A citation-based method for searching scientific literature

Julian Catchen, Paul A Hohenlohe, Susan Bassham, Angel Amores, William A Cresko. Mol Ecol 2013
Times Cited: 1502







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



Times Cited
  Times     Co-cited
Similarity


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
42

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
30



Inference of population structure using multilocus genotype data.
J K Pritchard, M Stephens, P Donnelly. Genetics 2000
27

Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species.
Brant K Peterson, Jesse N Weber, Emily H Kay, Heidi S Fisher, Hopi E Hoekstra. PLoS One 2012
26


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
23

Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Nathan A Baird, Paul D Etter, Tressa S Atwood, Mark C Currey, Anthony L Shiver, Zachary A Lewis, Eric U Selker, William A Cresko, Eric A Johnson. PLoS One 2008
23

Stacks: building and genotyping Loci de novo from short-read sequences.
Julian M Catchen, Angel Amores, Paul Hohenlohe, William Cresko, John H Postlethwait. G3 (Bethesda) 2011
967
21

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
18

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.
Thibaut Jombart, Ismaïl Ahmed. Bioinformatics 2011
17

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
17

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
17


A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
Robert J Elshire, Jeffrey C Glaubitz, Qi Sun, Jesse A Poland, Ken Kawamoto, Edward S Buckler, Sharon E Mitchell. PLoS One 2011
16




Fast model-based estimation of ancestry in unrelated individuals.
David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
13


Harnessing the power of RADseq for ecological and evolutionary genomics.
Kimberly R Andrews, Jeffrey M Good, Michael R Miller, Gordon Luikart, Paul A Hohenlohe. Nat Rev Genet 2016
510
13

Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics.
Nicolas C Rochette, Angel G Rivera-Colón, Julian M Catchen. Mol Ecol 2019
176
11



BEAST 2: a software platform for Bayesian evolutionary analysis.
Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A Suchard, Andrew Rambaut, Alexei J Drummond. PLoS Comput Biol 2014
9


Application of phylogenetic networks in evolutionary studies.
Daniel H Huson, David Bryant. Mol Biol Evol 2006
9

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
9



ANGSD: Analysis of Next Generation Sequencing Data.
Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen. BMC Bioinformatics 2014
906
9

2b-RAD: a simple and flexible method for genome-wide genotyping.
Shi Wang, Eli Meyer, John K McKay, Mikhail V Matz. Nat Methods 2012
278
8

Deriving genotypes from RAD-seq short-read data using Stacks.
Nicolas C Rochette, Julian M Catchen. Nat Protoc 2017
133
8

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
Naama M Kopelman, Jonathan Mayzel, Mattias Jakobsson, Noah A Rosenberg, Itay Mayrose. Mol Ecol Resour 2015
902
8

Fast and efficient estimation of individual ancestry coefficients.
Eric Frichot, François Mathieu, Théo Trouillon, Guillaume Bouchard, Olivier François. Genetics 2014
288
8

Genomics of local adaptation with gene flow.
Anna Tigano, Vicki L Friesen. Mol Ecol 2016
142
8


Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.
David Bryant, Remco Bouckaert, Joseph Felsenstein, Noah A Rosenberg, Arindam RoyChoudhury. Mol Biol Evol 2012
441
7

A high-performance computing toolset for relatedness and principal component analysis of SNP data.
Xiuwen Zheng, David Levine, Jess Shen, Stephanie M Gogarten, Cathy Laurie, Bruce S Weir. Bioinformatics 2012
915
7






Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
6

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
6

These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists.
Shannon J O'Leary, Jonathan B Puritz, Stuart C Willis, Christopher M Hollenbeck, David S Portnoy. Mol Ecol 2018
88
6

A One-Penny Imputed Genome from Next-Generation Reference Panels.
Brian L Browning, Ying Zhou, Sharon R Browning. Am J Hum Genet 2018
386
6

Robust demographic inference from genomic and SNP data.
Laurent Excoffier, Isabelle Dupanloup, Emilia Huerta-Sánchez, Vitor C Sousa, Matthieu Foll. PLoS Genet 2013
639
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.