A citation-based method for searching scientific literature

Pascal Schläpfer, Peifen Zhang, Chuan Wang, Taehyong Kim, Michael Banf, Lee Chae, Kate Dreher, Arvind K Chavali, Ricardo Nilo-Poyanco, Thomas Bernard, Daniel Kahn, Seung Y Rhee. Plant Physiol 2017
Times Cited: 159







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



Times Cited
  Times     Co-cited
Similarity


Plant metabolic clusters - from genetics to genomics.
Hans-Wilhelm Nützmann, Ancheng Huang, Anne Osbourn. New Phytol 2016
141
19

Genomic signatures of specialized metabolism in plants.
Lee Chae, Taehyong Kim, Ricardo Nilo-Poyanco, Seung Y Rhee. Science 2014
148
19

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
17

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

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
12

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

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
10

The MetaCyc database of metabolic pathways and enzymes.
Ron Caspi, Richard Billington, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Quang Ong, Wai Kit Ong,[...]. Nucleic Acids Res 2018
318
9



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

The pathway tools pathway prediction algorithm.
Peter D Karp, Mario Latendresse, Ron Caspi. Stand Genomic Sci 2011
65
12

Formation of plant metabolic gene clusters within dynamic chromosomal regions.
Ben Field, Anna-Sophie Fiston-Lavier, Ariane Kemen, Katrin Geisler, Hadi Quesneville, Anne E Osbourn. Proc Natl Acad Sci U S A 2011
130
8

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
9

Robust predictions of specialized metabolism genes through machine learning.
Bethany M Moore, Peipei Wang, Pengxiang Fan, Bryan Leong, Craig A Schenck, John P Lloyd, Melissa D Lehti-Shiu, Robert L Last, Eran Pichersky, Shin-Han Shiu. Proc Natl Acad Sci U S A 2019
38
21

Gene clustering in plant specialized metabolism.
Hans-Wilhelm Nützmann, Anne Osbourn. Curr Opin Biotechnol 2014
110
8

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
8

Delineation of metabolic gene clusters in plant genomes by chromatin signatures.
Nan Yu, Hans-Wilhelm Nützmann, James T MacDonald, Ben Moore, Ben Field, Souha Berriri, Martin Trick, Susan J Rosser, S Vinod Kumar, Paul S Freemont,[...]. Nucleic Acids Res 2016
45
17

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
8

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Peter D Karp, Mario Latendresse, Suzanne M Paley, Markus Krummenacker, Quang D Ong, Richard Billington, Anamika Kothari, Daniel Weaver, Thomas Lee, Pallavi Subhraveti,[...]. Brief Bioinform 2016
153
7

Phytozome: a comparative platform for green plant genomics.
David M Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam,[...]. Nucleic Acids Res 2012
7

PubChem 2019 update: improved access to chemical data.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2019
7

Plant Reactome: a resource for plant pathways and comparative analysis.
Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha D Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin L Elser, Joel Weiser,[...]. Nucleic Acids Res 2017
34
20

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck. Nucleic Acids Res 2016
312
7

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
7

KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research.
Farit Mochamad Afendi, Taketo Okada, Mami Yamazaki, Aki Hirai-Morita, Yukiko Nakamura, Kensuke Nakamura, Shun Ikeda, Hiroki Takahashi, Md Altaf-Ul-Amin, Latifah K Darusman,[...]. Plant Cell Physiol 2012
264
7


A specialized metabolic network selectively modulates Arabidopsis root microbiota.
Ancheng C Huang, Ting Jiang, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai, Anne Osbourn. Science 2019
149
7


Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Mingxun Wang, Jeremy J Carver, Vanessa V Phelan, Laura M Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A Kapono, Tal Luzzatto-Knaan,[...]. Nat Biotechnol 2016
7

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
20

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7


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
7

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
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

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
6

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
6

Genomic clustering of cyanogenic glucoside biosynthetic genes aids their identification in Lotus japonicus and suggests the repeated evolution of this chemical defence pathway.
Adam M Takos, Camilla Knudsen, Daniela Lai, Rubini Kannangara, Lisbeth Mikkelsen, Mohammed S Motawia, Carl E Olsen, Shusei Sato, Satoshi Tabata, Kirsten Jørgensen,[...]. Plant J 2011
103
6


Evolution of Gene Duplication in Plants.
Nicholas Panchy, Melissa Lehti-Shiu, Shin-Han Shiu. Plant Physiol 2016
449
6

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.
Björn Usadel, Takeshi Obayashi, Marek Mutwil, Federico M Giorgi, George W Bassel, Mimi Tanimoto, Amanda Chow, Dirk Steinhauser, Staffan Persson, Nicholas J Provart. Plant Cell Environ 2009
314
6

Identification of a biosynthetic gene cluster in rice for momilactones.
Kazuhiro Shimura, Atsushi Okada, Kazunori Okada, Yusuke Jikumaru, Kwang-Wook Ko, Tomonobu Toyomasu, Takeshi Sassa, Morifumi Hasegawa, Osamu Kodama, Naoto Shibuya,[...]. J Biol Chem 2007
168
6

The rise of operon-like gene clusters in plants.
Svetlana Boycheva, Laurent Daviet, Jean-Luc Wolfender, Teresa B Fitzpatrick. Trends Plant Sci 2014
87
6

High-throughput functional annotation and data mining with the Blast2GO suite.
Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Tim D Williams, Shivashankar H Nagaraj, María José Nueda, Montserrat Robles, Manuel Talón, Joaquín Dopazo, Ana Conesa. Nucleic Acids Res 2008
6

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity.
Pengxiang Fan, Peipei Wang, Yann-Ru Lou, Bryan J Leong, Bethany M Moore, Craig A Schenck, Rachel Combs, Pengfei Cao, Federica Brandizzi, Shin-Han Shiu,[...]. Elife 2020
17
35

Minimum Information about a Biosynthetic Gene cluster.
Marnix H Medema, Renzo Kottmann, Pelin Yilmaz, Matthew Cummings, John B Biggins, Kai Blin, Irene de Bruijn, Yit Heng Chooi, Jan Claesen, R Cameron Coates,[...]. Nat Chem Biol 2015
422
6


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.