A citation-based method for searching scientific literature

Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
Times Cited: 182







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



Times Cited
  Times     Co-cited
Similarity



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
627
24

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
22

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
21

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt. PLoS Comput Biol 2017
21

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
490
20

Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
564
19

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
168
18

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
512
17

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

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
405
14

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
13

NanoPack: visualizing and processing long-read sequencing data.
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
379
13

Detecting DNA cytosine methylation using nanopore sequencing.
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp. Nat Methods 2017
284
12

NCBI prokaryotic genome annotation pipeline.
Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D Pruitt, Mark Borodovsky, James Ostell. Nucleic Acids Res 2016
12


Opportunities and challenges in long-read sequencing data analysis.
Shanika L Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E Ritchie, Quentin Gouil. Genome Biol 2020
151
10

Real-time, portable genome sequencing for Ebola surveillance.
Joshua Quick, Nicholas J Loman, Sophie Duraffour, Jared T Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno, Gytis Dudas, Amy Mikhail,[...]. Nature 2016
591
10

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
241
9

Fast and accurate long-read assembly with wtdbg2.
Jue Ruan, Heng Li. Nat Methods 2020
238
9

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler,[...]. Nat Protoc 2017
369
9

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
9

Completing bacterial genome assemblies with multiplex MinION sequencing.
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt. Microb Genom 2017
187
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9


Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
8

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
8

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020
70
11


Mapping DNA methylation with high-throughput nanopore sequencing.
Arthur C Rand, Miten Jain, Jordan M Eizenga, Audrey Musselman-Brown, Hugh E Olsen, Mark Akeson, Benedict Paten. Nat Methods 2017
171
7

Highly parallel direct RNA sequencing on an array of nanopores.
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland,[...]. Nat Methods 2018
323
7

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
7

Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E Workman, Alison D Tang, Paul S Tang, Miten Jain, John R Tyson, Roham Razaghi, Philip C Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick,[...]. Nat Methods 2019
108
6

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.
Haotian Teng, Minh Duc Cao, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan J M Coin. Gigascience 2018
48
12

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.
Alexander Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose. Bioinformatics 2019
88
6

PacBio Sequencing and Its Applications.
Anthony Rhoads, Kin Fai Au. Genomics Proteomics Bioinformatics 2015
717
6

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
6

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.
Søren M Karst, Ryan M Ziels, Rasmus H Kirkegaard, Emil A Sørensen, Daniel McDonald, Qiyun Zhu, Rob Knight, Mads Albertsen. Nat Methods 2021
23
26

Ultra-deep, long-read nanopore sequencing of mock microbial community standards.
Samuel M Nicholls, Joshua C Quick, Shuiquan Tang, Nicholas J Loman. Gigascience 2019
71
8

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.
Ryan R Wick, Louise M Judd, Kathryn E Holt. PLoS Comput Biol 2018
55
10

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
140
6

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing.
Andrew M Smith, Miten Jain, Logan Mulroney, Daniel R Garalde, Mark Akeson. PLoS One 2019
45
11

Targeted nanopore sequencing with Cas9-guided adapter ligation.
Timothy Gilpatrick, Isac Lee, James E Graham, Etienne Raimondeau, Rebecca Bowen, Andrew Heron, Bradley Downs, Saraswati Sukumar, Fritz J Sedlazeck, Winston Timp. Nat Biotechnol 2020
62
8

Accurate detection of m6A RNA modifications in native RNA sequences.
Huanle Liu, Oguzhan Begik, Morghan C Lucas, Jose Miguel Ramirez, Christopher E Mason, David Wiener, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa. Nat Commun 2019
105
5

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.
Vladimír Boža, Broňa Brejová, Tomáš Vinař. PLoS One 2017
69
7


Adaptive seeds tame genomic sequence comparison.
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith. Genome Res 2011
559
5


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.