-
1
-
-
84891128670
-
Modern taxonomy of biotechnologically important Aspergillus and Penicillium species
-
Houbraken J, de Vries RP, Samson RA. 2014. Modern taxonomy of biotechnologically important Aspergillus and Penicillium species. Adv Appl Microbiol 86:199–249. https://doi.org/10.1016/B978-0-12-800262-9.00004-4.
-
(2014)
Adv Appl Microbiol
, vol.86
, pp. 199-249
-
-
Houbraken, J.1
De Vries, R.P.2
Samson, R.A.3
-
2
-
-
38549164691
-
GenBank
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2007. GenBank. Nucleic Acids Res 36:D25–D30. https://doi.org/10.1093/nar/gkm929.
-
(2007)
Nucleic Acids Res
, vol.36
, pp. D25-D30
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
3
-
-
58149200954
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37:D5–D15. https://doi.org/10.1093/nar/gkn741.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. DD5-D15
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Dicuccio, M.8
Edgar, R.9
Federhen, S.10
Feolo, M.11
Geer, L.Y.12
Helmberg, W.13
Kapustin, Y.14
Landsman, D.15
Lipman, D.J.16
Madden, T.L.17
Maglott, D.R.18
Miller, V.19
Mizrachi, I.20
Ostell, J.21
Pruitt, K.D.22
Schuler, G.D.23
Sequeira, E.24
Sherry, S.T.25
Shumway, M.26
Sirotkin, K.27
Souvorov, A.28
Starchenko, G.29
Tatusova, T.A.30
Wagner, L.31
Yaschenko, E.32
Ye, J.33
more..
-
4
-
-
0036237205
-
Biology and ecology of toxigenic Penicillium species
-
Pitt JI. 2002. Biology and ecology of toxigenic Penicillium species. Adv Exp Med Biol 504:29–41. https://doi.org/10.1007/978-1-4615-0629-4_4.
-
(2002)
Adv Exp Med Biol
, vol.504
, pp. 29-41
-
-
Pitt, J.I.1
-
5
-
-
0020625313
-
Factors affecting growth and cellulose hydrolysis by the thermotolerant Aspergillus nidulans from composts
-
Ogundero VW. 1983. Factors affecting growth and cellulose hydrolysis by the thermotolerant Aspergillus nidulans from composts. Acta Biotechnol 3:65–72. https://doi.org/10.1002/abio.370030116.
-
(1983)
Acta Biotechnol
, vol.3
, pp. 65-72
-
-
Ogundero, V.W.1
-
6
-
-
84871689083
-
The function and evolution of the Aspergillus genome
-
Gibbons JG, Rokas A. 2013. The function and evolution of the Aspergillus genome. Trends Microbiol 21:14–22. https://doi.org/10.1016/j.tim.2012.09.005.
-
(2013)
Trends Microbiol
, vol.21
, pp. 14-22
-
-
Gibbons, J.G.1
Rokas, A.2
-
7
-
-
56149109469
-
Genomics of Aspergillus oryzae: Learning from the history of Koji mold and exploration of its future
-
Machida M, Yamada O, Gomi K. 2008. Genomics of Aspergillus oryzae: Learning from the history of Koji mold and exploration of its future. DNA Res 15:173–183. https://doi.org/10.1093/dnares/dsn020.
-
(2008)
DNA Res
, vol.15
, pp. 173-183
-
-
Machida, M.1
Yamada, O.2
Gomi, K.3
-
8
-
-
84864599461
-
The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae
-
Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. 2012. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr Biol 22:1403–1409. https://doi.org/10.1016/j.cub.2012.05.033.
-
(2012)
Curr Biol
, vol.22
, pp. 1403-1409
-
-
Gibbons, J.G.1
Salichos, L.2
Slot, J.C.3
Rinker, D.C.4
McGary, K.L.5
King, J.G.6
Klich, M.A.7
Tabb, D.L.8
McDonald, W.H.9
Rokas, A.10
-
9
-
-
33947693407
-
Genomics of Aspergillus oryzae
-
Kobayashi T, Abe K, Asai K, Gomi K, Juvvadi PR, Kato M, Kitamoto K, Takeuchi M, Machida M. 2007. Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem 71:646–670. https://doi.org/10.1271/bbb.60550.
-
(2007)
Biosci Biotechnol Biochem
, vol.71
, pp. 646-670
-
-
Kobayashi, T.1
Abe, K.2
Asai, K.3
Gomi, K.4
Juvvadi, P.R.5
Kato, M.6
Kitamoto, K.7
Takeuchi, M.8
Machida, M.9
-
10
-
-
0018939225
-
Mevinolin: A highly potent competitive inhibitor of hydroxymethylglutaryl-coenzyme A reductase and a cholesterollowering agent
-
Albert AW, Chen J, Kuron G, Hunt V, Huff J, Hoffman C, Rothrock J, Lopez M, Joshua H, Harris E, Patchett A, Monaghan R, Currie S, Stapley E, Albers-Schonberg G, Hensens O, Hirshfield J, Hoogsteen K, Liesch J, Springer J. 1980. Mevinolin: A highly potent competitive inhibitor of hydroxymethylglutaryl-coenzyme A reductase and a cholesterollowering agent. Proc Natl Acad Sci U S A 77:3957–3961. https://doi.org/10.1073/pnas.77.7.3957.
-
(1980)
Proc Natl Acad Sci U S A
, vol.77
, pp. 3957-3961
-
-
Albert, A.W.1
Chen, J.2
Kuron, G.3
Hunt, V.4
Huff, J.5
Hoffman, C.6
Rothrock, J.7
Lopez, M.8
Joshua, H.9
Harris, E.10
Patchett, A.11
Monaghan, R.12
Currie, S.13
Stapley, E.14
Albers-Schonberg, G.15
Hensens, O.16
Hirshfield, J.17
Hoogsteen, K.18
Liesch, J.19
Springer, J.20
more..
-
11
-
-
0013475860
-
Production of blue cheese flavor via submerged fermentation by Penicillium roqueforti
-
Nelson JH. 1970. Production of blue cheese flavor via submerged fermentation by Penicillium roqueforti. J Agric Food Chem 18:567–569. https://doi.org/10.1021/jf60170a024.
-
(1970)
J Agric Food Chem
, vol.18
, pp. 567-569
-
-
Nelson, J.H.1
-
12
-
-
84857837751
-
The composition of Camembert cheese-ripening cultures modulates both mycelial growth and appearance
-
Lessard M-H, Bélanger G, St-Gelais D, Labrie S. 2012. The composition of Camembert cheese-ripening cultures modulates both mycelial growth and appearance. Appl Environ Microbiol 78:1813–1819. https://doi.org/10.1128/AEM.06645-11.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 1813-1819
-
-
Lessard, M.-H.1
Bélanger, G.2
St-Gelais, D.3
Labrie, S.4
-
13
-
-
77955114517
-
A historical perspective on the discovery of statins
-
Endo A. 2010. A historical perspective on the discovery of statins. Proc Jpn Acad Ser B Phys Biol Sci 86:484–493. https://doi.org/10.2183/pjab.86.484.
-
(2010)
Proc Jpn Acad Ser B Phys Biol Sci
, vol.86
, pp. 484-493
-
-
Endo, A.1
-
14
-
-
34250783965
-
Aspergillus flavus: Human pathogen, allergen and mycotoxin producer
-
Hedayati MT, Pasqualotto AC, Warn PA, Bowyer P, Denning DW. 2007. Aspergillus flavus: Human pathogen, allergen and mycotoxin producer. Microbiology 153:1677–1692. https://doi.org/10.1099/mic.0.2007/007641-0.
-
(2007)
Microbiology
, vol.153
, pp. 1677-1692
-
-
Hedayati, M.T.1
Pasqualotto, A.C.2
Warn, P.A.3
Bowyer, P.4
Denning, D.W.5
-
15
-
-
28644434509
-
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
-
Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV., Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafton A, Latgé J-P, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O’Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream M-A, Reichard U, Renauld H, Robson GD, de Córdoba SR, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, de Aldana CRV, Weidman J, White O, Woodward J, Yu J-H, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW. 2005. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438:1151–1156. https://doi.org/10.1038/nature04332.
-
(2005)
Nature
, vol.438
, pp. 1151-1156
-
-
Nierman, W.C.1
Pain, A.2
Erson, M.J.3
Wortman, J.R.4
Kim, H.S.5
Arroyo, J.6
Berriman, M.7
Abe, K.8
Archer, D.B.9
Bermejo, C.10
Bennett, J.11
Bowyer, P.12
Chen, D.13
Collins, M.14
Coulsen, R.15
Davies, R.16
Dyer, P.S.17
Farman, M.18
Fedorova, N.19
Fedorova, N.20
Feldblyum, T.V.21
Fischer, R.22
Fosker, N.23
Fraser, A.24
García, J.L.25
García, M.J.26
Goble, A.27
Goldman, G.H.28
Gomi, K.29
Griffith-Jones, S.30
Gwilliam, R.31
Haas, B.32
Haas, H.33
Harris, D.34
Horiuchi, H.35
Huang, J.36
Humphray, S.37
Jiménez, J.38
Keller, N.39
Khouri, H.40
Kitamoto, K.41
Kobayashi, T.42
Konzack, S.43
Kulkarni, R.44
Kumagai, T.45
Lafton, A.46
Latgé, J.-P.47
Li, W.48
Lord, A.49
Lu, C.50
Majoros, W.H.51
May, G.S.52
Miller, B.L.53
Mohamoud, Y.54
Molina, M.55
Monod, M.56
Mouyna, I.57
Mulligan, S.58
Murphy, L.59
O’Neil, S.60
Paulsen, I.61
Peñalva, M.A.62
Pertea, M.63
Price, C.64
Pritchard, B.L.65
Quail, M.A.66
Rabbinowitsch, E.67
Rawlins, N.68
Rajandream, M.-A.69
Reichard, U.70
Renauld, H.71
Robson, G.D.72
De Córdoba, S.R.73
Rodríguez-Peña, J.M.74
Ronning, C.M.75
Rutter, S.76
Salzberg, S.L.77
Sanchez, M.78
Sánchez-Ferrero, J.C.79
Saunders, D.80
Seeger, K.81
Squares, R.82
Squares, S.83
Takeuchi, M.84
Tekaia, F.85
Turner, G.86
De Aldana, C.87
Weidman, J.88
White, O.89
Woodward, J.90
Yu, J.-H.91
Fraser, C.92
Galagan, J.E.93
Asai, K.94
Machida, M.95
Hall, N.96
Barrell, B.97
Denning, D.W.98
more..
-
16
-
-
84923117708
-
Genome, Transcriptome, and functional analyses of Penicillium expansum provide new insights into secondary metabolism and pathogenicity
-
Ballester A-R, Marcet-Houben M, Levin E, Sela N, Selma-Lázaro C, Carmona L, Wisniewski M, Droby S, González-Candelas L, Gabaldón T. 2015. Genome, Transcriptome, and functional analyses of Penicillium expansum provide new insights into secondary metabolism and pathogenicity. Mol Plant Microbe Interact 28:232–248. https://doi.org/10.1094/MPMI-09-14-0261-FI.
-
(2015)
Mol Plant Microbe Interact
, vol.28
, pp. 232-248
-
-
Ballester, A.-R.1
Marcet-Houben, M.2
Levin, E.3
Sela, N.4
Selma-Lázaro, C.5
Carmona, L.6
Wisniewski, M.7
Droby, S.8
González-Candelas, L.9
Gabaldón, T.10
-
17
-
-
84869233554
-
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus
-
Marcet-Houben M, Ballester A-R, de la Fuente B, Harries E, Marcos JF, González-Candelas L, Gabaldón T. 2012. Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics 13:646. https://doi.org/10.1186/1471-2164-13-646.
-
(2012)
BMC Genomics
, vol.13
, pp. 646
-
-
Marcet-Houben, M.1
Ballester, A.-R.2
De La Fuente, B.3
Harries, E.4
Marcos, J.F.5
González-Candelas, L.6
Gabaldón, T.7
-
18
-
-
84929999792
-
Genomic characterization reveals insights into patulin biosynthesis and pathogenicity in Penicillium species
-
Li B, Zong Y, Du Z, Chen Y, Zhang Z, Qin G, Zhao W, Tian S. 2015. Genomic characterization reveals insights into patulin biosynthesis and pathogenicity in Penicillium species. Mol Plant Microbe Interact 28: 635–647. https://doi.org/10.1094/MPMI-12-14-0398-FI.
-
(2015)
Mol Plant Microbe Interact
, vol.28
, pp. 635-647
-
-
Li, B.1
Zong, Y.2
Du, Z.3
Chen, Y.4
Zhang, Z.5
Qin, G.6
Zhao, W.7
Tian, S.8
-
20
-
-
0031952976
-
Ecological determinants for germination and growth of some Aspergillus and Penicillium spp. From maize grain
-
Marín S, Sanchis V, Sáenz R, Ramos AJ, Vinas I, Magan N. 1998. Ecological determinants for germination and growth of some Aspergillus and Penicillium spp. from maize grain. J Appl Microbiol 84:25–36. https://doi.org/10.1046/j.1365-2672.1997.00297.x.
-
(1998)
J Appl Microbiol
, vol.84
, pp. 25-36
-
-
Marín, S.1
Sanchis, V.2
Sáenz, R.3
Ramos, A.J.4
Vinas, I.5
Magan, N.6
-
22
-
-
0001042972
-
Effects of gas composition and water activity on growth of field and storage fungi and their interactions
-
Magan N, Lacey J. 1984. Effects of gas composition and water activity on growth of field and storage fungi and their interactions. Trans Br Mycol Soc 82:305–314. https://doi.org/10.1016/S0007-1536(84) 80074-1.
-
(1984)
Trans Br Mycol Soc
, vol.82
, pp. 305-314
-
-
Magan, N.1
Lacey, J.2
-
23
-
-
85013301401
-
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
-
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park H-S, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčic´ K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV de C, Vesth TC, Visser J, Yu J-H, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, VanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. 2017. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18:28. https://doi.org/10.1186/s13059-017-1151-0.24.
-
(2017)
Genome Biol
, vol.18
, pp. 28
-
-
De Vries, R.P.1
Riley, R.2
Wiebenga, A.3
Aguilar-Osorio, G.4
Amillis, S.5
Uchima, C.A.6
Erluh, G.7
Asadollahi, M.8
Askin, M.9
Barry, K.10
Battaglia, E.11
Bayram, Ö.12
Benocci, T.13
Braus-Stromeyer, S.A.14
Caldana, C.15
Cánovas, D.16
Cerqueira, G.C.17
Chen, F.18
Chen, W.19
Choi, C.20
Clum, A.21
Dos Santos, R.22
Damásio, A.R.23
Diallinas, G.24
Emri, T.25
Fekete, E.26
Flipphi, M.27
Freyberg, S.28
Gallo, A.29
Gournas, C.30
Habgood, R.31
Hainaut, M.32
Harispe, M.L.33
Henrissat, B.34
Hildén, K.S.35
Hope, R.36
Hossain, A.37
Karabika, E.38
Karaffa, L.39
Karányi, Z.40
Kraševec, N.41
Kuo, A.42
Kusch, H.43
Labutti, K.44
Lagendijk, E.L.45
Lapidus, A.46
Levasseur, A.47
Lindquist, E.48
Lipzen, A.49
Logrieco, A.F.50
Maccabe, A.51
Mäkelä, M.R.52
Malavazi, I.53
Melin, P.54
Meyer, V.55
Mielnichuk, N.56
Miskei, M.57
Molnár, Á.P.58
Mulé, G.59
Ngan, C.Y.60
Orejas, M.61
Orosz, E.62
Ouedraogo, J.P.63
Overkamp, K.M.64
Park, H.-S.65
Perrone, G.66
Piumi, F.67
Punt, P.J.68
Ram, A.69
Ramón, A.70
Rauscher, S.71
Record, E.72
Riaño-Pachón, D.M.73
Robert, V.74
Röhrig, J.75
Ruller, R.76
Salamov, A.77
Salih, N.S.78
Samson, R.A.79
Sándor, E.80
Sanguinetti, M.81
Schütze, T.82
Sepčic´, K.83
Shelest, E.84
Sherlock, G.85
Sophianopoulou, V.86
Squina, F.M.87
Sun, H.88
Susca, A.89
Todd, R.B.90
Tsang, A.91
Unkles, S.E.92
Van De Wiele, N.93
Van Rossen-Uffink, D.94
Oliveira Jv De, C.95
Vesth, T.C.96
Visser, J.97
Yu, J.-H.98
Zhou, M.99
Ersen, M.R.100
Archer, D.B.101
Baker, S.E.102
Benoit, I.103
Brakhage, A.A.104
Braus, G.H.105
Fischer, R.106
Frisvad, J.C.107
Goldman, G.H.108
Houbraken, J.109
Oakley, B.110
Pócsi, I.111
Scazzocchio, C.112
Seiboth, B.113
Vankuyk, P.A.114
Wortman, J.115
Dyer, P.S.116
Grigoriev, I.V.117
more..
-
24
-
-
30544434099
-
Fungal secondary metabolism— from biochemistry to genomics
-
Keller NP, Turner G, Bennett JW. 2005. Fungal secondary metabolism— from biochemistry to genomics. Nat Rev Microbiol 3:937–947. https://doi.org/10.1038/nrmicro1286.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 937-947
-
-
Keller, N.P.1
Turner, G.2
Bennett, J.W.3
-
25
-
-
85000815540
-
Regulation and role of fungal secondary metabolites
-
Macheleidt J, Mattern DJ, Fischer J, Netzker T, Weber J, Schroeckh V, Valiante V, Brakhage AA. 2016. Regulation and role of fungal secondary metabolites. Annu Rev Genet 50:371–392. https://doi.org/10.1146/annurev-genet-120215-035203.
-
(2016)
Annu Rev Genet
, vol.50
, pp. 371-392
-
-
Macheleidt, J.1
Mattern, D.J.2
Fischer, J.3
Netzker, T.4
Weber, J.5
Schroeckh, V.6
Valiante, V.7
Brakhage, A.A.8
-
26
-
-
84907132888
-
The current role of Aspergillus and Penicillium in human and animal health
-
Pitt JI. 1994. The current role of Aspergillus and Penicillium in human and animal health. Med Mycol 32:17–32. https://doi.org/10.1080/02681219480000701.
-
(1994)
Med Mycol
, vol.32
, pp. 17-32
-
-
Pitt, J.I.1
-
27
-
-
84941187997
-
Chemodiversity in the genus Aspergillus
-
Frisvad JC, Larsen TO. 2015. Chemodiversity in the genus Aspergillus. Appl Microbiol Biotechnol 99:7859–7877. https://doi.org/10.1007/s00253-015-6839-z.
-
(2015)
Appl Microbiol Biotechnol
, vol.99
, pp. 7859-7877
-
-
Frisvad, J.C.1
Larsen, T.O.2
-
28
-
-
85053444983
-
The birth, evolution and death of metabolic gene clusters in fungi
-
Rokas A, Wisecaver JH, Lind AL. 2018. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 16:731–744. https://doi.org/10.1038/s41579-018-0075-3.
-
(2018)
Nat Rev Microbiol
, vol.16
, pp. 731-744
-
-
Rokas, A.1
Wisecaver, J.H.2
Lind, A.L.3
-
29
-
-
84979913002
-
New sections in Penicillium containing novel species producing patulin, pyripyropens or other bioactive compounds
-
Houbraken J, Wang L, Lee HB, Frisvad JC. 2016. New sections in Penicillium containing novel species producing patulin, pyripyropens or other bioactive compounds. Persoonia Fungi 36:299–314. https://doi.org/10.3767/003158516X692040.
-
(2016)
Persoonia Fungi
, vol.36
, pp. 299-314
-
-
Houbraken, J.1
Wang, L.2
Lee, H.B.3
Frisvad, J.C.4
-
30
-
-
35548929808
-
Secondary chemicals protect mould from fungivory
-
Rohlfs M, Albert M, Keller NP, Kempken F. 2007. Secondary chemicals protect mould from fungivory. Biol Lett 3:523–525. https://doi.org/10.1098/rsbl.2007.0338.
-
(2007)
Biol Lett
, vol.3
, pp. 523-525
-
-
Rohlfs, M.1
Albert, M.2
Keller, N.P.3
Kempken, F.4
-
31
-
-
56949083532
-
Secondary metabolism: Regulation and role in fungal biology
-
Fox EM, Howlett BJ. 2008. Secondary metabolism: Regulation and role in fungal biology. Curr Opin Microbiol 11:481–487. https://doi.org/10.1016/j.mib.2008.10.007.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 481-487
-
-
Fox, E.M.1
Howlett, B.J.2
-
32
-
-
84954230552
-
Bioactive secondary metabolites produced by the fungal endophytes of conifers
-
Stierle AA, Stierle DB. 2015. Bioactive secondary metabolites produced by the fungal endophytes of conifers. Nat Prod Commun 10: 1671–1682.
-
(2015)
Nat Prod Commun
, vol.10
, pp. 1671-1682
-
-
Stierle, A.A.1
Stierle, D.B.2
-
33
-
-
78650202413
-
Fungal secondary metabolites as modulators of interactions with insects and other arthropods
-
Rohlfs M, Churchill A. 2011. Fungal secondary metabolites as modulators of interactions with insects and other arthropods. Fungal Genet Biol 48:23–34. https://doi.org/10.1016/j.fgb.2010.08.008.
-
(2011)
Fungal Genet Biol
, vol.48
, pp. 23-34
-
-
Rohlfs, M.1
Churchill, A.2
-
34
-
-
0019727999
-
Ranking animal carcinogens: A proposed regulatory approach
-
Squire R. 1981. Ranking animal carcinogens: A proposed regulatory approach. Science 214:877–880. https://doi.org/10.1126/science.7302565.
-
(1981)
Science
, vol.214
, pp. 877-880
-
-
Squire, R.1
-
35
-
-
0018847617
-
On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. Influenzae
-
Fleming A. 1980. On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae. Clin Infect Dis 2:129–139. https://doi.org/10.1093/clinids/2.1.129.
-
(1980)
Clin Infect Dis
, vol.2
, pp. 129-139
-
-
Fleming, A.1
-
36
-
-
50349107247
-
Penicillin as a chemotherapeutic agent
-
Chain E, Florey HW, Gardner AD, Heatley NG, Jennings MA, Orr-Ewing J, Sanders AG. 1940. Penicillin as a chemotherapeutic agent. Lancet 236:226–228. https://doi.org/10.1016/S0140-6736(01)08728-1.
-
(1940)
Lancet
, vol.236
, pp. 226-228
-
-
Chain, E.1
Florey, H.W.2
Gardner, A.D.3
Heatley, N.G.4
Jennings, M.A.5
Orr-Ewing, J.6
Sanders, A.G.7
-
37
-
-
79960399031
-
A brief history of the antibiotic era: Lessons learned and challenges for the future
-
Aminov RI. 2010. A brief history of the antibiotic era: Lessons learned and challenges for the future. Front Microbiol 1:134. https://doi.org/10.3389/fmicb.2010.00134.
-
(2010)
Front Microbiol
, vol.1
, pp. 134
-
-
Aminov, R.I.1
-
38
-
-
84872842340
-
Sexual reproduction and mating-type-mediated strain development in the penicillinproducing fungus Penicillium chrysogenum
-
Böhm J, Hoff B, O’Gorman CM, Wolfers S, Klix V, Binger D, Zadra I, Kürnsteiner H, Pöggeler S, Dyer PS, Kück U. 2013. Sexual reproduction and mating-type-mediated strain development in the penicillinproducing fungus Penicillium chrysogenum. Proc Natl Acad Sci U S A 110:1476–1481. https://doi.org/10.1073/pnas.1217943110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 1476-1481
-
-
Böhm, J.1
Hoff, B.2
O’Gorman, C.M.3
Wolfers, S.4
Klix, V.5
Binger, D.6
Zadra, I.7
Kürnsteiner, H.8
Pöggeler, S.9
Dyer, P.S.10
Kück, U.11
-
40
-
-
85055530331
-
Systematic dissection of the evolutionarily conserved WetA developmental regulator across a genus of filamentous fungi
-
Wu M-Y, Mead ME, Lee M-K, Ostrem Loss EM, Kim S-C, Rokas A, Yu J-H. 2018. Systematic dissection of the evolutionarily conserved WetA developmental regulator across a genus of filamentous fungi. mBio 9:e01130-18. https://doi.org/10.1128/mBio.01130-18.
-
(2018)
Mbio
, vol.9
-
-
Wu, M.-Y.1
Mead, M.E.2
Lee, M.-K.3
Ostrem Loss, E.M.4
Kim, S.-C.5
Rokas, A.6
Yu, J.-H.7
-
41
-
-
84864401552
-
Molecular epidemiology of Aspergillus fumigatus isolates harboring the TR34/L98H azole resistance mechanism
-
Camps SMT, Rijs AJMM, Klaassen CHW, Meis JF, O’Gorman CM, Dyer PS, Melchers WJG, Verweij PE. 2012. Molecular epidemiology of Aspergillus fumigatus isolates harboring the TR34/L98H azole resistance mechanism. J Clin Microbiol 50:2674–2680. https://doi.org/10.1128/JCM.00335-12.
-
(2012)
J Clin Microbiol
, vol.50
, pp. 2674-2680
-
-
Camps, S.1
Rijs, A.2
Klaassen, C.3
Meis, J.F.4
O’Gorman, C.M.5
Dyer, P.S.6
Melchers, W.7
Verweij, P.E.8
-
42
-
-
0032916340
-
Aspergillus fumigatus and aspergillosis
-
Latgé JP. 1999. Aspergillus fumigatus and aspergillosis. Clin Microbiol Rev 12:310–350. https://doi.org/10.1128/CMR.12.2.310.
-
(1999)
Clin Microbiol Rev
, vol.12
, pp. 310-350
-
-
Latgé, J.P.1
-
43
-
-
84907579478
-
Aspergillus, its sexual states and the new International Code of Nomenclature
-
Pitt JI, Taylor JW. 2014. Aspergillus, its sexual states and the new International Code of Nomenclature. Mycologia 106:1051–1062. https://doi.org/10.3852/14-060.
-
(2014)
Mycologia
, vol.106
, pp. 1051-1062
-
-
Pitt, J.I.1
Taylor, J.W.2
-
44
-
-
84908295357
-
Phylogeny, identification and nomenclature of the genus Aspergillus
-
Samson RA, Visagie CM, Houbraken J, Hong S-B, Hubka V, Klaassen CHW, Perrone G, Seifert KA, Susca A, Tanney JB, Varga J, Kocsubé S, Szigeti G, Yaguchi T, Frisvad JC. 2014. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol 78:141–173. https://doi.org/10.1016/j.simyco.2014.07.004.
-
(2014)
Stud Mycol
, vol.78
, pp. 141-173
-
-
Samson, R.A.1
Visagie, C.M.2
Houbraken, J.3
Hong, S.-B.4
Hubka, V.5
Klaassen, C.6
Perrone, G.7
Seifert, K.A.8
Susca, A.9
Tanney, J.B.10
Varga, J.11
Kocsubé, S.12
Szigeti, G.13
Yaguchi, T.14
Frisvad, J.C.15
-
45
-
-
84878113118
-
Inferring ancient divergences requires genes with strong phylogenetic signals
-
Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327–331. https://doi.org/10.1038/nature12130.
-
(2013)
Nature
, vol.497
, pp. 327-331
-
-
Salichos, L.1
Rokas, A.2
-
46
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798–804. https://doi.org/10.1038/nature02053.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
47
-
-
85016928653
-
Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species
-
Nielsen JC, Grijseels S, Prigent S, Ji B, Dainat J, Nielsen KF, Frisvad JC, Workman M, Nielsen J. 2017. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nat Microbiol 2:17044. https://doi.org/10.1038/nmicrobiol.2017.44.
-
(2017)
Nat Microbiol
, vol.2
, pp. 17044
-
-
Nielsen, J.C.1
Grijseels, S.2
Prigent, S.3
Ji, B.4
Dainat, J.5
Nielsen, K.F.6
Frisvad, J.C.7
Workman, M.8
Nielsen, J.9
-
48
-
-
85040860340
-
Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species
-
Kjærbølling I, Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kuo A, Bowyer P, Matsuda Y, Mondo S, Lyhne EK, Kogle ME, Clum A, Lipzen A, Salamov A, Ngan CY, Daum C, Chiniquy J, Barry K, LaButti K, Haridas S, Simmons BA, Magnuson JK, Mortensen UH, Larsen TO, Grigoriev IV, Baker SE, Andersen MR. 2018. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A 115:E753–E761. https://doi.org/10.1073/pnas.1715954115.
-
(2018)
Proc Natl Acad Sci U S A
, vol.115
, pp. E753-E761
-
-
Kjærbølling, I.1
Vesth, T.C.2
Frisvad, J.C.3
Nybo, J.L.4
Theobald, S.5
Kuo, A.6
Bowyer, P.7
Matsuda, Y.8
Mondo, S.9
Lyhne, E.K.10
Kogle, M.E.11
Clum, A.12
Lipzen, A.13
Salamov, A.14
Ngan, C.Y.15
Daum, C.16
Chiniquy, J.17
Barry, K.18
Labutti, K.19
Haridas, S.20
Simmons, B.A.21
Magnuson, J.K.22
Mortensen, U.H.23
Larsen, T.O.24
Grigoriev, I.V.25
Baker, S.E.26
Ersen, M.R.27
more..
-
49
-
-
84996931915
-
Genome sequencing and comparative genomics analysis revealed pathogenic potential in Penicillium capsulatum as a novel fungal pathogen belonging to Eurotiales
-
Yang Y, Chen M, Li Z, Al-Hatmi AMS, de Hoog S, Pan W, Ye Q, Bo X, Li Z, Wang S, Wang J, Chen H, Liao W. 2016. Genome sequencing and comparative genomics analysis revealed pathogenic potential in Penicillium capsulatum as a novel fungal pathogen belonging to Eurotiales. Front Microbiol 7:1541. https://doi.org/10.3389/fmicb.2016.01541.
-
(2016)
Front Microbiol
, vol.7
, pp. 1541
-
-
Yang, Y.1
Chen, M.2
Li, Z.3
Al-Hatmi, A.4
De Hoog, S.5
Pan, W.6
Ye, Q.7
Bo, X.8
Li, Z.9
Wang, S.10
Wang, J.11
Chen, H.12
Liao, W.13
-
50
-
-
84862928655
-
Statistics and truth in phylogenomics
-
Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. 2012. Statistics and truth in phylogenomics. Mol Biol Evol 29:457–472. https://doi.org/10.1093/molbev/msr202.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 457-472
-
-
Kumar, S.1
Filipski, A.J.2
Battistuzzi, F.U.3
Kosakovsky Pond, S.L.4
Tamura, K.5
-
51
-
-
3042550872
-
Genome-scale phylogeny and the detection of systematic biases
-
Phillips MJ, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455–1458. https://doi.org/10.1093/molbev/msh137.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1455-1458
-
-
Phillips, M.J.1
Delsuc, F.2
Penny, D.3
-
52
-
-
79961133759
-
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited
-
Hess J, Goldman N. 2011. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited. PLoS One 6:e22783. https://doi.org/10.1371/journal.pone.0022783.
-
(2011)
Plos One
, vol.6
-
-
Hess, J.1
Goldman, N.2
-
53
-
-
84883284590
-
Origin of land plants using the multispecies coalescent model
-
Zhong B, Liu L, Yan Z, Penny D. 2013. Origin of land plants using the multispecies coalescent model. Trends Plant Sci 18:492–495. https://doi.org/10.1016/j.tplants.2013.04.009.
-
(2013)
Trends Plant Sci
, vol.18
, pp. 492-495
-
-
Zhong, B.1
Liu, L.2
Yan, Z.3
Penny, D.4
-
54
-
-
84866289853
-
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
-
Song S, Liu L, Edwards SV, Wu S. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A 109:14942–14947. https://doi.org/10.1073/pnas.1211733109.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 14942-14947
-
-
Song, S.1
Liu, L.2
Edwards, S.V.3
Wu, S.4
-
55
-
-
85008500372
-
-
Shen X-X, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 6:3927–3939. https://doi.org/10.1534/g3.116.034744.
-
(2016)
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
, vol.6
, pp. 3927-3939
-
-
Shen, X.-X.1
Zhou, X.2
Kominek, J.3
Kurtzman, C.P.4
Hittinger, C.T.5
Rokas, A.6
-
56
-
-
84988935122
-
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
-
Suh A. 2016. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zool Scr 45(S1):50–62. https://doi.org/10.1111/zsc.12213.
-
(2016)
Zool Scr
, vol.45
, Issue.1
, pp. 50-62
-
-
Suh, A.1
-
57
-
-
85021988665
-
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
-
Arcila D, Ortí G, Vari R, Armbruster JW, Stiassny MLJ, Ko KD, Sabaj MH, Lundberg J, Revell LJ, Betancur- R R. 2017. Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nat Ecol Evol 1:20. https://doi.org/10.1038/s41559-016-0020.
-
(2017)
Nat Ecol Evol
, vol.1
, pp. 20
-
-
Arcila, D.1
Ortí, G.2
Vari, R.3
Armbruster, J.W.4
Stiassny, M.5
Ko, K.D.6
Sabaj, M.H.7
Lundberg, J.8
Revell, L.J.9
Betancur-, R.R.10
-
58
-
-
85030862322
-
Embracing uncertainty in reconstructing early animal evolution
-
King N, Rokas A. 2017. Embracing uncertainty in reconstructing early animal evolution. Curr Biol 27:R1081–R1088. https://doi.org/10.1016/j.cub.2017.08.054.
-
(2017)
Curr Biol
, vol.27
, pp. R1081-R1088
-
-
King, N.1
Rokas, A.2
-
59
-
-
85021804124
-
Contentious relationships in phylogenomic studies can be driven by a handful of genes
-
Shen X-X, Hittinger CT, Rokas A. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol 1:126. https://doi.org/10.1038/s41559-017-0126.
-
(2017)
Nat Ecol Evol
, vol.1
, pp. 126
-
-
Shen, X.-X.1
Hittinger, C.T.2
Rokas, A.3
-
60
-
-
85058593949
-
Tempo and mode of genome evolution in the budding yeast subphylum
-
Shen X-X, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe R, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A. 2018. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175:1533–1545.e20. https://doi.org/10.1016/j.cell.2018.10.023.
-
(2018)
Cell
, vol.175
, pp. 1533-1545
-
-
Shen, X.-X.1
Opulente, D.A.2
Kominek, J.3
Zhou, X.4
Steenwyk, J.L.5
Buh, K.V.6
Haase, M.7
Wisecaver, J.H.8
Wang, M.9
Doering, D.T.10
Boudouris, J.T.11
Schneider, R.M.12
Langdon, Q.K.13
Ohkuma, M.14
Endoh, R.15
Takashima, M.16
Manabe, R.17
Čadež, N.18
Libkind, D.19
Rosa, C.A.20
Devirgilio, J.21
Hulfachor, A.B.22
Groenewald, M.23
Kurtzman, C.P.24
Hittinger, C.T.25
Rokas, A.26
more..
-
61
-
-
85008392540
-
Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles
-
Kocsubé S, Perrone G, Magistà D, Houbraken J, Varga J, Szigeti G, Hubka V, Hong S-B, Frisvad JC, Samson RA. 2016. Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles. Stud Mycol 85:199–213. https://doi.org/10.1016/j.simyco.2016.11.006.
-
(2016)
Stud Mycol
, vol.85
, pp. 199-213
-
-
Kocsubé, S.1
Perrone, G.2
Magistà, D.3
Houbraken, J.4
Varga, J.5
Szigeti, G.6
Hubka, V.7
Hong, S.-B.8
Frisvad, J.C.9
Samson, R.A.10
-
62
-
-
84977488777
-
Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella
-
Taylor JW, Göker M, Pitt JI. 2016. Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella. Taxon 65:593–601. https://doi.org/10.12705/653.10.
-
(2016)
Taxon
, vol.65
, pp. 593-601
-
-
Taylor, J.W.1
Göker, M.2
Pitt, J.I.3
-
63
-
-
84973324653
-
Computing the internode certainty and related measures from partial gene trees
-
Kobert K, Salichos L, Rokas A, Stamatakis A. 2016. Computing the internode certainty and related measures from partial gene trees. Mol Biol Evol 33:1606–1617. https://doi.org/10.1093/molbev/msw040.
-
(2016)
Mol Biol Evol
, vol.33
, pp. 1606-1617
-
-
Kobert, K.1
Salichos, L.2
Rokas, A.3
Stamatakis, A.4
-
64
-
-
84898641369
-
Novel information theory-based measures for quantifying incongruence among phylogenetic trees
-
Salichos L, Stamatakis A, Rokas A. 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol 31:1261–1271. https://doi.org/10.1093/molbev/msu061.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1261-1271
-
-
Salichos, L.1
Stamatakis, A.2
Rokas, A.3
-
65
-
-
84876566349
-
OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs
-
Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV. 2013. OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 41:D358–D365. https://doi.org/10.1093/nar/gks1116.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D358-D365
-
-
Waterhouse, R.M.1
Tegenfeldt, F.2
Li, J.3
Zdobnov, E.M.4
Kriventseva, E.V.5
-
66
-
-
84255189126
-
Phylogeny of Penicillium and the segregation of Trichocomaceae into three families
-
Houbraken J, Samson RA. 2011. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol 70:1–51. https://doi.org/10.3114/sim.2011.70.01.
-
(2011)
Stud Mycol
, vol.70
, pp. 1-51
-
-
Houbraken, J.1
Samson, R.A.2
-
67
-
-
85041125468
-
UFBoot2: Improving the ultrafast bootstrap approximation
-
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. 2018. UFBoot2: Improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522. https://doi.org/10.1093/molbev/msx281.
-
(2018)
Mol Biol Evol
, vol.35
, pp. 518-522
-
-
Hoang, D.T.1
Chernomor, O.2
Von Haeseler, A.3
Minh, B.Q.4
Vinh, L.S.5
-
68
-
-
49549112511
-
Database indexing for production MegaBLAST searches
-
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. 2008. Database indexing for production MegaBLAST searches. Bioinformatics 24:1757–1764. https://doi.org/10.1093/bioinformatics/btn322.
-
(2008)
Bioinformatics
, vol.24
, pp. 1757-1764
-
-
Morgulis, A.1
Coulouris, G.2
Raytselis, Y.3
Madden, T.L.4
Agarwala, R.5
Schäffer, A.A.6
-
69
-
-
0032766857
-
Multiple comparisons of loglikelihoods with applications to phylogenetic inference
-
Shimodaira H, Hasegawa M. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114. https://doi.org/10.1093/oxfordjournals.molbev.a026201.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1114
-
-
Shimodaira, H.1
Hasegawa, M.2
-
70
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492–508. https://doi.org/10.1080/10635150290069913.
-
(2002)
Syst Biol
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
71
-
-
85028559263
-
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
-
Liu L, Zhang J, Rheindt FE, Lei F, Qu Y, Wang Y, Zhang Y, Sullivan C, Nie W, Wang J, Yang F, Chen J, Edwards SV, Meng J, Wu S. 2017. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proc Natl Acad Sci U S A 114:E7282–E7290. https://doi.org/10.1073/pnas.1616744114.
-
(2017)
Proc Natl Acad Sci U S A
, vol.114
, pp. E7282-E7290
-
-
Liu, L.1
Zhang, J.2
Rheindt, F.E.3
Lei, F.4
Qu, Y.5
Wang, Y.6
Zhang, Y.7
Sullivan, C.8
Nie, W.9
Wang, J.10
Yang, F.11
Chen, J.12
Edwards, S.V.13
Meng, J.14
Wu, S.15
-
72
-
-
0017055252
-
ML-236A, ML-236B, and ML-236C, new inhibitors of cholesterogenesis produced by Penicillium citrinum
-
Endo A, Kuroda M, Tsujita Y. 1976. ML-236A, ML-236B, and ML-236C, new inhibitors of cholesterogenesis produced by Penicillium citrinum. J Antibiot (Tokyo) 29:1346–1348. https://doi.org/10.7164/antibiotics.29.1346.
-
(1976)
J Antibiot (Tokyo)
, vol.29
, pp. 1346-1348
-
-
Endo, A.1
Kuroda, M.2
Tsujita, Y.3
-
73
-
-
85061988258
-
-
Mead ME, Knowles SL, Raja HA, Beattie SR, Kowalski CH, Steenwyk JL, Silva LP, Chiaratto J, Ries LNA, Goldman GH, Cramer RA, Oberlies NH, Rokas A. 2019. Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, a close relative of the major human fungal pathogen Aspergillus fumigatus. mSphere 4:e00018-19. https://doi.org/10.1128/mSphere.00018-19.
-
(2019)
Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus Fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus Fumigatus. Msphere
, vol.4
-
-
Mead, M.E.1
Knowles, S.L.2
Raja, H.A.3
Beattie, S.R.4
Kowalski, C.H.5
Steenwyk, J.L.6
Silva, L.P.7
Chiaratto, J.8
Ries, L.9
Goldman, G.H.10
Cramer, R.A.11
Oberlies, N.H.12
Rokas, A.13
-
74
-
-
84859217905
-
A taxonomic and ecological overview of cheese fungi
-
Ropars J, Cruaud C, Lacoste S, Dupont J. 2012. A taxonomic and ecological overview of cheese fungi. Int J Food Microbiol 155:199–210. https://doi.org/10.1016/j.ijfoodmicro.2012.02.005.
-
(2012)
Int J Food Microbiol
, vol.155
, pp. 199-210
-
-
Ropars, J.1
Cruaud, C.2
Lacoste, S.3
Dupont, J.4
-
75
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan JH, Salter LA. 2005. Gene tree distributions under the coalescent process. Evolution 59:24–37. https://doi.org/10.1111/j.0014-3820.2005.tb00891.x.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
76
-
-
0034350321
-
Testing hybridization hypotheses based on incongruent gene trees
-
Sang T, Zhong Y. 2000. Testing hybridization hypotheses based on incongruent gene trees. Syst Biol 49:422–434. https://doi.org/10.1080/10635159950127321.
-
(2000)
Syst Biol
, vol.49
, pp. 422-434
-
-
Sang, T.1
Zhong, Y.2
-
77
-
-
2442573762
-
Simultaneous identification of duplications and lateral transfers
-
ACM Press, New York, NY
-
Hallett M, Lagergren J, Tofigh A. 2004. Simultaneous identification of duplications and lateral transfers, p. 347–356. In Proceedings of the Eighth Annual International Conference on Computational Molecular Biology—RECOMB ‘04. ACM Press, New York, NY.
-
(2004)
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology—RECOMB ‘04
, pp. 347-356
-
-
Hallett, M.1
Lagergren, J.2
Tofigh, A.3
-
78
-
-
33847790997
-
Pattern pluralism and the tree of life hypothesis
-
Doolittle WF, Bapteste E. 2007. Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci U S A 104:2043–2049. https://doi.org/10.1073/pnas.0610699104.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
79
-
-
67049119180
-
Evidence for an ancient adaptive episode of convergent molecular evolution
-
Castoe TA, de Koning APJ, Kim H-M, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD. 2009. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci U S A 106:8986–8991. https://doi.org/10.1073/pnas.0900233106.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 8986-8991
-
-
Castoe, T.A.1
De Koning, A.2
Kim, H.-M.3
Gu, W.4
Noonan, B.P.5
Naylor, G.6
Jiang, Z.J.7
Parkinson, C.L.8
Pollock, D.D.9
-
80
-
-
74549195621
-
The hearing gene Prestin unites echolocating bats and whales
-
Li Y, Liu Z, Shi P, Zhang J. 2010. The hearing gene Prestin unites echolocating bats and whales. Curr Biol 20:R55–R56. https://doi.org/10.1016/j.cub.2009.11.042.
-
(2010)
Curr Biol
, vol.20
, pp. R55-R56
-
-
Li, Y.1
Liu, Z.2
Shi, P.3
Zhang, J.4
-
81
-
-
33745591114
-
Genetic evidence for complex speciation of humans and chimpanzees
-
Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103–1108. https://doi.org/10.1038/nature04789.
-
(2006)
Nature
, vol.441
, pp. 1103-1108
-
-
Patterson, N.1
Richter, D.J.2
Gnerre, S.3
Lander, E.S.4
Reich, D.5
-
82
-
-
33847253862
-
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
-
Hobolth A, Christensen OF, Mailund T, Schierup MH. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 3:e7. https://doi.org/10.1371/journal.pgen.0030007.
-
(2007)
Plos Genet
, vol.3
-
-
Hobolth, A.1
Christensen, O.F.2
Mailund, T.3
Schierup, M.H.4
-
83
-
-
84886085175
-
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
-
Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD. 2013. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Res 23:1817–1828. https://doi.org/10.1101/gr.159426.113.
-
(2013)
Genome Res
, vol.23
, pp. 1817-1828
-
-
Martin, S.H.1
Dasmahapatra, K.K.2
Nadeau, N.J.3
Salazar, C.4
Walters, J.R.5
Simpson, F.6
Blaxter, M.7
Manica, A.8
Mallet, J.9
Jiggins, C.D.10
-
84
-
-
84855712054
-
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
-
Nabhan AR, Sarkar IN. 2012. The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Brief Bioinform 13:122–134. https://doi.org/10.1093/bib/bbr014.
-
(2012)
Brief Bioinform
, vol.13
, pp. 122-134
-
-
Nabhan, A.R.1
Sarkar, I.N.2
-
85
-
-
17744398025
-
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
-
Rokas A, Carroll SB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22:1337–1344. https://doi.org/10.1093/molbev/msi121.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1337-1344
-
-
Rokas, A.1
Carroll, S.B.2
-
86
-
-
65249099546
-
Phylogenomics revives traditional views on deep animal relationships
-
Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Wörheide G, Manuel M. 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19:706–712. https://doi.org/10.1016/j.cub.2009.02.052.
-
(2009)
Curr Biol
, vol.19
, pp. 706-712
-
-
Philippe, H.1
Derelle, R.2
Lopez, P.3
Pick, K.4
Borchiellini, C.5
Boury-Esnault, N.6
Vacelet, J.7
Renard, E.8
Houliston, E.9
Quéinnec, E.10
Da Silva, C.11
Wincker, P.12
Le Guyader, H.13
Leys, S.14
Jackson, D.J.15
Schreiber, F.16
Erpenbeck, D.17
Morgenstern, B.18
Wörheide, G.19
Manuel, M.20
more..
-
87
-
-
34547883900
-
Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans
-
Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF. 2007. Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans. Curr Biol 17: 1420–1425. https://doi.org/10.1016/j.cub.2007.07.036.
-
(2007)
Curr Biol
, vol.17
, pp. 1420-1425
-
-
Rodríguez-Ezpeleta, N.1
Brinkmann, H.2
Burger, G.3
Roger, A.J.4
Gray, M.W.5
Philippe, H.6
Lang, B.F.7
-
88
-
-
84946130803
-
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
-
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. 2015. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Syst Biol 64:778–791. https://doi.org/10.1093/sysbio/syv033.
-
(2015)
Syst Biol
, vol.64
, pp. 778-791
-
-
Tan, G.1
Muffato, M.2
Ledergerber, C.3
Herrero, J.4
Goldman, N.5
Gil, M.6
Dessimoz, C.7
-
89
-
-
0036593395
-
Ancient phylogenetic relationships
-
Gribaldo S, Philippe H. 2002. Ancient phylogenetic relationships. Theor Popul Biol 61:391–408. https://doi.org/10.1006/tpbi.2002.1593.
-
(2002)
Theor Popul Biol
, vol.61
, pp. 391-408
-
-
Gribaldo, S.1
Philippe, H.2
-
90
-
-
74549221461
-
Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing
-
Giraud F, Giraud T, Aguileta G, Fournier E, Samson R, Cruaud C, Lacoste S, Ropars J, Tellier A, Dupont J. 2010. Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing. Int J Food Microbiol 137:204–213. https://doi.org/10.1016/j.ijfoodmicro.2009.11.014.
-
(2010)
Int J Food Microbiol
, vol.137
, pp. 204-213
-
-
Giraud, F.1
Giraud, T.2
Aguileta, G.3
Fournier, E.4
Samson, R.5
Cruaud, C.6
Lacoste, S.7
Ropars, J.8
Tellier, A.9
Dupont, J.10
-
91
-
-
33751381461
-
TimeTree: A public knowledgebase of divergence times among organisms
-
Hedges SB, Dudley J, Kumar S. 2006. TimeTree: A public knowledgebase of divergence times among organisms. Bioinformatics 22: 2971–2972. https://doi.org/10.1093/bioinformatics/btl505.
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
92
-
-
0001225414
-
Fungal molecular evolution: Gene trees and geologic time
-
In McLaughlin DJ, McLaughlin EG, Lemke PA, Springer, Berlin, Germany
-
Berbee ML, Taylor JW. 2001. Fungal molecular evolution: Gene trees and geologic time. In McLaughlin DJ, McLaughlin EG, Lemke PA (ed), Systematics and evolution. The Mycota (a comprehensive treatise on fungi as experimental systems for basic and applied research), vol 7B. Springer, Berlin, Germany.
-
(2001)
Systematics and Evolution. the Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research)
, vol.7
-
-
Berbee, M.L.1
Taylor, J.W.2
-
93
-
-
33846551800
-
Molecular taxonomy, origins and evolution of freshwater ascomycetes
-
Vijaykrishna D, Jeewon R, Hyde K. 2006. Molecular taxonomy, origins and evolution of freshwater ascomycetes. Fungal Divers 23:351–390.
-
(2006)
Fungal Divers
, vol.23
, pp. 351-390
-
-
Vijaykrishna, D.1
Jeewon, R.2
Hyde, K.3
-
94
-
-
70349645483
-
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
-
Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C-Y, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19:1722–1731. https://doi.org/10.1101/gr.087551.108.
-
(2009)
Genome Res
, vol.19
, pp. 1722-1731
-
-
Sharpton, T.J.1
Stajich, J.E.2
Rounsley, S.D.3
Gardner, M.J.4
Wortman, J.R.5
Jordar, V.S.6
Maiti, R.7
Kodira, C.D.8
Neafsey, D.E.9
Zeng, Q.10
Hung, C.-Y.11
McMahan, C.12
Muszewska, A.13
Grynberg, M.14
Mandel, M.A.15
Kellner, E.M.16
Barker, B.M.17
Galgiani, J.N.18
Orbach, M.J.19
Kirkland, T.N.20
Cole, G.T.21
Henn, M.R.22
Birren, B.W.23
Taylor, J.W.24
more..
-
95
-
-
84874534961
-
Gene make-up: Rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes
-
Da Lage J-L, Binder M, Hua-Van A, Janeček Š, Casane D. 2013. Gene make-up: Rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes. BMC Evol Biol 13:40. https://doi.org/10.1186/1471-2148-13-40.
-
(2013)
BMC Evol Biol
, vol.13
, pp. 40
-
-
Da Lage, J.-L.1
Binder, M.2
Hua-Van, A.3
Janeček, Š.4
Casane, D.5
-
96
-
-
42649099266
-
Conservation of divergent transcription in fungi
-
Kensche PR, Oti M, Dutilh BE, Huynen MA. 2008. Conservation of divergent transcription in fungi. Trends Genet 24:207–211. https://doi.org/10.1016/j.tig.2008.02.003.
-
(2008)
Trends Genet
, vol.24
, pp. 207-211
-
-
Kensche, P.R.1
Oti, M.2
Dutilh, B.E.3
Huynen, M.A.4
-
97
-
-
84905195191
-
Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data
-
Beimforde C, Feldberg K, Nylinder S, Rikkinen J, Tuovila H, Dörfelt H, Gube M, Jackson DJ, Reitner J, Seyfullah LJ, Schmidt AR. 2014. Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data. Mol Phylogenet Evol 78:386–398. https://doi.org/10.1016/j.ympev.2014.04.024.
-
(2014)
Mol Phylogenet Evol
, vol.78
, pp. 386-398
-
-
Beimforde, C.1
Feldberg, K.2
Nylinder, S.3
Rikkinen, J.4
Tuovila, H.5
Dörfelt, H.6
Gube, M.7
Jackson, D.J.8
Reitner, J.9
Seyfullah, L.J.10
Schmidt, A.R.11
-
98
-
-
84959275744
-
Genomic analysis of an ascomycete fungus from the rice planthopper reveals how it adapts to an endosymbiotic lifestyle
-
Fan H-W, Noda H, Xie H-Q, Suetsugu Y, Zhu Q-H, Zhang C-X. 2015. Genomic analysis of an ascomycete fungus from the rice planthopper reveals how it adapts to an endosymbiotic lifestyle. Genome Biol Evol 7:2623–2634. https://doi.org/10.1093/gbe/evv169.
-
(2015)
Genome Biol Evol
, vol.7
, pp. 2623-2634
-
-
Fan, H.-W.1
Noda, H.2
Xie, H.-Q.3
Suetsugu, Y.4
Zhu, Q.-H.5
Zhang, C.-X.6
-
99
-
-
84941696041
-
The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a barkto-rock substrate shift
-
Gaya E, Fernández-Brime S, Vargas R, Lachlan RF, Gueidan C, Ramírez-Mejía M, Lutzoni F. 2015. The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a barkto-rock substrate shift. Proc Natl Acad Sci U S A 112:11600–11605. https://doi.org/10.1073/pnas.1507072112.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, pp. 11600-11605
-
-
Gaya, E.1
Fernández-Brime, S.2
Vargas, R.3
Lachlan, R.F.4
Gueidan, C.5
Ramírez-Mejía, M.6
Lutzoni, F.7
-
100
-
-
84884508060
-
Fusarium pathogenomics
-
Ma L-J, Geiser DM, Proctor RH, Rooney AP, O’Donnell K, Trail F, Gardiner DM, Manners JM, Kazan K. 2013. Fusarium pathogenomics. Annu Rev Microbiol 67:399–416. https://doi.org/10.1146/annurev-micro-092412-155650.
-
(2013)
Annu Rev Microbiol
, vol.67
, pp. 399-416
-
-
Ma, L.-J.1
Geiser, D.M.2
Proctor, R.H.3
Rooney, A.P.4
O’Donnell, K.5
Trail, F.6
Gardiner, D.M.7
Manners, J.M.8
Kazan, K.9
-
101
-
-
84874989125
-
Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria
-
O’Donnell K, Rooney AP, Proctor RH, Brown DW, McCormick SP, Ward TJ, Frandsen RJN, Lysøe E, Rehner SA, Aoki T, Robert V, Crous PW, Groenewald JZ, Kang S, Geiser DM. 2013. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol 52: 20–31. https://doi.org/10.1016/j.fgb.2012.12.004.
-
(2013)
Fungal Genet Biol
, vol.52
, pp. 20-31
-
-
O’Donnell, K.1
Rooney, A.P.2
Proctor, R.H.3
Brown, D.W.4
McCormick, S.P.5
Ward, T.J.6
Frandsen, R.7
Lysøe, E.8
Rehner, S.A.9
Aoki, T.10
Robert, V.11
Crous, P.W.12
Groenewald, J.Z.13
Kang, S.14
Geiser, D.M.15
-
102
-
-
84996590420
-
-
Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. 2016. In silico Whole Genome Sequencer and Analyzer (iWGS): A computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 6:3655–3662. https://doi.org/10.1534/g3.116.034249.
-
(2016)
In Silico Whole Genome Sequencer and Analyzer (Iwgs): A Computational Pipeline to Guide the Design and Analysis of De Novo Genome Sequencing Studies
, vol.6
, pp. 3655-3662
-
-
Zhou, X.1
Peris, D.2
Kominek, J.3
Kurtzman, C.P.4
Hittinger, C.T.5
Rokas, A.6
-
103
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.
-
(2012)
J Comput Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
Pyshkin, A.V.11
Sirotkin, A.V.12
Vyahhi, N.13
Tesler, G.14
Alekseyev, M.A.15
Pevzner, P.A.16
-
104
-
-
84891349005
-
Informed and automated k-mer size selection for genome assembly
-
Chikhi R, Medvedev P. 2014. Informed and automated k-mer size selection for genome assembly. Bioinformatics 30:31–37. https://doi.org/10.1093/bioinformatics/btt310.
-
(2014)
Bioinformatics
, vol.30
, pp. 31-37
-
-
Chikhi, R.1
Medvedev, P.2
-
105
-
-
84876266928
-
QUAST: Quality assessment tool for genome assemblies
-
Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086.
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
106
-
-
85045577622
-
BUSCO applications from quality assessments to gene prediction and phylogenomics
-
Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548. https://doi.org/10.1093/molbev/msx319.
-
(2018)
Mol Biol Evol
, vol.35
, pp. 543-548
-
-
Waterhouse, R.M.1
Seppey, M.2
Simão, F.A.3
Manni, M.4
Ioannidis, P.5
Klioutchnikov, G.6
Kriventseva, E.V.7
Zdobnov, E.M.8
-
107
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195.
-
(2011)
Plos Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
108
-
-
85073370262
-
The BLAST sequence analysis tool. The NCBI handbook
-
Bethesda, MD
-
Madden T. 2013. The BLAST sequence analysis tool. The NCBI handbook. National Library of Medicine, Bethesda, MD.
-
(2013)
National Library of Medicine
-
-
Madden, T.1
-
109
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
110
-
-
2942527473
-
Gene prediction with a hidden Markov model and a new intron submodel
-
Stanke M, Waack S. 2003. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19:ii215–ii225. https://doi.org/10.1093/bioinformatics/btg1080.
-
(2003)
Bioinformatics
, vol.19
-
-
Stanke, M.1
Waack, S.2
-
111
-
-
85019711462
-
Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders
-
Ioannidis P, Simao FA, Waterhouse RM, Manni M, Seppey M, Robertson HM, Misof B, Niehuis O, Zdobnov EM. 2017. Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders. Genome Biol Evol 9:415–430. https://doi.org/10.1093/gbe/evx006.
-
(2017)
Genome Biol Evol
, vol.9
, pp. 415-430
-
-
Ioannidis, P.1
Simao, F.A.2
Waterhouse, R.M.3
Manni, M.4
Seppey, M.5
Robertson, H.M.6
Misof, B.7
Niehuis, O.8
Zdobnov, E.M.9
-
112
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
113
-
-
55249096440
-
Using BLOSUM in sequence alignments
-
Mount DW. 2008. Using BLOSUM in sequence alignments. CSH Protoc 2008:pdb.top39. https://doi.org/10.1101/pdb.top39.
-
(2008)
CSH Protoc
, vol.2008
-
-
Mount, D.W.1
-
114
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon M. 2009. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. https://doi.org/10.1093/bioinformatics/btp163.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
Dalke, A.6
Friedberg, I.7
Hamelryck, T.8
Kauff, F.9
Wilczynski, B.10
De Hoon, M.11
-
115
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutierrez, S.1
Silla-Martinez, J.M.2
Gabaldon, T.3
-
116
-
-
85008426692
-
A genome-scale investigation of how sequence, function, and tree-based gene properties influence phylogenetic inference
-
Shen X-X, Salichos L, Rokas A. 2016. A genome-scale investigation of how sequence, function, and tree-based gene properties influence phylogenetic inference. Genome Biol Evol 8:2565–2580. https://doi.org/10.1093/gbe/evw179.
-
(2016)
Genome Biol Evol
, vol.8
, pp. 2565-2580
-
-
Shen, X.-X.1
Salichos, L.2
Rokas, A.3
-
117
-
-
0141721426
-
The root of the mammalian tree inferred from whole mitochondrial genomes
-
Phillips MJ, Penny D. 2003. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol 28:171–185. https://doi.org/10.1016/S1055-7903(03)00057-5.
-
(2003)
Mol Phylogenet Evol
, vol.28
, pp. 171-185
-
-
Phillips, M.J.1
Penny, D.2
-
118
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
119
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards SV. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63:1–19. https://doi.org/10.1111/j.1558-5646.2008.00549.x.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
120
-
-
84931034856
-
ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
-
Mirarab S, Warnow T. 2015. ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31:i44–i52. https://doi.org/10.1093/bioinformatics/btv234.
-
(2015)
Bioinformatics
, vol.31
, pp. i44-i52
-
-
Mirarab, S.1
Warnow, T.2
-
121
-
-
84922362345
-
IQ-TREE: A fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies
-
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/msu300.
-
(2015)
Mol Biol Evol
, vol.32
, pp. 268-274
-
-
Nguyen, L.-T.1
Schmidt, H.A.2
Von Haeseler, A.3
Minh, B.Q.4
-
122
-
-
85019875027
-
ModelFinder: Fast model selection for accurate phylogenetic estimates
-
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589. https://doi.org/10.1038/nmeth.4285.
-
(2017)
Nat Methods
, vol.14
, pp. 587-589
-
-
Kalyaanamoorthy, S.1
Minh, B.Q.2
Wong, T.3
Von Haeseler, A.4
Jermiin, L.S.5
-
123
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
124
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306–314. https://doi.org/10.1007/BF00160154.
-
(1994)
J Mol Evol
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
125
-
-
0030451420
-
Among-site rate variation and its impact on phylogenetic analyses
-
Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 11:367–372. https://doi.org/10.1016/0169-5347(96)10041-0.
-
(1996)
Trends Ecol Evol
, vol.11
, pp. 367-372
-
-
Yang, Z.1
-
126
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci 17:57–86.
-
(1986)
Lect Math Life Sci
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
127
-
-
79951849225
-
A ‘missing’ family of classical orthogonal polynomials
-
Vinet L, Zhedanov A. 2011. A ‘missing’ family of classical orthogonal polynomials. J Phys A Math Theor 44:085201. https://doi.org/10.1088/1751-8113/44/8/085201.
-
(2011)
J Phys a Math Theor
, vol.44
-
-
Vinet, L.1
Zhedanov, A.2
-
128
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8:275–282. https://doi.org/10.1093/bioinformatics/8.3.275.
-
(1992)
Bioinformatics
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
129
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol 25:1307–1320. https://doi.org/10.1093/molbev/msn067.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
130
-
-
12344269158
-
Different versions of the Dayhoff rate matrix
-
Kosiol C, Goldman N. 2005. Different versions of the Dayhoff rate matrix. Mol Biol Evol 22:193–199. https://doi.org/10.1093/molbev/msi005.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 193-199
-
-
Kosiol, C.1
Goldman, N.2
-
131
-
-
85041094722
-
Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets
-
Zhou X, Shen X-X, Hittinger CT, Rokas A. 2018. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol Biol Evol 35:486–503. https://doi.org/10.1093/molbev/msx302.
-
(2018)
Mol Biol Evol
, vol.35
, pp. 486-503
-
-
Zhou, X.1
Shen, X.-X.2
Hittinger, C.T.3
Rokas, A.4
-
132
-
-
84994448773
-
Terrace aware data structure for phylogenomic inference from supermatrices
-
Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol 65:997–1008. https://doi.org/10.1093/sysbio/syw037.
-
(2016)
Syst Biol
, vol.65
, pp. 997-1008
-
-
Chernomor, O.1
Von Haeseler, A.2
Minh, B.Q.3
-
133
-
-
0031297695
-
General time-reversible distances with unequal rates across sites: Mixing and inverse Gaussian distributions with invariant sites
-
Waddell PJ, Steel M. 1997. General time-reversible distances with unequal rates across sites: Mixing and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol 8:398–414. https://doi.org/10.1006/mpev.1997.0452.
-
(1997)
Mol Phylogenet Evol
, vol.8
, pp. 398-414
-
-
Waddell, P.J.1
Steel, M.2
-
135
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266: 418–427. https://doi.org/10.1016/S0076-6879(96)66026-1.
-
(1996)
Methods Enzymol
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
136
-
-
53749090508
-
Empirical profile mixture models for phylogenetic reconstruction
-
Quang LS, Gascuel O, Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24:2317–2323. https://doi.org/10.1093/bioinformatics/btn445.
-
(2008)
Bioinformatics
, vol.24
, pp. 2317-2323
-
-
Quang, L.S.1
Gascuel, O.2
Lartillot, N.3
-
137
-
-
85041590310
-
Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation
-
Wang H-C, Minh BQ, Susko E, Roger AJ. 2018. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst Biol 67:216–235. https://doi.org/10.1093/sysbio/syx068.
-
(2018)
Syst Biol
, vol.67
, pp. 216-235
-
-
Wang, H.-C.1
Minh, B.Q.2
Susko, E.3
Roger, A.J.4
-
139
-
-
46749110034
-
FactoMineR: An R package for multivariate analysis
-
Lê S, Josse J, Husson F. 2008. FactoMineR: An R package for multivariate analysis. J Stat Softw 25:1–18.
-
(2008)
J Stat Softw
, vol.25
, pp. 1-18
-
-
Lê, S.1
Josse, J.2
Husson, F.3
-
141
-
-
85046568532
-
Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence
-
Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz M, von, Rokas A. 2017. Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence. bioRxiv https://www.biorxiv.org/content/10.1101/168526v1.
-
(2017)
Biorxiv
-
-
Zhou, X.1
Lutteropp, S.2
Czech, L.3
Stamatakis, A.4
Looz, M.5
Von, R.A.6
-
142
-
-
77954209892
-
The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell
-
Junier T, Zdobnov EM. 2010. The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26: 1669–1670. https://doi.org/10.1093/bioinformatics/btq243.
-
(2010)
Bioinformatics
, vol.26
, pp. 1669-1670
-
-
Junier, T.1
Zdobnov, E.M.2
-
143
-
-
77954403053
-
BMGE (Block mapping and gathering with entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments
-
Criscuolo A, Gribaldo S. 2010. BMGE (block mapping and gathering with entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10:210. https://doi.org/10.1186/1471-2148-10-210.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 210
-
-
Criscuolo, A.1
Gribaldo, S.2
-
144
-
-
0025181359
-
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
-
Kishino H, Miyata T, Hasegawa M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 31: 151–160. https://doi.org/10.1007/BF02109483.
-
(1990)
J Mol Evol
, vol.31
, pp. 151-160
-
-
Kishino, H.1
Miyata, T.2
Hasegawa, M.3
-
145
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591. https://doi.org/10.1093/molbev/msm088.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
146
-
-
84873505893
-
The unbearable uncertainty of Bayesian divergence time estimation
-
Dos Reis M, Yang Z. 2013. The unbearable uncertainty of Bayesian divergence time estimation. J Syst Evol 51:30–43. https://doi.org/10.1111/j.1759-6831.2012.00236.x.
-
(2013)
J Syst Evol
, vol.51
, pp. 30-43
-
-
Dos Reis, M.1
Yang, Z.2
-
147
-
-
0000783674
-
The number of iterations, convergence diagnostics and generic Metropolis algorithms
-
In Gilks WR, Richardson S, Spiegelhalter DJ, Chapman and Hall/CRC, Boca Raton, FL
-
Raftery AE, Lewis SM. 1995. The number of iterations, convergence diagnostics and generic Metropolis algorithms, p 115–130. In Gilks WR, Richardson S, Spiegelhalter DJ (ed), Markov chain Monte Carlo in practice. Chapman and Hall/CRC, Boca Raton, FL.
-
(1995)
Markov Chain Monte Carlo in Practice
, pp. 115-130
-
-
Raftery, A.E.1
Lewis, S.M.2
-
148
-
-
84914162769
-
Spearman’s rank correlation coefficient
-
Sedgwick P. 2014. Spearman’s rank correlation coefficient. BMJ 349: G7327. https://doi.org/10.1136/bmj.g7327.
-
(2014)
BMJ
, vol.349
, pp. g7327
-
-
Sedgwick, P.1
-
149
-
-
85073384542
-
-
Package “Hmisc” v4 00
-
Harrell FE, Jr. 2015. Package “Hmisc” v4 00.
-
(2015)
-
-
Harrell, F.E.1
-
151
-
-
85028383131
-
UpSetR: An R package for the visualization of intersecting sets and their properties
-
Conway JR, Lex A, Gehlenborg N. 2017. UpSetR: An R package for the visualization of intersecting sets and their properties. Bioinformatics 33:2938–2940. https://doi.org/10.1093/bioinformatics/btx364.
-
(2017)
Bioinformatics
, vol.33
, pp. 2938-2940
-
-
Conway, J.R.1
Lex, A.2
Gehlenborg, N.3
-
152
-
-
85031745642
-
Package ‘pheatmap’
-
Kolde R. 2012. Package ‘pheatmap’. Bioconductor.
-
(2012)
Bioconductor
-
-
Kolde, R.1
-
153
-
-
42149156736
-
FigTree, a graphical viewer of phylogenetic trees
-
University of Edinburgh, Edinburgh, United Kingdom
-
Rambaut A. 2009. FigTree, a graphical viewer of phylogenetic trees. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
-
(2009)
Institute of Evolutionary Biology
-
-
Rambaut, A.1
-
154
-
-
84924065334
-
Strap: An R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence
-
Bell MA, Lloyd GT. 2015. strap: An R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology 58:379–389. https://doi.org/10.1111/pala.12142.
-
(2015)
Palaeontology
, vol.58
, pp. 379-389
-
-
Bell, M.A.1
Lloyd, G.T.2
|