A citation-based method for searching scientific literature

Jianmin Wang, Charles G Mullighan, John Easton, Stefan Roberts, Sue L Heatley, Jing Ma, Michael C Rusch, Ken Chen, Christopher C Harris, Li Ding, Linda Holmfeldt, Debbie Payne-Turner, Xian Fan, Lei Wei, David Zhao, John C Obenauer, Clayton Naeve, Elaine R Mardis, Richard K Wilson, James R Downing, Jinghui Zhang. Nat Methods 2011
Times Cited: 367







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



Times Cited
  Times     Co-cited
Similarity



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
39

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
27

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
25

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
25

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
24

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
23

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
657
23


LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
660
21

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
519
21

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
927
20

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
20

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
18

CONSERTING: integrating copy-number analysis with structural-variation detection.
Xiang Chen, Pankaj Gupta, Jianmin Wang, Joy Nakitandwe, Kathryn Roberts, James D Dalton, Matthew Parker, Samir Patel, Linda Holmfeldt, Debbie Payne,[...]. Nat Methods 2015
49
36

An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
17

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
16



Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
802
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
15

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.
Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B Alexandrov, Michael N Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C Rusch, John Easton,[...]. Nature 2018
377
11

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
11

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
137
11

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

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
10

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.
Daniel L Cameron, Jan Schröder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss. Genome Res 2017
116
10

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.
Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo, Yoichiro Kamatani. Genome Biol 2019
148
10


Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
9

The repertoire of mutational signatures in human cancer.
Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R Covington, Dmitry A Gordenin, Erik N Bergstrom,[...]. Nature 2020
901
9

BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping.
Xian Fan, Travis E Abbott, David Larson, Ken Chen. Curr Protoc Bioinformatics 2014
88
9

Diverse mechanisms of somatic structural variations in human cancer genomes.
Lixing Yang, Lovelace J Luquette, Nils Gehlenborg, Ruibin Xi, Psalm S Haseley, Chih-Heng Hsieh, Chengsheng Zhang, Xiaojia Ren, Alexei Protopopov, Lynda Chin,[...]. Cell 2013
213
8

Structural variation in the human genome.
Lars Feuk, Andrew R Carson, Stephen W Scherer. Nat Rev Genet 2006
8

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
Paul A Northcott, Catherine Lee, Thomas Zichner, Adrian M Stütz, Serap Erkek, Daisuke Kawauchi, David J H Shih, Volker Hovestadt, Marc Zapatka, Dominik Sturm,[...]. Nature 2014
362
8

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Bruno Zeitouni, Valentina Boeva, Isabelle Janoueix-Lerosey, Sophie Loeillet, Patricia Legoix-né, Alain Nicolas, Olivier Delattre, Emmanuel Barillot. Bioinformatics 2010
133
8

Mapping copy number variation by population-scale genome sequencing.
Ryan E Mills, Klaudia Walter, Chip Stewart, Robert E Handsaker, Ken Chen, Can Alkan, Alexej Abyzov, Seungtai Chris Yoon, Kai Ye, R Keira Cheetham,[...]. Nature 2011
739
8

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
8

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
Jinghui Zhang, Li Ding, Linda Holmfeldt, Gang Wu, Sue L Heatley, Debbie Payne-Turner, John Easton, Xiang Chen, Jianmin Wang, Michael Rusch,[...]. Nature 2012
8

The Pediatric Cancer Genome Project.
James R Downing, Richard K Wilson, Jinghui Zhang, Elaine R Mardis, Ching-Hon Pui, Li Ding, Timothy J Ley, William E Evans. Nat Genet 2012
220
8

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
497
8


Resolving the complexity of the human genome using single-molecule sequencing.
Mark J P Chaisson, John Huddleston, Megan Y Dennis, Peter H Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano,[...]. Nature 2015
418
7

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
7

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.
Faiyaz Notta, Michelle Chan-Seng-Yue, Mathieu Lemire, Yilong Li, Gavin W Wilson, Ashton A Connor, Robert E Denroche, Sheng-Ben Liang, Andrew M K Brown, Jaeseung C Kim,[...]. Nature 2016
298
7

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma.
Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan,[...]. JAMA Oncol 2017
159
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S Taylor, Charles Swanton. Genome Biol 2016
573
7

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
7

Clock-like mutational processes in human somatic cells.
Ludmil B Alexandrov, Philip H Jones, David C Wedge, Julian E Sale, Peter J Campbell, Serena Nik-Zainal, Michael R Stratton. Nat Genet 2015
497
7


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.