A citation-based method for searching scientific literature

Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
Times Cited: 2706







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



Times Cited
  Times     Co-cited
Similarity


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
31

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
28

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
27

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
24

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
22

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
22


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
19

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
299
19

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
18


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
580
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
17

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
16

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
15

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
457
15

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

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
14

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.
Gherman V Uritskiy, Jocelyne DiRuggiero, James Taylor. Microbiome 2018
223
14

metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
853
14

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
528
13

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

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
218
13

[Vomiting of pregnancy].
V A Kulavskiĭ. Feldsher Akush 1972
39
30

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
390
12



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



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
581
11

Accelerated Profile HMM Searches.
Sean R Eddy. PLoS Comput Biol 2011
10

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
379
10

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

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold.
Takuya Aramaki, Romain Blanc-Mathieu, Hisashi Endo, Koichi Ohkubo, Minoru Kanehisa, Susumu Goto, Hiroyuki Ogata. Bioinformatics 2020
162
9

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
9

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
9


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
8

The carbohydrate-active enzymes database (CAZy) in 2013.
Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M Coutinho, Bernard Henrissat. Nucleic Acids Res 2014
8


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
8

Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Peter Menzel, Kim Lee Ng, Anders Krogh. Nat Commun 2016
483
8


A new genomic blueprint of the human gut microbiota.
Alexandre Almeida, Alex L Mitchell, Miguel Boland, Samuel C Forster, Gregory B Gloor, Aleksandra Tarkowska, Trevor D Lawley, Robert D Finn. Nature 2019
344
8

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
7

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
7

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
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.