A citation-based method for searching scientific literature

Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
Times Cited: 7808







List of co-cited articles
323 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
23


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
15

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
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
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

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
10

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

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
9


CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9




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

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
8

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
8

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
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
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
7

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
7

Pfam: The protein families database in 2021.
Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson,[...]. Nucleic Acids Res 2021
661
7

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010
6



Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
6


Automated generation of heuristics for biological sequence comparison.
Guy St C Slater, Ewan Birney. BMC Bioinformatics 2005
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
5

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
5

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
5

Mash: fast genome and metagenome distance estimation using MinHash.
Brian D Ondov, Todd J Treangen, Páll Melsted, Adam B Mallonee, Nicholas H Bergman, Sergey Koren, Adam M Phillippy. Genome Biol 2016
983
5

The sequence read archive.
Rasko Leinonen, Hideaki Sugawara, Martin Shumway. Nucleic Acids Res 2011
5

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
5


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

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Jiarong Guo, Ben Bolduc, Ahmed A Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O Delmont, Akbar Adjie Pratama, M Consuelo Gazitúa, Dean Vik, Matthew B Sullivan,[...]. Microbiome 2021
64
7

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
5

Accelerated Profile HMM Searches.
Sean R Eddy. PLoS Comput Biol 2011
5

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
5


The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
4

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
4

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
4

Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Peter Menzel, Kim Lee Ng, Anders Krogh. Nat Commun 2016
598
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.