-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
0034098730
-
Using GeneWise in the Drosophila annotation experiment
-
Birney E., Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Research 2000, 10:547-548.
-
(2000)
Genome Research
, vol.10
, pp. 547-548
-
-
Birney, E.1
Durbin, R.2
-
4
-
-
77955551021
-
Fermentation characteristics of Dekkera bruxellensis strains
-
Blomqvist J., Eberhard T., Schnürer J., Passoth V. Fermentation characteristics of Dekkera bruxellensis strains. Applied Microbiology and Biotechnology 2010, 87:1487-1497.
-
(2010)
Applied Microbiology and Biotechnology
, vol.87
, pp. 1487-1497
-
-
Blomqvist, J.1
Eberhard, T.2
Schnürer, J.3
Passoth, V.4
-
5
-
-
67650757433
-
TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez S., Silla-Martínez J.M., Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009, 25:1972-1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
6
-
-
67149116767
-
Genome sequence of the recombinant protein production host Pichia pastoris
-
De Schutter K., Lin Y.C., Tiels P., Van Hecke A., Glinka S., Weber-Lehmann J., Rouzé P., Van de Peer Y., Callewaert N. Genome sequence of the recombinant protein production host Pichia pastoris. Nature Biotechnology 2009, 27:561-566.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 561-566
-
-
De Schutter, K.1
Lin, Y.C.2
Tiels, P.3
Van Hecke, A.4
Glinka, S.5
Weber-Lehmann, J.6
Rouzé, P.7
Van de Peer, Y.8
Callewaert, N.9
-
7
-
-
0003155807
-
Microbial spoilage and preservation of wine: using weapons from nature's own arsenal
-
Du Toit M., Pretorius I.S. Microbial spoilage and preservation of wine: using weapons from nature's own arsenal. South African Journal of Enology and Viticulture 2000, 21:74-96.
-
(2000)
South African Journal of Enology and Viticulture
, vol.21
, pp. 74-96
-
-
Du Toit, M.1
Pretorius, I.S.2
-
8
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy S.R. Accelerated profile HMM searches. PLoS Computational Biology 2011, 7:e1002195.
-
(2011)
PLoS Computational Biology
, vol.7
-
-
Eddy, S.R.1
-
9
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
10
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002, 30:1575-1584.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
11
-
-
0003437302
-
-
Distributed by the author, Department of Genome Sciences, University of Washington, Seattle
-
Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 2005, Distributed by the author, Department of Genome Sciences, University of Washington, Seattle.
-
(2005)
PHYLIP (Phylogeny Inference Package) version 3.6
-
-
Felsenstein, J.1
-
12
-
-
74049118261
-
Large-scale assignment of orthology: back to phylogenetics?
-
Gabaldón T. Large-scale assignment of orthology: back to phylogenetics?. Genome Biology 2008, 9:235.
-
(2008)
Genome Biology
, vol.9
, pp. 235
-
-
Gabaldón, T.1
-
13
-
-
80051701328
-
Dekkera/Brettanomyces yeasts for ethanol production from renewable sources under oxygen-limited and low-pH conditions
-
Galafassi S., Merico A., Pizza F., Hellborg L., Molinari F., Piskur J., Compagno C. Dekkera/Brettanomyces yeasts for ethanol production from renewable sources under oxygen-limited and low-pH conditions. Journal of Industrial Microbiology & Biotechnology 2011, 38:1079-1088.
-
(2011)
Journal of Industrial Microbiology & Biotechnology
, vol.38
, pp. 1079-1088
-
-
Galafassi, S.1
Merico, A.2
Pizza, F.3
Hellborg, L.4
Molinari, F.5
Piskur, J.6
Compagno, C.7
-
14
-
-
0030807655
-
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
-
Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 1997, 14:685-695.
-
(1997)
Molecular Biology and Evolution
, vol.14
, pp. 685-695
-
-
Gascuel, O.1
-
15
-
-
3042677643
-
Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts
-
Gojković Z., Knecht W., Zameitat E., Warneboldt J., Coutelis J.B., Pynyaha Y., Neuveglise C., Møller K., Löffler M., Piskur J. Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Molecular Genetics and Genomics 2004, 271:387-393.
-
(2004)
Molecular Genetics and Genomics
, vol.271
, pp. 387-393
-
-
Gojković, Z.1
Knecht, W.2
Zameitat, E.3
Warneboldt, J.4
Coutelis, J.B.5
Pynyaha, Y.6
Neuveglise, C.7
Møller, K.8
Löffler, M.9
Piskur, J.10
-
16
-
-
84862174834
-
The Genome Portal of the Department of Energy Joint Genome Institute
-
Grigoriev I.V., Nordberg H., Shabalov I., Aerts A., Cantor M., Goodstein D., Kuo A., Minovitsky S., Nikitin R., Ohm R.A., Otillar R., Poliakov A., Ratnere I., Riley R., Smirnova T., Rokhsar D., Dubchak I. The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Research 2012, 40(1):D26-D32.
-
(2012)
Nucleic Acids Research
, vol.40
, Issue.1
-
-
Grigoriev, I.V.1
Nordberg, H.2
Shabalov, I.3
Aerts, A.4
Cantor, M.5
Goodstein, D.6
Kuo, A.7
Minovitsky, S.8
Nikitin, R.9
Ohm, R.A.10
Otillar, R.11
Poliakov, A.12
Ratnere, I.13
Riley, R.14
Smirnova, T.15
Rokhsar, D.16
Dubchak, I.17
-
17
-
-
68049139485
-
Estimating maximum likelihood phylogenies with PhyML
-
Guindon S., Delsuc F., Dufayard J.F., Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods in Molecular Biology 2009, 537:113-137.
-
(2009)
Methods in Molecular Biology
, vol.537
, pp. 113-137
-
-
Guindon, S.1
Delsuc, F.2
Dufayard, J.F.3
Gascuel, O.4
-
18
-
-
72449150687
-
Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis
-
Hellborg L., Piskur J. Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. Eukaryotic Cell 2009, 8:1739-1749.
-
(2009)
Eukaryotic Cell
, vol.8
, pp. 1739-1749
-
-
Hellborg, L.1
Piskur, J.2
-
19
-
-
0022895192
-
Metabolism of volatile phenolic compounds from hydroxycinnamic acids by Brettanomyces strains
-
Heresztyn T. Metabolism of volatile phenolic compounds from hydroxycinnamic acids by Brettanomyces strains. Archives of Microbiology 1986, 146:96-98.
-
(1986)
Archives of Microbiology
, vol.146
, pp. 96-98
-
-
Heresztyn, T.1
-
20
-
-
78650583195
-
Assigning duplication events to relative temporal scales in genome-wide studies
-
Huerta-Cepas J., Gabaldón T. Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics 2011, 27:38-45.
-
(2011)
Bioinformatics
, vol.27
, pp. 38-45
-
-
Huerta-Cepas, J.1
Gabaldón, T.2
-
22
-
-
78651300216
-
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
-
Huerta-Cepas J., Capella-Gutierrez S., Pryszcz L.P., Denisov I., Kormes D., Marcet-Houben M., Gabaldón T. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Research 2011, 39:D556-D560.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Huerta-Cepas, J.1
Capella-Gutierrez, S.2
Pryszcz, L.P.3
Denisov, I.4
Kormes, D.5
Marcet-Houben, M.6
Gabaldón, T.7
-
23
-
-
23244467882
-
Rewiring of the yeast transcriptional network through the evolution of motif usage
-
Ihmels J., Bergmann S., Gerami-Nejad M., Yanai I., McClellan M., Berman J., Barkai N. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005, 309:938-940.
-
(2005)
Science
, vol.309
, pp. 938-940
-
-
Ihmels, J.1
Bergmann, S.2
Gerami-Nejad, M.3
Yanai, I.4
McClellan, M.5
Berman, J.6
Barkai, N.7
-
24
-
-
0028696343
-
Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark
-
Isono K., McIninch J.D., Borodovsky M. Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark. DNA Research 1994, 1:263-269.
-
(1994)
DNA Research
, vol.1
, pp. 263-269
-
-
Isono, K.1
McIninch, J.D.2
Borodovsky, M.3
-
25
-
-
23844525077
-
Repbase update, a database of eukaryotic repetitive elements
-
Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenetics and Genome Research 2005, 110:462-467.
-
(2005)
Cytogenetics and Genome Research
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
26
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Research 2008, 36:D480-D484.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
27
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 2008, 9:286-298.
-
(2008)
Briefings in Bioinformatics
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
28
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent W.J. BLAT-the BLAST-like alignment tool. Genome Research 2002, 12:656-664.
-
(2002)
Genome Research
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
29
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin E.V., Fedorova N.D., Jackson J.D., Jacobs A.R., Krylov D.M., Makarova K.S., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Rogozin I.B., Smirnov S., Sorokin A.V., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., Natale D.A. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology 2004, 5:R7.
-
(2004)
Genome Biology
, vol.5
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Krylov, D.M.5
Makarova, K.S.6
Mazumder, R.7
Mekhedov, S.L.8
Nikolskaya, A.N.9
Rao, B.S.10
Rogozin, I.B.11
Smirnov, S.12
Sorokin, A.V.13
Sverdlov, A.V.14
Vasudevan, S.15
Wolf, Y.I.16
Yin, J.J.17
Natale, D.A.18
-
30
-
-
33845873289
-
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
-
Letunic I., Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23:127-128.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
32
-
-
0344406716
-
Reliability measures for membrane protein topology prediction algorithms
-
Melén K., Krogh A., von Heijne G. Reliability measures for membrane protein topology prediction algorithms. Journal of Molecular Biology 2003, 327:735-744.
-
(2003)
Journal of Molecular Biology
, vol.327
, pp. 735-744
-
-
Melén, K.1
Krogh, A.2
von Heijne, G.3
-
33
-
-
0030614959
-
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
-
Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 1997, 10:1-6.
-
(1997)
Protein Engineering
, vol.10
, pp. 1-6
-
-
Nielsen, H.1
Engelbrecht, J.2
Brunak, S.3
von Heijne, G.4
-
34
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
Parkhomchuk D., Borodina T., Amstislavskiy V., Banaru M., Hallen L., Krobitsch S., Lehrach H., Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Research 2009, 37:e123.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
Lehrach, H.7
Soldatov, A.8
-
35
-
-
3242886892
-
Yeast genome sequencing: the power of comparative genomics
-
Piskur J., Langkjaer R.B. Yeast genome sequencing: the power of comparative genomics. Molecular Microbiology 2004, 53:381-389.
-
(2004)
Molecular Microbiology
, vol.53
, pp. 381-389
-
-
Piskur, J.1
Langkjaer, R.B.2
-
36
-
-
33645862582
-
How did Saccharomyces evolve to become a good brewer?
-
Piskur J., Rozpedowska E., Polakova S., Merico A., Compagno C. How did Saccharomyces evolve to become a good brewer?. Trends in Genetics 2006, 22:183-186.
-
(2006)
Trends in Genetics
, vol.22
, pp. 183-186
-
-
Piskur, J.1
Rozpedowska, E.2
Polakova, S.3
Merico, A.4
Compagno, C.5
-
37
-
-
29144455282
-
De novo identification of repeat families in large genomes
-
Price A.L., Jones N.C., Pevzner P.A. De novo identification of repeat families in large genomes. Bioinformatics 2005, 21(Suppl. 1):i351-i358.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Price, A.L.1
Jones, N.C.2
Pevzner, P.A.3
-
38
-
-
79955879462
-
Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts
-
Rozpedowska E., Hellborg L., Ishchuk O.P., Orhan F., Galafassi S., Merico A., Woolfit M., Compagno C., Piskur J. Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts. Nature Communications 2011, 2:302.
-
(2011)
Nature Communications
, vol.2
, pp. 302
-
-
Rozpedowska, E.1
Hellborg, L.2
Ishchuk, O.P.3
Orhan, F.4
Galafassi, S.5
Merico, A.6
Woolfit, M.7
Compagno, C.8
Piskur, J.9
-
39
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
Salamov A.A., Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Research 2000, 10:516-522.
-
(2000)
Genome Research
, vol.10
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
42
-
-
14644397888
-
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis A., Ludwig T., Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
44
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
The UniProt Consortium.
-
The UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Research 2011, 39:D214-D219.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
-
45
-
-
20044383583
-
Resurrecting ancestral alcohol dehydrogenases from yeast
-
Thomson J.M., Gaucher E.A., Burgan M.F., De Kee D.W., Li T., Aris J.P., Benner S.A. Resurrecting ancestral alcohol dehydrogenases from yeast. Nature Genetics 2005, 37:630-635.
-
(2005)
Nature Genetics
, vol.37
, pp. 630-635
-
-
Thomson, J.M.1
Gaucher, E.A.2
Burgan, M.F.3
De Kee, D.W.4
Li, T.5
Aris, J.P.6
Benner, S.A.7
-
46
-
-
54049130043
-
Physiological and oenological traits of different Dekkera/Brettanomyces bruxellensis strains under wine-model conditions
-
Vigentini I., Romano A., Compagno C., Merico A., Molinari F., Tirelli A., Foschino R., Volonterio G. Physiological and oenological traits of different Dekkera/Brettanomyces bruxellensis strains under wine-model conditions. FEMS Yeast Research 2008, 8:1087-1096.
-
(2008)
FEMS Yeast Research
, vol.8
, pp. 1087-1096
-
-
Vigentini, I.1
Romano, A.2
Compagno, C.3
Merico, A.4
Molinari, F.5
Tirelli, A.6
Foschino, R.7
Volonterio, G.8
-
47
-
-
33645507429
-
M-Coffee: combining multiple sequence alignment methods with T-Coffee
-
Wallace I.M., O'Sullivan O., Higgins D.G., Notredame C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Research 2006, 34:1692-1699.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 1692-1699
-
-
Wallace, I.M.1
O'Sullivan, O.2
Higgins, D.G.3
Notredame, C.4
-
49
-
-
46249126320
-
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
-
Wehe A., Bansal M.S., Burleigh J.G., Eulenstein O. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 2008, 24:1540-1541.
-
(2008)
Bioinformatics
, vol.24
, pp. 1540-1541
-
-
Wehe, A.1
Bansal, M.S.2
Burleigh, J.G.3
Eulenstein, O.4
-
50
-
-
34247874564
-
Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis
-
Woolfit M., Rozpedowska E., Piskur J., Wolfe K.H. Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. Eukaryotic Cell 2007, 6:721-733.
-
(2007)
Eukaryotic Cell
, vol.6
, pp. 721-733
-
-
Woolfit, M.1
Rozpedowska, E.2
Piskur, J.3
Wolfe, K.H.4
-
51
-
-
0034800374
-
InterProScan-an integration platform for the signature-recognition methods in InterPro
-
Zdobnov E.M., Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
|