A citation-based method for searching scientific literature

Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon, Valerie A Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G Bouffard, Alexander M Chang, Nancy F Hansen, Amy B Wilfert, Françoise Thibaud-Nissen, Anthony D Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y Dennis, Daniela C Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa Ana Risques, Tina A Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C Mullikin, Pavel A Pevzner, Jennifer L Gerton, Beth A Sullivan, Evan E Eichler, Adam M Phillippy. Nature 2020
Times Cited: 300







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



Times Cited
  Times     Co-cited
Similarity


The structure, function and evolution of a complete human chromosome 8.
Glennis A Logsdon, Mitchell R Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C Dishuck, Arang Rhie,[...]. Nature 2021
95
36

The complete sequence of a human genome.
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman,[...]. Science 2022
245
29


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
471
23

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
22

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
159
22

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
299
21

Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
224
20

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
814
17

Towards complete and error-free genome assemblies of all vertebrate species.
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim,[...]. Nature 2021
232
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
15

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
15

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
143
15


Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
13

Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
963
13

Epigenetic patterns in a complete human genome.
Ariel Gershman, Michael E G Sauria, Xavi Guitart, Mitchell R Vollger, Paul W Hook, Savannah J Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren,[...]. Science 2022
33
36

Complete genomic and epigenetic maps of human centromeres.
Nicolas Altemose, Glennis A Logsdon, Andrey V Bzikadze, Pragya Sidhwani, Sasha A Langley, Gina V Caldas, Savannah J Hoyt, Lev Uralsky, Fedor D Ryabov, Colin J Shew,[...]. Science 2022
45
26

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
11

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Arang Rhie, Brian P Walenz, Sergey Koren, Adam M Phillippy. Genome Biol 2020
153
11

Linear assembly of a human centromere on the Y chromosome.
Miten Jain, Hugh E Olsen, Daniel J Turner, David Stoddart, Kira V Bulazel, Benedict Paten, David Haussler, Huntington F Willard, Mark Akeson, Karen H Miga. Nat Biotechnol 2018
133
11

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10

Weighted minimizer sampling improves long read mapping.
Chirag Jain, Arang Rhie, Haowen Zhang, Claudia Chu, Brian P Walenz, Sergey Koren, Adam M Phillippy. Bioinformatics 2020
48
20

The design and construction of reference pangenome graphs with minigraph.
Heng Li, Xiaowen Feng, Chong Chu. Genome Biol 2020
79
12

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
10

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
574
9

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
9

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
8

RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J Sedlazeck, Zachary B Lippman, Michael C Schatz. Genome Biol 2019
234
8

The genetic and epigenetic landscape of the Arabidopsis centromeres.
Matthew Naish, Michael Alonge, Piotr Wlodzimierz, Andrew J Tock, Bradley W Abramson, Anna Schmücker, Terezie Mandáková, Bhagyshree Jamge, Christophe Lambing, Pallas Kuo,[...]. Science 2021
49
16

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
444
8

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
344
8

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.
Savannah J Hoyt, Jessica M Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo G de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez,[...]. Science 2022
36
22

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
354
7

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James P Drake, Jane M Landolin, Adam M Phillippy. Nat Biotechnol 2015
530
7

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
7



TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats.
Alla Mikheenko, Andrey V Bzikadze, Alexey Gurevich, Karen H Miga, Pavel A Pevzner. Bioinformatics 2020
23
30

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
644
7

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
50
14

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

De novo assembly of haplotype-resolved genomes with trio binning.
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy. Nat Biotechnol 2018
173
7

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
169
7

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
137
7

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
203
7


Segmental duplications and their variation in a complete human genome.
Mitchell R Vollger, Xavi Guitart, Philip C Dishuck, Ludovica Mercuri, William T Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M Munson, Alexandra P Lewis,[...]. Science 2022
27
25

Centromere reference models for human chromosomes X and Y satellite arrays.
Karen H Miga, Yulia Newton, Miten Jain, Nicolas Altemose, Huntington F Willard, W James Kent. Genome Res 2014
145
7


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.