A citation-based method for searching scientific literature

Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao. BMC Bioinformatics 2013
Times Cited: 254







List of co-cited articles
588 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
27

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
736
22

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
535
21


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
803
20

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
863
17

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
342
17

Global variation in copy number in the human genome.
Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, T Daniel Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen,[...]. Nature 2006
17

Whole-genome CNV analysis: advances in computational approaches.
Mehdi Pirooznia, Fernando S Goes, Peter P Zandi. Front Genet 2015
79
20

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
936
16

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.
Vincent Plagnol, James Curtis, Michael Epstein, Kin Y Mok, Emma Stebbings, Sofia Grigoriadou, Nicholas W Wood, Sophie Hambleton, Siobhan O Burns, Adrian J Thrasher,[...]. Bioinformatics 2012
293
15

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
368
14



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
13

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
444
13

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
12

The Database of Genomic Variants: a curated collection of structural variation in the human genome.
Jeffrey R MacDonald, Robert Ziman, Ryan K C Yuen, Lars Feuk, Stephen W Scherer. Nucleic Acids Res 2014
632
12

Copy number variation in human health, disease, and evolution.
Feng Zhang, Wenli Gu, Matthew E Hurles, James R Lupski. Annu Rev Genomics Hum Genet 2009
693
12

Structural variation in the human genome.
Lars Feuk, Andrew R Carson, Stephen W Scherer. Nat Rev Genet 2006
11

Structural variation in the human genome and its role in disease.
Paweł Stankiewicz, James R Lupski. Annu Rev Med 2010
670
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
480
11

Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.
Menachem Fromer, Jennifer L Moran, Kimberly Chambert, Eric Banks, Sarah E Bergen, Douglas M Ruderfer, Robert E Handsaker, Steven A McCarroll, Michael C O'Donovan, Michael J Owen,[...]. Am J Hum Genet 2012
331
11

Detection of Genomic Structural Variants from Next-Generation Sequencing Data.
Lorenzo Tattini, Romina D'Aurizio, Alberto Magi. Front Bioeng Biotechnol 2015
131
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

Circular binary segmentation for the analysis of array-based DNA copy number data.
Adam B Olshen, E S Venkatraman, Robert Lucito, Michael Wigler. Biostatistics 2004
10

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.
Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter. Nucleic Acids Res 2012
233
9


Computational methods for discovering structural variation with next-generation sequencing.
Paul Medvedev, Monica Stanciu, Michael Brudno. Nat Methods 2009
331
9

Copy number variation detection and genotyping from exome sequence data.
Niklas Krumm, Peter H Sudmant, Arthur Ko, Brian J O'Roak, Maika Malig, Bradley P Coe, Aaron R Quinlan, Deborah A Nickerson, Evan E Eichler. Genome Res 2012
359
9

High-resolution mapping of copy-number alterations with massively parallel sequencing.
Derek Y Chiang, Gad Getz, David B Jaffe, Michael J T O'Kelly, Xiaojun Zhao, Scott L Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson, Eric S Lander. Nat Methods 2009
349
9

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
57
15

Origins and functional impact of copy number variation in the human genome.
Donald F Conrad, Dalila Pinto, Richard Redon, Lars Feuk, Omer Gokcumen, Yujun Zhang, Jan Aerts, T Daniel Andrews, Chris Barnes, Peter Campbell,[...]. Nature 2010
9

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
69
13

A map of human genome variation from population-scale sequencing.
Gonçalo R Abecasis, David Altshuler, Adam Auton, Lisa D Brooks, Richard M Durbin, Richard A Gibbs, Matt E Hurles, Gil A McVean. Nature 2010
9

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
Christopher A Miller, Oliver Hampton, Cristian Coarfa, Aleksandar Milosavljevic. PLoS One 2011
117
9

Statistical challenges associated with detecting copy number variations with next-generation sequencing.
Shu Mei Teo, Yudi Pawitan, Chee Seng Ku, Kee Seng Chia, Agus Salim. Bioinformatics 2012
119
9

Large multiallelic copy number variations in humans.
Robert E Handsaker, Vanessa Van Doren, Jennifer R Berman, Giulio Genovese, Seva Kashin, Linda M Boettger, Steven A McCarroll. Nat Genet 2015
187
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8

Copy number variation: new insights in genome diversity.
Jennifer L Freeman, George H Perry, Lars Feuk, Richard Redon, Steven A McCarroll, David M Altshuler, Hiroyuki Aburatani, Keith W Jones, Chris Tyler-Smith, Matthew E Hurles,[...]. Genome Res 2006
488
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


SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data.
Yong Chen, Li Zhao, Yi Wang, Ming Cao, Violet Gelowani, Mingchu Xu, Smriti A Agrawal, Yumei Li, Stephen P Daiger, Richard Gibbs,[...]. BMC Bioinformatics 2017
29
27



Summarizing and correcting the GC content bias in high-throughput sequencing.
Yuval Benjamini, Terence P Speed. Nucleic Acids Res 2012
405
7

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.
Kai Wang, Mingyao Li, Dexter Hadley, Rui Liu, Joseph Glessner, Struan F A Grant, Hakon Hakonarson, Maja Bucan. Genome Res 2007
7

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A J Horst, Georg Brunner, Alistair J Cochran, Scott Binder, John Quackenbush, Stanley F Nelson. Bioinformatics 2011
266
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.