-
1
-
-
33747718071
-
Algorithmic construction of sets for k-restrictions
-
DOI 10.1145/1150334.1150336
-
Alon, N., Moshkovitz, D., and Safra, S. (2006). Algorithmic construction of sets for k-restrictions. ACM Trans. Algorithms, 2(2):153-177. (Pubitemid 44273960)
-
(2006)
ACM Transactions on Algorithms
, vol.2
, Issue.2
, pp. 153-177
-
-
Alon, N.1
Moshkovitz, D.2
Safra, S.3
-
2
-
-
35548931140
-
Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
-
Arvas, M., Kivioja, T., Mitchell, A., Saloheimo, M., Ussery, D., Penttilä, M., and Oliver, S. (2007). Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics, 8(1):325.
-
(2007)
BMC Genomics
, vol.8
, Issue.1
, pp. 325
-
-
Arvas, M.1
Kivioja, T.2
Mitchell, A.3
Saloheimo, M.4
Ussery, D.5
Penttilä, M.6
Oliver, S.7
-
3
-
-
55749087868
-
Large-scale reconstruction and phylogenetic analysis of metabolic environments
-
Borenstein, E., Kupiec, M., Feldman, M. W., and Ruppin, E. (2008). Large-scale reconstruction and phylogenetic analysis of metabolic environments. PNAS, 105(38):14482-14487.
-
(2008)
PNAS
, vol.105
, Issue.38
, pp. 14482-14487
-
-
Borenstein, E.1
Kupiec, M.2
Feldman, M.W.3
Ruppin, E.4
-
4
-
-
10944257452
-
Improving gene network inference by comparing expression time-series across species, developmental stages or tissues
-
DOI 10.1142/S0219720004000892, PII S0219720004000892
-
Bourque, G. and Sankoff, D. (2004). Improving gene network inference by comparing expression time-series across species, developmental stages or tissues. J Bioinform Comput Biol, 2(4):765-783. (Pubitemid 40017366)
-
(2004)
Journal of Bioinformatics and Computational Biology
, vol.2
, Issue.4
, pp. 765-783
-
-
Bourque, G.1
Sankoff, D.2
-
5
-
-
56949085134
-
The origin and evolution of modern metabolism
-
Caetano-Anollés, G., Yafremava, L., Gee, H., Caetano- Anollés, D., Kim, H., and Mittenthal, J. (2009). The origin and evolution of modern metabolism. The International Journal of Biochemistry & Cell Biology, 41(2):285-297.
-
(2009)
The International Journal of Biochemistry & Cell Biology
, vol.41
, Issue.2
, pp. 285-297
-
-
Caetano-Anollés, G.1
Yafremava, L.2
Gee, H.3
Caetano-Anollés, D.4
Kim, H.5
Mittenthal, J.6
-
6
-
-
33846672559
-
Phylogenetic reconstruction from non-genomic data
-
Clemente, J., Satou, K., and Valiente, G. (2007). Phylogenetic reconstruction from non-genomic data. Bioinformatics, 23(2):e110.
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Clemente, J.1
Satou, K.2
Valiente, G.3
-
7
-
-
63849126532
-
Optimized ancestral state reconstruction using sankoff parsimony
-
Clemente, J. C., Ikeo, K., Valiente, G., and Gojobori, T. (2009). Optimized ancestral state reconstruction using sankoff parsimony. BMC Bioinformatics, 10(51).
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.51
-
-
Clemente, J.C.1
Ikeo, K.2
Valiente, G.3
Gojobori, T.4
-
8
-
-
0033215210
-
Pathway alignment: Application to the comparative analysis of glycolytic enzymes
-
DOI 10.1042/0264-6021:3430115
-
Dandekar, T., Schuster, S., Snel, B., Huynen, M., and Bork, P. (1999). Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J., 343(Pt 1):115-124. (Pubitemid 29473885)
-
(1999)
Biochemical Journal
, vol.343
, Issue.1
, pp. 115-124
-
-
Dandekar, T.1
Schuster, S.2
Snel, B.3
Huynen, M.4
Bork, P.5
-
10
-
-
84959747425
-
Toward defining the course of evolution: Minimum change for a specific tree topology
-
Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20:406-416.
-
(1971)
Syst. Zool.
, vol.20
, pp. 406-416
-
-
Fitch, W.M.1
-
11
-
-
33845452848
-
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
-
Fitzpatrick, D., Logue, M., Stajich, J., and Butler, G. (2006). A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology, 6(1):99.
-
(2006)
BMC Evolutionary Biology
, vol.6
, Issue.1
, pp. 99
-
-
Fitzpatrick, D.1
Logue, M.2
Stajich, J.3
Butler, G.4
-
14
-
-
43649084234
-
An environmental perspective on metabolism
-
Handorf, T., Christian, N., Ebenhöh, O., and Kahn, D. (2008). An environmental perspective on metabolism. Journal of Theoretical Biology, 252(3):530-537.
-
(2008)
Journal of Theoretical Biology
, vol.252
, Issue.3
, pp. 530-537
-
-
Handorf, T.1
Christian, N.2
Ebenhöh, O.3
Kahn, D.4
-
15
-
-
34447317247
-
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
-
Jamshidi, N. and Palsson, B. O. (2007). Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Systems Biology, 1(26).
-
(2007)
BMC Systems Biology
, vol.1
, Issue.26
-
-
Jamshidi, N.1
Palsson, B.O.2
-
16
-
-
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., and Yamanishi, Y. (2008). Kegg for linking genomes to life and the environment. Nucleic Acids Res., 36.D480-D484.
-
(2008)
Nucleic Acids Res.
, 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
-
17
-
-
44349157798
-
The evolution of modularity in bacterial metabolic networks
-
Kreimer, A., Borenstein, E., Gophna, U., and Ruppin, E. (2008). The evolution of modularity in bacterial metabolic networks. Proceedings of the National Academy of Sciences, 105(19):6976.
-
(2008)
Proceedings of the National Academy of Sciences
, vol.105
, Issue.19
, pp. 6976
-
-
Kreimer, A.1
Borenstein, E.2
Gophna, U.3
Ruppin, E.4
-
18
-
-
55949089680
-
An introduction to metabolic networks and their structural analysis
-
Lacroix, V., Cottret, L., Thebault, P., and Sagot, M.-F. (2008). An introduction to metabolic networks and their structural analysis. IEEE Transactions on Computational Biology and Bioinformatics, 5(4):594-617.
-
(2008)
IEEE Transactions on Computational Biology and Bioinformatics
, vol.5
, Issue.4
, pp. 594-617
-
-
Lacroix, V.1
Cottret, L.2
Thebault, P.3
Sagot, M.-F.4
-
19
-
-
75149156665
-
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
-
Mano, A., Tuller, T., Bj, O., and Pinter, R. Y. (2010). Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinformatics, 11(Suppl 1):S38.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Mano, A.1
Tuller, T.2
Bj, O.3
Pinter, R.Y.4
-
20
-
-
78049435631
-
A bayesian approach to the evolution of metabolic networks on a phylogeny
-
Mithani, A., Preston, G., and Hein, J. (2010). A bayesian approach to the evolution of metabolic networks on a phylogeny. PLoS Computational Biology, 6(8).
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.8
-
-
Mithani, A.1
Preston, G.2
Hein, J.3
-
21
-
-
66349136048
-
A stochastic model for the evolution of metabolic networks with neighbor dependence
-
Mithani, A., Preston, G. M., and Hein, J. (2009). A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics, 25(12):1528-1535.
-
(2009)
Bioinformatics
, vol.25
, Issue.12
, pp. 1528-1535
-
-
Mithani, A.1
Preston, G.M.2
Hein, J.3
-
23
-
-
33646527159
-
Finding feasible pathways in metabolic networks
-
Advances in Informatics: 10th Panhellenic Conference on Informatics (PCI 2005).
-
Pitkänen, E., Rantanen, A., Rousu, J., and Ukkonen, E. (2005). Finding feasible pathways in metabolic networks. In Advances in Informatics: 10th Panhellenic Conference on Informatics (PCI 2005). Lecture Notes in Computer Science 3746, pages 123-133.
-
(2005)
Lecture Notes in Computer Science
, vol.3746
, pp. 123-133
-
-
Pitkänen, E.1
Rantanen, A.2
Rousu, J.3
Ukkonen, E.4
-
24
-
-
84855621976
-
A computational method for reconstructing gapless metabolic networks
-
Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD'08), Springer
-
Pitkänen, E., Rantanen, A., Rousu, J., and Ukkonen, E. (2008). A computational method for reconstructing gapless metabolic networks. In Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD'08), volume 13 of Communications in Computer and Information Science. Springer.
-
(2008)
Communications in Computer and Information Science
, vol.13
-
-
Pitkänen, E.1
Rantanen, A.2
Rousu, J.3
Ukkonen, E.4
-
25
-
-
77950629548
-
Computational methods for metabolic reconstruction
-
Pitkänen, E., Rousu, J., and Ukkonen, E. (2010). Computational methods for metabolic reconstruction. Current Opinion in Biotechnology, 21(1):70-77.
-
(2010)
Current Opinion in Biotechnology
, vol.21
, Issue.1
, pp. 70-77
-
-
Pitkänen, E.1
Rousu, J.2
Ukkonen, E.3
-
26
-
-
67449096729
-
Flux balance analysis of biological systems: Applications and challenges
-
Raman, K. and Chandra, N. (2009). Flux balance analysis of biological systems: applications and challenges. Briefings in Bioinformatics, 10(4):435-449.
-
(2009)
Briefings in Bioinformatics
, vol.10
, Issue.4
, pp. 435-449
-
-
Raman, K.1
Chandra, N.2
-
27
-
-
45749090110
-
An analytic and systematic framework for estimating metabolic flux ratios from 13 C tracer experiments
-
Rantanen, A., Rousu, J., Jouhten, P., Zamboni, N., Maaheimo, H., and Ukkonen, E. (2008). An analytic and systematic framework for estimating metabolic flux ratios from 13 C tracer experiments. BMC Bioinformatics, 9(1):266.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 266
-
-
Rantanen, A.1
Rousu, J.2
Jouhten, P.3
Zamboni, N.4
Maaheimo, H.5
Ukkonen, E.6
-
28
-
-
0030714232
-
A sub-constant error-probability low-degree test, and a sub-constant error-probability PCP characterization of NP
-
Raz, R. and Safra, S. (1997). A sub-constant error-probability low-degree test, and a sub-constant error-probability PCP characterization of NP. In Proceedings of the Twenty-Ninth Annual ACM Symposium on Theory of Computing, pages 475-484.
-
(1997)
Proceedings of the Twenty-Ninth Annual ACM Symposium on Theory of Computing
, pp. 475-484
-
-
Raz, R.1
Safra, S.2
-
29
-
-
0016424695
-
Minimal mutation trees of sequences
-
Sankoff, D. (1975). Minimal mutation trees of sequences. SIAM J. Appl, 28:35-12.
-
(1975)
SIAM J. Appl
, vol.28
, pp. 35-112
-
-
Sankoff, D.1
-
30
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan, R. and Ideker, T. (2006). Modeling cellular machinery through biological network comparison. Nature Biotechnology, 24:427-133.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 427-1133
-
-
Sharan, R.1
Ideker, T.2
-
31
-
-
66349089524
-
Genome-scale network analysis of imprinted human metabolic genes
-
Sigurdsson, M. I., Jamshidi, N., Jonsson, J. J., and Palsson, B. O. (2009). Genome-scale network analysis of imprinted human metabolic genes. Epigenetics, 4(1):43-46.
-
(2009)
Epigenetics
, vol.4
, Issue.1
, pp. 43-46
-
-
Sigurdsson, M.I.1
Jamshidi, N.2
Jonsson, J.J.3
Palsson, B.O.4
-
32
-
-
0034565517
-
A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy
-
Tohsato, Y., Matsuda, H., and Hashimoto, A. (2000). A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, pages 376-383.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
, pp. 376-383
-
-
Tohsato, Y.1
Matsuda, H.2
Hashimoto, A.3
-
33
-
-
74949120671
-
Reconstructing ancestral gene content by coevolution
-
Tuller, T., Birin, H., Gophna, U., Kupiec, M., and Ruppin, E. (2010). Reconstructing ancestral gene content by coevolution. Genome Res., 20(1):122-132.
-
(2010)
Genome Res.
, vol.20
, Issue.1
, pp. 122-132
-
-
Tuller, T.1
Birin, H.2
Gophna, U.3
Kupiec, M.4
Ruppin, E.5
-
34
-
-
70349686781
-
Evolutionary constraints permeate large metabolic networks
-
Wagner, A. (2009). Evolutionary constraints permeate large metabolic networks. BMC Evolutionary Biology, 9(1):231.
-
(2009)
BMC Evolutionary Biology
, vol.9
, Issue.1
, pp. 231
-
-
Wagner, A.1
|