A citation-based method for searching scientific literature

Valentina Boeva, Tatiana Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot. Bioinformatics 2012
Times Cited: 525







List of co-cited articles
475 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
35

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
22

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
20

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
19

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
989
14

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
14


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
13

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
12

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
12

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
680
11

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
977
11

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
731
10

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
10

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
670
9


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9

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
9


Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
808
8

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
8

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
8

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
8

CREST maps somatic structural variation in cancer genomes with base-pair resolution.
Jianmin Wang, Charles G Mullighan, John Easton, Stefan Roberts, Sue L Heatley, Jing Ma, Michael C Rusch, Ken Chen, Christopher C Harris, Li Ding,[...]. Nat Methods 2011
369
8

Absolute quantification of somatic DNA alterations in human cancer.
Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir,[...]. Nat Biotechnol 2012
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

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.
Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao. BMC Bioinformatics 2013
289
7

Sensitive and accurate detection of copy number variants using read depth of coverage.
Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye, Jonathan Sebat. Genome Res 2009
369
7


SvABA: genome-wide detection of structural variants and indels by local assembly.
Jeremiah A Wala, Pratiti Bandopadhayay, Noah F Greenwald, Ryan O'Rourke, Ted Sharpe, Chip Stewart, Steve Schumacher, Yilong Li, Joachim Weischenfeldt, Xiaotong Yao,[...]. Genome Res 2018
143
7

MuSiC: identifying mutational significance in cancer genomes.
Nathan D Dees, Qunyuan Zhang, Cyriac Kandoth, Michael C Wendl, William Schierding, Daniel C Koboldt, Thomas B Mooney, Matthew B Callaway, David Dooling, Elaine R Mardis,[...]. Genome Res 2012
417
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
7


IntSIM: An Integrated Simulator of Next-Generation Sequencing Data.
Xiguo Yuan, Junying Zhang, Liying Yang. IEEE Trans Biomed Eng 2017
30
20

iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.
Prashanthi Dharanipragada, Sriharsha Vogeti, Nita Parekh. PLoS One 2018
25
24

CONDEL: Detecting Copy Number Variation and Genotyping Deletion Zygosity from Single Tumor Samples Using Sequence Data.
Xiguo Yuan, Jun Bai, Junying Zhang, Liying Yang, Junbo Duan, Yaoyao Li, Meihong Gao. IEEE/ACM Trans Comput Biol Bioinform 2020
27
22

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang, Devin P Locke,[...]. Nat Methods 2009
931
6

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
420
6


OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
David Tamborero, Abel Gonzalez-Perez, Nuria Lopez-Bigas. Bioinformatics 2013
267
6

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.
F Favero, T Joshi, A M Marquard, N J Birkbak, M Krzystanek, Q Li, Z Szallasi, A C Eklund. Ann Oncol 2015
301
6

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
6

Allele-specific copy number analysis of tumors.
Peter Van Loo, Silje H Nordgard, Ole Christian Lingjærde, Hege G Russnes, Inga H Rye, Wei Sun, Victor J Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume,[...]. Proc Natl Acad Sci U S A 2010
656
6

Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
515
6

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
6

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.
Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny, Sheida Nabavi. BMC Bioinformatics 2017
79
6

A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data.
Brett Trost, Susan Walker, Zhuozhi Wang, Bhooma Thiruvahindrapuram, Jeffrey R MacDonald, Wilson W L Sung, Sergio L Pereira, Joe Whitney, Ada J S Chan, Giovanna Pellecchia,[...]. Am J Hum Genet 2018
97
5


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.