-
1
-
-
1042280957
-
Phylogenomic inference of protein molecular function: advances and challenges
-
Sjölander,K. (2004) Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20, 170-179.
-
(2004)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjölander, K.1
-
2
-
-
84968054140
-
Nothing in biology makes sense except in the light of evolution
-
Dobzhansky,C.T. (1973) Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach., 35, 125-129.
-
(1973)
Am. Biol. Teach.
, vol.35
, pp. 125-129
-
-
Dobzhansky, C.T.1
-
3
-
-
76749158462
-
Getting started in structural phylogenomics
-
Sjölander,K. (2010) Getting started in structural phylogenomics. PLoS Comput. Biol., 6, e1000621.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Sjölander, K.1
-
4
-
-
67849116905
-
Berkeley PHOG: PhyloFacts orthology group prediction web server
-
Datta,R.S., Meacham,C., Samad,B., Neyer,C. and Sjölander,K. (2009) Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res., 37, W84-W89.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Datta, R.S.1
Meacham, C.2
Samad, B.3
Neyer, C.4
Sjölander, K.5
-
5
-
-
74049118261
-
Large-scale assignment of orthology: back to phylogenetics?
-
Gabaldon,T. (2008) Large-scale assignment of orthology: back to phylogenetics? Genome Biol., 9, 235.
-
(2008)
Genome Biol.
, vol.9
, pp. 235
-
-
Gabaldon, T.1
-
6
-
-
54949145058
-
INTREPID-INformation-theoretic TREe traversal for protein functional site IDentification
-
Sankararaman,S. and Sjölander,K. (2008) INTREPID-INformation-theoretic TREe traversal for protein functional site IDentification. Bioinformatics, 24, 2445-2452.
-
(2008)
Bioinformatics
, vol.24
, pp. 2445-2452
-
-
Sankararaman, S.1
Sjölander, K.2
-
7
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
-
Capra,J.A., Laskowski,R.A., Thornton,J.M., Singh,M. and Funkhouser,T.A. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
8
-
-
77949602893
-
Active site prediction using evolutionary and structural information
-
Sankararaman,S., Sha,F., Kirsch,J.F., Jordan,M.I. and Sjölander,K. (2010) Active site prediction using evolutionary and structural information. Bioinformatics, 26, 617-624.
-
(2010)
Bioinformatics
, vol.26
, pp. 617-624
-
-
Sankararaman, S.1
Sha, F.2
Kirsch, J.F.3
Jordan, M.I.4
Sjölander, K.5
-
9
-
-
33745630672
-
Functional classification using phylogenomic inference
-
Brown,D. and Sjölander,K. (2006) Functional classification using phylogenomic inference. PLoS Comput. Biol., 2, e77.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Brown, D.1
Sjölander, K.2
-
10
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
-
(1986)
EMBO J.
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
11
-
-
67649240664
-
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
-
Liu,K., Raghavan,S., Nelesen,S., Linder,C.R. and Warnow,T. (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science, 324, 1561-1564.
-
(2009)
Science
, vol.324
, pp. 1561-1564
-
-
Liu, K.1
Raghavan, S.2
Nelesen, S.3
Linder, C.R.4
Warnow, T.5
-
12
-
-
73649145874
-
POY version 4: phylogenetic analysis using dynamic homologies
-
Varón,A., Vinh,L.S. and Wheeler,W.C. (2010) POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, 26, 72-85.
-
(2010)
Cladistics
, vol.26
, pp. 72-85
-
-
Varón, A.1
Vinh, L.S.2
Wheeler, W.C.3
-
13
-
-
59649130312
-
Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy
-
Liu,K., Nelesen,S., Raghavan,S., Linder,C.R. and Warnow,T. (2009) Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 7-21.
-
(2009)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.6
, pp. 7-21
-
-
Liu, K.1
Nelesen, S.2
Raghavan, S.3
Linder, C.R.4
Warnow, T.5
-
14
-
-
0028181441
-
Hidden Markov models in computational biology. Applications to protein modeling
-
Krogh,A., Brown,M., Mian,I.S., Sjölander,K. and Haussler,D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjölander, K.4
Haussler, D.5
-
15
-
-
34548392746
-
Automated protein subfamily identification and classification
-
Brown,D.P., Krishnamurthy,N. and Sjölander,K. (2007) Automated protein subfamily identification and classification. PLoS Comput. Biol., 3, e160.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Brown, D.P.1
Krishnamurthy, N.2
Sjölander, K.3
-
16
-
-
0034044314
-
The PSIPRED protein structure prediction server
-
McGuffin,L.J., Bryson,K. and Jones,D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
-
(2000)
Bioinformatics
, vol.16
, pp. 404-405
-
-
McGuffin, L.J.1
Bryson, K.2
Jones, D.T.3
-
17
-
-
0042594474
-
SATCHMO: sequence alignment and tree construction using hidden Markov models
-
Edgar,R.C. and Sjölander,K. (2003) SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
-
(2003)
Bioinformatics
, vol.19
, pp. 1404-1411
-
-
Edgar, R.C.1
Sjölander, K.2
-
18
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh,K. and Toh,H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
19
-
-
0036857358
-
QuickTree: building huge Neighbour-Joining trees of protein sequences
-
Howe,K., Bateman,A. and Durbin,R. (2002) QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics, 18, 1546-1547.
-
(2002)
Bioinformatics
, vol.18
, pp. 1546-1547
-
-
Howe, K.1
Bateman, A.2
Durbin, R.3
-
20
-
-
14644397888
-
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis,A., Ludwig,T. and Meier,H. (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
21
-
-
65449188232
-
Jalview Version 2-a multiple sequence alignment editor and analysis workbench
-
Waterhouse,A.M., Procter,J.B., Martin,D.M., Clamp,M. and Barton,G.J. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.3
Clamp, M.4
Barton, G.J.5
-
22
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar,R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
23
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin,M.A., Blackshields,G., Brown,N.P., Chenna,R., McGettigan,P.A., McWilliam,H., Valentin,F., Wallace,I.M., Wilm,A., Lopez,R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
24
-
-
34248145506
-
FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function
-
Krishnamurthy,N., Brown,D. and Sjölander,K. (2007) FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function. BMC Evol. Biol., 7(Suppl. 1), S12.
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Krishnamurthy, N.1
Brown, D.2
Sjölander, K.3
-
25
-
-
2442663920
-
Scoring profile-to-profile sequence alignments
-
Wang,G. and Dunbrack,R.L. Jr (2004) Scoring profile-to-profile sequence alignments. Protein Sci., 13, 1612-1626.
-
(2004)
Protein Sci.
, vol.13
, pp. 1612-1626
-
-
Wang, G.1
Dunbrack R.L., Jr.2
-
26
-
-
0036188264
-
Predicting reliable regions in protein sequence alignments
-
Cline,M., Hughey,R. and Karplus,K. (2002) Predicting reliable regions in protein sequence alignments. Bioinformatics, 18, 306-314.
-
(2002)
Bioinformatics
, vol.18
, pp. 306-314
-
-
Cline, M.1
Hughey, R.2
Karplus, K.3
-
27
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do,C.B., Mahabhashyam,M.S.P., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
-
(2005)
Genome Res.
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.P.2
Brudno, M.3
Batzoglou, S.4
-
28
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
|