A citation-based method for searching scientific literature

Johannes Köster, Sven Rahmann. Bioinformatics 2012
Times Cited: 860







List of co-cited articles
376 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
21

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
16

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
16

MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
16

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
15

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11


Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, Cedric Notredame. Nat Biotechnol 2017
450
10



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
8

Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster. Nat Methods 2018
327
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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
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

Singularity: Scientific containers for mobility of compute.
Gregory M Kurtzer, Vanessa Sochat, Michael W Bauer. PLoS One 2017
252
7


GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
6


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
6

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
6


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
6

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5



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
5

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
5

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
5


Twelve years of SAMtools and BCFtools.
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies,[...]. Gigascience 2021
480
5

Sustainable data analysis with Snakemake.
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B Hall, Christopher H Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O Twardziok, Alexander Kanitz,[...]. F1000Res 2021
89
5


metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
5

Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
862
5

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
5

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
4


PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007
4

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
4

ART: a next-generation sequencing read simulator.
Weichun Huang, Leping Li, Jason R Myers, Gabor T Marth. Bioinformatics 2012
651
4


VSEARCH: a versatile open source tool for metagenomics.
Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé. PeerJ 2016
4

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
4

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
4

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
4


Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar,[...]. Nat Biotechnol 2019
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.