A citation-based method for searching scientific literature

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, Gilean McVean, Richard Durbin. Bioinformatics 2011
Times Cited: 4476







List of co-cited articles
340 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
41


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
25

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
24

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
22

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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
15

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
13



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
10

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
9


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
8

Stacks: an analysis tool set for population genomics.
Julian Catchen, Paul A Hohenlohe, Susan Bassham, Angel Amores, William A Cresko. Mol Ecol 2013
8


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

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
7

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
168
7

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
7

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
7

Application of phylogenetic networks in evolutionary studies.
Daniel H Huson, David Bryant. Mol Biol Evol 2006
7

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
Jeffrey C Glaubitz, Terry M Casstevens, Fei Lu, James Harriman, Robert J Elshire, Qi Sun, Edward S Buckler. PLoS One 2014
651
6

DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M Stütz, Vladimir Benes, Jan O Korbel. Bioinformatics 2012
834
6


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
6

R/qtl: QTL mapping in experimental crosses.
Karl W Broman, Hao Wu, Saunak Sen, Gary A Churchill. Bioinformatics 2003
6



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
6

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
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
5

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
947
5


Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Wensheng Wang, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, Tianqing Zheng, Roven Rommel Fuentes, Fan Zhang,[...]. Nature 2018
374
5

Testing for ancient admixture between closely related populations.
Eric Y Durand, Nick Patterson, David Reich, Montgomery Slatkin. Mol Biol Evol 2011
506
5

Haploview: analysis and visualization of LD and haplotype maps.
J C Barrett, B Fry, J Maller, M J Daly. Bioinformatics 2005
5

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
5


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
5


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
5


Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
5

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations.
Brenna R Forester, Jesse R Lasky, Helene H Wagner, Dean L Urban. Mol Ecol 2018
112
5



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
910
4

The genomic basis of adaptive evolution in threespine sticklebacks.
Felicity C Jones, Manfred G Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C Zody, Simon White,[...]. Nature 2012
957
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.