A citation-based method for searching scientific literature

Yanqing Sun, Lianguang Shang, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo. Trends Plant Sci 2022
Times Cited: 28







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



Times Cited
  Times     Co-cited
Similarity


Representation and participation across 20 years of plant genome sequencing.
Rose A Marks, Scott Hotaling, Paul B Frandsen, Robert VanBuren. Nat Plants 2021
45
35

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
25

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
25

Plant pan-genomes are the new reference.
Philipp E Bayer, Agnieszka A Golicz, Armin Scheben, Jacqueline Batley, David Edwards. Nat Plants 2020
146
17

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
17

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.
Peng Qin, Hongwei Lu, Huilong Du, Hao Wang, Weilan Chen, Zhuo Chen, Qiang He, Shujun Ou, Hongyu Zhang, Xuanzhao Li,[...]. Cell 2021
92
14

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14


Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
14

Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms.
Shengdan Wu, Baocai Han, Yuannian Jiao. Mol Plant 2020
85
14


Exploring and Exploiting Pan-genomics for Crop Improvement.
Yongfu Tao, Xianrong Zhao, Emma Mace, Robert Henry, David Jordan. Mol Plant 2019
88
14

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
Daniel Lang, Kristian K Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg,[...]. Plant J 2018
192
14

Plant genome sequences: past, present, future.
Paul Julian Kersey. Curr Opin Plant Biol 2019
64
14

Ancestral polyploidy in seed plants and angiosperms.
Yuannian Jiao, Norman J Wickett, Saravanaraj Ayyampalayam, André S Chanderbali, Lena Landherr, Paula E Ralph, Lynn P Tomsho, Yi Hu, Haiying Liang, Pamela S Soltis,[...]. Nature 2011
14


Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.
Sean P Gordon, Bruno Contreras-Moreira, Daniel P Woods, David L Des Marais, Diane Burgess, Shengqiang Shu, Christoph Stritt, Anne C Roulin, Wendy Schackwitz, Ludmila Tyler,[...]. Nat Commun 2017
156
14

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.
Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M Tieman, Elizabeth A Burzynski-Chang, Tara L Fish, Kaitlin A Stromberg, Gavin L Sacks,[...]. Nat Genet 2019
229
14

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
Hervé Tettelin, Vega Masignani, Michael J Cieslewicz, Claudio Donati, Duccio Medini, Naomi L Ward, Samuel V Angiuoli, Jonathan Crabtree, Amanda L Jones, A Scott Durkin,[...]. Proc Natl Acad Sci U S A 2005
14

The barley pan-genome reveals the hidden legacy of mutation breeding.
Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Cécile Monat, Thomas Lux, Nadia Kamal, Daniel Lang, Axel Himmelbach,[...]. Nature 2020
126
14

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.
Qiang Zhao, Qi Feng, Hengyun Lu, Yan Li, Ahong Wang, Qilin Tian, Qilin Zhan, Yiqi Lu, Lei Zhang, Tao Huang,[...]. Nat Genet 2018
260
14

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.
Jia-Ming Song, Zhilin Guan, Jianlin Hu, Chaocheng Guo, Zhiquan Yang, Shuo Wang, Dongxu Liu, Bo Wang, Shaoping Lu, Run Zhou,[...]. Nat Plants 2020
223
14

Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin,[...]. Nat Biotechnol 2018
169
14

The B73 maize genome: complexity, diversity, and dynamics.
Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves,[...]. Science 2009
10

Plant Pan-Genomics Comes of Age.
Li Lei, Eugene Goltsman, David Goodstein, Guohong Albert Wu, Daniel S Rokhsar, John P Vogel. Annu Rev Plant Biol 2021
19
15


The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
10

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.
Patricia P Chan, Todd M Lowe. Methods Mol Biol 2019
552
10

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
10


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
10

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms.
Gregory W Stull, Xiao-Jian Qu, Caroline Parins-Fukuchi, Ying-Ying Yang, Jun-Bo Yang, Zhi-Yun Yang, Yi Hu, Hong Ma, Pamela S Soltis, Douglas E Soltis,[...]. Nat Plants 2021
22
13

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.
Xin Qiao, Qionghou Li, Hao Yin, Kaijie Qi, Leiting Li, Runze Wang, Shaoling Zhang, Andrew H Paterson. Genome Biol 2019
256
10

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006
827
10

Infernal 1.1: 100-fold faster RNA homology searches.
Eric P Nawrocki, Sean R Eddy. Bioinformatics 2013
10

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
692
10


The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress.
Liangsheng Zhang, Shengdan Wu, Xiaojun Chang, Xiuyun Wang, Yunpeng Zhao, Yiping Xia, Robert N Trigiano, Yuannian Jiao, Fei Chen. Plant Cell Environ 2020
35
10

The timescale of early land plant evolution.
Jennifer L Morris, Mark N Puttick, James W Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H Wellman, Ziheng Yang, Harald Schneider, Philip C J Donoghue. Proc Natl Acad Sci U S A 2018
322
10

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns.
Chien-Hsun Huang, Xinping Qi, Duoyuan Chen, Ji Qi, Hong Ma. J Integr Plant Biol 2020
21
14

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
Stefan A Rensing, Daniel Lang, Andreas D Zimmer, Astrid Terry, Asaf Salamov, Harris Shapiro, Tomoaki Nishiyama, Pierre-François Perroud, Erika A Lindquist, Yasuko Kamisugi,[...]. Science 2008
10

Fern genomes elucidate land plant evolution and cyanobacterial symbioses.
Fay-Wei Li, Paul Brouwer, Lorenzo Carretero-Paulet, Shifeng Cheng, Jan de Vries, Pierre-Marc Delaux, Ariana Eily, Nils Koppers, Li-Yaung Kuo, Zheng Li,[...]. Nat Plants 2018
181
10

Triticum population sequencing provides insights into wheat adaptation.
Yao Zhou, Xuebo Zhao, Yiwen Li, Jun Xu, Aoyue Bi, Lipeng Kang, Daxing Xu, Haofeng Chen, Ying Wang, Yuan-Ge Wang,[...]. Nat Genet 2020
62
10

Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots.
Yuannian Jiao, Jingping Li, Haibao Tang, Andrew H Paterson. Plant Cell 2014
136
10

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection.
Jianying Li, Daojun Yuan, Pengcheng Wang, Qiongqiong Wang, Mengling Sun, Zhenping Liu, Huan Si, Zhongping Xu, Yizan Ma, Boyang Zhang,[...]. Genome Biol 2021
33
10

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Wensheng Wang, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, Tianqing Zheng, Roven Rommel Fuentes, Fan Zhang,[...]. Nature 2018
556
10

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan, Florian Maumus, Danielle Ciren,[...]. Cell 2020
214
10

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
Ying-hui Li, Guangyu Zhou, Jianxin Ma, Wenkai Jiang, Long-guo Jin, Zhouhao Zhang, Yong Guo, Jinbo Zhang, Yi Sui, Liangtao Zheng,[...]. Nat Biotechnol 2014
306
10

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
300
10

The Chinese pine genome and methylome unveil key features of conifer evolution.
Shihui Niu, Jiang Li, Wenhao Bo, Weifei Yang, Andrea Zuccolo, Stefania Giacomello, Xi Chen, Fangxu Han, Junhe Yang, Yitong Song,[...]. Cell 2022
42
10


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.