A citation-based method for searching scientific literature

Linchun Shi, Haimei Chen, Mei Jiang, Liqiang Wang, Xi Wu, Linfang Huang, Chang Liu. Nucleic Acids Res 2019
Times Cited: 298







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



Times Cited
  Times     Co-cited
Similarity



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
592
46


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
30

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
27

MISA-web: a web server for microsatellite prediction.
Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher. Bioinformatics 2017
486
24

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
21

IRscope: an online program to visualize the junction sites of chloroplast genomes.
Ali Amiryousefi, Jaakko Hyvönen, Peter Poczai. Bioinformatics 2018
211
20

NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits. Nucleic Acids Res 2017
20

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
20

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
916
18

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
16


VISTA: computational tools for comparative genomics.
Kelly A Frazer, Lior Pachter, Alexander Poliakov, Edward M Rubin, Inna Dubchak. Nucleic Acids Res 2004
16

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.
Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio, Sara Guirao-Rico, Pablo Librado, Sebastián E Ramos-Onsins, Alejandro Sánchez-Gracia. Mol Biol Evol 2017
15

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
15

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.
Susann Wicke, Gerald M Schneeweiss, Claude W dePamphilis, Kai F Müller, Dietmar Quandt. Plant Mol Biol 2011
592
13

Bandage: interactive visualization of de novo genome assemblies.
Ryan R Wick, Mark B Schultz, Justin Zobel, Kathryn E Holt. Bioinformatics 2015
755
13

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
13


MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
12

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A Suchard, John P Huelsenbeck. Syst Biol 2012
11

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
Peter Schattner, Angela N Brooks, Todd M Lowe. Nucleic Acids Res 2005
10

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
10

Chloroplast genomes: diversity, evolution, and applications in genetic engineering.
Henry Daniell, Choun-Sea Lin, Ming Yu, Wan-Jung Chang. Genome Biol 2016
464
8

jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
8

ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
8

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear. Mol Biol Evol 2020
8

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
271
8

EMBOSS: the European Molecular Biology Open Software Suite.
P Rice, I Longden, A Bleasby. Trends Genet 2000
7

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes.
Xiao-Jian Qu, Michael J Moore, De-Zhu Li, Ting-Shuang Yi. Plant Methods 2019
375
6

Plant DNA barcoding: from gene to genome.
Xiwen Li, Yang Yang, Robert J Henry, Maurizio Rossetto, Yitao Wang, Shilin Chen. Biol Rev Camb Philos Soc 2015
288
6


Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.
Robert K Jansen, Zhengqiu Cai, Linda A Raubeson, Henry Daniell, Claude W Depamphilis, James Leebens-Mack, Kai F Müller, Mary Guisinger-Bellian, Rosemarie C Haberle, Anne K Hansen,[...]. Proc Natl Acad Sci U S A 2007
604
6

Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Aaron C E Darling, Bob Mau, Frederick R Blattner, Nicole T Perna. Genome Res 2004
6



Chloroplast genome sequences from total DNA for plant identification.
Catherine J Nock, Daniel L E Waters, Mark A Edwards, Stirling G Bowen, Nicole Rice, Giovanni M Cordeiro, Robert J Henry. Plant Biotechnol J 2011
176
5



Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Jan Krumsiek, Roland Arnold, Thomas Rattei. Bioinformatics 2007
430
5

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu,[...]. Gigascience 2012
5

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots.
Michael J Moore, Pamela S Soltis, Charles D Bell, J Gordon Burleigh, Douglas E Soltis. Proc Natl Acad Sci U S A 2010
376
5


A DNA barcode for land plants.
. Proc Natl Acad Sci U S A 2009
5


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
40
12



Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes.
Shuyu Zheng, Peter Poczai, Jaakko Hyvönen, Jing Tang, Ali Amiryousefi. Front Genet 2020
32
15


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.