-
1
-
-
33748776559
-
Automated protein function prediction-The genomic challenge
-
Friedberg, I. (2006) Automated protein function prediction-the genomic challenge. Brief. Bioinform., 7, 225-242.
-
(2006)
Brief. Bioinform
, vol.7
, pp. 225-242
-
-
Friedberg, I.1
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
3
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
Radivojac, P., Clark, W.T., Oron, T.R., Schnoes, A.M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A. et al. (2013) A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227.
-
(2013)
Nat. Methods
, vol.10
, pp. 221-227
-
-
Radivojac, P.1
Clark, W.T.2
Oron, T.R.3
Schnoes, A.M.4
Wittkop, T.5
Sokolov, A.6
Graim, K.7
Funk, C.8
Verspoor, K.9
Ben-Hur, A.10
-
4
-
-
60749125063
-
Protein function annotation by homology-based inference
-
Loewenstein, Y., Raimondo, D., Redfern, O.C., Watson, J., Frishman, D., Linial, M., Orengo, C., Thornton, J. and Tramontano, A. (2009) Protein function annotation by homology-based inference. Genome Biol., 10, 207.
-
(2009)
Genome Biol.
, vol.10
, pp. 207
-
-
Loewenstein, Y.1
Raimondo, D.2
Redfern, O.C.3
Watson, J.4
Frishman, D.5
Linial, M.6
Orengo, C.7
Thornton, J.8
Tramontano, A.9
-
5
-
-
79959918507
-
BAR-PLUS: The Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
-
Piovesan, D., Luigi Martelli, P., Fariselli, P., Zauli, A., Rossi, I. and Casadio, R. (2011) BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res., 39, W197-W202.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W197-W202
-
-
Piovesan, D.1
Luigi Martelli, P.2
Fariselli, P.3
Zauli, A.4
Rossi, I.5
Casadio, R.6
-
6
-
-
84879314610
-
How to inherit statistically validated annotation within BAR+ protein clusters
-
Piovesan, D., Martelli, P.L., Fariselli, P., Profiti, G., Zauli, A., Rossi, I. and Casadio, R. (2013) How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinformatics, 14(Suppl. 3), S4.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S4
-
-
Piovesan, D.1
Martelli, P.L.2
Fariselli, P.3
Profiti, G.4
Zauli, A.5
Rossi, I.6
Casadio, R.7
-
7
-
-
67649868148
-
ESG: Extended similarity group method for automated protein function prediction
-
Chitale, M., Hawkins, T., Park, C. and Kihara, D. (2009) ESG: extended similarity group method for automated protein function prediction. Bioinformatics, 25, 1739-1745.
-
(2009)
Bioinformatics
, vol.25
, pp. 1739-1745
-
-
Chitale, M.1
Hawkins, T.2
Park, C.3
Kihara, D.4
-
8
-
-
80555156606
-
Genome-scale phylogenetic function annotation of large and diverse protein families
-
Engelhardt, B.E., Jordan, M.I., Srouji, J.R. and Brenner, S.E. (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res., 21, 1969-1980.
-
(2011)
Genome Res.
, vol.21
, pp. 1969-1980
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Srouji, J.R.3
Brenner, S.E.4
-
9
-
-
58149203231
-
InterPro: The integrative protein signature database
-
Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D211-D215
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Das, U.8
Daugherty, L.9
Duquenne, L.10
-
10
-
-
66549096455
-
Exploiting structural classifications for function prediction: Towards a domain grammar for protein function
-
Dessailly, B.H., Redfern, O.C., Cuff, A. and Orengo, C.A. (2009) Exploiting structural classifications for function prediction: towards a domain grammar for protein function. Curr. Opin. Struct. Biol., 19, 349-356.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 349-356
-
-
Dessailly, B.H.1
Redfern, O.C.2
Cuff, A.3
Orengo, C.A.4
-
11
-
-
78651274743
-
SUPERFAMILY 1.75 including a domain-centric gene ontology method
-
De Lima Morais, D.A., Fang, H., Rackham, O.J.L., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res., 39, D427-D434.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D427-D434
-
-
De-Lima-Morais, D.A.1
Fang, H.2
Rackham, O.J.L.3
Wilson, D.4
Pethica, R.5
Chothia, C.6
Gough, J.7
-
12
-
-
84876298530
-
Protein function prediction using domain families
-
Rentzsch, R. and Orengo, C.A. (2013) Protein function prediction using domain families. BMC Bioinformatics, 14 (Suppl. 3), S5.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S5
-
-
Rentzsch, R.1
Orengo, C.A.2
-
13
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W. (1999) From molecular to modular cell biology. Nature, 402, C47-C52.
-
(1999)
Nature
, vol.402
, pp. C47-C52
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
14
-
-
1442329655
-
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
-
Brun, C., Chevenet, F., Martin, D., Wojcik, J., Guénoche, A. and Jacq, B. (2003) Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol., 5, R6.
-
(2003)
Genome Biol.
, vol.5
, pp. R6
-
-
Brun, C.1
Chevenet, F.2
Martin, D.3
Wojcik, J.4
Guénoche, A.5
Jacq, B.6
-
15
-
-
34447639783
-
Using indirect protein interactions for the prediction of Gene Ontology functions
-
Chua, H.N., Sung, W.-K. and Wong, L. (2007) Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics, 8(Suppl. 4), S8.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. S8
-
-
Chua, H.N.1
Sung, W.-K.2
Wong, L.3
-
16
-
-
78650373804
-
Network medicine: A network-based approach to human disease
-
Barabási, A.-L., Gulbahce, N. and Loscalzo, J. (2011) Network medicine: a network-based approach to human disease. Nat. Rev. Genet., 12, 56-68.
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 56-68
-
-
Barabási, A.-L.1
Gulbahce, N.2
Loscalzo, J.3
-
17
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.-L., Millar, A., Taylor, P., Bennett, K., Boutilier, K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.-L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
-
18
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M. and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
19
-
-
84878083062
-
Protein function prediction by massive integration of evolutionary analyses and multiple data sources
-
Cozzetto, D., Buchan, D.W.A., Bryson, K. and Jones, D.T. (2013) Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics, 14(Suppl. 3), S1.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S1
-
-
Cozzetto, D.1
Buchan, D.W.A.2
Bryson, K.3
Jones, D.T.4
-
20
-
-
84874396916
-
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology
-
Fontana, P., Cestaro, A., Velasco, R., Formentin, E. and Toppo, S. (2009) Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS One, 4, e4619.
-
(2009)
PLoS One
, vol.4
, pp. e4619
-
-
Fontana, P.1
Cestaro, A.2
Velasco, R.3
Formentin, E.4
Toppo, S.5
-
21
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
-
22
-
-
84891783174
-
Activities at the Universal Protein Resource (UniProt)
-
The UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D191-D198
-
-
-
23
-
-
50849114838
-
Arrangements in the modular evolution of proteins
-
Moore, A.D., Björklund, A.K., Ekman, D., Bornberg-Bauer, E. and Elofsson, A. (2008) Arrangements in the modular evolution of proteins. Trends Biochem. Sci., 33, 444-451.
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 444-451
-
-
Moore, A.D.1
Björklund, A.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
24
-
-
84858077472
-
The Pfam protein families database
-
Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D290-D301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
-
25
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn, R.D., Clements, J. and Eddy, S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W29-W37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
26
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. (1990) Basic Local Alignment Search Tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.1
-
27
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
-
28
-
-
0024403904
-
Neural cadherin: Role in selective cell-cell adhesion
-
Miyatani, S., Shimamura, K., Hatta, M., Nagafuchi, A., Nose, A., Matsunaga, M., Hatta, K. and Takeichi, M. (1989) Neural cadherin: role in selective cell-cell adhesion. Science, 245, 631-635.
-
(1989)
Science
, vol.245
, pp. 631-635
-
-
Miyatani, S.1
Shimamura, K.2
Hatta, M.3
Nagafuchi, A.4
Nose, A.5
Matsunaga, M.6
Hatta, K.7
Takeichi, M.8
-
29
-
-
44349150359
-
X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment
-
Dibbens, L.M., Tarpey, P.S., Hynes, K., Bayly, M.A., Scheffer, I.E., Smith, R., Bomar, J., Sutton, E., Vandeleur, L., Shoubridge, C. et al. (2008) X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment. Nat. Genet., 40, 776-781.
-
(2008)
Nat. Genet
, vol.40
, pp. 776-781
-
-
Dibbens, L.M.1
Tarpey, P.S.2
Hynes, K.3
Bayly, M.A.4
Scheffer, I.E.5
Smith, R.6
Bomar, J.7
Sutton, E.8
Vandeleur, L.9
Shoubridge, C.10
-
30
-
-
84908207041
-
Identification of four novel PCDH19 mutations and prediction of their functional impact
-
Leonardi, E., Sartori, S., Vecchi, M., Bettella, E., Polli, R., Palma, L.D., Boniver, C. and Murgia, A. (2014) Identification of Four Novel PCDH19 Mutations and Prediction of Their Functional Impact. Ann. Hum. Genet., 78, 389-398.
-
(2014)
Ann. Hum. Genet
, vol.78
, pp. 389-398
-
-
Leonardi, E.1
Sartori, S.2
Vecchi, M.3
Bettella, E.4
Polli, R.5
Palma, L.D.6
Boniver, C.7
Murgia, A.8
-
31
-
-
84908205182
-
Protocadherin-17 mediates collective axon extension by recruiting actin regulator complexes to interaxonal contacts
-
Hayashi, S., Inoue, Y., Kiyonari, H., Abe, T., Misaki, K., Moriguchi, H., Tanaka, Y. and Takeichi, M. (2014) Protocadherin-17 mediates collective axon extension by recruiting actin regulator complexes to interaxonal contacts. Dev. Cell, 30, 673-687.
-
(2014)
Dev. Cell
, vol.30
, pp. 673-687
-
-
Hayashi, S.1
Inoue, Y.2
Kiyonari, H.3
Abe, T.4
Misaki, K.5
Moriguchi, H.6
Tanaka, Y.7
Takeichi, M.8
-
32
-
-
78649676371
-
Protocadherin-19 and N-cadherin interact to control cell movements during anterior neurulation
-
Biswas, S., Emond, M.R. and Jontes, J.D. (2010) Protocadherin-19 and N-cadherin interact to control cell movements during anterior neurulation. J. Cell Biol., 191, 1029-1041.
-
(2010)
J. Cell Biol.
, vol.191
, pp. 1029-1041
-
-
Biswas, S.1
Emond, M.R.2
Jontes, J.D.3
|