Handa, David Gilmour. Genes Dev 2003
217
16

3D chromatin architecture and transcription regulation in cancer.
Siwei Deng, Yuliang Feng, Siim Pauklin. J Hematol Oncol 2022
3
33

The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex.
Chris A Helliwell, Craig C Wood, Masumi Robertson, W James Peacock, Elizabeth S Dennis. Plant J 2006
312
16

The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis.
Teddy Jégu, David Latrasse, Marianne Delarue, Heribert Hirt, Séverine Domenichini, Federico Ariel, Martin Crespi, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed. Plant Cell 2014
64
16

The spen family protein FPA controls alternative cleavage and polyadenylation of RNA.
Csaba Hornyik, Lionel C Terzi, Gordon G Simpson. Dev Cell 2010
160
16

Supervital Mutants of Arabidopsis.
G P Rédei. Genetics 1962
155
16


Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time.
Victor Quesada, Richard Macknight, Caroline Dean, Gordon G Simpson. EMBO J 2003
186
16

Integration of flowering signals in winter-annual Arabidopsis.
Scott D Michaels, Edward Himelblau, Sang Yeol Kim, Fritz M Schomburg, Richard M Amasino. Plant Physiol 2005
198
16


Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.
Daniel Enderle, Christian Beisel, Michael B Stadler, Moritz Gerstung, Prashanth Athri, Renato Paro. Genome Res 2011
123
16


FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition.
Gordon G Simpson, Paul P Dijkwel, Victor Quesada, Ian Henderson, Caroline Dean. Cell 2003
274
16

The FLC Locus: A Platform for Discoveries in Epigenetics and Adaptation.
Charles Whittaker, Caroline Dean. Annu Rev Cell Dev Biol 2017
144
16


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.