A citation-based method for searching scientific literature

Mamunur Rashid, Carla Daniela Robles-Espinoza, Alistair G Rust, David J Adams. Bioinformatics 2013
Times Cited: 24







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



Times Cited
  Times     Co-cited
Similarity


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
75

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
62

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
356
62

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
54

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
936
45

A comparative analysis of algorithms for somatic SNV detection in cancer.
Nicola D Roberts, R Daniel Kortschak, Wendy T Parker, Andreas W Schreiber, Susan Branford, Hamish S Scott, Garique Glonek, David L Adelson. Bioinformatics 2013
62
37

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Takafumi N Yamaguchi, J Christopher Bare, Christine P'ng, Daryl Waggott, Veronica Y Sabelnykova,[...]. Nat Methods 2015
167
33

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
29

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
29


JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Andrew Roth, Jiarui Ding, Ryan Morin, Anamaria Crisan, Gavin Ha, Ryan Giuliany, Ali Bashashati, Martin Hirst, Gulisa Turashvili, Arusha Oloumi,[...]. Bioinformatics 2012
113
29

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers.
Qingguo Wang, Peilin Jia, Fei Li, Haiquan Chen, Hongbin Ji, Donald Hucks, Kimberly Brown Dahlman, William Pao, Zhongming Zhao. Genome Med 2013
116
29

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.
Huilei Xu, John DiCarlo, Ravi Vijaya Satya, Quan Peng, Yexun Wang. BMC Genomics 2014
96
29

An ensemble approach to accurately detect somatic mutations using SomaticSeq.
Li Tai Fang, Pegah Tootoonchi Afshar, Aparna Chhibber, Marghoob Mohiyuddin, Yu Fan, John C Mu, Greg Gibeling, Sharon Barr, Narges Bani Asadi, Mark B Gerstein,[...]. Genome Biol 2015
47
29

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
Anne Bruun Krøigård, Mads Thomassen, Anne-Vibeke Lænkholm, Torben A Kruse, Martin Jakob Larsen. PLoS One 2016
88
29

Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
25

Combining calls from multiple somatic mutation-callers.
Su Yeon Kim, Laurent Jacob, Terence P Speed. BMC Bioinformatics 2014
13
46

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.
Tyler S Alioto, Ivo Buchhalter, Sophia Derdak, Barbara Hutter, Matthew D Eldridge, Eivind Hovig, Lawrence E Heisler, Timothy A Beck, Jared T Simpson, Laurie Tonon,[...]. Nat Commun 2015
174
25

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
285
20

Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
Nancy F Hansen, Jared J Gartner, Lan Mei, Yardena Samuels, James C Mullikin. Bioinformatics 2013
41
20

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
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
20

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
121
20

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.
Yu Fan, Liu Xi, Daniel S T Hughes, Jianjun Zhang, Jianhua Zhang, P Andrew Futreal, David A Wheeler, Wenyi Wang. Genome Biol 2016
105
20

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A Marra, Anne Condon,[...]. Bioinformatics 2012
91
20

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
346
20

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
439
16

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger, Andrew J Rowan, Stuart Horswell, M Math, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart,[...]. N Engl J Med 2012
16

A simple consensus approach improves somatic mutation prediction accuracy.
David L Goode, Sally M Hunter, Maria A Doyle, Tao Ma, Simone M Rowley, David Choong, Georgina L Ryland, Ian G Campbell. Genome Med 2013
23
17

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
16

Virmid: accurate detection of somatic mutations with sample impurity inference.
Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G Gleeson, Vineet Bafna. Genome Biol 2013
45
16

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.
Brandi L Cantarel, Daniel Weaver, Nathan McNeill, Jianhua Zhang, Aaron J Mackey, Justin Reese. BMC Bioinformatics 2014
34
16

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
16

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
16



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
373
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
12

Comparing somatic mutation-callers: beyond Venn diagrams.
Su Yeon Kim, Terence P Speed. BMC Bioinformatics 2013
50
12

The Catalogue of Somatic Mutations in Cancer (COSMIC).
S A Forbes, G Bhamra, S Bamford, E Dawson, C Kok, J Clements, A Menzies, J W Teague, P A Futreal, M R Stratton. Curr Protoc Hum Genet 2008
566
12

A comprehensive catalogue of somatic mutations from a human cancer genome.
Erin D Pleasance, R Keira Cheetham, Philip J Stephens, David J McBride, Sean J Humphray, Chris D Greenman, Ignacio Varela, Meng-Lay Lin, Gonzalo R Ordóñez, Graham R Bignell,[...]. Nature 2010
12

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.
Valentina Boeva, Tatiana Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot. Bioinformatics 2012
504
12

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
12


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
12

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.
Michael N Edmonson, Jinghui Zhang, Chunhua Yan, Richard P Finney, Daoud M Meerzaman, Kenneth H Buetow. Bioinformatics 2011
78
12

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.
Alexis Christoforides, John D Carpten, Glen J Weiss, Michael J Demeure, Daniel D Von Hoff, David W Craig. BMC Genomics 2013
56
12

Somatic point mutation calling in low cellularity tumors.
Karin S Kassahn, Oliver Holmes, Katia Nones, Ann-Marie Patch, David K Miller, Angelika N Christ, Ivon Harliwong, Timothy J Bruxner, Qinying Xu, Matthew Anderson,[...]. PLoS One 2013
46
12

Genetic basis for clinical response to CTLA-4 blockade in melanoma.
Alexandra Snyder, Vladimir Makarov, Taha Merghoub, Jianda Yuan, Jesse M Zaretsky, Alexis Desrichard, Logan A Walsh, Michael A Postow, Phillip Wong, Teresa S Ho,[...]. N Engl J Med 2014
12

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Eliezer M Van Allen, Diana Miao, Bastian Schilling, Sachet A Shukla, Christian Blank, Lisa Zimmer, Antje Sucker, Uwe Hillen, Marnix H Geukes Foppen, Simone M Goldinger,[...]. Science 2015
12


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.