A citation-based method for searching scientific literature

Guillaume Holley, Doruk Beyter, Helga Ingimundardottir, Peter L Møller, Snædis Kristmundsdottir, Hannes P Eggertsson, Bjarni V Halldorsson. Genome Biol 2021
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
691
100

NanoPack: visualizing and processing long-read sequencing data.
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
531
80

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
96
60

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
705
60

Fast and accurate long-read assembly with wtdbg2.
Jue Ruan, Heng Li. Nat Methods 2020
315
60


Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
732
60

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
465
40

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
40

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
40

Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis,[...]. Nat Biotechnol 2012
601
40

Versatile and open software for comparing large genomes.
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
40


FMLRC: Hybrid long read error correction using an FM-index.
Jeremy R Wang, James Holt, Leonard McMillan, Corbin D Jones. BMC Bioinformatics 2018
33
40

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
40

Characterization of individual polynucleotide molecules using a membrane channel.
J J Kasianowicz, E Brandin, D Branton, D W Deamer. Proc Natl Acad Sci U S A 1996
40

MinIONQC: fast and simple quality control for MinION sequencing data.
R Lanfear, M Schalamun, D Kainer, W Wang, B Schwessinger. Bioinformatics 2019
45
40

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.
Davide Bolognini, Alberto Magi, Vladimir Benes, Jan O Korbel, Tobias Rausch. Gigascience 2020
6
40

Phased diploid genome assembly with single-molecule real-time sequencing.
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
781
40

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
223
40

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
89
40

NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.
Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J Fullwood, Bryan T H Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre Thiery, Daniel G Tenen,[...]. Genome Biol 2020
23
40

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
278
40

Adaptive seeds tame genomic sequence comparison.
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith. Genome Res 2011
603
40

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
116
40

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.
Alexander Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose. Bioinformatics 2019
104
40


SVIM: structural variant identification using mapped long reads.
David Heller, Martin Vingron. Bioinformatics 2019
55
40

metaFlye: scalable long-read metagenome assembly using repeat graphs.
Mikhail Kolmogorov, Derek M Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P L Smith,[...]. Nat Methods 2020
71
40

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
447
40

Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
253
40


lra: A long read aligner for sequences and contigs.
Jingwen Ren, Mark J P Chaisson. PLoS Comput Biol 2021
7
40

GraphAligner: rapid and versatile sequence-to-graph alignment.
Mikko Rautiainen, Tobias Marschall. Genome Biol 2020
18
40

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.
Carolin A Müller, Michael A Boemo, Paolo Spingardi, Benedikt M Kessler, Skirmantas Kriaucionis, Jared T Simpson, Conrad A Nieduszynski. Nat Methods 2019
33
40

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION.
Melissa Leija-Salazar, Fritz J Sedlazeck, Marco Toffoli, Stephen Mullin, Katya Mokretar, Maria Athanasopoulou, Aimee Donald, Reena Sharma, Derralynn Hughes, Anthony H V Schapira,[...]. Mol Genet Genomic Med 2019
35
40

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
30
40

Long-read-based human genomic structural variation detection with cuteSV.
Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu, Yadong Wang. Genome Biol 2020
29
40

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Christine Van Broeckhoven,[...]. Genome Biol 2019
25
40


BUSCO: Assessing Genome Assembly and Annotation Completeness.
Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov. Methods Mol Biol 2019
548
20

Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies.
Liliana Florea, Alexander Souvorov, Theodore S Kalbfleisch, Steven L Salzberg. PLoS One 2011
40
20

Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
20

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Sebastian Proost, Jan Fostier, Dieter De Witte, Bart Dhoedt, Piet Demeester, Yves Van de Peer, Klaas Vandepoele. Nucleic Acids Res 2012
113
20

The value of new genome references.
Kim C Worley, Stephen Richards, Jeffrey Rogers. Exp Cell Res 2017
8
20

Carbon translocation from a plant to an insect-pathogenic endophytic fungus.
Scott W Behie, Camila C Moreira, Irina Sementchoukova, Larissa Barelli, Paul M Zelisko, Michael J Bidochka. Nat Commun 2017
43
20

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation.
Wei Shen, Shuai Le, Yan Li, Fuquan Hu. PLoS One 2016
373
20

The evolution of genome mining in microbes - a review.
Nadine Ziemert, Mohammad Alanjary, Tilmann Weber. Nat Prod Rep 2016
292
20

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
Ling Xu, Zhaobin Dong, Lu Fang, Yongjiang Luo, Zhaoyuan Wei, Hailong Guo, Guoqing Zhang, Yong Q Gu, Devin Coleman-Derr, Qingyou Xia,[...]. Nucleic Acids Res 2019
228
20



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.