A citation-based method for searching scientific literature

S E Lewis, S M J Searle, N Harris, M Gibson, V Lyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, M A Crosby, J S Kaminker, B B Matthews, S E Prochnik, C D Smithy, J L Tupy, G M Rubin, S Misra, C J Mungall, M E Clamp. Genome Biol 2002
Times Cited: 269







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



Times Cited
  Times     Co-cited
Similarity


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
26

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
16


MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Brandi L Cantarel, Ian Korf, Sofia M C Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell. Genome Res 2008
922
13

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
Chang Liu, Linchun Shi, Yingjie Zhu, Haimei Chen, Jianhui Zhang, Xiaohan Lin, Xiaojun Guan. BMC Genomics 2012
356
12

REPuter: the manifold applications of repeat analysis on a genomic scale.
S Kurtz, J V Choudhuri, E Ohlebusch, C Schleiermacher, J Stoye, R Giegerich. Nucleic Acids Res 2001
893
12




MISA-web: a web server for microsatellite prediction.
Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher. Bioinformatics 2017
458
11


Repbase Update, a database of eukaryotic repetitive elements.
J Jurka, V V Kapitonov, A Pavlicek, P Klonowski, O Kohany, J Walichiewicz. Cytogenet Genome Res 2005
10

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
10



MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
10

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
9

CPGAVAS2, an integrated plastome sequence annotator and analyzer.
Linchun Shi, Haimei Chen, Mei Jiang, Liqiang Wang, Xi Wu, Linfang Huang, Chang Liu. Nucleic Acids Res 2019
277
9

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
8

Artemis: sequence visualization and annotation.
K Rutherford, J Parkhill, J Crook, T Horsnell, P Rice, M A Rajandream, B Barrell. Bioinformatics 2000
8


Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004
8

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010
8


Automated generation of heuristics for biological sequence comparison.
Guy St C Slater, Ewan Birney. BMC Bioinformatics 2005
8

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
8

EMBOSS: the European Molecular Biology Open Software Suite.
P Rice, I Longden, A Bleasby. Trends Genet 2000
8

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
8

JBrowse: a next-generation genome browser.
Mitchell E Skinner, Andrew V Uzilov, Lincoln D Stein, Christopher J Mungall, Ian H Holmes. Genome Res 2009
495
7


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
7

A whole-genome assembly of the domestic cow, Bos taurus.
Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard,[...]. Genome Biol 2009
754
7

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
7

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
7

A preliminary genetic map in Solea senegalensis (Pleuronectiformes, Soleidae) using BAC-FISH and next-generation sequencing.
A García-Cegarra, M A Merlo, M Ponce, S Portela-Bens, I Cross, M Manchado, L Rebordinos. Cytogenet Genome Res 2013
18
38

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.
Dong Zhang, Fangluan Gao, Ivan Jakovlić, Hong Zou, Jin Zhang, Wen X Li, Gui T Wang. Mol Ecol Resour 2020
558
7

The generic genome browser: a building block for a model organism system database.
Lincoln D Stein, Christopher Mungall, ShengQiang Shu, Michael Caudy, Marco Mangone, Allen Day, Elizabeth Nickerson, Jason E Stajich, Todd W Harris, Adrian Arva,[...]. Genome Res 2002
833
6

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
6

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Genis Parra, Keith Bradnam, Ian Korf. Bioinformatics 2007
6

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
6

BLAT--the BLAST-like alignment tool.
W James Kent. Genome Res 2002
6


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis.
Silvia Portela-Bens, Manuel Alejandro Merlo, María Esther Rodríguez, Ismael Cross, Manuel Manchado, Nadezda Kosyakova, Thomas Liehr, Laureana Rebordinos. Chromosoma 2017
17
35


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
6

GeSeq - versatile and accurate annotation of organelle genomes.
Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner. Nucleic Acids Res 2017
989
6

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W dePamphilis, Ting-Shuang Yi, De-Zhu Li. Genome Biol 2020
554
6

MRBAYES: Bayesian inference of phylogenetic trees.
J P Huelsenbeck, F Ronquist. Bioinformatics 2001
5



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.