A citation-based method for searching scientific literature

Stephen J Bush, Dona Foster, David W Eyre, Emily L Clark, Nicola De Maio, Liam P Shaw, Nicole Stoesser, Tim E A Peto, Derrick W Crook, A Sarah Walker. Gigascience 2020
Times Cited: 27







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



Times Cited
  Times     Co-cited
Similarity


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
48

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
29

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
22



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
830
18


Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
544
18

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
18


Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP.
Dai Yoshimura, Rei Kajitani, Yasuhiro Gotoh, Katsuyuki Katahira, Miki Okuno, Yoshitoshi Ogura, Tetsuya Hayashi, Takehiko Itoh. Microb Genom 2019
21
19

Best practices for evaluating single nucleotide variant calling methods for microbial genomics.
Nathan D Olson, Steven P Lund, Rebecca E Colman, Jeffrey T Foster, Jason W Sahl, James M Schupp, Paul Keim, Jayne B Morrow, Marc L Salit, Justin M Zook. Front Genet 2015
83
14

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
Stephen Nayfach, Beltran Rodriguez-Mueller, Nandita Garud, Katherine S Pollard. Genome Res 2016
186
14

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
Johan Goris, Konstantinos T Konstantinidis, Joel A Klappenbach, Tom Coenye, Peter Vandamme, James M Tiedje. Int J Syst Evol Microbiol 2007
14

Adaptive Evolution within Gut Microbiomes of Healthy People.
Shijie Zhao, Tami D Lieberman, Mathilde Poyet, Kathryn M Kauffman, Sean M Gibbons, Mathieu Groussin, Ramnik J Xavier, Eric J Alm. Cell Host Microbe 2019
106
14

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
14

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


Centrifuge: rapid and sensitive classification of metagenomic sequences.
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. Genome Res 2016
365
14

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
14

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
14

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.
Matthew R Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian A Firek, Michael J Morowitz, Jillian F Banfield. Nat Biotechnol 2021
23
17

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.
Marc W Allard, Errol Strain, David Melka, Kelly Bunning, Steven M Musser, Eric W Brown, Ruth Timme. J Clin Microbiol 2016
161
11

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
11

MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
11


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
11

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
11

Microbial strain-level population structure and genetic diversity from metagenomes.
Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, Nicola Segata. Genome Res 2017
241
11

Shifting the genomic gold standard for the prokaryotic species definition.
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
11

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.
Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S Katz,[...]. Microb Genom 2017
77
11

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
11

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

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.
Alexandra Moura, Alexis Criscuolo, Hannes Pouseele, Mylène M Maury, Alexandre Leclercq, Cheryl Tarr, Jonas T Björkman, Timothy Dallman, Aleisha Reimer, Vincent Enouf,[...]. Nat Microbiol 2016
253
11


ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Xavier Didelot, Daniel J Wilson. PLoS Comput Biol 2015
378
11

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
11

The GEM mapper: fast, accurate and versatile alignment by filtration.
Santiago Marco-Sola, Michael Sammeth, Roderic Guigó, Paolo Ribeca. Nat Methods 2012
292
11

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
11

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
Nicola De Maio, Liam P Shaw, Alasdair Hubbard, Sophie George, Nicholas D Sanderson, Jeremy Swann, Ryan Wick, Manal AbuOun, Emma Stubberfield, Sarah J Hoosdally,[...]. Microb Genom 2019
70
11

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.
Ea Zankari, Rosa Allesøe, Katrine G Joensen, Lina M Cavaco, Ole Lund, Frank M Aarestrup. J Antimicrob Chemother 2017
134
11




Genome-scale rates of evolutionary change in bacteria.
Sebastian Duchêne, Kathryn E Holt, François-Xavier Weill, Simon Le Hello, Jane Hawkey, David J Edwards, Mathieu Fourment, Edward C Holmes. Microb Genom 2016
117
11


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
11

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.
Nandita R Garud, Benjamin H Good, Oskar Hallatschek, Katherine S Pollard. PLoS Biol 2019
82
11

Genomic variation landscape of the human gut microbiome.
Siegfried Schloissnig, Manimozhiyan Arumugam, Shinichi Sunagawa, Makedonka Mitreva, Julien Tap, Ana Zhu, Alison Waller, Daniel R Mende, Jens Roat Kultima, John Martin,[...]. Nature 2013
455
11

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.
David W Eyre, Tanya Golubchik, N Claire Gordon, Rory Bowden, Paolo Piazza, Elizabeth M Batty, Camilla L C Ip, Daniel J Wilson, Xavier Didelot, Lily O'Connor,[...]. BMJ Open 2012
180
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.