A citation-based method for searching scientific literature

Li Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A Bowser, Ian A Graham, Kai Ye. Science 2018
Times Cited: 88







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



Times Cited
  Times     Co-cited
Similarity


A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine.
Thilo Winzer, Valeria Gazda, Zhesi He, Filip Kaminski, Marcelo Kern, Tony R Larson, Yi Li, Fergus Meade, Roxana Teodor, Fabián E Vaistij,[...]. Science 2012
179
23

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
20

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
18



MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Yupeng Wang, Haibao Tang, Jeremy D Debarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo,[...]. Nucleic Acids Res 2012
17

The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism.
Xiubin Liu, Yisong Liu, Peng Huang, Yongshuo Ma, Zhixing Qing, Qi Tang, Huifen Cao, Pi Cheng, Yajie Zheng, Zejun Yuan,[...]. Mol Plant 2017
50
28

The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history.
Danièle L Filiault, Evangeline S Ballerini, Terezie Mandáková, Gökçe Aköz, Nathan J Derieg, Jeremy Schmutz, Jerry Jenkins, Jane Grimwood, Shengqiang Shu, Richard D Hayes,[...]. Elife 2018
56
23

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.
Satria A Kautsar, Hernando G Suarez Duran, Kai Blin, Anne Osbourn, Marnix H Medema. Nucleic Acids Res 2017
96
14

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin,[...]. Nature 2007
14


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
13

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006
674
13

Plant metabolic clusters - from genetics to genomics.
Hans-Wilhelm Nützmann, Ancheng Huang, Anne Osbourn. New Phytol 2016
141
13

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell,[...]. Genome Biol 2013
185
12

Gene clustering in plant specialized metabolism.
Hans-Wilhelm Nützmann, Anne Osbourn. Curr Opin Biotechnol 2014
110
12

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.
Hélène Badouin, Jérôme Gouzy, Christopher J Grassa, Florent Murat, S Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L Owens, Sébastien Carrère, Baptiste Mayjonade,[...]. Nature 2017
260
12

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
12

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
12


Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy.
Qiushi Li, Sukanya Ramasamy, Pooja Singh, Jillian M Hagel, Sonja M Dunemann, Xue Chen, Rongji Chen, Lisa Yu, Joseph E Tucker, Peter J Facchini,[...]. Nat Commun 2020
19
57

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.
Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa, Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki,[...]. Nat Commun 2021
22
50

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
11

OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
11


Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
11

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.
France Denoeud, Lorenzo Carretero-Paulet, Alexis Dereeper, Gaëtan Droc, Romain Guyot, Marco Pietrella, Chunfang Zheng, Adriana Alberti, François Anthony, Giuseppe Aprea,[...]. Science 2014
253
11

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
559
11

Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber.
Yi Shang, Yongshuo Ma, Yuan Zhou, Huimin Zhang, Lixin Duan, Huiming Chen, Jianguo Zeng, Qian Zhou, Shenhao Wang, Wenjia Gu,[...]. Science 2014
186
10

De novo identification of repeat families in large genomes.
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
935
10

Genome-guided investigation of plant natural product biosynthesis.
Franziska Kellner, Jeongwoon Kim, Bernardo J Clavijo, John P Hamilton, Kevin L Childs, Brieanne Vaillancourt, Jason Cepela, Marc Habermann, Burkhard Steuernagel, Leah Clissold,[...]. Plant J 2015
105
10

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
10

Benzylisoquinoline alkaloid metabolism: a century of discovery and a brave new world.
Jillian M Hagel, Peter J Facchini. Plant Cell Physiol 2013
173
10


Complete biosynthesis of noscapine and halogenated alkaloids in yeast.
Yanran Li, Sijin Li, Kate Thodey, Isis Trenchard, Aaron Cravens, Christina D Smolke. Proc Natl Acad Sci U S A 2018
112
10

A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis.
Xue Chen, Jillian M Hagel, Limei Chang, Joseph E Tucker, Stacey A Shiigi, Yuora Yelpaala, Hsiang-Yun Chen, Rodrigo Estrada, Jeffrey Colbeck, Maria Enquist-Newman,[...]. Nat Chem Biol 2018
40
22


Metabolic Gene Clusters in Eukaryotes.
Hans-Wilhelm Nützmann, Claudio Scazzocchio, Anne Osbourn. Annu Rev Genet 2018
64
14

The evolutionary significance of polyploidy.
Yves Van de Peer, Eshchar Mizrachi, Kathleen Marchal. Nat Rev Genet 2017
480
9

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza.
Haibin Xu, Jingyuan Song, Hongmei Luo, Yujun Zhang, Qiushi Li, Yingjie Zhu, Jiang Xu, Ying Li, Chi Song, Bo Wang,[...]. Mol Plant 2016
125
9


StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
9

Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004
9

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

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.
Pascal Schläpfer, Peifen Zhang, Chuan Wang, Taehyong Kim, Michael Banf, Lee Chae, Kate Dreher, Arvind K Chavali, Ricardo Nilo-Poyanco, Thomas Bernard,[...]. Plant Physiol 2017
159
9

The PhytoClust tool for metabolic gene clusters discovery in plant genomes.
Nadine Töpfer, Lisa-Maria Fuchs, Asaph Aharoni. Nucleic Acids Res 2017
37
21


Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
9

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
Olga Dudchenko, Sanjit S Batra, Arina D Omer, Sarah K Nyquist, Marie Hoeger, Neva C Durand, Muhammad S Shamim, Ido Machol, Eric S Lander, Aviva Presser Aiden,[...]. Science 2017
507
9

Investigation of terpene diversification across multiple sequenced plant genomes.
Alexander M Boutanaev, Tessa Moses, Jiachen Zi, David R Nelson, Sam T Mugford, Reuben J Peters, Anne Osbourn. Proc Natl Acad Sci U S A 2015
143
9


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.