A citation-based method for searching scientific literature

Joseph K Pickrell, Jonathan K Pritchard. PLoS Genet 2012
Times Cited: 905







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



Times Cited
  Times     Co-cited
Similarity


Fast model-based estimation of ancestry in unrelated individuals.
David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
44

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
38

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
36


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
868
30

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
29

Reconstructing Indian population history.
David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes L Price, Lalji Singh. Nature 2009
858
26

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
24

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
21


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
20


Stacks: an analysis tool set for population genomics.
Julian Catchen, Paul A Hohenlohe, Susan Bassham, Angel Amores, William A Cresko. Mol Ecol 2013
17

Population structure and eigenanalysis.
Nick Patterson, Alkes L Price, David Reich. PLoS Genet 2006
16

ANGSD: Analysis of Next Generation Sequencing Data.
Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen. BMC Bioinformatics 2014
755
15

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
13


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
12

Robust demographic inference from genomic and SNP data.
Laurent Excoffier, Isabelle Dupanloup, Emilia Huerta-Sánchez, Vitor C Sousa, Matthieu Foll. PLoS Genet 2013
563
12

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
776
11

Application of phylogenetic networks in evolutionary studies.
Daniel H Huson, David Bryant. Mol Biol Evol 2006
11



Inference of population structure using multilocus genotype data.
J K Pritchard, M Stephens, P Donnelly. Genetics 2000
9

A draft sequence of the Neandertal genome.
Richard E Green, Johannes Krause, Adrian W Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz,[...]. Science 2010
9

Testing for ancient admixture between closely related populations.
Eric Y Durand, Nick Patterson, David Reich, Montgomery Slatkin. Mol Biol Evol 2011
506
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9

Evaluating the use of ABBA-BABA statistics to locate introgressed loci.
Simon H Martin, John W Davey, Chris D Jiggins. Mol Biol Evol 2015
229
9

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.
Thibaut Jombart, Ismaïl Ahmed. Bioinformatics 2011
945
8


Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard. Syst Biol 2018
8

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.
Maanasa Raghavan, Pontus Skoglund, Kelly E Graf, Mait Metspalu, Anders Albrechtsen, Ida Moltke, Simon Rasmussen, Thomas W Stafford, Ludovic Orlando, Ene Metspalu,[...]. Nature 2014
342
8

fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Anil Raj, Matthew Stephens, Jonathan K Pritchard. Genetics 2014
579
8

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
8

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
8

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
7

Quartet inference from SNP data under the coalescent model.
Julia Chifman, Laura Kubatko. Bioinformatics 2014
373
7


Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA.
Emilia Huerta-Sánchez, Xin Jin, Asan, Zhuoma Bianba, Benjamin M Peter, Nicolas Vinckenbosch, Yu Liang, Xin Yi, Mingze He, Mehmet Somel,[...]. Nature 2014
419
7


Inference of population structure using dense haplotype data.
Daniel John Lawson, Garrett Hellenthal, Simon Myers, Daniel Falush. PLoS Genet 2012
486
7

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
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
773
7

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
7

ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
7

Dsuite - Fast D-statistics and related admixture evidence from VCF files.
Milan Malinsky, Michael Matschiner, Hannes Svardal. Mol Ecol Resour 2021
37
16

ipyrad: Interactive assembly and analysis of RADseq datasets.
Deren A R Eaton, Isaac Overcast. Bioinformatics 2020
63
9

UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
6

Genomic architecture and introgression shape a butterfly radiation.
Nathaniel B Edelman, Paul B Frandsen, Miriam Miyagi, Bernardo Clavijo, John Davey, Rebecca B Dikow, Gonzalo García-Accinelli, Steven M Van Belleghem, Nick Patterson, Daniel E Neafsey,[...]. Science 2019
84
7

Reconstructing Native American population history.
David Reich, Nick Patterson, Desmond Campbell, Arti Tandon, Stéphane Mazieres, Nicolas Ray, Maria V Parra, Winston Rojas, Constanza Duque, Natalia Mesa,[...]. Nature 2012
362
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.