A citation-based method for searching scientific literature

David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
Times Cited: 3175







List of co-cited articles
501 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

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
40

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
28


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
26

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
16


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
16

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
15

Population structure and eigenanalysis.
Nick Patterson, Alkes L Price, David Reich. PLoS Genet 2006
14


Stacks: an analysis tool set for population genomics.
Julian Catchen, Paul A Hohenlohe, Susan Bassham, Angel Amores, William A Cresko. Mol Ecol 2013
11


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
11

Ancient admixture in human history.
Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, David Reich. Genetics 2012
998
11

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
10

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.
Chi Zhang, Shan-Shan Dong, Jun-Yang Xu, Wei-Ming He, Tie-Lin Yang. Bioinformatics 2019
262
10


GCTA: a tool for genome-wide complex trait analysis.
Jian Yang, S Hong Lee, Michael E Goddard, Peter M Visscher. Am J Hum Genet 2011
10

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
9


Robust relationship inference in genome-wide association studies.
Ani Manichaikul, Josyf C Mychaleckyj, Stephen S Rich, Kathy Daly, Michèle Sale, Wei-Min Chen. Bioinformatics 2010
8


BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8

TASSEL: software for association mapping of complex traits in diverse samples.
Peter J Bradbury, Zhiwu Zhang, Dallas E Kroon, Terry M Casstevens, Yogesh Ramdoss, Edward S Buckler. Bioinformatics 2007
8

A linear complexity phasing method for thousands of genomes.
Olivier Delaneau, Jonathan Marchini, Jean-François Zagury. Nat Methods 2011
7

Principal components analysis corrects for stratification in genome-wide association studies.
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick, David Reich. Nat Genet 2006
7


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
7


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
7


The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon,[...]. Nature 2016
572
7


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
6


Inference of population structure using dense haplotype data.
Daniel John Lawson, Garrett Hellenthal, Simon Myers, Daniel Falush. PLoS Genet 2012
538
6

Next-generation genotype imputation service and methods.
Sayantan Das, Lukas Forer, Sebastian Schönherr, Carlo Sidore, Adam E Locke, Alan Kwong, Scott I Vrieze, Emily Y Chew, Shawn Levy, Matt McGue,[...]. Nat Genet 2016
6

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
6

Inference of population structure using multilocus genotype data.
J K Pritchard, M Stephens, P Donnelly. Genetics 2000
6


vcfr: a package to manipulate and visualize variant call format data in R.
Brian J Knaus, Niklaus J Grünwald. Mol Ecol Resour 2017
238
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
392
5

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
5


Robust demographic inference from genomic and SNP data.
Laurent Excoffier, Isabelle Dupanloup, Emilia Huerta-Sánchez, Vitor C Sousa, Matthieu Foll. PLoS Genet 2013
639
5

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
5




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.