A citation-based method for searching scientific literature

Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo, Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin Lloyd Hibberd, Niranjan Nagarajan. Nucleic Acids Res 2012
Times Cited: 630







List of co-cited articles
378 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
32


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
23

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
16

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
16


Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
13

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
13

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
Andrew Rambaut, Edward C Holmes, Áine O'Toole, Verity Hill, John T McCrone, Christopher Ruis, Louis du Plessis, Oliver G Pybus. Nat Microbiol 2020
12



Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Strelka2: fast and accurate calling of germline and somatic variants.
Sangtae Kim, Konrad Scheffler, Aaron L Halpern, Mitchell A Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Yeonbin Kim, Doruk Beyter, Peter Krusche,[...]. Nat Methods 2018
406
10

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Nathan D Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L Matteson, Jaqueline Goes De Jesus, Bradley J Main, Amanda L Tan, Lauren M Paul, Doug E Brackney, Saran Grewal,[...]. Genome Biol 2019
289
10

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
Áine O'Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor,[...]. Virus Evol 2021
241
10

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
9

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
9

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
965
9

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear. Mol Biol Evol 2020
9

Nextstrain: real-time tracking of pathogen evolution.
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher. Bioinformatics 2018
8

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
8

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
8

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.
Qianqian Li, Jiajing Wu, Jianhui Nie, Li Zhang, Huan Hao, Shuo Liu, Chenyan Zhao, Qi Zhang, Huan Liu, Lingling Nie,[...]. Cell 2020
801
8

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Bette Korber, Will M Fischer, Sandrasegaram Gnanakaran, Hyejin Yoon, James Theiler, Werner Abfalterer, Nick Hengartner, Elena E Giorgi, Tanmoy Bhattacharya, Brian Foley,[...]. Cell 2020
8


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

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
7


Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.
Alexandra Popa, Jakob-Wendelin Genger, Michael D Nicholson, Thomas Penz, Daniela Schmid, Stephan W Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaço,[...]. Sci Transl Med 2020
111
7

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
6

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
Zhongwu Lai, Aleksandra Markovets, Miika Ahdesmaki, Brad Chapman, Oliver Hofmann, Robert McEwen, Justin Johnson, Brian Dougherty, J Carl Barrett, Jonathan R Dry. Nucleic Acids Res 2016
371
6

SARS-CoV-2 evolution during treatment of chronic infection.
Steven A Kemp, Dami A Collier, Rawlings P Datir, Isabella A T M Ferreira, Salma Gayed, Aminu Jahun, Myra Hosmillo, Chloe Rees-Spear, Petra Mlcochova, Ines Ushiro Lumb,[...]. Nature 2021
410
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
974
6

SARS-CoV-2 variants, spike mutations and immune escape.
William T Harvey, Alessandro M Carabelli, Ben Jackson, Ravindra K Gupta, Emma C Thomson, Ewan M Harrison, Catherine Ludden, Richard Reeve, Andrew Rambaut, Sharon J Peacock,[...]. Nat Rev Microbiol 2021
910
6

SARS-CoV-2 within-host diversity and transmission.
Katrina A Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett, Amy Trebes, Monique Andersson, Newton Otecko, Emma L Wise, Nathan Moore,[...]. Science 2021
112
6

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
6

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
5

Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population.
Marco Vignuzzi, Jeffrey K Stone, Jamie J Arnold, Craig E Cameron, Raul Andino. Nature 2006
721
5

Genetic bottlenecks in intraspecies virus transmission.
John T McCrone, Adam S Lauring. Curr Opin Virol 2018
67
7


Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R F Twigg, Andrew O M Wilkie, Gil McVean, Gerton Lunter. Nat Genet 2014
581
5

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
Eric Talevich, A Hunter Shain, Thomas Botton, Boris C Bastian. PLoS Comput Biol 2016
709
5

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice.
Shuai Jin, Yuan Zong, Qiang Gao, Zixu Zhu, Yanpeng Wang, Peng Qin, Chengzhi Liang, Daowen Wang, Jin-Long Qiu, Feng Zhang,[...]. Science 2019
288
5

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis.
Changyang Zhou, Yidi Sun, Rui Yan, Yajing Liu, Erwei Zuo, Chan Gu, Linxiao Han, Yu Wei, Xinde Hu, Rong Zeng,[...]. Nature 2019
197
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
534
5


Quasispecies theory and the behavior of RNA viruses.
Adam S Lauring, Raul Andino. PLoS Pathog 2010
495
5

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences.
Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura. BMC Bioinformatics 2021
10
50

UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
4

Virological assessment of hospitalized patients with COVID-2019.
Roman Wölfel, Victor M Corman, Wolfgang Guggemos, Michael Seilmaier, Sabine Zange, Marcel A Müller, Daniela Niemeyer, Terry C Jones, Patrick Vollmar, Camilla Rothe,[...]. Nature 2020
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.