A citation-based method for searching scientific literature

Jakob Franke, Jeongwoon Kim, John P Hamilton, Dongyan Zhao, Gina M Pham, Krystle Wiegert-Rininger, Emily Crisovan, Linsey Newton, Brieanne Vaillancourt, Evangelos Tatsis, C Robin Buell, Sarah E O'Connor. Chembiochem 2019
Times Cited: 25







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



Times Cited
  Times     Co-cited
Similarity


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
44

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
28

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides.
Genevieve M Hoopes, John P Hamilton, Jeongwoon Kim, Dongyan Zhao, Krystle Wiegert-Rininger, Emily Crisovan, C Robin Buell. G3 (Bethesda) 2018
15
40

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
24

A BAHD acyltransferase catalyzing 19-O-acetylation of tabersonine derivatives in roots of Catharanthus roseus enables combinatorial synthesis of monoterpene indole alkaloids.
Inês Carqueijeiro, Thomas Dugé de Bernonville, Arnaud Lanoue, Thu-Thuy Dang, Christiana N Teijaro, Christian Paetz, Kevin Billet, Angela Mosquera, Audrey Oudin, Sébastien Besseau,[...]. Plant J 2018
29
20

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
20

Folivory elicits a strong defense reaction in Catharanthus roseus: metabolomic and transcriptomic analyses reveal distinct local and systemic responses.
Thomas Dugé de Bernonville, Inês Carqueijeiro, Arnaud Lanoue, Florent Lafontaine, Paloma Sánchez Bel, Franziska Liesecke, Karine Musset, Audrey Oudin, Gaëlle Glévarec, Olivier Pichon,[...]. Sci Rep 2017
24
20

The bHLH transcription factor BIS1 controls the iridoid branch of the monoterpenoid indole alkaloid pathway in Catharanthus roseus.
Alex Van Moerkercke, Priscille Steensma, Fabian Schweizer, Jacob Pollier, Ivo Gariboldi, Richard Payne, Robin Vanden Bossche, Karel Miettinen, Javiera Espoz, Purin Candra Purnama,[...]. Proc Natl Acad Sci U S A 2015
88
20

The basic helix-loop-helix transcription factor BIS2 is essential for monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus.
Alex Van Moerkercke, Priscille Steensma, Ivo Gariboldi, Javiera Espoz, Purin C Purnama, Fabian Schweizer, Karel Miettinen, Robin Vanden Bossche, Rebecca De Clercq, Johan Memelink,[...]. Plant J 2016
52
20

Plant metabolic clusters - from genetics to genomics.
Hans-Wilhelm Nützmann, Ancheng Huang, Anne Osbourn. New Phytol 2016
141
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
20

A look inside an alkaloid multisite plant: the Catharanthus logistics.
Vincent Courdavault, Nicolas Papon, Marc Clastre, Nathalie Giglioli-Guivarc'h, Benoit St-Pierre, Vincent Burlat. Curr Opin Plant Biol 2014
66
20

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
20

Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity.
Anna Stavrinides, Evangelos C Tatsis, Lorenzo Caputi, Emilien Foureau, Clare E M Stevenson, David M Lawson, Vincent Courdavault, Sarah E O'Connor. Nat Commun 2016
33
16

De novo production of the plant-derived alkaloid strictosidine in yeast.
Stephanie Brown, Marc Clastre, Vincent Courdavault, Sarah E O'Connor. Proc Natl Acad Sci U S A 2015
216
16


A pair of tabersonine 16-hydroxylases initiates the synthesis of vindoline in an organ-dependent manner in Catharanthus roseus.
Sébastien Besseau, Franziska Kellner, Arnaud Lanoue, Antje M K Thamm, Vonny Salim, Bernd Schneider, Fernando Geu-Flores, René Höfer, Grégory Guirimand, Anthony Guihur,[...]. Plant Physiol 2013
59
16

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
16

An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole.
Richard M E Payne, Deyang Xu, Emilien Foureau, Marta Ines Soares Teto Carqueijeiro, Audrey Oudin, Thomas Dugé de Bernonville, Vlastimil Novak, Meike Burow, Carl-Erik Olsen, D Marc Jones,[...]. Nat Plants 2017
64
16


The basic helix-loop-helix transcription factor CrMYC2 controls the jasmonate-responsive expression of the ORCA genes that regulate alkaloid biosynthesis in Catharanthus roseus.
Hongtao Zhang, Sabah Hedhili, Grégory Montiel, Yanxia Zhang, Guillaume Chatel, Martial Pré, Pascal Gantet, Johan Memelink. Plant J 2011
166
16


GATA and Phytochrome Interacting Factor Transcription Factors Regulate Light-Induced Vindoline Biosynthesis in Catharanthus roseus.
Yongliang Liu, Barunava Patra, Sitakanta Pattanaik, Ying Wang, Ling Yuan. Plant Physiol 2019
20
20


Zinc finger proteins act as transcriptional repressors of alkaloid biosynthesis genes in Catharanthus roseus.
Bea Pauw, Frédérique A O Hilliou, Virginia Sandonis Martin, Guillaume Chatel, Cocky J F de Wolf, Antony Champion, Martial Pré, Bert van Duijn, Jan W Kijne, Leslie van der Fits,[...]. J Biol Chem 2004
93
16

Homolog of tocopherol C methyltransferases catalyzes N methylation in anticancer alkaloid biosynthesis.
David K Liscombe, Aimee R Usera, Sarah E O'Connor. Proc Natl Acad Sci U S A 2010
50
16

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
16

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
16

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
16

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
16


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
16


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
16

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
16

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
16

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.
Qing Zhao, Jun Yang, Meng-Ying Cui, Jie Liu, Yumin Fang, Mengxiao Yan, Wenqing Qiu, Huiwen Shang, Zhicheng Xu, Reheman Yidiresi,[...]. Mol Plant 2019
44
16

Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine.
Thomas Dugé de Bernonville, Marc Clastre, Sébastien Besseau, Audrey Oudin, Vincent Burlat, Gaëlle Glévarec, Arnaud Lanoue, Nicolas Papon, Nathalie Giglioli-Guivarc'h, Benoit St-Pierre,[...]. Phytochemistry 2015
47
16

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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
16

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
16

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
16

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
18

Chemistry and biology of monoterpene indole alkaloid biosynthesis.
Sarah E O'Connor, Justin J Maresh. Nat Prod Rep 2006
437
12

A three enzyme system to generate the Strychnos alkaloid scaffold from a central biosynthetic intermediate.
Evangelos C Tatsis, Inês Carqueijeiro, Thomas Dugé de Bernonville, Jakob Franke, Thu-Thuy T Dang, Audrey Oudin, Arnaud Lanoue, Florent Lafontaine, Anna K Stavrinides, Marc Clastre,[...]. Nat Commun 2017
49
12

The Catharanthus alkaloids: pharmacognosy and biotechnology.
Robert van Der Heijden, Denise I Jacobs, Wim Snoeijer, Didier Hallard, Robert Verpoorte. Curr Med Chem 2004
287
12

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.
Xiaozhou Luo, Michael A Reiter, Leo d'Espaux, Jeff Wong, Charles M Denby, Anna Lechner, Yunfeng Zhang, Adrian T Grzybowski, Simon Harth, Weiyin Lin,[...]. Nature 2019
204
12

A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules.
James Reed, Michael J Stephenson, Karel Miettinen, Bastiaan Brouwer, Aymeric Leveau, Paul Brett, Rebecca J M Goss, Alain Goossens, Maria A O'Connell, Anne Osbourn. Metab Eng 2017
83
12


Completion of the seven-step pathway from tabersonine to the anticancer drug precursor vindoline and its assembly in yeast.
Yang Qu, Michael L A E Easson, Jordan Froese, Razvan Simionescu, Tomas Hudlicky, Vincenzo De Luca. Proc Natl Acad Sci U S A 2015
102
12


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.