A citation-based method for searching scientific literature

Shuaibin Wang, Dawei Li, Xiaohong Yao, Qingwei Song, Zupeng Wang, Qiong Zhang, Caihong Zhong, Yifei Liu, Hongwen Huang. Genome Biol Evol 2019
Times Cited: 14







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



Times Cited
  Times     Co-cited
Similarity


The alternative reality of plant mitochondrial DNA: One ring does not rule them all.
Alexander Kozik, Beth A Rowan, Dean Lavelle, Lidija Berke, M Eric Schranz, Richard W Michelmore, Alan C Christensen. PLoS Genet 2019
72
64

The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.
Shanshan Dong, Chaoxian Zhao, Fei Chen, Yanhui Liu, Shouzhou Zhang, Hong Wu, Liangsheng Zhang, Yang Liu. BMC Genomics 2018
39
50

GeSeq - versatile and accurate annotation of organelle genomes.
Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner. Nucleic Acids Res 2017
989
50

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
42

Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber.
Andrew J Alverson, Danny W Rice, Stephanie Dickinson, Kerrie Barry, Jeffrey D Palmer. Plant Cell 2011
147
42

Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).
Andrew J Alverson, XiaoXin Wei, Danny W Rice, David B Stern, Kerrie Barry, Jeffrey D Palmer. Mol Biol Evol 2010
235
35

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.
Elizabeth Skippington, Todd J Barkman, Danny W Rice, Jeffrey D Palmer. Proc Natl Acad Sci U S A 2015
122
35

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
Daniel B Sloan, Andrew J Alverson, John P Chuckalovcak, Martin Wu, David E McCauley, Jeffrey D Palmer, Douglas R Taylor. PLoS Biol 2012
290
35

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
35



REPuter: the manifold applications of repeat analysis on a genomic scale.
S Kurtz, J V Choudhuri, E Ohlebusch, C Schleiermacher, J Stoye, R Giegerich. Nucleic Acids Res 2001
893
35



PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.
Dong Zhang, Fangluan Gao, Ivan Jakovlić, Hong Zou, Jin Zhang, Wen X Li, Gui T Wang. Mol Ecol Resour 2020
592
35

Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca.
Yan Cheng, Xiaoxue He, S V G N Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng,[...]. BMC Genomics 2021
11
45

MISA-web: a web server for microsatellite prediction.
Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher. Bioinformatics 2017
458
35

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W dePamphilis, Ting-Shuang Yi, De-Zhu Li. Genome Biol 2020
554
35

Bandage: interactive visualization of de novo genome assemblies.
Ryan R Wick, Mark B Schultz, Justin Zobel, Kathryn E Holt. Bioinformatics 2015
735
28

High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants.
Logan W Cole, Wenhu Guo, Jeffrey P Mower, Jeffrey D Palmer. Mol Biol Evol 2018
28
28

Inheritance and recombination of mitochondrial genomes in plants, fungi and animals.
Camille M Barr, Maurine Neiman, Douglas R Taylor. New Phytol 2005
195
28

Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation.
José M Gualberto, Kathleen J Newton. Annu Rev Plant Biol 2017
159
28

Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.
Wenhu Guo, Felix Grewe, Weishu Fan, Gregory J Young, Volker Knoop, Jeffrey D Palmer, Jeffrey P Mower. Mol Biol Evol 2016
76
28

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
28


IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
28


High speed BLASTN: an accelerated MegaBLAST search tool.
Ying Chen, Weicai Ye, Yongdong Zhang, Yuesheng Xu. Nucleic Acids Res 2015
121
28



Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome.
Jean-Stéphane Varré, Nunzio D'Agostino, Pascal Touzet, Sophie Gallina, Rachele Tamburino, Concita Cantarella, Elodie Ubrig, Teodoro Cardi, Laurence Drouard, José Manuel Gualberto,[...]. Int J Mol Sci 2019
21
28

Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis.
Ning Ye, Xuelin Wang, Juan Li, Changwei Bi, Yiqing Xu, Dongyang Wu, Qiaolin Ye. PeerJ 2017
24
28

CPGAVAS2, an integrated plastome sequence annotator and analyzer.
Linchun Shi, Haimei Chen, Mei Jiang, Liqiang Wang, Xi Wu, Linfang Huang, Chang Liu. Nucleic Acids Res 2019
277
28

Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.
Danny W Rice, Andrew J Alverson, Aaron O Richardson, Gregory J Young, M Virginia Sanchez-Puerta, Jérôme Munzinger, Kerrie Barry, Jeffrey L Boore, Yan Zhang, Claude W dePamphilis,[...]. Science 2013
178
21


SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
21

The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes.
Zhiqiang Wu, Jocelyn M Cuthbert, Douglas R Taylor, Daniel B Sloan. Proc Natl Acad Sci U S A 2015
55
21

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.
Patricia P Chan, Todd M Lowe. Methods Mol Biol 2019
452
21

The plant mitochondrial genome: dynamics and maintenance.
José M Gualberto, Daria Mileshina, Clémentine Wallet, Adnan Khan Niazi, Frédérique Weber-Lotfi, André Dietrich. Biochimie 2014
115
21

Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues.
Jean-René Arseneau, Royce Steeves, Mark Laflamme. Mol Ecol Resour 2017
40
21

Using Apollo to browse and edit genome annotations.
Sima Misra, Nomi Harris. Curr Protoc Bioinformatics 2006
24
21

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
21

Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.
Zheng-Shan He, Andan Zhu, Jun-Bo Yang, Weishu Fan, De-Zhu Li. Int J Mol Sci 2021
3
100

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches.
Changwei Bi, Andrew H Paterson, Xuelin Wang, Yiqing Xu, Dongyang Wu, Yanshu Qu, Anna Jiang, Qiaolin Ye, Ning Ye. Biomed Res Int 2016
24
21

The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.
Y Notsu, S Masood, T Nishikawa, N Kubo, G Akiduki, M Nakazono, A Hirai, K Kadowaki. Mol Genet Genomics 2002
307
21


Apollo: a sequence annotation editor.
S E Lewis, S M J Searle, N Harris, M Gibson, V Lyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, M A Crosby,[...]. Genome Biol 2002
269
21



Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.
Shaun D Jackman, Lauren Coombe, René L Warren, Heather Kirk, Eva Trinh, Tina MacLeod, Stephen Pleasance, Pawan Pandoh, Yongjun Zhao, Robin J Coope,[...]. Genome Biol Evol 2020
14
21


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.