A citation-based method for searching scientific literature

Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
Times Cited: 4372







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



Times Cited
  Times     Co-cited
Similarity


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
27

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
25

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
24

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
22

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
21

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
20

metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
18

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
17

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
14

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
14

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
14

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
13

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.
Dongwan D Kang, Feng Li, Edward Kirton, Ashleigh Thomas, Rob Egan, Hong An, Zhong Wang. PeerJ 2019
479
13

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen,[...]. Nucleic Acids Res 2019
818
12

FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
11


Accelerated Profile HMM Searches.
Sean R Eddy. PLoS Comput Biol 2011
11

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
636
11

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Yu Peng, Henry C M Leung, S M Yiu, Francis Y L Chin. Bioinformatics 2012
10

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson. Nat Microbiol 2017
625
10

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
10


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
10

Shifting the genomic gold standard for the prokaryotic species definition.
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
10

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
10

Binning metagenomic contigs by coverage and composition.
Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z Ijaz, Leo Lahti, Nicholas J Loman, Anders F Andersson, Christopher Quince. Nat Methods 2014
694
9

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, Adam R Rivers, Emiley A Eloe-Fadrosh,[...]. Nat Biotechnol 2017
577
9



MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
9

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
9

RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Staerfeldt, Torbjørn Rognes, David W Ussery. Nucleic Acids Res 2007
9

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
8


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
8


Anvi'o: an advanced analysis and visualization platform for 'omics data.
A Murat Eren, Özcan C Esen, Christopher Quince, Joseph H Vineis, Hilary G Morrison, Mitchell L Sogin, Tom O Delmont. PeerJ 2015
671
8

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

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
8

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.
Christian M K Sieber, Alexander J Probst, Allison Sharrar, Brian C Thomas, Matthias Hess, Susannah G Tringe, Jillian F Banfield. Nat Microbiol 2018
298
8


Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
862
7

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
996
7

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi,[...]. Cell 2019
497
7

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
991
7

A complete domain-to-species taxonomy for Bacteria and Archaea.
Donovan H Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J Mussig, Philip Hugenholtz. Nat Biotechnol 2020
322
7


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