A citation-based method for searching scientific literature

Geòrgia Escaramís, Elisa Docampo, Raquel Rabionet. Brief Funct Genomics 2015
Times Cited: 49







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



Times Cited
  Times     Co-cited
Similarity


LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
582
30

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
759
28

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
999
28

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
861
24


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
528
20


Structural variation in the human genome.
Lars Feuk, Andrew R Carson, Stephen W Scherer. Nat Rev Genet 2006
16


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
16

A copy number variation map of the human genome.
Mehdi Zarrei, Jeffrey R MacDonald, Daniele Merico, Stephen W Scherer. Nat Rev Genet 2015
383
14

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
218
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
247
14

Detection of Genomic Structural Variants from Next-Generation Sequencing Data.
Lorenzo Tattini, Romina D'Aurizio, Alberto Magi. Front Bioeng Biotechnol 2015
133
12

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
390
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
655
10

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
259
10

Structural variation in the human genome and its role in disease.
Paweł Stankiewicz, James R Lupski. Annu Rev Med 2010
676
10

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
10

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
10

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
267
10

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
714
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
426
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
892
10

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
10

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
10



Paired-end mapping reveals extensive structural variation in the human genome.
Jan O Korbel, Alexander Eckehart Urban, Jason P Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik Simons, Philip M Kim, Dean Palejev, Nicholas J Carriero, Lei Du,[...]. Science 2007
769
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
820
8

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Hugo Y K Lam, Xinmeng Jasmine Mu, Adrian M Stütz, Andrea Tanzer, Philip D Cayting, Michael Snyder, Philip M Kim, Jan O Korbel, Mark B Gerstein. Nat Biotechnol 2010
121
8

Genome sequencing identifies major causes of severe intellectual disability.
Christian Gilissen, Jayne Y Hehir-Kwa, Djie Tjwan Thung, Maartje van de Vorst, Bregje W M van Bon, Marjolein H Willemsen, Michael Kwint, Irene M Janssen, Alexander Hoischen, Annette Schenck,[...]. Nature 2014
641
8

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
8

Mechanisms of change in gene copy number.
P J Hastings, James R Lupski, Susan M Rosenberg, Grzegorz Ira. Nat Rev Genet 2009
731
8

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
8

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
125
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

Whole-genome CNV analysis: advances in computational approaches.
Mehdi Pirooznia, Fernando S Goes, Peter P Zandi. Front Genet 2015
84
8

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Giuseppe Narzisi, Jason A O'Rawe, Ivan Iossifov, Han Fang, Yoon-Ha Lee, Zihua Wang, Yiyang Wu, Gholson J Lyon, Michael Wigler, Michael C Schatz. Nat Methods 2014
128
8

Human Structural Variation: Mechanisms of Chromosome Rearrangements.
Brooke Weckselblatt, M Katharine Rudd. Trends Genet 2015
101
8

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.
Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, Michael C Schatz. Nat Rev Genet 2018
172
8

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.
Zhonghua Zhang, Linyong Mao, Huiming Chen, Fengjiao Bu, Guangcun Li, Jinjing Sun, Shuai Li, Honghe Sun, Chen Jiao, Rachel Blakely,[...]. Plant Cell 2015
68
8

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
393
8

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Jan Schröder, Arthur Hsu, Samantha E Boyle, Geoff Macintyre, Marek Cmero, Richard W Tothill, Ricky W Johnstone, Mark Shackleton, Anthony T Papenfuss. Bioinformatics 2014
48
8

Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives.
Biao Liu, Jeffrey M Conroy, Carl D Morrison, Adekunle O Odunsi, Maochun Qin, Lei Wei, Donald L Trump, Candace S Johnson, Song Liu, Jianmin Wang. Oncotarget 2015
21
19

SVIM: structural variant identification using mapped long reads.
David Heller, Martin Vingron. Bioinformatics 2019
47
8

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
159
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.