-
2
-
-
84870918230
-
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature
-
Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep. 2013;30:108-60.
-
(2013)
Nat Prod Rep
, vol.30
, pp. 108-160
-
-
Arnison, P.G.1
Bibb, M.J.2
Bierbaum, G.3
Bowers, A.A.4
Bugni, T.S.5
Bulaj, G.6
-
3
-
-
84902002754
-
Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus
-
Umemura M, Nagano N, Koke H, Kawano J, Ishii T, Miyamura Y, et al. Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus. Fung Genet Biol. 2014;68:23-30.
-
(2014)
Fung Genet Biol
, vol.68
, pp. 23-30
-
-
Umemura, M.1
Nagano, N.2
Koke, H.3
Kawano, J.4
Ishii, T.5
Miyamura, Y.6
-
4
-
-
84950279555
-
Class of cyclic ribosomal peptide synthetic genes in filamentous fungi
-
Nagano N, Umemura M, Izumikawa M, Kawano J, Ishii T, Kikuchi M, et al. Class of cyclic ribosomal peptide synthetic genes in filamentous fungi. Fungal Genet Biol. 2016;86:58-70.
-
(2016)
Fungal Genet Biol
, vol.86
, pp. 58-70
-
-
Nagano, N.1
Umemura, M.2
Izumikawa, M.3
Kawano, J.4
Ishii, T.5
Kikuchi, M.6
-
5
-
-
84962719801
-
Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes
-
Ding W, Liu WQ, Jia Y, Li Y, van der Donk W, Zhang Q. Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes. Proc Natl Acad Sci U S A. 2016;113:3521-6.
-
(2016)
Proc Natl Acad Sci U S A
, vol.113
, pp. 3521-3526
-
-
Ding, W.1
Liu, W.Q.2
Jia, Y.3
Li, Y.4
Donk, W.5
Zhang, Q.6
-
6
-
-
84896980201
-
The molecular diversity of toxin gene families in lethal Amanita mushrooms
-
Li P, Deng WQ, Li TH. The molecular diversity of toxin gene families in lethal Amanita mushrooms. Toxicon. 2014;83:59-68.
-
(2014)
Toxicon
, vol.83
, pp. 59-68
-
-
Li, P.1
Deng, W.Q.2
Li, T.H.3
-
8
-
-
84903975698
-
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/brown rot paradigm for wood decay fungi
-
Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/brown rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A. 2014;111:9923-8.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 9923-9928
-
-
Riley, R.1
Salamov, A.A.2
Brown, D.W.3
Nagy, L.G.4
Floudas, D.5
Held, B.W.6
-
9
-
-
84919903118
-
Peptide macrocyclization catalyzed by a prolyl oligopeptidase involved in α-amanitin biosynthesis
-
Luo H, Hong SY, Sgambelluri RM, Angelos E, Li X, Walton JD. Peptide macrocyclization catalyzed by a prolyl oligopeptidase involved in α-amanitin biosynthesis. Chem Biol. 2014;21:1610-7.
-
(2014)
Chem Biol
, vol.21
, pp. 1610-1617
-
-
Luo, H.1
Hong, S.Y.2
Sgambelluri, R.M.3
Angelos, E.4
Li, X.5
Walton, J.D.6
-
10
-
-
78649816006
-
Co-localization of amanitin and a candidate toxin-processing prolyl oligopeptidase in Amanita basidiocarps
-
Luo H, Hallen-Adams HE, Scott-Craig JS, Walton JD. Co-localization of amanitin and a candidate toxin-processing prolyl oligopeptidase in Amanita basidiocarps. Eukaryot Cell. 2010;9:1891-900.
-
(2010)
Eukaryot Cell
, vol.9
, pp. 1891-1900
-
-
Luo, H.1
Hallen-Adams, H.E.2
Scott-Craig, J.S.3
Walton, J.D.4
-
11
-
-
84897110016
-
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
-
Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Front Genet. 2013;4:237.
-
(2013)
Front Genet
, vol.4
, pp. 237
-
-
Kumar, S.1
Jones, M.2
Koutsovoulos, G.3
Clarke, M.4
Blaxter, M.5
-
12
-
-
84940907209
-
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
-
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210-2.
-
(2015)
Bioinformatics
, vol.31
, pp. 3210-3212
-
-
Simão, F.A.1
Waterhouse, R.M.2
Ioannidis, P.3
Kriventseva, E.V.4
Zdobnov, E.M.5
-
13
-
-
38049057159
-
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes
-
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18:188-96.
-
(2008)
Genome Res
, vol.18
, pp. 188-196
-
-
Cantarel, B.L.1
Korf, I.2
Robb, S.M.C.3
Parra, G.4
Ross, E.5
Moore, B.6
Holt, C.7
Alvarado, A.S.8
Yandell, M.9
-
14
-
-
84893466287
-
MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations
-
Campbell MS, Law MY, Holt C, Stein JC, Moghe G, Hufnagel DE, et al. MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014;164:513-24.
-
(2014)
Plant Physiol
, vol.164
, pp. 513-524
-
-
Campbell, M.S.1
Law, M.Y.2
Holt, C.3
Stein, J.C.4
Moghe, G.5
Hufnagel, D.E.6
-
15
-
-
0003894409
-
Peptides of poisonous Amanita mushrooms
-
New York: Springer
-
Wieland T. Peptides of poisonous Amanita mushrooms. New York: Springer; 1986.
-
(1986)
-
-
Wieland, T.1
-
16
-
-
84925005930
-
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
-
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, et al. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015;47:410-5.
-
(2015)
Nat Genet
, vol.47
, pp. 410-415
-
-
Kohler, A.1
Kuo, A.2
Nagy, L.G.3
Morin, E.4
Barry, K.W.5
Buscot, F.6
-
17
-
-
35048844271
-
Tryptathionine bridges in peptide synthesis
-
May JP, Perrin DM. Tryptathionine bridges in peptide synthesis. Biopolymers. 2007;88:714-24.
-
(2007)
Biopolymers
, vol.88
, pp. 714-724
-
-
May, J.P.1
Perrin, D.M.2
-
18
-
-
84885378072
-
Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps
-
Li P, Deng WQ, Li TH, Song B, Shen YH. Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps. Gene. 2013;532:63-71.
-
(2013)
Gene
, vol.532
, pp. 63-71
-
-
Li, P.1
Deng, W.Q.2
Li, T.H.3
Song, B.4
Shen, Y.H.5
-
19
-
-
84885382611
-
Cyclopeptides from Amanita exitialis
-
Xue JH, Wu P, Chi YL, Xu LX, Wei XY. Cyclopeptides from Amanita exitialis. Nat Prod Bioprospect. 2011;1:52-6.
-
(2011)
Nat Prod Bioprospect
, vol.1
, pp. 52-56
-
-
Xue, J.H.1
Wu, P.2
Chi, Y.L.3
Xu, L.X.4
Wei, X.Y.5
-
21
-
-
0027464731
-
Immunosuppressive activity in the series of cycloamanide peptides from mushrooms
-
Wieczorek Z, Siemion IZ, Zimecki M, Bolewska-Pedyczak E, Wieland T. Immunosuppressive activity in the series of cycloamanide peptides from mushrooms. Peptides. 1993;14:1-5.
-
(1993)
Peptides
, vol.14
, pp. 1-5
-
-
Wieczorek, Z.1
Siemion, I.Z.2
Zimecki, M.3
Bolewska-Pedyczak, E.4
Wieland, T.5
-
22
-
-
79551567024
-
Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore
-
Azzolin L, Antolini N, Calderan A, Ruzza P, Sciacovelli M, Marin O, et al. Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore. PLoS One. 2011;28:e16280.
-
(2011)
PLoS One
, vol.28
-
-
Azzolin, L.1
Antolini, N.2
Calderan, A.3
Ruzza, P.4
Sciacovelli, M.5
Marin, O.6
-
23
-
-
84919923378
-
Profiling of amatoxins and phallotoxins in the genus Lepiota by liquid chromatography combined with UV absorbance and mass spectrometry
-
Sgambelluri RM, Epis S, Sassera D, Luo H, Angelos ER, Walton JD. Profiling of amatoxins and phallotoxins in the genus Lepiota by liquid chromatography combined with UV absorbance and mass spectrometry. Toxins. 2014;6:2336-47.
-
(2014)
Toxins
, vol.6
, pp. 2336-2347
-
-
Sgambelluri, R.M.1
Epis, S.2
Sassera, D.3
Luo, H.4
Angelos, E.R.5
Walton, J.D.6
-
24
-
-
84866373857
-
mMass as a software tool for the annotation of cyclic peptide tandem mass spectra
-
Niedermeyer THJ, Strohalm M. mMass as a software tool for the annotation of cyclic peptide tandem mass spectra. PLoS One. 2012;7:e44913.
-
(2012)
PLoS One
, vol.7
-
-
Niedermeyer, T.H.J.1
Strohalm, M.2
-
25
-
-
67650594524
-
Processing of the phalloidin proprotein by prolyl oligopeptidase from the mushroom Conocybe albipes
-
Luo H, Hallen-Adams HE, Walton JD. Processing of the phalloidin proprotein by prolyl oligopeptidase from the mushroom Conocybe albipes. J Biol Chem. 2009;284:18070-7.
-
(2009)
J Biol Chem
, vol.284
, pp. 18070-18077
-
-
Luo, H.1
Hallen-Adams, H.E.2
Walton, J.D.3
-
26
-
-
84887661754
-
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)
-
Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, Young ND. Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). BMC Bioinformatics. 2013;14:335.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 335
-
-
Zhou, P.1
Silverstein, K.A.2
Gao, L.3
Walton, J.D.4
Nallu, S.5
Guhlin, J.6
Young, N.D.7
-
27
-
-
41949135032
-
Structure, function and biological relevance of prolyl oligopeptidase
-
Szeltner Z, Polgár L. Structure, function and biological relevance of prolyl oligopeptidase. Curr Protein Pept Sci. 2008;9:96-107.
-
(2008)
Curr Protein Pept Sci
, vol.9
, pp. 96-107
-
-
Szeltner, Z.1
Polgár, L.2
-
28
-
-
74549127669
-
Distribution and abundance of the introduced ectomycorrhizal fungus Amanita phalloides in North America
-
Wolfe BE, Richard F, Cross HB, Pringle A. Distribution and abundance of the introduced ectomycorrhizal fungus Amanita phalloides in North America. New Phytol. 2010;185:803-16.
-
(2010)
New Phytol
, vol.185
, pp. 803-816
-
-
Wolfe, B.E.1
Richard, F.2
Cross, H.B.3
Pringle, A.4
-
29
-
-
0003645786
-
A colour atlas of poisonous fungi
-
Regensburg: Wolfe
-
Bresinsky A, Besl H. A colour atlas of poisonous fungi. Regensburg: Wolfe; 1990.
-
-
-
Bresinsky, A.1
Besl, H.2
-
30
-
-
84952673564
-
Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks
-
Mohimani H, Pevzner PA. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Nat Prod Rep. 2016;33:73-86.
-
(2016)
Nat Prod Rep
, vol.33
, pp. 73-86
-
-
Mohimani, H.1
Pevzner, P.A.2
-
31
-
-
27444445936
-
Production and characterization of amanitin toxins from a pure culture of Amanita exitialis
-
Zhang P, Chen Z, Hu J, Wei B, Zhang Z, Hu W. Production and characterization of amanitin toxins from a pure culture of Amanita exitialis. FEMS Microbiol Lett. 2005;252:223-8.
-
(2005)
FEMS Microbiol Lett
, vol.252
, pp. 223-228
-
-
Zhang, P.1
Chen, Z.2
Hu, J.3
Wei, B.4
Zhang, Z.5
Hu, W.6
-
32
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114-20.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
33
-
-
84892405230
-
NextClip: an analysis and read preparation tool for Nextera long mate pair libraries
-
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M. NextClip: an analysis and read preparation tool for Nextera long mate pair libraries. Bioinformatics. 2013;30:566-8.
-
(2013)
Bioinformatics
, vol.30
, pp. 566-568
-
-
Leggett, R.M.1
Clavijo, B.J.2
Clissold, L.3
Clark, M.D.4
Caccamo, M.5
-
34
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-9.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
35
-
-
84942887758
-
SOAPdenovo2: an empirically improved memory-efficent short-read de novo assembler
-
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficent short-read de novo assembler. GigaScience. 2012;1:18.
-
(2012)
GigaScience
, vol.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
Yuan, J.6
-
36
-
-
79960264362
-
Full-length transcriptome assembly from RNA-seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011;29:644-52.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
-
37
-
-
2942527473
-
Gene prediction with a hidden Markov model and a new intron submodel
-
Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003;19:ii215-25.
-
(2003)
Bioinformatics
, vol.19
, pp. 11215-11225
-
-
Stanke, M.1
Waack, S.2
-
38
-
-
2942544417
-
Gene finding in novel genomes
-
Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5:59.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 59
-
-
Korf, I.1
-
39
-
-
84857623318
-
Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES
-
Borodovsky M, Lomsadze A. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Curr Protoc Bioinformatics. 2011;4:610.
-
(2011)
Curr Protoc Bioinformatics
, vol.4
, pp. 610
-
-
Borodovsky, M.1
Lomsadze, A.2
-
40
-
-
84891783174
-
Activities at the Universal Protein Resource (UniProt)
-
UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucl Acids Res. 2014;42:D191-8.
-
(2014)
Nucl Acids Res
, vol.42
, pp. D191-D198
-
-
-
41
-
-
79959931985
-
HMMER web server: interactive sequence similarity searching
-
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucl Acids Res. 2011;39:W29-37.
-
(2011)
Nucl Acids Res
, vol.39
, pp. W29-37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
42
-
-
80053345905
-
SignalP 4.0 discriminating singal peptides from transmembrane regions
-
Petersen TN, Brunak S, von Heijne G, Neilsen H. SignalP 4.0 discriminating singal peptides from transmembrane regions. Nature Meth. 2011;8:785-6.
-
(2011)
Nature Meth
, vol.8
, pp. 785-786
-
-
Petersen, T.N.1
Brunak, S.2
Heijne, G.3
Neilsen, H.4
-
43
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov Model: application to complete genomes
-
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov Model: application to complete genomes. J Mol Biol. 2001;305:567-80.
-
(2001)
J Mol Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Heijne, G.3
Sonnhammer, E.L.4
-
44
-
-
69749083447
-
JBrowse: a next-generation genome browser
-
Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Gen Res. 2009;19:1630-8.
-
(2009)
Gen Res
, vol.19
, pp. 1630-1638
-
-
Skinner, M.E.1
Uzilov, A.V.2
Stein, L.D.3
Mungall, C.J.4
Holmes, I.H.5
-
45
-
-
84890330527
-
MEGA6: molecular evolutionary genetics analysis version 6.0.
-
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725-9.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
-
46
-
-
36448991500
-
Clustal W and Clustal X Version 2.0.
-
Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, et al. Clustal W and Clustal X Version 2.0. Bioinformatics. 2007;23:2947-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.1
Blackshields, G.2
Brown, N.3
Chenna, R.4
McGettigan, P.5
McWilliam, H.6
Valentin, F.7
Wallace, I.8
-
47
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert Jr CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178-9.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2179
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
|