A citation-based method for searching scientific literature

Fuguang Li, Guangyi Fan, Cairui Lu, Guanghui Xiao, Changsong Zou, Russell J Kohel, Zhiying Ma, Haihong Shang, Xiongfeng Ma, Jianyong Wu, Xinming Liang, Gai Huang, Richard G Percy, Kun Liu, Weihua Yang, Wenbin Chen, Xiongming Du, Chengcheng Shi, Youlu Yuan, Wuwei Ye, Xin Liu, Xueyan Zhang, Weiqing Liu, Hengling Wei, Shoujun Wei, Guodong Huang, Xianlong Zhang, Shuijin Zhu, He Zhang, Fengming Sun, Xingfen Wang, Jie Liang, Jiahao Wang, Qiang He, Leihuan Huang, Jun Wang, Jinjie Cui, Guoli Song, Kunbo Wang, Xun Xu, John Z Yu, Yuxian Zhu, Shuxun Yu. Nat Biotechnol 2015
Times Cited: 538







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



Times Cited
  Times     Co-cited
Similarity


Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Tianzhen Zhang, Yan Hu, Wenkai Jiang, Lei Fang, Xueying Guan, Jiedan Chen, Jinbo Zhang, Christopher A Saski, Brian E Scheffler, David M Stelly,[...]. Nat Biotechnol 2015
806
56

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.
Yan Hu, Jiedan Chen, Lei Fang, Zhiyuan Zhang, Wei Ma, Yongchao Niu, Longzhen Ju, Jieqiong Deng, Ting Zhao, Jinmin Lian,[...]. Nat Genet 2019
212
41

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
Andrew H Paterson, Jonathan F Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C Showmaker, Shengqiang Shu, Joshua Udall,[...]. Nature 2012
683
39

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.
Maojun Wang, Lili Tu, Daojun Yuan, De Zhu, Chao Shen, Jianying Li, Fuyan Liu, Liuling Pei, Pengcheng Wang, Guannan Zhao,[...]. Nat Genet 2019
211
38

Genome sequence of the cultivated cotton Gossypium arboreum.
Fuguang Li, Guangyi Fan, Kunbo Wang, Fengming Sun, Youlu Yuan, Guoli Song, Qin Li, Zhiying Ma, Cairui Lu, Changsong Zou,[...]. Nat Genet 2014
486
35

The draft genome of a diploid cotton Gossypium raimondii.
Kunbo Wang, Zhiwen Wang, Fuguang Li, Wuwei Ye, Junyi Wang, Guoli Song, Zhen Yue, Lin Cong, Haihong Shang, Shilin Zhu,[...]. Nat Genet 2012
531
28

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution.
Gai Huang, Zhiguo Wu, Richard G Percy, Mingzhou Bai, Yang Li, James E Frelichowski, Jiang Hu, Kun Wang, John Z Yu, Yuxian Zhu. Nat Genet 2020
74
36

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Yupeng Wang, Haibao Tang, Jeremy D Debarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo,[...]. Nucleic Acids Res 2012
27


Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits.
Xiongming Du, Gai Huang, Shoupu He, Zhaoen Yang, Gaofei Sun, Xiongfeng Ma, Nan Li, Xueyan Zhang, Junling Sun, Min Liu,[...]. Nat Genet 2018
200
25

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R Thomas, Margaret H Frank, Yehua He, Rui Xia. Mol Plant 2020
24

GSDS 2.0: an upgraded gene feature visualization server.
Bo Hu, Jinpu Jin, An-Yuan Guo, He Zhang, Jingchu Luo, Ge Gao. Bioinformatics 2015
20

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
18

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.
Xia Liu, Bo Zhao, Hua-Jun Zheng, Yan Hu, Gang Lu, Chang-Qing Yang, Jie-Dan Chen, Jun-Jian Chen, Dian-Yang Chen, Liang Zhang,[...]. Sci Rep 2015
141
16

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres.
Daojun Yuan, Zhonghui Tang, Maojun Wang, Wenhui Gao, Lili Tu, Xin Jin, Lingling Chen, Yonghui He, Lin Zhang, Longfu Zhu,[...]. Sci Rep 2015
157
16

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars.
Zhaoen Yang, Xiaoyang Ge, Zuoren Yang, Wenqiang Qin, Gaofei Sun, Zhi Wang, Zhi Li, Ji Liu, Jie Wu, Ye Wang,[...]. Nat Commun 2019
58
25

Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
15

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits.
Lei Fang, Qiong Wang, Yan Hu, Yinhua Jia, Jiedan Chen, Bingliang Liu, Zhiyuan Zhang, Xueying Guan, Shuqi Chen, Baoliang Zhou,[...]. Nat Genet 2017
147
14

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts. Nucleic Acids Res 2002
14

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.
Z Jeffrey Chen, Avinash Sreedasyam, Atsumi Ando, Qingxin Song, Luis M De Santiago, Amanda M Hulse-Kemp, Mingquan Ding, Wenxue Ye, Ryan C Kirkbride, Jerry Jenkins,[...]. Nat Genet 2020
75
17

CottonGen: a genomics, genetics and breeding database for cotton research.
Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen P Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G Percy, Dorrie Main. Nucleic Acids Res 2014
136
13

MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
12

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement.
Zuoren Yang, Ghulam Qanmber, Zhi Wang, Zhaoen Yang, Fuguang Li. Trends Plant Sci 2020
30
40

CottonFGD: an integrated functional genomics database for cotton.
Tao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo, Rui Zhang. BMC Plant Biol 2017
93
12

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

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield.
Zhiying Ma, Shoupu He, Xingfen Wang, Junling Sun, Yan Zhang, Guiyin Zhang, Liqiang Wu, Zhikun Li, Zhihao Liu, Gaofei Sun,[...]. Nat Genet 2018
136
11

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.
Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, Pengcheng Wang, Qingyong Yang, Zhengxiu Ye, Chao Shen, Jianying Li, Lin Zhang,[...]. Nat Genet 2017
198
11

Toward sequencing cotton (Gossypium) genomes.
Z Jeffrey Chen, Brian E Scheffler, Elizabeth Dennis, Barbara A Triplett, Tianzhen Zhang, Wangzhen Guo, Xiaoya Chen, David M Stelly, Pablo D Rabinowicz, Christopher D Town,[...]. Plant Physiol 2007
208
11

Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality.
Mi Zhang, Xuelian Zheng, Shuiqing Song, Qiwei Zeng, Lei Hou, Demou Li, Juan Zhao, Yuan Wei, Xianbi Li, Ming Luo,[...]. Nat Biotechnol 2011
144
10

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
10

The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
9

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
9

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
9


How cotton fibers elongate: a tale of linear cell-growth mode.
Yong-Mei Qin, Yu-Xian Zhu. Curr Opin Plant Biol 2011
142
9

Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation.
Yong-Hui Shi, Sheng-Wei Zhu, Xi-Zeng Mao, Jian-Xun Feng, Yong-Mei Qin, Liang Zhang, Jing Cheng, Li-Ping Wei, Zhi-Yong Wang, Yu-Xian Zhu. Plant Cell 2006
320
9

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri.
Joshua A Udall, Evan Long, Chris Hanson, Daojun Yuan, Thiruvarangan Ramaraj, Justin L Conover, Lei Gong, Mark A Arick, Corrinne E Grover, Daniel G Peterson,[...]. G3 (Bethesda) 2019
27
33

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
9

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
9

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016
9

GhMYB25-like: a key factor in early cotton fibre development.
Sally-Ann Walford, Yingru Wu, Danny J Llewellyn, Elizabeth S Dennis. Plant J 2011
140
8


The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
8


Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
Boulos Chalhoub, France Denoeud, Shengyi Liu, Isobel A P Parkin, Haibao Tang, Xiyin Wang, Julien Chiquet, Harry Belcram, Chaobo Tong, Birgit Samans,[...]. Science 2014
8

Recent Advances and Future Perspectives in Cotton Research.
Gai Huang, Jin-Quan Huang, Xiao-Ya Chen, Yu-Xian Zhu. Annu Rev Plant Biol 2021
23
34

Cotton fiber: a powerful single-cell model for cell wall and cellulose research.
Candace H Haigler, Lissete Betancur, Michael R Stiff, John R Tuttle. Front Plant Sci 2012
130
8


InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
7

Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis.
Yong-Mei Qin, Chun-Yang Hu, Yu Pang, Alexander J Kastaniotis, J Kalervo Hiltunen, Yu-Xian Zhu. Plant Cell 2007
147
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.