A citation-based method for searching scientific literature

Jordan M Eizenga, Adam M Novak, Jonas A Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, Josiah D Seaman, Robin Rounthwaite, Jana Ebler, Mikko Rautiainen, Shilpa Garg, Benedict Paten, Tobias Marschall, Jouni Sirén, Erik Garrison. Annu Rev Genomics Hum Genet 2020
Times Cited: 29







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



Times Cited
  Times     Co-cited
Similarity


Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin,[...]. Nat Biotechnol 2018
162
62

The design and construction of reference pangenome graphs with minigraph.
Heng Li, Xiaowen Feng, Chong Chu. Genome Biol 2020
71
51

Pan-genomics in the human genome era.
Rachel M Sherman, Steven L Salzberg. Nat Rev Genet 2020
78
44

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
Hervé Tettelin, Vega Masignani, Michael J Cieslewicz, Claudio Donati, Duccio Medini, Naomi L Ward, Samuel V Angiuoli, Jonathan Crabtree, Amanda L Jones, A Scott Durkin,[...]. Proc Natl Acad Sci U S A 2005
44


Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T Dawson, Erik Garrison, Adam M Novak, Benedict Paten. Genome Biol 2020
65
44

Genome graphs and the evolution of genome inference.
Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison. Genome Res 2017
129
44

Fast and accurate genomic analyses using genome graphs.
Goran Rakocevic, Vladimir Semenyuk, Wan-Ping Lee, James Spencer, John Browning, Ivan J Johnson, Vladan Arsenijevic, Jelena Nadj, Kaushik Ghose, Maria C Suciu,[...]. Nat Genet 2019
82
37

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan, Florian Maumus, Danielle Ciren,[...]. Cell 2020
192
34

Pan-Genome of Wild and Cultivated Soybeans.
Yucheng Liu, Huilong Du, Pengcheng Li, Yanting Shen, Hua Peng, Shulin Liu, Guo-An Zhou, Haikuan Zhang, Zhi Liu, Miao Shi,[...]. Cell 2020
202
34

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
34

Paragraph: a graph-based structural variant genotyper for short-read sequence data.
Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R Bentley, Michael C Schatz, Fritz J Sedlazeck,[...]. Genome Biol 2019
52
34

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
194
31

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
287
31

Plant pan-genomes are the new reference.
Philipp E Bayer, Agnieszka A Golicz, Armin Scheben, Jacqueline Batley, David Edwards. Nat Plants 2020
135
31

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
31

GraphAligner: rapid and versatile sequence-to-graph alignment.
Mikko Rautiainen, Tobias Marschall. Genome Biol 2020
25
36

Graphtyper enables population-scale genotyping using pangenome graphs.
Hannes P Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir,[...]. Nat Genet 2017
98
27

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
147
27

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
162
27

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
431
24

Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
203
24


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
24

Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
Rachel M Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E Ortega,[...]. Nat Genet 2019
153
24

The pangenome of hexaploid bread wheat.
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley,[...]. Plant J 2017
163
24

Haplotype-aware graph indexes.
Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin. Bioinformatics 2020
29
24

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement.
Ning Yang, Jie Liu, Qiang Gao, Songtao Gui, Lu Chen, Linfeng Yang, Juan Huang, Tianquan Deng, Jingyun Luo, Lijuan He,[...]. Nat Genet 2019
92
20

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.
Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M Tieman, Elizabeth A Burzynski-Chang, Tara L Fish, Kaitlin A Stromberg, Gavin L Sacks,[...]. Nat Genet 2019
210
20

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.
Sean P Gordon, Bruno Contreras-Moreira, Daniel P Woods, David L Des Marais, Diane Burgess, Shengqiang Shu, Christoph Stritt, Anne C Roulin, Wendy Schackwitz, Ludmila Tyler,[...]. Nat Commun 2017
152
20

The barley pan-genome reveals the hidden legacy of mutation breeding.
Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Cécile Monat, Thomas Lux, Nadia Kamal, Daniel Lang, Axel Himmelbach,[...]. Nature 2020
106
20

Structural variation in the sequencing era.
Steve S Ho, Alexander E Urban, Ryan E Mills. Nat Rev Genet 2020
152
20

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.
Jia-Ming Song, Zhilin Guan, Jianlin Hu, Chaocheng Guo, Zhiquan Yang, Shuo Wang, Dongxu Liu, Bo Wang, Shaoping Lu, Run Zhou,[...]. Nat Plants 2020
202
20

The pangenome of an agronomically important crop plant Brassica oleracea.
Agnieszka A Golicz, Philipp E Bayer, Guy C Barker, Patrick P Edger, HyeRan Kim, Paula A Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W Richard McCombie, Isobel A P Parkin,[...]. Nat Commun 2016
185
20

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
88
20

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
20

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
20

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
330
20

Is it time to change the reference genome?
Sara Ballouz, Alexander Dobin, Jesse A Gillis. Genome Biol 2019
68
20

Bandage: interactive visualization of de novo genome assemblies.
Ryan R Wick, Mark B Schultz, Justin Zobel, Kathryn E Holt. Bioinformatics 2015
798
20

Building the sequence map of the human pan-genome.
Ruiqiang Li, Yingrui Li, Hancheng Zheng, Ruibang Luo, Hongmei Zhu, Qibin Li, Wubin Qian, Yuanyuan Ren, Geng Tian, Jinxiang Li,[...]. Nat Biotechnol 2010
153
20

Ten years of pan-genome analyses.
George Vernikos, Duccio Medini, David R Riley, Hervé Tettelin. Curr Opin Microbiol 2015
317
20

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
130
20

De novo assembly and genotyping of variants using colored de Bruijn graphs.
Zamin Iqbal, Mario Caccamo, Isaac Turner, Paul Flicek, Gil McVean. Nat Genet 2012
312
20

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.
Hannes P Eggertsson, Snaedis Kristmundsdottir, Doruk Beyter, Hakon Jonsson, Astros Skuladottir, Marteinn T Hardarson, Daniel F Gudbjartsson, Kari Stefansson, Bjarni V Halldorsson, Pall Melsted. Nat Commun 2019
40
20

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
204
17

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren. Genome Res 2020
143
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
433
17

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
Ying-hui Li, Guangyu Zhou, Jianxin Ma, Wenkai Jiang, Long-guo Jin, Zhouhao Zhang, Yong Guo, Jinbo Zhang, Yi Sui, Liangtao Zheng,[...]. Nat Biotechnol 2014
296
17

Accurate genotyping across variant classes and lengths using variant graphs.
Jonas Andreas Sibbesen, Lasse Maretty, Anders Krogh. Nat Genet 2018
29
17


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.