A citation-based method for searching scientific literature

Rachel M Sherman, Steven L Salzberg. Nat Rev Genet 2020
Times Cited: 74







List of co-cited articles
556 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
154
29

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
22

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
22


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
146
20

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
63
22


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
269
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
17

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
17

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
182
17

Pangenome Graphs.
Jordan M Eizenga, Adam M Novak, Jonas A Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, Josiah D Seaman, Robin Rounthwaite, Jana Ebler,[...]. Annu Rev Genomics Hum Genet 2020
27
48

Is it time to change the reference genome?
Sara Ballouz, Alexander Dobin, Jesse A Gillis. Genome Biol 2019
64
18

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
188
16

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
16

Plant pan-genomes are the new reference.
Philipp E Bayer, Agnieszka A Golicz, Armin Scheben, Jacqueline Batley, David Edwards. Nat Plants 2020
131
16

The design and construction of reference pangenome graphs with minigraph.
Heng Li, Xiaowen Feng, Chong Chu. Genome Biol 2020
70
17

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
114
16

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
49
22

Genome graphs and the evolution of genome inference.
Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison. Genome Res 2017
126
14

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
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
314
14

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
37
27

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
204
13

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
13

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
13

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
179
13

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
409
13

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon,[...]. Nature 2016
605
12

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
182
12

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
12

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
289
12

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Wensheng Wang, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, Tianqing Zheng, Roven Rommel Fuentes, Fan Zhang,[...]. Nature 2018
510
12

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications.
Agnieszka A Golicz, Philipp E Bayer, Prem L Bhalla, Jacqueline Batley, David Edwards. Trends Genet 2020
55
16

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
311
10

Haplotype-aware graph indexes.
Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin. Bioinformatics 2020
28
28

GraphAligner: rapid and versatile sequence-to-graph alignment.
Mikko Rautiainen, Tobias Marschall. Genome Biol 2020
22
36

Ten years of pan-genome analyses.
George Vernikos, Duccio Medini, David R Riley, Hervé Tettelin. Curr Opin Microbiol 2015
309
10

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Valerie A Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt, Françoise Thibaud-Nissen, Derek Albracht,[...]. Genome Res 2017
321
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
766
10

Long-read sequencing and de novo assembly of a Chinese genome.
Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong,[...]. Nat Commun 2016
146
10

The sequence of the human genome.
J C Venter, M D Adams, E W Myers, P W Li, R J Mural, G G Sutton, H O Smith, M Yandell, C A Evans, R A Holt,[...]. Science 2001
10

Exploring and Exploiting Pan-genomics for Crop Improvement.
Yongfu Tao, Xianrong Zhao, Emma Mace, Robert Henry, David Jordan. Mol Plant 2019
82
10

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
188
10

Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
178
10

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
94
9

HUPAN: a pan-genome analysis pipeline for human genomes.
Zhongqu Duan, Yuyang Qiao, Jinyuan Lu, Huimin Lu, Wenmin Zhang, Fazhe Yan, Chen Sun, Zhiqiang Hu, Zhen Zhang, Guichao Li,[...]. Genome Biol 2019
33
21


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
198
9

De novo assembly and phasing of a Korean human genome.
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim,[...]. Nature 2016
187
9


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.