Mamunur Rashid, Carla Daniela Robles-Espinoza, Alistair G Rust, David J Adams. Bioinformatics 2013
Times Cited: 24
Times Cited: 24
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
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
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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
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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
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
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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
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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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
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
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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
Nicola D Roberts, R Daniel Kortschak, Wendy T Parker, Andreas W Schreiber, Susan Branford, Hamish S Scott, Garique Glonek, David L Adelson. Bioinformatics 2013
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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
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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
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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
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
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JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
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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
Qingguo Wang, Peilin Jia, Fei Li, Haiquan Chen, Hongbin Ji, Donald Hucks, Kimberly Brown Dahlman, William Pao, Zhongming Zhao. Genome Med 2013
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Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.
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An ensemble approach to accurately detect somatic mutations using SomaticSeq.
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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
Anne Bruun Krøigård, Mads Thomassen, Anne-Vibeke Lænkholm, Torben A Kruse, Martin Jakob Larsen. PLoS One 2016
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Signatures of mutational processes in human cancer.
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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
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Combining calls from multiple somatic mutation-callers.
Su Yeon Kim, Laurent Jacob, Terence P Speed. BMC Bioinformatics 2014
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A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.
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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.
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Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
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Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
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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
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
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An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.
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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
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Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
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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
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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
Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Nat Biotechnol 2014
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Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
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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
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
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From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
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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
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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
Brandi L Cantarel, Daniel Weaver, Nathan McNeill, Jianhua Zhang, Aaron J Mackey, Justin Reese. BMC Bioinformatics 2014
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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
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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
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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Kai Ye, Marcel H Schulz, Quan Long, Rolf Apweiler, Zemin Ning. Bioinformatics 2009
Kai Ye, Marcel H Schulz, Quan Long, Rolf Apweiler, Zemin Ning. Bioinformatics 2009
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In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data.
Lei Cai, Wei Yuan, Zhou Zhang, Lin He, Kuo-Chen Chou. Sci Rep 2016
Lei Cai, Wei Yuan, Zhou Zhang, Lin He, Kuo-Chen Chou. Sci Rep 2016
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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
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The variant call format and VCFtools.
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Comparing somatic mutation-callers: beyond Venn diagrams.
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The Catalogue of Somatic Mutations in Cancer (COSMIC).
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A comprehensive catalogue of somatic mutations from a human cancer genome.
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Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.
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Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
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BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
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dbSNP: the NCBI database of genetic variation.
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Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.
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Somatic point mutation calling in low cellularity tumors.
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Genetic basis for clinical response to CTLA-4 blockade in melanoma.
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Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
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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.