A citation-based method for searching scientific literature

Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher. Bioinformatics 2017
Times Cited: 458







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



Times Cited
  Times     Co-cited
Similarity


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
36

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
31


IRscope: an online program to visualize the junction sites of chloroplast genomes.
Ali Amiryousefi, Jaakko Hyvönen, Peter Poczai. Bioinformatics 2018
194
26


VISTA: computational tools for comparative genomics.
Kelly A Frazer, Lior Pachter, Alexander Poliakov, Edward M Rubin, Inna Dubchak. Nucleic Acids Res 2004
25

NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits. Nucleic Acids Res 2017
23

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
20

Chloroplast genomes: diversity, evolution, and applications in genetic engineering.
Henry Daniell, Choun-Sea Lin, Ming Yu, Wan-Jung Chang. Genome Biol 2016
448
20

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
20


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
18

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
17

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
17

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
17


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
577
17

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
17

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
15

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
14


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
12

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
11

Automatic annotation of organellar genomes with DOGMA.
Stacia K Wyman, Robert K Jansen, Jeffrey L Boore. Bioinformatics 2004
11

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
603
11

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
10

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
558
10

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
10

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
358
9

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
9


Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.
Linda A Raubeson, Rhiannon Peery, Timothy W Chumley, Chris Dziubek, H Matthew Fourcade, Jeffrey L Boore, Robert K Jansen. BMC Genomics 2007
224
9

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
9

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
8

Primer3--new capabilities and interfaces.
Andreas Untergasser, Ioana Cutcutache, Triinu Koressaar, Jian Ye, Brant C Faircloth, Maido Remm, Steven G Rozen. Nucleic Acids Res 2012
8


Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Aaron C E Darling, Bob Mau, Frederick R Blattner, Nicole T Perna. Genome Res 2004
8

The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.
Timothy W Chumley, Jeffrey D Palmer, Jeffrey P Mower, H Matthew Fourcade, Patrick J Calie, Jeffrey L Boore, Robert K Jansen. Mol Biol Evol 2006
263
8

Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species.
Yanci Yang, Tao Zhou, Dong Duan, Jia Yang, Li Feng, Guifang Zhao. Front Plant Sci 2016
109
8


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
8


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
8


CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
Chang Liu, Linchun Shi, Yingjie Zhu, Haimei Chen, Jianhui Zhang, Xiaohan Lin, Xiaojun Guan. BMC Genomics 2012
356
7

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

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
7

Chloroplast microsatellites: new tools for studies in plant ecology and evolution.
J Provan, W Powell, P M. Hollingsworth. Trends Ecol Evol 2001
256
7

KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.
Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu. Genomics Proteomics Bioinformatics 2010
607
7

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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.