A citation-based method for searching scientific literature

Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J Lyon, Hakon Hakonarson. Nucleic Acids Res 2011
Times Cited: 168







List of co-cited articles
500 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
52

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
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
620
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
34


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
31

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
29

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
26

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
20

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

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
576
16


VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Daniel C Koboldt, Ken Chen, Todd Wylie, David E Larson, Michael D McLellan, Elaine R Mardis, George M Weinstock, Richard K Wilson, Li Ding. Bioinformatics 2009
799
15


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
362
14

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
13

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.
Jason O'Rawe, Tao Jiang, Guangqing Sun, Yiyang Wu, Wei Wang, Jingchu Hu, Paul Bodily, Lifeng Tian, Hakon Hakonarson, W Evan Johnson,[...]. Genome Med 2013
287
12


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
11

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
10

dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
10

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.
Sarah Sandmann, Aniek O de Graaf, Mohsen Karimi, Bert A van der Reijden, Eva Hellström-Lindberg, Joop H Jansen, Martin Dugas. Sci Rep 2017
103
10



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
952
9

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
9

A survey of tools for variant analysis of next-generation genome sequencing data.
Stephan Pabinger, Andreas Dander, Maria Fischer, Rene Snajder, Michael Sperk, Mirjana Efremova, Birgit Krabichler, Michael R Speicher, Johannes Zschocke, Zlatko Trajanoski. Brief Bioinform 2014
308
8

Detection of ultra-rare mutations by next-generation sequencing.
Michael W Schmitt, Scott R Kennedy, Jesse J Salk, Edward J Fox, Joseph B Hiatt, Lawrence A Loeb. Proc Natl Acad Sci U S A 2012
581
8

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7


Variant callers for next-generation sequencing data: a comparison study.
Xiangtao Liu, Shizhong Han, Zuoheng Wang, Joel Gelernter, Bao-Zhu Yang. PLoS One 2013
94
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

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Nat Biotechnol 2014
445
7

SomaticSniper: identification of somatic point mutations in whole genome sequencing data.
David E Larson, Christopher C Harris, Ken Chen, Daniel C Koboldt, Travis E Abbott, David J Dooling, Timothy J Ley, Elaine R Mardis, Richard K Wilson, Li Ding. Bioinformatics 2012
366
7

Systematic comparison of variant calling pipelines using gold standard personal exome variants.
Sohyun Hwang, Eiru Kim, Insuk Lee, Edward M Marcotte. Sci Rep 2015
169
7


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
6

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
6


DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
6

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.
Dianne I Lou, Jeffrey A Hussmann, Ross M McBee, Ashley Acevedo, Raul Andino, William H Press, Sara L Sawyer. Proc Natl Acad Sci U S A 2013
177
6

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID.
Cassandra B Jabara, Corbin D Jones, Jeffrey Roach, Jeffrey A Anderson, Ronald Swanstrom. Proc Natl Acad Sci U S A 2011
272
6

Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.
Christian Schlötterer, Raymond Tobler, Robert Kofler, Viola Nolte. Nat Rev Genet 2014
364
6

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.
Yuichi Shiraishi, Yusuke Sato, Kenichi Chiba, Yusuke Okuno, Yasunobu Nagata, Kenichi Yoshida, Norio Shiba, Yasuhide Hayashi, Haruki Kume, Yukio Homma,[...]. Nucleic Acids Res 2013
125
6

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt. BMC Syst Biol 2016
19
31

A universal SNP and small-indel variant caller using deep neural networks.
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar,[...]. Nat Biotechnol 2018
264
6

SOAP2: an improved ultrafast tool for short read alignment.
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang. Bioinformatics 2009
5

Searching for SNPs with cloud computing.
Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg. Genome Biol 2009
5

SNP detection for massively parallel whole-genome resequencing.
Ruiqiang Li, Yingrui Li, Xiaodong Fang, Huanming Yang, Jian Wang, Karsten Kristiansen, Jun Wang. Genome Res 2009
625
5

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.
Nathan L Clement, Quinn Snell, Mark J Clement, Peter C Hollenhorst, Jahnvi Purwar, Barbara J Graves, Bradley R Cairns, W Evan Johnson. Bioinformatics 2010
47
10

Validation and assessment of variant calling pipelines for next-generation sequencing.
Mehdi Pirooznia, Melissa Kramer, Jennifer Parla, Fernando S Goes, James B Potash, W Richard McCombie, Peter P Zandi. Hum Genomics 2014
75
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.