A citation-based method for searching scientific literature

Marcel Margulies, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B Dewell, Lei Du, Joseph M Fierro, Xavier V Gomes, Brian C Godwin, Wen He, Scott Helgesen, Chun Heen Ho, Gerard P Irzyk, Szilveszter C Jando, Maria L I Alenquer, Thomas P Jarvie, Kshama B Jirage, Jong-Bum Kim, James R Knight, Janna R Lanza, John H Leamon, Steven M Lefkowitz, Ming Lei, Jing Li, Kenton L Lohman, Hong Lu, Vinod B Makhijani, Keith E McDade, Michael P McKenna, Eugene W Myers, Elizabeth Nickerson, John R Nobile, Ramona Plant, Bernard P Puc, Michael T Ronan, George T Roth, Gary J Sarkis, Jan Fredrik Simons, John W Simpson, Maithreyan Srinivasan, Karrie R Tartaro, Alexander Tomasz, Kari A Vogt, Greg A Volkmer, Shally H Wang, Yong Wang, Michael P Weiner, Pengguang Yu, Richard F Begley, Jonathan M Rothberg. Nature 2005
Times Cited: 4452







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



Times Cited
  Times     Co-cited
Similarity


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
12

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
11


Accurate whole human genome sequencing using reversible terminator chemistry.
David R Bentley, Shankar Balasubramanian, Harold P Swerdlow, Geoffrey P Smith, John Milton, Clive G Brown, Kevin P Hall, Dirk J Evers, Colin L Barnes, Helen R Bignell,[...]. Nature 2008
10

DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
10

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
10

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
9

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
9

An integrated semiconductor device enabling non-optical genome sequencing.
Jonathan M Rothberg, Wolfgang Hinz, Todd M Rearick, Jonathan Schultz, William Mileski, Mel Davey, John H Leamon, Kim Johnson, Mark J Milgrew, Matthew Edwards,[...]. Nature 2011
901
9

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
9

Next-generation DNA sequencing.
Jay Shendure, Hanlee Ji. Nat Biotechnol 2008
8

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow, Yong Gu. BMC Genomics 2012
971
8

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
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

Accurate multiplex polony sequencing of an evolved bacterial genome.
Jay Shendure, Gregory J Porreca, Nikos B Reppas, Xiaoxia Lin, John P McCutcheon, Abraham M Rosenbaum, Michael D Wang, Kun Zhang, Robi D Mitra, George M Church. Science 2005
690
7

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
7

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
6

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.
Devin Dressman, Hai Yan, Giovanni Traverso, Kenneth W Kinzler, Bert Vogelstein. Proc Natl Acad Sci U S A 2003
452
6

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu,[...]. Gigascience 2012
6

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles. Bioinformatics 2005
6


Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
6

Progress in ion torrent semiconductor chip based sequencing.
Barry Merriman, Jonathan M Rothberg. Electrophoresis 2012
146
5

Field guide to next-generation DNA sequencers.
Travis C Glenn. Mol Ecol Resour 2011
537
5

Landscape of next-generation sequencing technologies.
Thomas P Niedringhaus, Denitsa Milanova, Matthew B Kerby, Michael P Snyder, Annelise E Barron. Anal Chem 2011
127
5

Ten years of next-generation sequencing technology.
Erwin L van Dijk, Hélène Auger, Yan Jaszczyszyn, Claude Thermes. Trends Genet 2014
576
5


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5

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
5



The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
351
5

Consed: a graphical editor for next-generation sequencing.
David Gordon, Phil Green. Bioinformatics 2013
133
5

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
5

InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
5

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
5

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
457
4

Impact of transposable elements on the organization and function of allopolyploid genomes.
Christian Parisod, Karine Alix, Jérémy Just, Maud Petit, Véronique Sarilar, Corinne Mhiri, Malika Ainouche, Boulos Chalhoub, Marie-Angèle Grandbastien. New Phytol 2010
127
4


The evolutionary significance of polyploidy.
Yves Van de Peer, Eshchar Mizrachi, Kathleen Marchal. Nat Rev Genet 2017
346
4

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
4

The RAST Server: rapid annotations using subsystems technology.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal,[...]. BMC Genomics 2008
4

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
4


MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4

The Third Revolution in Sequencing Technology.
Erwin L van Dijk, Yan Jaszczyszyn, Delphine Naquin, Claude Thermes. Trends Genet 2018
209
4

Advancements in Next-Generation Sequencing.
Shawn E Levy, Richard M Myers. Annu Rev Genomics Hum Genet 2016
165
4

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
4

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
4


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.