A citation-based method for searching scientific literature

Ryan E Mills, Klaudia Walter, Chip Stewart, Robert E Handsaker, Ken Chen, Can Alkan, Alexej Abyzov, Seungtai Chris Yoon, Kai Ye, R Keira Cheetham, Asif Chinwalla, Donald F Conrad, Yutao Fu, Fabian Grubert, Iman Hajirasouliha, Fereydoun Hormozdiari, Lilia M Iakoucheva, Zamin Iqbal, Shuli Kang, Jeffrey M Kidd, Miriam K Konkel, Joshua Korn, Ekta Khurana, Deniz Kural, Hugo Y K Lam, Jing Leng, Ruiqiang Li, Yingrui Li, Chang-Yun Lin, Ruibang Luo, Xinmeng Jasmine Mu, James Nemesh, Heather E Peckham, Tobias Rausch, Aylwyn Scally, Xinghua Shi, Michael P Stromberg, Adrian M Stütz, Alexander Eckehart Urban, Jerilyn A Walker, Jiantao Wu, Yujun Zhang, Zhengdong D Zhang, Mark A Batzer, Li Ding, Gabor T Marth, Gil McVean, Jonathan Sebat, Michael Snyder, Jun Wang, Kenny Ye, Evan E Eichler, Mark B Gerstein, Matthew E Hurles, Charles Lee, Steven A McCarroll, Jan O Korbel. Nature 2011
Times Cited: 703







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



Times Cited
  Times     Co-cited
Similarity


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
947
37

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
26

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
23

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
20

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
743
20




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
350
17

Characterizing the Major Structural Variant Alleles of the Human Genome.
Peter A Audano, Arvis Sulovari, Tina A Graves-Lindsay, Stuart Cantsilieris, Melanie Sorensen, AnneMarie E Welch, Max L Dougherty, Bradley J Nelson, Ankeeta Shah, Susan K Dutcher,[...]. Cell 2019
137
17

Global diversity, population stratification, and selection of human copy-number variation.
Peter H Sudmant, Swapan Mallick, Bradley J Nelson, Fereydoun Hormozdiari, Niklas Krumm, John Huddleston, Bradley P Coe, Carl Baker, Susanne Nordenfelt, Michael Bamshad,[...]. Science 2015
175
16

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
545
16

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
819
15

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
14

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
382
14

Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins,[...]. Nat Commun 2019
219
14

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
14

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


Large-scale copy number polymorphism in the human genome.
Jonathan Sebat, B Lakshmi, Jennifer Troge, Joan Alexander, Janet Young, Pär Lundin, Susanne Månér, Hillary Massa, Megan Walker, Maoyen Chi,[...]. Science 2004
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
481
12

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
370
11

Structural variation in the human genome and its role in disease.
Paweł Stankiewicz, James R Lupski. Annu Rev Med 2010
674
11

Phenotypic impact of genomic structural variation: insights from and for human disease.
Joachim Weischenfeldt, Orsolya Symmons, François Spitz, Jan O Korbel. Nat Rev Genet 2013
250
11

Relative impact of nucleotide and copy number variation on gene expression phenotypes.
Barbara E Stranger, Matthew S Forrest, Mark Dunning, Catherine E Ingle, Claude Beazley, Natalie Thorne, Richard Redon, Christine P Bird, Anna de Grassi, Charles Lee,[...]. Science 2007
11

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
11

Detection of large-scale variation in the human genome.
A John Iafrate, Lars Feuk, Miguel N Rivera, Marc L Listewnik, Patricia K Donahoe, Ying Qi, Stephen W Scherer, Charles Lee. Nat Genet 2004
11

Analysis of copy number variations among diverse cattle breeds.
George E Liu, Yali Hou, Bin Zhu, Maria Francesca Cardone, Lu Jiang, Angelo Cellamare, Apratim Mitra, Leeson J Alexander, Luiz L Coutinho, Maria Elena Dell'Aquila,[...]. Genome Res 2010
185
10

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
872
10

Discovery and genotyping of structural variation from long-read haploid genome sequence data.
John Huddleston, Mark J P Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives,[...]. Genome Res 2017
154
10

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
615
10

The impact of structural variation on human gene expression.
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily K Tsang, Xin Li, Yungil Kim, Tarik Hadzic, Farhan N Damani, Liron Ganel, Stephen B Montgomery,[...]. Nat Genet 2017
116
10

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Robert E Handsaker, Joshua M Korn, James Nemesh, Steven A McCarroll. Nat Genet 2011
211
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
94
10

Copy number variation of individual cattle genomes using next-generation sequencing.
Derek M Bickhart, Yali Hou, Steven G Schroeder, Can Alkan, Maria Francesca Cardone, Lakshmi K Matukumalli, Jiuzhou Song, Robert D Schnabel, Mario Ventura, Jeremy F Taylor,[...]. Genome Res 2012
175
9

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
9

Diversity of human copy number variation and multicopy genes.
Peter H Sudmant, Jacob O Kitzman, Francesca Antonacci, Can Alkan, Maika Malig, Anya Tsalenko, Nick Sampas, Laurakay Bruhn, Jay Shendure, Evan E Eichler. Science 2010
433
9

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan,[...]. Nat Commun 2017
131
9

SpeedSeq: ultra-fast personal genome analysis and interpretation.
Colby Chiang, Ryan M Layer, Gregory G Faust, Michael R Lindberg, David B Rose, Erik P Garrison, Gabor T Marth, Aaron R Quinlan, Ira M Hall. Nat Methods 2015
204
9

Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, Ajay Ummat, Oscar Franzen, Tobias Rausch, Adrian M Stütz, William Stedman, Thomas Anantharaman, Alex Hastie,[...]. Nat Methods 2015
268
8

An initial comparative map of copy number variations in the goat (Capra hircus) genome.
Luca Fontanesi, Pier Luigi Martelli, Francesca Beretti, Valentina Riggio, Stefania Dall'Olio, Michela Colombo, Rita Casadio, Vincenzo Russo, Baldassare Portolano. BMC Genomics 2010
82
9

Detection of copy number variations and their effects in Chinese bulls.
Liangzhi Zhang, Shangang Jia, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou,[...]. BMC Genomics 2014
32
25

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
8

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
Marghoob Mohiyuddin, John C Mu, Jian Li, Narges Bani Asadi, Mark B Gerstein, Alexej Abyzov, Wing H Wong, Hugo Y K Lam. Bioinformatics 2015
64
12

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

Mechanisms of change in gene copy number.
P J Hastings, James R Lupski, Susan M Rosenberg, Grzegorz Ira. Nat Rev Genet 2009
719
8

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
7

Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus.
Yang Zhou, Yuri T Utsunomiya, Lingyang Xu, El Hamidi Abdel Hay, Derek M Bickhart, Pamela Almeida Alexandre, Benjamin D Rosen, Steven G Schroeder, Roberto Carvalheiro, Haroldo Henrique de Rezende Neves,[...]. BMC Genomics 2016
32
21

Population-genetic properties of differentiated copy number variations in cattle.
Lingyang Xu, Yali Hou, Derek M Bickhart, Yang Zhou, El Hamidi Abdel Hay, Jiuzhou Song, Tad S Sonstegard, Curtis P Van Tassell, George E Liu. Sci Rep 2016
40
17

Mapping and sequencing of structural variation from eight human genomes.
Jeffrey M Kidd, Gregory M Cooper, William F Donahue, Hillary S Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci,[...]. Nature 2008
767
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.