A citation-based method for searching scientific literature

Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp. Nat Methods 2017
Times Cited: 342







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



Times Cited
  Times     Co-cited
Similarity


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
197
38


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
728
20

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
391
20

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
96
20

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
19

Direct detection of DNA methylation during single-molecule, real-time sequencing.
Benjamin A Flusberg, Dale R Webster, Jessica H Lee, Kevin J Travers, Eric C Olivares, Tyson A Clark, Jonas Korlach, Stephen W Turner. Nat Methods 2010
784
17

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Qian Liu, Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang. Nat Commun 2019
100
16

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.
Peng Ni, Neng Huang, Zhi Zhang, De-Peng Wang, Fan Liang, Yu Miao, Chuan-Le Xiao, Feng Luo, Jianxin Wang. Bioinformatics 2019
70
22

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
482
14

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
158
14

Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
270
13

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
13

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
595
12

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
213
12



A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
M Frommer, L E McDonald, D S Millar, C M Collis, F Watt, G W Grigg, P L Molloy, C L Paul. Proc Natl Acad Sci U S A 1992
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
11

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J Sedlazeck, Kasper D Hansen, Jared T Simpson, Winston Timp. Nat Methods 2020
34
32

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
649
10

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
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
241
10

Using long-read sequencing to detect imprinted DNA methylation.
Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence P Speed, Marnie E Blewitt,[...]. Nucleic Acids Res 2019
45
20

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
9

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
477
9

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
271
9

Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
150
9

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
144
8

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.
Emily K Schutsky, Jamie E DeNizio, Peng Hu, Monica Yun Liu, Christopher S Nabel, Emily B Fabyanic, Young Hwang, Frederic D Bushman, Hao Wu, Rahul M Kohli. Nat Biotechnol 2018
74
10

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
Shinsuke Ito, Li Shen, Qing Dai, Susan C Wu, Leonard B Collins, James A Swenberg, Chuan He, Yi Zhang. Science 2011
8

Real-time DNA sequencing from single polymerase molecules.
John Eid, Adrian Fehr, Jeremy Gray, Khai Luong, John Lyle, Geoff Otto, Paul Peluso, David Rank, Primo Baybayan, Brad Bettman,[...]. Science 2009
8

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
8



Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.
Alexa B R McIntyre, Noah Alexander, Kirill Grigorev, Daniela Bezdan, Heike Sichtig, Charles Y Chiu, Christopher E Mason. Nat Commun 2019
64
12

Three decades of nanopore sequencing.
David Deamer, Mark Akeson, Daniel Branton. Nat Biotechnol 2016
363
7

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.
Ashley Byrne, Anna E Beaudin, Hugh E Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M DuBois, E Camilla Forsberg, Mark Akeson, Christopher Vollmers. Nat Commun 2017
180
7

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
65
10

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz. Genome Res 2019
92
7

Deciphering bacterial epigenomes using modern sequencing technologies.
John Beaulaurier, Eric E Schadt, Gang Fang. Nat Rev Genet 2019
53
13

The Third Revolution in Sequencing Technology.
Erwin L van Dijk, Yan Jaszczyszyn, Delphine Naquin, Claude Thermes. Trends Genet 2018
326
7


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
7

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
762
7

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
7

Real-time selective sequencing using nanopore technology.
Matthew Loose, Sunir Malla, Michael Stout. Nat Methods 2016
103
6

Improved data analysis for the MinION nanopore sequencer.
Miten Jain, Ian T Fiddes, Karen H Miga, Hugh E Olsen, Benedict Paten, Mark Akeson. Nat Methods 2015
311
6

Decoding the epitranscriptional landscape from native RNA sequences.
Piroon Jenjaroenpun, Thidathip Wongsurawat, Taylor D Wadley, Trudy M Wassenaar, Jun Liu, Qing Dai, Visanu Wanchai, Nisreen S Akel, Azemat Jamshidi-Parsian, Aime T Franco,[...]. Nucleic Acids Res 2021
58
10

Dynamic RNA Modifications in Gene Expression Regulation.
Ian A Roundtree, Molly E Evans, Tao Pan, Chuan He. Cell 2017
6


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.