A citation-based method for searching scientific literature

J C Barrett, B Fry, J Maller, M J Daly. Bioinformatics 2005
Times Cited: 11191







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



Times Cited
  Times     Co-cited
Similarity


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
31

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
18

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
13

The structure of haplotype blocks in the human genome.
Stacey B Gabriel, Stephen F Schaffner, Huy Nguyen, Jamie M Moore, Jessica Roy, Brendan Blumenstiel, John Higgins, Matthew DeFelice, Amy Lochner, Maura Faggart,[...]. Science 2002
12

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
11

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
10

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
10

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
10


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

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
6

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

A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.
Jianming Yu, Gael Pressoir, William H Briggs, Irie Vroh Bi, Masanori Yamasaki, John F Doebley, Michael D McMullen, Brandon S Gaut, Dahlia M Nielsen, James B Holland,[...]. Nat Genet 2006
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5


GAPIT: genome association and prediction integrated tool.
Alexander E Lipka, Feng Tian, Qishan Wang, Jason Peiffer, Meng Li, Peter J Bradbury, Michael A Gore, Edward S Buckler, Zhiwu Zhang. Bioinformatics 2012
788
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5



StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
4

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
855
4


From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Geraldine A Van der Auwera, Mauricio O Carneiro, Christopher Hartl, Ryan Poplin, Guillermo Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault,[...]. Curr Protoc Bioinformatics 2013
4

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4



A new statistical method for haplotype reconstruction from population data.
M Stephens, N J Smith, P Donnelly. Am J Hum Genet 2001
4

A One-Penny Imputed Genome from Next-Generation Reference Panels.
Brian L Browning, Ying Zhou, Sharon R Browning. Am J Hum Genet 2018
238
4

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
848
3


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
3


HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
3


The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
3

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
3

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
3

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
3


Annotation of functional variation in personal genomes using RegulomeDB.
Alan P Boyle, Eurie L Hong, Manoj Hariharan, Yong Cheng, Marc A Schaub, Maya Kasowski, Konrad J Karczewski, Julie Park, Benjamin C Hitz, Shuai Weng,[...]. Genome Res 2012
3


Shifting the limits in wheat research and breeding using a fully annotated reference genome.
Rudi Appels, Kellye Eversole, Catherine Feuillet, Beat Keller, Jane Rogers, Nils Stein, Curtis J Pozniak, Nils Stein, Frédéric Choulet, Assaf Distelfeld,[...]. Science 2018
950
3


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
931
3

An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
947
3

Variance component model to account for sample structure in genome-wide association studies.
Hyun Min Kang, Jae Hoon Sul, Susan K Service, Noah A Zaitlen, Sit-Yee Kong, Nelson B Freimer, Chiara Sabatti, Eleazar Eskin. Nat Genet 2010
3

Association of genetic polymorphisms with age at menarche in Russian women.
Irina Ponomarenko, Evgeny Reshetnikov, Oksana Altuchova, Alexey Polonikov, Inna Sorokina, Anna Yermachenko, Volodymyr Dvornyk, Oleg Golovchenko, Mikhail Churnosov. Gene 2019
16
18

An adaptive permutation approach for genome-wide association study: evaluation and recommendations for use.
Ronglin Che, John R Jack, Alison A Motsinger-Reif, Chad C Brown. BioData Min 2014
35
8

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
3


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.