A citation-based method for searching scientific literature

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, Miriam K Konkel, Ankit Malhotra, Adrian M Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J P Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y K Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A Gibbs, Gabor Marth, Christopher E Mason, Androniki Menelaou, Donna M Muzny, Bradley J Nelson, Amina Noor, Nicholas F Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A Shabalin, Andreas Untergasser, Jerilyn A Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner, Jonathan Sebat, Mark A Batzer, Steven A McCarroll, Ryan E Mills, Mark B Gerstein, Ali Bashir, Oliver Stegle, Scott E Devine, Charles Lee, Evan E Eichler, Jan O Korbel. Nature 2015
Times Cited: 1066







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



Times Cited
  Times     Co-cited
Similarity


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
28

A structural variation reference for medical and population genetics.
Ryan L Collins, Harrison Brand, Konrad J Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C Francioli, Amit V Khera, Chelsea Lowther, Laura D Gauthier, Harold Wang,[...]. Nature 2020
179
25

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
593
18

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
620
18

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
916
18

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
18

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
278
16

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
16

Mapping and characterization of structural variation in 17,795 human genomes.
Haley J Abel, David E Larson, Allison A Regier, Colby Chiang, Indraniel Das, Krishna L Kanchi, Ryan M Layer, Benjamin M Neale, William J Salerno, Catherine Reeves,[...]. Nature 2020
60
23

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
13



PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007
13

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
782
12

Structural variation in the human genome.
Lars Feuk, Andrew R Carson, Stephen W Scherer. Nat Rev Genet 2006
12

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
138
12


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
139
11

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
11

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
447
11

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
11

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter Ebert, Peter A Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari,[...]. Science 2021
81
13

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
10

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
209
10

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
691
10

A robust benchmark for detection of germline large deletions and insertions.
Justin M Zook, Nancy F Hansen, Nathan D Olson, Lesley Chapman, James C Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M Phillippy, Paul C Boutros,[...]. Nat Biotechnol 2020
71
14

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Annalisa Buniello, Jacqueline A L MacArthur, Maria Cerezo, Laura W Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon, Joannella Morales, Edward Mountjoy, Elliot Sollis,[...]. Nucleic Acids Res 2019
10

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
9


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
168
9

Mechanisms underlying structural variant formation in genomic disorders.
Claudia M B Carvalho, James R Lupski. Nat Rev Genet 2016
292
9

Structural variation in the sequencing era.
Steve S Ho, Alexander E Urban, Ryan E Mills. Nat Rev Genet 2020
103
9

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
9

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
728
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
8


The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
8

Structural variant calling: the long and the short of it.
Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J Sedlazeck. Genome Biol 2019
109
8

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
8


From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Geraldine A Van der Auwera, Mauricio O Carneiro, Christopher Hartl, Ryan Poplin, Guillermo Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault,[...]. Curr Protoc Bioinformatics 2013
7

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
7

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
407
7

An integrated map of genetic variation from 1,092 human genomes.
Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean. Nature 2012
7

Structural variation in the human genome and its role in disease.
Paweł Stankiewicz, James R Lupski. Annu Rev Med 2010
690
7

Reference-based phasing using the Haplotype Reference Consortium panel.
Po-Ru Loh, Petr Danecek, Pier Francesco Palamara, Christian Fuchsberger, Yakir A Reshef, Hilary K Finucane, Sebastian Schoenherr, Lukas Forer, Shane McCarthy, Goncalo R Abecasis,[...]. Nat Genet 2016
564
7

A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
7

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
237
7

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
7

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
272
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.