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: 694







List of co-cited articles
810 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
903
39

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
24

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

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
724
22


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
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
774
19

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
317
19

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
124
19

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
511
18

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
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
168
17


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
373
17

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
198
17


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
433
15

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
14


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
241
12

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
183
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

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
171
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
683
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

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
141
11

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
571
11

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
107
11

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
11

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
81
13

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
357
10

Structural variation in the human genome and its role in disease.
Paweł Stankiewicz, James R Lupski. Annu Rev Med 2010
666
10

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
428
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
209
10

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
191
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
850
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

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
178
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
120
9

Structural variation in the human genome.
Lars Feuk, Andrew R Carson, Stephen W Scherer. Nat Rev Genet 2006
9

Mechanisms of change in gene copy number.
P J Hastings, James R Lupski, Susan M Rosenberg, Grzegorz Ira. Nat Rev Genet 2009
709
9

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

A copy number variation morbidity map of developmental delay.
Gregory M Cooper, Bradley P Coe, Santhosh Girirajan, Jill A Rosenfeld, Tiffany H Vu, Carl Baker, Charles Williams, Heather Stalker, Rizwan Hamid, Vickie Hannig,[...]. Nat Genet 2011
794
8

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
25

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
8

A human genome structural variation sequencing resource reveals insights into mutational mechanisms.
Jeffrey M Kidd, Tina Graves, Tera L Newman, Robert Fulton, Hillary S Hayden, Maika Malig, Joelle Kallicki, Rajinder Kaul, Richard K Wilson, Evan E Eichler. Cell 2010
185
8

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
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.