A citation-based method for searching scientific literature

Richard E Green, Johannes Krause, Adrian W Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F Hansen, Eric Y Durand, Anna-Sapfo Malaspinas, Jeffrey D Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A Burbano, Jeffrey M Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Vladimir B Doronichev, Liubov V Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W Schmitz, Philip L F Johnson, Evan E Eichler, Daniel Falush, Ewan Birney, James C Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich, Svante Pääbo. Science 2010
Times Cited: 1632







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



Times Cited
  Times     Co-cited
Similarity


Testing for ancient admixture between closely related populations.
Eric Y Durand, Nick Patterson, David Reich, Montgomery Slatkin. Mol Biol Evol 2011
522
31

The complete genome sequence of a Neanderthal from the Altai Mountains.
Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H Sudmant, Cesare de Filippo,[...]. Nature 2014
882
27

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
910
25

A high-coverage genome sequence from an archaic Denisovan individual.
Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G Schraiber, Flora Jay, Kay Prüfer, Cesare de Filippo,[...]. Science 2012
851
23


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

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
21


Evaluating the use of ABBA-BABA statistics to locate introgressed loci.
Simon H Martin, John W Davey, Chris D Jiggins. Mol Biol Evol 2015
238
18

A high-coverage Neandertal genome from Vindija Cave in Croatia.
Kay Prüfer, Cesare de Filippo, Steffi Grote, Fabrizio Mafessoni, Petra Korlević, Mateja Hajdinjak, Benjamin Vernot, Laurits Skov, Pinghsun Hsieh, Stéphane Peyrégne,[...]. Science 2017
201
18

The genomic landscape of Neanderthal ancestry in present-day humans.
Sriram Sankararaman, Swapan Mallick, Michael Dannemann, Kay Prüfer, Janet Kelso, Svante Pääbo, Nick Patterson, David Reich. Nature 2014
421
17

Fast model-based estimation of ancestry in unrelated individuals.
David H Alexander, John Novembre, Kenneth Lange. Genome Res 2009
16

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
16

Genetic history of an archaic hominin group from Denisova Cave in Siberia.
David Reich, Richard E Green, Martin Kircher, Johannes Krause, Nick Patterson, Eric Y Durand, Bence Viola, Adrian W Briggs, Udo Stenzel, Philip L F Johnson,[...]. Nature 2010
688
15

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.
Benjamin Vernot, Serena Tucci, Janet Kelso, Joshua G Schraiber, Aaron B Wolf, Rachel M Gittelman, Michael Dannemann, Steffi Grote, Rajiv C McCoy, Heather Norton,[...]. Science 2016
167
15

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14

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
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
13


ANGSD: Analysis of Next Generation Sequencing Data.
Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen. BMC Bioinformatics 2014
791
12


Gene tree discordance, phylogenetic inference and the multispecies coalescent.
James H Degnan, Noah A Rosenberg. Trends Ecol Evol 2009
817
11


Hybridization as an invasion of the genome.
James Mallet. Trends Ecol Evol 2005
859
11


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
96
11

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
517
11

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
11

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans.
Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich. Curr Biol 2016
172
11

An early modern human from Romania with a recent Neanderthal ancestor.
Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel,[...]. Nature 2015
251
11

A genomic perspective on hybridization and speciation.
Bret A Payseur, Loren H Rieseberg. Mol Ecol 2016
189
10

The date of interbreeding between Neandertals and modern humans.
Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, David Reich. PLoS Genet 2012
183
10


Reconstructing Indian population history.
David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes L Price, Lalji Singh. Nature 2009
872
10


The Strength of Selection against Neanderthal Introgression.
Ivan Juric, Simon Aeschbacher, Graham Coop. PLoS Genet 2016
137
10

A high-coverage Neandertal genome from Chagyrskaya Cave.
Fabrizio Mafessoni, Steffi Grote, Cesare de Filippo, Viviane Slon, Kseniya A Kolobova, Bence Viola, Sergey V Markin, Manjusha Chintalapati, Stephane Peyrégne, Laurits Skov,[...]. Proc Natl Acad Sci U S A 2020
43
23


Inferring Phylogenetic Networks Using PhyloNet.
Dingqiao Wen, Yun Yu, Jiafan Zhu, Luay Nakhleh. Syst Biol 2018
76
11


ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab. BMC Bioinformatics 2018
388
9

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares.
Matthew R Jones, L Scott Mills, Paulo Célio Alves, Colin M Callahan, Joel M Alves, Diana J R Lafferty, Francis M Jiggins, Jeffrey D Jensen, José Melo-Ferreira, Jeffrey M Good. Science 2018
96
9

Hybrid speciation.
James Mallet. Nature 2007
764
9

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.
James B Pease, David C Haak, Matthew W Hahn, Leonie C Moyle. PLoS Biol 2016
167
9

Bayesian inference of ancient human demography from individual genome sequences.
Ilan Gronau, Melissa J Hubisz, Brad Gulko, Charles G Danko, Adam Siepel. Nat Genet 2011
300
9

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


Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.
Matthias Meyer, Juan-Luis Arsuaga, Cesare de Filippo, Sarah Nagel, Ayinuer Aximu-Petri, Birgit Nickel, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell,[...]. Nature 2016
189
9

Multiple episodes of interbreeding between Neanderthal and modern humans.
Fernando A Villanea, Joshua G Schraiber. Nat Ecol Evol 2019
44
20


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.