A citation-based method for searching scientific literature

Torsten Seemann. Bioinformatics 2014
Times Cited: 5396







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



Times Cited
  Times     Co-cited
Similarity


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
26

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
26

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

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
18

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
15

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

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
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

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
12

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
11

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
11


Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork. Mol Biol Evol 2017
786
10

FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
10

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
9


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
8

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
8

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
8

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
8

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
Brian P Alcock, Amogelang R Raphenya, Tammy T Y Lau, Kara K Tsang, Mégane Bouchard, Arman Edalatmand, William Huynh, Anna-Lisa V Nguyen, Annie A Cheng, Sihan Liu,[...]. Nucleic Acids Res 2020
421
8

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Chirag Jain, Luis M Rodriguez-R, Adam M Phillippy, Konstantinos T Konstantinidis, Srinivas Aluru. Nat Commun 2018
712
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

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
Nabil-Fareed Alikhan, Nicola K Petty, Nouri L Ben Zakour, Scott A Beatson. BMC Genomics 2011
7

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
6

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
980
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

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.
A-P Magiorakos, A Srinivasan, R B Carey, Y Carmeli, M E Falagas, C G Giske, S Harbarth, J F Hindler, G Kahlmeter, B Olsson-Liljequist,[...]. Clin Microbiol Infect 2012
6

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
6


The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Ross Overbeek, Robert Olson, Gordon D Pusch, Gary J Olsen, James J Davis, Terry Disz, Robert A Edwards, Svetlana Gerdes, Bruce Parrello, Maulik Shukla,[...]. Nucleic Acids Res 2014
6

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
6

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
6

Easyfig: a genome comparison visualizer.
Mitchell J Sullivan, Nicola K Petty, Scott A Beatson. Bioinformatics 2011
6


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

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.
Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz. Nat Biotechnol 2018
895
5


BIGSdb: Scalable analysis of bacterial genome variation at the population level.
Keith A Jolley, Martin C J Maiden. BMC Bioinformatics 2010
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


VFDB: a reference database for bacterial virulence factors.
Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin. Nucleic Acids Res 2005
602
5

Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates.
Michael Feldgarden, Vyacheslav Brover, Daniel H Haft, Arjun B Prasad, Douglas J Slotta, Igor Tolstoy, Gregory H Tyson, Shaohua Zhao, Chih-Hao Hsu, Patrick F McDermott,[...]. Antimicrob Agents Chemother 2019
248
5

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
Thomas Brettin, James J Davis, Terry Disz, Robert A Edwards, Svetlana Gerdes, Gary J Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch,[...]. Sci Rep 2015
954
5


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
5

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
5


The comprehensive antibiotic resistance database.
Andrew G McArthur, Nicholas Waglechner, Fazmin Nizam, Austin Yan, Marisa A Azad, Alison J Baylay, Kirandeep Bhullar, Marc J Canova, Gianfranco De Pascale, Linda Ejim,[...]. Antimicrob Agents Chemother 2013
861
4


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.