A citation-based method for searching scientific literature

Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam. Bioinformatics 2015
Times Cited: 1310







List of co-cited articles
546 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
37

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
29

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
28

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
27

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
24

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

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


CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
15

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
14


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
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
299
13

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.
Gherman V Uritskiy, Jocelyne DiRuggiero, James Taylor. Microbiome 2018
223
13


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
12

metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
853
12


Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Peter Menzel, Kim Lee Ng, Anders Krogh. Nat Commun 2016
483
10

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
10

Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
544
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
580
10

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
522
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


MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, Nicola Segata. Nat Methods 2015
830
9

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
9


DADA2: High-resolution sample inference from Illumina amplicon data.
Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes. Nat Methods 2016
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

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

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
8

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
8

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
8

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
7

FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
7

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.
Robert D Stewart, Marc D Auffret, Amanda Warr, Andrew H Wiser, Maximilian O Press, Kyle W Langford, Ivan Liachko, Timothy J Snelling, Richard J Dewhurst, Alan W Walker,[...]. Nat Commun 2018
163
7

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.
Yu-Wei Wu, Yung-Hsu Tang, Susannah G Tringe, Blake A Simmons, Steven W Singer. Microbiome 2014
261
7

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
7

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
H Bjørn Nielsen, Mathieu Almeida, Agnieszka Sierakowska Juncker, Simon Rasmussen, Junhua Li, Shinichi Sunagawa, Damian R Plichta, Laurent Gautier, Anders G Pedersen, Emmanuelle Le Chatelier,[...]. Nat Biotechnol 2014
480
7

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
7


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6




QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
6

QIIME allows analysis of high-throughput community sequencing data.
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon,[...]. Nat Methods 2010
6

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
6

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.
Nicola Segata, Daniela Börnigen, Xochitl C Morgan, Curtis Huttenhower. Nat Commun 2013
427
6


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.