A citation-based method for searching scientific literature

Antonis Rokas, Jennifer H Wisecaver, Abigail L Lind. Nat Rev Microbiol 2018
Times Cited: 77







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



Times Cited
  Times     Co-cited
Similarity



Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species.
Abigail L Lind, Jennifer H Wisecaver, Catarina Lameiras, Philipp Wiemann, Jonathan M Palmer, Nancy P Keller, Fernando Rodrigues, Gustavo H Goldman, Antonis Rokas. PLoS Biol 2017
89
20

Fungal secondary metabolism - from biochemistry to genomics.
Nancy P Keller, Geoffrey Turner, Joan W Bennett. Nat Rev Microbiol 2005
861
18

Metabolic Gene Clusters in Eukaryotes.
Hans-Wilhelm Nützmann, Claudio Scazzocchio, Anne Osbourn. Annu Rev Genet 2018
64
20

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.
Jens Christian Nielsen, Sietske Grijseels, Sylvain Prigent, Boyang Ji, Jacques Dainat, Kristian Fog Nielsen, Jens Christian Frisvad, Mhairi Workman, Jens Nielsen. Nat Microbiol 2017
110
15

Fungal metabolic gene clusters-caravans traveling across genomes and environments.
Jennifer H Wisecaver, Antonis Rokas. Front Microbiol 2015
76
15

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.
Inge Kjærbølling, Tammi C Vesth, Jens C Frisvad, Jane L Nybo, Sebastian Theobald, Alan Kuo, Paul Bowyer, Yudai Matsuda, Stephen Mondo, Ellen K Lyhne,[...]. Proc Natl Acad Sci U S A 2018
64
17

Regulation of fungal secondary metabolism.
Axel A Brakhage. Nat Rev Microbiol 2013
496
14

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
14

Prototype of an intertwined secondary-metabolite supercluster.
Philipp Wiemann, Chun-Jun Guo, Jonathan M Palmer, Relebohile Sekonyela, Clay C C Wang, Nancy P Keller. Proc Natl Acad Sci U S A 2013
123
14

MycoCosm portal: gearing up for 1000 fungal genomes.
Igor V Grigoriev, Roman Nikitin, Sajeet Haridas, Alan Kuo, Robin Ohm, Robert Otillar, Robert Riley, Asaf Salamov, Xueling Zhao, Frank Korzeniewski,[...]. Nucleic Acids Res 2014
633
14

Biosynthetic gene clusters and the evolution of fungal chemodiversity.
Antonis Rokas, Matthew E Mead, Jacob L Steenwyk, Huzefa A Raja, Nicholas H Oberlies. Nat Prod Rep 2020
29
37


antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Kai Blin, Thomas Wolf, Marc G Chevrette, Xiaowen Lu, Christopher J Schwalen, Satria A Kautsar, Hernando G Suarez Duran, Emmanuel L C de Los Santos, Hyun Uk Kim, Mariana Nave,[...]. Nucleic Acids Res 2017
738
12



Plant metabolic clusters - from genetics to genomics.
Hans-Wilhelm Nützmann, Ancheng Huang, Anne Osbourn. New Phytol 2016
141
12

SMURF: Genomic mapping of fungal secondary metabolite clusters.
Nora Khaldi, Fayaz T Seifuddin, Geoff Turner, Daniel Haft, William C Nierman, Kenneth H Wolfe, Natalie D Fedorova. Fungal Genet Biol 2010
444
12

The evolution of fungal metabolic pathways.
Jennifer H Wisecaver, Jason C Slot, Antonis Rokas. PLoS Genet 2014
95
12


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
11

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.
Ronald P de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry,[...]. Genome Biol 2017
222
11

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.
Xing-Xing Shen, Dana A Opulente, Jacek Kominek, Xiaofan Zhou, Jacob L Steenwyk, Kelly V Buh, Max A B Haase, Jennifer H Wisecaver, Mingshuang Wang, Drew T Doering,[...]. Cell 2018
172
11


VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism.
Ozgür Bayram, Sven Krappmann, Min Ni, Jin Woo Bok, Kerstin Helmstaedt, Oliver Valerius, Susanna Braus-Stromeyer, Nak-Jung Kwon, Nancy P Keller, Jae-Hyuk Yu,[...]. Science 2008
527
10


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10


SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
10



antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H Medema, Tilmann Weber. Nucleic Acids Res 2019
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
9

A scalable platform to identify fungal secondary metabolites and their gene clusters.
Kenneth D Clevenger, Jin Woo Bok, Rosa Ye, Galen P Miley, Maria H Verdan, Thomas Velk, Cynthia Chen, KaHoua Yang, Matthew T Robey, Peng Gao,[...]. Nat Chem Biol 2017
80
9

Regulation and Role of Fungal Secondary Metabolites.
Juliane Macheleidt, Derek J Mattern, Juliane Fischer, Tina Netzker, Jakob Weber, Volker Schroeckh, Vito Valiante, Axel A Brakhage. Annu Rev Genet 2016
136
9

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
Tammi C Vesth, Jane L Nybo, Sebastian Theobald, Jens C Frisvad, Thomas O Larsen, Kristian F Nielsen, Jakob B Hoof, Julian Brandl, Asaf Salamov, Robert Riley,[...]. Nat Genet 2018
77
9

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium.
Jacob L Steenwyk, Xing-Xing Shen, Abigail L Lind, Gustavo H Goldman, Antonis Rokas. mBio 2019
43
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
9

Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes.
Scott Kroken, N Louise Glass, John W Taylor, O C Yoder, B Gillian Turgeon. Proc Natl Acad Sci U S A 2003
349
7

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.
Peter Cimermancic, Marnix H Medema, Jan Claesen, Kenji Kurita, Laura C Wieland Brown, Konstantinos Mavrommatis, Amrita Pati, Paul A Godfrey, Michael Koehrsen, Jon Clardy,[...]. Cell 2014
484
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

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
7

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
7


Fungal Diversity Revisited: 2.2 to 3.8 Million Species.
David L Hawksworth, Robert Lücking. Microbiol Spectr 2017
229
7

Horizontal transfer and death of a fungal secondary metabolic gene cluster.
Matthew A Campbell, Antonis Rokas, Jason C Slot. Genome Biol Evol 2012
69
8

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Tilmann Weber, Kai Blin, Srikanth Duddela, Daniel Krug, Hyun Uk Kim, Robert Bruccoleri, Sang Yup Lee, Michael A Fischbach, Rolf Müller, Wolfgang Wohlleben,[...]. Nucleic Acids Res 2015
7



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.