A citation-based method for searching scientific literature

Yucheng Liu, Huilong Du, Pengcheng Li, Yanting Shen, Hua Peng, Shulin Liu, Guo-An Zhou, Haikuan Zhang, Zhi Liu, Miao Shi, Xuehui Huang, Yan Li, Min Zhang, Zheng Wang, Baoge Zhu, Bin Han, Chengzhi Liang, Zhixi Tian. Cell 2020
Times Cited: 175







List of co-cited articles
1136 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.
Zhengkui Zhou, Yu Jiang, Zheng Wang, Zhiheng Gou, Jun Lyu, Weiyu Li, Yanjun Yu, Liping Shu, Yingjun Zhao, Yanming Ma,[...]. Nat Biotechnol 2015
496
35

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
199
29

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
166
28

Genome sequence of the palaeopolyploid soybean.
Jeremy Schmutz, Steven B Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L Hyten, Qijian Song, Jay J Thelen, Jianlin Cheng,[...]. Nature 2010
26

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
288
26

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
495
24

Plant pan-genomes are the new reference.
Philipp E Bayer, Agnieszka A Golicz, Armin Scheben, Jacqueline Batley, David Edwards. Nat Plants 2020
123
24

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
21

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
58
36

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
234
20

A reference-grade wild soybean genome.
Min Xie, Claire Yik-Lok Chung, Man-Wah Li, Fuk-Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden King-Yung Leung, Tin-Hang Wong, Suk-Wah Tong,[...]. Nat Commun 2019
88
22

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
181
19

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
19

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
95
18


Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.
Hon-Ming Lam, Xun Xu, Xin Liu, Wenbin Chen, Guohua Yang, Fuk-Ling Wong, Man-Wah Li, Weiming He, Nan Qin, Bo Wang,[...]. Nat Genet 2010
552
17

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean.
Chao Fang, Yanming Ma, Shiwen Wu, Zhi Liu, Zheng Wang, Rui Yang, Guanghui Hu, Zhengkui Zhou, Hong Yu, Min Zhang,[...]. Genome Biol 2017
151
17

The pangenome of hexaploid bread wheat.
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley,[...]. Plant J 2017
159
16


De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.
Matthew B Hufford, Arun S Seetharam, Margaret R Woodhouse, Kapeel M Chougule, Shujun Ou, Jianing Liu, William A Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu,[...]. Science 2021
55
29

The molecular genetics of crop domestication.
John F Doebley, Brandon S Gaut, Bruce D Smith. Cell 2006
911
15

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
153
15

The pangenome of an agronomically important crop plant Brassica oleracea.
Agnieszka A Golicz, Philipp E Bayer, Guy C Barker, Patrick P Edger, HyeRan Kim, Paula A Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W Richard McCombie, Isobel A P Parkin,[...]. Nat Commun 2016
178
15

MUMmer4: A fast and versatile genome alignment system.
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin. PLoS Comput Biol 2018
508
15

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement.
Aamir W Khan, Vanika Garg, Manish Roorkiwal, Agnieszka A Golicz, David Edwards, Rajeev K Varshney. Trends Plant Sci 2020
75
20

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
14

Exploring and Exploiting Pan-genomics for Crop Improvement.
Yongfu Tao, Xianrong Zhao, Emma Mace, Robert Henry, David Jordan. Mol Plant 2019
80
17

Parallel selection on a dormancy gene during domestication of crops from multiple families.
Min Wang, Wenzhen Li, Chao Fang, Fan Xu, Yucheng Liu, Zheng Wang, Rui Yang, Min Zhang, Shulin Liu, Sijia Lu,[...]. Nat Genet 2018
88
15

Insights into the maize pan-genome and pan-transcriptome.
Candice N Hirsch, Jillian M Foerster, James M Johnson, Rajandeep S Sekhon, German Muttoni, Brieanne Vaillancourt, Francisco Peñagaricano, Erika Lindquist, Mary Ann Pedraza, Kerrie Barry,[...]. Plant Cell 2014
266
14

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
14

PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007
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

De novo assembly of a Chinese soybean genome.
Yanting Shen, Jing Liu, Haiying Geng, Jixiang Zhang, Yucheng Liu, Haikuan Zhang, Shilai Xing, Jianchang Du, Shisong Ma, Zhixi Tian. Sci China Life Sci 2018
70
18

Construction and comparison of three reference-quality genome assemblies for soybean.
Babu Valliyodan, Steven B Cannon, Philipp E Bayer, Shengqiang Shu, Anne V Brown, Longhui Ren, Jerry Jenkins, Claire Y-L Chung, Ting-Fung Chan, Christopher G Daum,[...]. Plant J 2019
33
39

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.
Bhavna Hurgobin, Agnieszka A Golicz, Philipp E Bayer, Chon-Kit Kenneth Chan, Soodeh Tirnaz, Aria Dolatabadian, Sarah V Schiessl, Birgit Samans, Juan D Montenegro, Isobel A P Parkin,[...]. Plant Biotechnol J 2018
109
13

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.
Sariel Hübner, Natalia Bercovich, Marco Todesco, Jennifer R Mandel, Jens Odenheimer, Emanuel Ziegler, Joon S Lee, Gregory J Baute, Gregory L Owens, Christopher J Grassa,[...]. Nat Plants 2019
82
15

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
13

Impacts of genetic bottlenecks on soybean genome diversity.
David L Hyten, Qijian Song, Youlin Zhu, Ik-Young Choi, Randall L Nelson, Jose M Costa, James E Specht, Randy C Shoemaker, Perry B Cregan. Proc Natl Acad Sci U S A 2006
300
13

How the pan-genome is changing crop genomics and improvement.
Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B Hufford, Candice N Hirsch. Genome Biol 2021
49
26


De novo domestication of wild tomato using genome editing.
Agustin Zsögön, Tomáš Čermák, Emmanuel Rezende Naves, Marcela Morato Notini, Kai H Edel, Stefan Weinl, Luciano Freschi, Daniel F Voytas, Jörg Kudla, Lázaro Eustáquio Pereira Peres. Nat Biotechnol 2018
242
12

Towards plant pangenomics.
Agnieszka A Golicz, Jacqueline Batley, David Edwards. Plant Biotechnol J 2016
102
12

Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication.
Sijia Lu, Lidong Dong, Chao Fang, Shulin Liu, Lingping Kong, Qun Cheng, Liyu Chen, Tong Su, Haiyang Nan, Dan Zhang,[...]. Nat Genet 2020
79
15

Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean.
David E Cook, Tong Geon Lee, Xiaoli Guo, Sara Melito, Kai Wang, Adam M Bayless, Jianping Wang, Teresa J Hughes, David K Willis, Thomas E Clemente,[...]. Science 2012
312
11

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
11

Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication.
Shoudong Wang, Shulin Liu, Jie Wang, Kengo Yokosho, Bin Zhou, Ya-Chi Yu, Zhi Liu, Wolf B Frommer, Jian Feng Ma, Li-Qing Chen,[...]. Natl Sci Rev 2020
28
39

TASSEL: software for association mapping of complex traits in diverse samples.
Peter J Bradbury, Zhiwu Zhang, Dallas E Kroon, Terry M Casstevens, Yogesh Ramdoss, Edward S Buckler. Bioinformatics 2007
11

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding.
Philipp E Bayer, Babu Valliyodan, Haifei Hu, Jacob I Marsh, Yuxuan Yuan, Tri D Vuong, Gunvant Patil, Qijian Song, Jacqueline Batley, Rajeev K Varshney,[...]. Plant Genome 2022
15
73

Development and evaluation of SoySNP50K, a high-density genotyping array for soybean.
Qijian Song, David L Hyten, Gaofeng Jia, Charles V Quigley, Edward W Fickus, Randall L Nelson, Perry B Cregan. PLoS One 2013
262
10

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
145
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.