A citation-based method for searching scientific literature

Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa, Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki, Runa Fukushi, Yoko Kusuya, Hiroki Takahashi, Hiroshi Uchiyama, Atsushi Toyoda, Shoko Hikosaka, Eiji Goto, Kazuki Saito, Mami Yamazaki. Nat Commun 2021
Times Cited: 22







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



Times Cited
  Times     Co-cited
Similarity


The opium poppy genome and morphinan production.
Li Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A Bowser, Ian A Graham,[...]. Science 2018
88
50

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
36

Plant metabolic clusters - from genetics to genomics.
Hans-Wilhelm Nützmann, Ancheng Huang, Anne Osbourn. New Phytol 2016
141
31

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
31

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
31

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
27

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
27

Metabolic Gene Clusters in Eukaryotes.
Hans-Wilhelm Nützmann, Claudio Scazzocchio, Anne Osbourn. Annu Rev Genet 2018
64
27

Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes.
M Itkin, U Heinig, O Tzfadia, A J Bhide, B Shinde, P D Cardenas, S E Bocobza, T Unger, S Malitsky, R Finkers,[...]. Science 2013
275
22

De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin.
Dongyan Zhao, John P Hamilton, Gina M Pham, Emily Crisovan, Krystle Wiegert-Rininger, Brieanne Vaillancourt, Dean DellaPenna, C Robin Buell. Gigascience 2017
32
22

Bifunctional Cytochrome P450 Enzymes Involved in Camptothecin Biosynthesis.
Yun Yang, Wei Li, Jing Pang, Liangzhen Jiang, Xixing Qu, Xiang Pu, Guolin Zhang, Yinggang Luo. ACS Chem Biol 2019
20
25

Metabolite Diversity in Alkaloid Biosynthesis: A Multilane (Diastereomer) Highway for Camptothecin Synthesis in Camptotheca acuminata.
Radin Sadre, Maria Magallanes-Lundback, Sujana Pradhan, Vonny Salim, Alex Mesberg, A Daniel Jones, Dean DellaPenna. Plant Cell 2016
52
22

The seco-iridoid pathway from Catharanthus roseus.
Karel Miettinen, Lemeng Dong, Nicolas Navrot, Thomas Schneider, Vincent Burlat, Jacob Pollier, Lotte Woittiez, Sander van der Krol, Raphaël Lugan, Tina Ilc,[...]. Nat Commun 2014
214
22

The PhytoClust tool for metabolic gene clusters discovery in plant genomes.
Nadine Töpfer, Lisa-Maria Fuchs, Asaph Aharoni. Nucleic Acids Res 2017
37
22

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
18

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
18

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae.
Benjamin R Lichman, Grant T Godden, Carol Robin Buell. Curr Opin Plant Biol 2020
13
30

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
18

Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics.
Nirin Udomsom, Amit Rai, Hideyuki Suzuki, Jun Okuyama, Ryosuke Imai, Tetsuya Mori, Ryo Nakabayashi, Kazuki Saito, Mami Yamazaki. Front Plant Sci 2016
24
18

Evolution of Gene Duplication in Plants.
Nicholas Panchy, Melissa Lehti-Shiu, Shin-Han Shiu. Plant Physiol 2016
449
18

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
18


Transcription Factor OpWRKY3 Is Involved in the Development and Biosynthesis of Camptothecin and Its Precursors in Ophiorrhiza pumila Hairy Roots.
Can Wang, Chao Wu, Yao Wang, Chenhong Xie, Min Shi, Shivraj Nile, Zhigang Zhou, Guoyin Kai. Int J Mol Sci 2019
10
40

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states.
Hans-Wilhelm Nützmann, Daniel Doerr, América Ramírez-Colmenero, Jesús Emiliano Sotelo-Fonseca, Eva Wegel, Marco Di Stefano, Steven W Wingett, Peter Fraser, Laurence Hurst, Selene L Fernandez-Valverde,[...]. Proc Natl Acad Sci U S A 2020
26
18

A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants.
Jennifer H Wisecaver, Alexander T Borowsky, Vered Tzin, Georg Jander, Daniel J Kliebenstein, Antonis Rokas. Plant Cell 2017
104
18

Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis.
Jakob Franke, Jeongwoon Kim, John P Hamilton, Dongyan Zhao, Gina M Pham, Krystle Wiegert-Rininger, Emily Crisovan, Linsey Newton, Brieanne Vaillancourt, Evangelos Tatsis,[...]. Chembiochem 2019
25
18


A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants.
X Qi, S Bakht, M Leggett, C Maxwell, R Melton, A Osbourn. Proc Natl Acad Sci U S A 2004
189
18

Formation and diversification of a paradigm biosynthetic gene cluster in plants.
Zhenhua Liu, Jitender Cheema, Marielle Vigouroux, Lionel Hill, James Reed, Pirita Paajanen, Levi Yant, Anne Osbourn. Nat Commun 2020
11
36

Analysis of a chemical plant defense mechanism in grasses.
M Frey, P Chomet, E Glawischnig, C Stettner, S Grün, A Winklmair, W Eisenreich, A Bacher, R B Meeley, S P Briggs,[...]. Science 1997
372
18

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
18

Gene clustering in plant specialized metabolism.
Hans-Wilhelm Nützmann, Anne Osbourn. Curr Opin Biotechnol 2014
110
18

Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle.
Lorenzo Caputi, Jakob Franke, Scott C Farrow, Khoa Chung, Richard M E Payne, Trinh-Don Nguyen, Thu-Thuy T Dang, Inês Soares Teto Carqueijeiro, Konstantinos Koudounas, Thomas Dugé de Bernonville,[...]. Science 2018
111
18

The impact of third generation genomic technologies on plant genome assembly.
Wen-Biao Jiao, Korbinian Schneeberger. Curr Opin Plant Biol 2017
87
13


Solution of the multistep pathway for assembly of corynanthean, strychnos, iboga, and aspidosperma monoterpenoid indole alkaloids from 19E-geissoschizine.
Yang Qu, Michael E A M Easson, Razvan Simionescu, Josef Hajicek, Antje M K Thamm, Vonny Salim, Vincenzo De Luca. Proc Natl Acad Sci U S A 2018
51
13

The evolutionary dynamics of plant duplicate genes.
Richard C Moore, Michael D Purugganan. Curr Opin Plant Biol 2005
306
13

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
13

Metabolomics with 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants.
Ryo Nakabayashi, Tetsuya Mori, Noriko Takeda, Kiminori Toyooka, Hiroshi Sudo, Hiroshi Tsugawa, Kazuki Saito. Anal Chem 2020
9
33

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
13

Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume.
Keiichi Mochida, Tetsuya Sakurai, Hikaru Seki, Takuhiro Yoshida, Kotaro Takahagi, Satoru Sawai, Hiroshi Uchiyama, Toshiya Muranaka, Kazuki Saito. Plant J 2017
71
13


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
13

Building near-complete plant genomes.
Todd P Michael, Robert VanBuren. Curr Opin Plant Biol 2020
60
13

The transcription factor OpWRKY2 positively regulates the biosynthesis of the anticancer drug camptothecin in Ophiorrhiza pumila.
Xiaolong Hao, Chenhong Xie, Qingyan Ruan, Xichen Zhang, Chao Wu, Bing Han, Jun Qian, Wei Zhou, Hans-Wilhelm Nützmann, Guoyin Kai. Hortic Res 2021
12
25

The long story of camptothecin: From traditional medicine to drugs.
Emanuela Martino, Serena Della Volpe, Elisa Terribile, Emanuele Benetti, Mirena Sakaj, Adriana Centamore, Andrea Sala, Simona Collina. Bioorg Med Chem Lett 2017
84
13

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
13


A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato.
Ju Eun Jeon, Jung-Gun Kim, Curt R Fischer, Niraj Mehta, Cosima Dufour-Schroif, Kimberly Wemmer, Mary Beth Mudgett, Elizabeth Sattely. Cell 2020
34
13

Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae.
Yuan Zhou, Yongshuo Ma, Jianguo Zeng, Lixin Duan, Xiaofeng Xue, Huaisong Wang, Tao Lin, Zhiqiang Liu, Kewu Zeng, Yang Zhong,[...]. Nat Plants 2016
85
13


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.