A citation-based method for searching scientific literature

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, Alexey V Pyshkin, Alexander V Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A Alekseyev, Pavel A Pevzner. J Comput Biol 2012
Times Cited: 11415







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



Times Cited
  Times     Co-cited
Similarity


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
33

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
23


QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
15

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
13

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
13

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


The RAST Server: rapid annotations using subsystems technology.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal,[...]. BMC Genomics 2008
11

Prodigal: prokaryotic gene recognition and translation initiation site identification.
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
10

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
9

Roary: rapid large-scale prokaryote pan genome analysis.
Andrew J Page, Carla A Cummins, Martin Hunt, Vanessa K Wong, Sandra Reuter, Matthew T G Holden, Maria Fookes, Daniel Falush, Jacqueline A Keane, Julian Parkhill. Bioinformatics 2015
9

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
9

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt. PLoS Comput Biol 2017
9

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
8

In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.
Alessandra Carattoli, Ea Zankari, Aurora García-Fernández, Mette Voldby Larsen, Ole Lund, Laura Villa, Frank Møller Aarestrup, Henrik Hasman. Antimicrob Agents Chemother 2014
8

Identification of acquired antimicrobial resistance genes.
Ea Zankari, Henrik Hasman, Salvatore Cosentino, Martin Vestergaard, Simon Rasmussen, Ole Lund, Frank M Aarestrup, Mette Voldby Larsen. J Antimicrob Chemother 2012
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


Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
7


InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
7

NCBI prokaryotic genome annotation pipeline.
Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D Pruitt, Mark Borodovsky, James Ostell. Nucleic Acids Res 2016
7

PHASTER: a better, faster version of the PHAST phage search tool.
David Arndt, Jason R Grant, Ana Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S Wishart. Nucleic Acids Res 2016
7

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
6

A large-scale evaluation of algorithms to calculate average nucleotide identity.
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun. Antonie Van Leeuwenhoek 2017
6

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun. Int J Syst Evol Microbiol 2017
6

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
6

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
6

ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes.
Sushim Kumar Gupta, Babu Roshan Padmanabhan, Seydina M Diene, Rafael Lopez-Rojas, Marie Kempf, Luce Landraud, Jean-Marc Rolain. Antimicrob Agents Chemother 2014
696
6

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
5

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam. Bioinformatics 2015
5

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata. Nucleic Acids Res 2002
5

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
762
5

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
5

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H Medema, Tilmann Weber. Nucleic Acids Res 2019
5

FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
5

Multilocus sequence typing of total-genome-sequenced bacteria.
Mette V Larsen, Salvatore Cosentino, Simon Rasmussen, Carsten Friis, Henrik Hasman, Rasmus Lykke Marvig, Lars Jelsbak, Thomas Sicheritz-Pontén, David W Ussery, Frank M Aarestrup,[...]. J Clin Microbiol 2012
5

ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia, Rolf S Kaas, Etienne Ruppe, Marilyn C Roberts, Stefan Schwarz, Vincent Cattoir, Alain Philippon, Rosa L Allesoe, Ana Rita Rebelo, Alfred Ferrer Florensa,[...]. J Antimicrob Chemother 2020
446
5

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin. Nucleic Acids Res 2018
642
5


Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk, Markus Göker. BMC Bioinformatics 2013
5

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Baofeng Jia, Amogelang R Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, Kara K Tsang, Briony A Lago, Biren M Dave, Sheldon Pereira, Arjun N Sharma,[...]. Nucleic Acids Res 2017
5

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks. Bioinformatics 2019
562
5

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
5

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
449
5

SignalP 5.0 improves signal peptide predictions using deep neural networks.
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
5


Easyfig: a genome comparison visualizer.
Mitchell J Sullivan, Nicola K Petty, Scott A Beatson. Bioinformatics 2011
5


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.