A citation-based method for searching scientific literature

Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au. F1000Res 2017
Times Cited: 178







List of co-cited articles
672 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
705
25

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
25

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
336
23

PacBio Sequencing and Its Applications.
Anthony Rhoads, Kin Fai Au. Genomics Proteomics Bioinformatics 2015
788
21

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
19

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
18

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
177
17

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
206
17

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
580
15

Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
732
15

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
378
15

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
239
14

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations.
Spyros Oikonomopoulos, Yu Chang Wang, Haig Djambazian, Dunarel Badescu, Jiannis Ragoussis. Sci Rep 2016
75
16

Assessment of transcript reconstruction methods for RNA-seq.
Tamara Steijger, Josep F Abril, Pär G Engström, Felix Kokocinski, Tim J Hubbard, Roderic Guigó, Jennifer Harrow, Paul Bertone. Nat Methods 2013
367
12

A single-molecule long-read survey of the human transcriptome.
Donald Sharon, Hagen Tilgner, Fabian Grubert, Michael Snyder. Nat Biotechnol 2013
332
12


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11

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
11

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
11

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes.
Charlotte Soneson, Yao Yao, Anna Bratus-Neuenschwander, Andrea Patrignani, Mark D Robinson, Shobbir Hussain. Nat Commun 2019
68
16

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
147
11

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
11


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
10

Characterization of the human ESC transcriptome by hybrid sequencing.
Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A Williams, Harm van Bakel, Eric E Schadt, Renee A Reijo-Pera, Jason G Underwood,[...]. Proc Natl Acad Sci U S A 2013
187
10

A survey of the sorghum transcriptome using single-molecule long reads.
Salah E Abdel-Ghany, Michael Hamilton, Jennifer L Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur, Anireddy S N Reddy. Nat Commun 2016
243
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
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
447
10

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics.
Simon Ardui, Adam Ameur, Joris R Vermeesch, Matthew S Hestand. Nucleic Acids Res 2018
212
9

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
332
9

Alternative isoform regulation in human tissue transcriptomes.
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
9

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.
Manuel Tardaguila, Lorena de la Fuente, Cristina Marti, Cécile Pereira, Francisco Jose Pardo-Palacios, Hector Del Risco, Marc Ferrell, Maravillas Mellado, Marissa Macchietto, Kenneth Verheggen,[...]. Genome Res 2018
87
10

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
691
9

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns.
Alison D Tang, Cameron M Soulette, Marijke J van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J Wu, Angela N Brooks. Nat Commun 2020
79
11

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA.
Roger Volden, Theron Palmer, Ashley Byrne, Charles Cole, Robert J Schmitz, Richard E Green, Christopher Vollmers. Proc Natl Acad Sci U S A 2018
75
10

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events.
Hagen Tilgner, Fereshteh Jahanbani, Tim Blauwkamp, Ali Moshrefi, Erich Jaeger, Feng Chen, Itamar Harel, Carlos D Bustamante, Morten Rasmussen, Michael P Snyder. Nat Biotechnol 2015
111
8

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.
Ishaan Gupta, Paul G Collier, Bettina Haase, Ahmed Mahfouz, Anoushka Joglekar, Taylor Floyd, Frank Koopmans, Ben Barres, August B Smit, Steven A Sloan,[...]. Nat Biotechnol 2018
106
8

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
8

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
407
8

Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
253
8

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
8

Evaluation and application of RNA-Seq by MinION.
Masahide Seki, Eri Katsumata, Ayako Suzuki, Sarun Sereewattanawoot, Yoshitaka Sakamoto, Junko Mizushima-Sugano, Sumio Sugano, Takashi Kohno, Martin C Frith, Katsuya Tsuchihara,[...]. DNA Res 2019
26
30

The Third Revolution in Sequencing Technology.
Erwin L van Dijk, Yan Jaszczyszyn, Delphine Naquin, Claude Thermes. Trends Genet 2018
308
8

Landscape of transcription in human cells.
Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger,[...]. Nature 2012
7

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
7

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
Bo Wang, Elizabeth Tseng, Michael Regulski, Tyson A Clark, Ting Hon, Yinping Jiao, Zhenyuan Lu, Andrew Olson, Joshua C Stein, Doreen Ware. Nat Commun 2016
272
7

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler,[...]. Nat Methods 2013
7

Improving PacBio long read accuracy by short read alignment.
Kin Fai Au, Jason G Underwood, Lawrence Lee, Wing Hung Wong. PLoS One 2012
184
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.