A citation-based method for searching scientific literature

Yuchao Jiang, Derek A Oldridge, Sharon J Diskin, Nancy R Zhang. Nucleic Acids Res 2015
Times Cited: 73







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



Times Cited
  Times     Co-cited
Similarity


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
332
43

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
362
42


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
28

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
299
28

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
267
26

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
26


An evaluation of copy number variation detection tools from whole-exome sequencing data.
Renjie Tan, Yadong Wang, Sarah E Kleinstein, Yongzhuang Liu, Xiaolin Zhu, Hongzhe Guo, Qinghua Jiang, Andrew S Allen, Mingfu Zhu. Hum Mutat 2014
124
20

EXCAVATOR: detecting copy number variants from whole-exome sequencing data.
Alberto Magi, Lorenzo Tattini, Ingrid Cifola, Romina D'Aurizio, Matteo Benelli, Eleonora Mangano, Cristina Battaglia, Elena Bonora, Ants Kurg, Marco Seri,[...]. Genome Biol 2013
147
19

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.
Jonathan S Packer, Evan K Maxwell, Colm O'Dushlaine, Alexander E Lopez, Frederick E Dewey, Rostislav Chernomorsky, Aris Baras, John D Overton, Lukas Habegger, Jeffrey G Reid. Bioinformatics 2016
31
45

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
345
17

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
256
16

CANOES: detecting rare copy number variants from whole exome sequencing data.
Daniel Backenroth, Jason Homsy, Laura R Murillo, Joe Glessner, Edwin Lin, Martina Brueckner, Richard Lifton, Elizabeth Goldmuntz, Wendy K Chung, Yufeng Shen. Nucleic Acids Res 2014
61
19

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
234
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
15

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
15

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
15

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
15

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
498
15

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
350
13

CONTRA: copy number analysis for targeted resequencing.
Jason Li, Richard Lupat, Kaushalya C Amarasinghe, Ella R Thompson, Maria A Doyle, Georgina L Ryland, Richard W Tothill, Saman K Halgamuge, Ian G Campbell, Kylie L Gorringe. Bioinformatics 2012
197
13


Summarizing and correcting the GC content bias in high-throughput sequencing.
Yuval Benjamini, Terence P Speed. Nucleic Acids Res 2012
412
13

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
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
637
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
695
10

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
10

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.
Yaping Yang, Donna M Muzny, Jeffrey G Reid, Matthew N Bainbridge, Alecia Willis, Patricia A Ward, Alicia Braxton, Joke Beuten, Fan Xia, Zhiyv Niu,[...]. N Engl J Med 2013
9

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

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
121
9

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
743
9

Modeling read counts for CNV detection in exome sequencing data.
Michael I Love, Alena Myšičková, Ruping Sun, Vera Kalscheuer, Martin Vingron, Stefan A Haas. Stat Appl Genet Mol Biol 2011
39
17

CopywriteR: DNA copy number detection from off-target sequence data.
Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P Lolkema,[...]. Genome Biol 2015
110
9

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
370
9

Integrated detection and population-genetic analysis of SNPs and copy number variation.
Steven A McCarroll, Finny G Kuruvilla, Joshua M Korn, Simon Cawley, James Nemesh, Alec Wysoker, Michael H Shapero, Paul I W de Bakker, Julian B Maller, Andrew Kirby,[...]. Nat Genet 2008
687
9

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
9

CoNVaDING: Single Exon Variation Detection in Targeted NGS Data.
Lennart F Johansson, Freerk van Dijk, Eddy N de Boer, Krista K van Dijk-Bos, Jan D H Jongbloed, Annemieke H van der Hout, Helga Westers, Richard J Sinke, Morris A Swertz, Rolf H Sijmons,[...]. Hum Mutat 2016
47
14

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
9

Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.
Ruen Yao, Cheng Zhang, Tingting Yu, Niu Li, Xuyun Hu, Xiumin Wang, Jian Wang, Yiping Shen. Mol Cytogenet 2017
43
16

Targeted capture and massively parallel sequencing of 12 human exomes.
Sarah B Ng, Emily H Turner, Peggy D Robertson, Steven D Flygare, Abigail W Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E Eichler,[...]. Nature 2009
8

Sequencing depth and coverage: key considerations in genomic analyses.
David Sims, Ian Sudbery, Nicholas E Ilott, Andreas Heger, Chris P Ponting. Nat Rev Genet 2014
616
8

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
545
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
703
8

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
120
8


Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.
Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke. Genome Biol 2011
612
8

Detection of clinically relevant copy number variants with whole-exome sequencing.
Joep de Ligt, Philip M Boone, Rolph Pfundt, Lisenka E L M Vissers, Todd Richmond, Joel Geoghegan, Kathleen O'Moore, Nicole de Leeuw, Christine Shaw, Han G Brunner,[...]. Hum Mutat 2013
78
8

CoNVEX: copy number variation estimation in exome sequencing data using HMM.
Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge. BMC Bioinformatics 2013
39
15

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
8


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.