-
1
-
-
58149182735
-
TB database: an integrated platform for tuberculosis research
-
10.1093/nar/gkn652, 2686437, 18835847
-
Reddy T, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, et al. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res 2009, 37:D499-D508. 10.1093/nar/gkn652, 2686437, 18835847.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Reddy, T.1
Riley, R.2
Wymore, F.3
Montgomery, P.4
DeCaprio, D.5
Engels, R.6
Gellesch, M.7
Hubble, J.8
Jen, D.9
Jin, H.10
-
2
-
-
33746622429
-
Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association
-
10.1073/pnas.0602817103, 1544089, 16844784
-
Singh A, Mai D, Kumar A, Steyn A. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc Natl Acad Sci USA 2006, 103:11346-11351. 10.1073/pnas.0602817103, 1544089, 16844784.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11346-11351
-
-
Singh, A.1
Mai, D.2
Kumar, A.3
Steyn, A.4
-
3
-
-
33745160404
-
Large-scale identification of protein-protein interaction of Escherichia coli K-12
-
10.1101/gr.4527806, 1457052, 16606699
-
Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang H, Hirai A, et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 2006, 16:686-691. 10.1101/gr.4527806, 1457052, 16606699.
-
(2006)
Genome Res
, vol.16
, pp. 686-691
-
-
Arifuzzaman, M.1
Maeda, M.2
Itoh, A.3
Nishikata, K.4
Takita, C.5
Saito, R.6
Ara, T.7
Nakahigashi, K.8
Huang, H.9
Hirai, A.10
-
4
-
-
58149185127
-
EcID. A database for the inference of functional interactions in E. coli
-
10.1093/nar/gkn853, 2686479, 19004873
-
Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D. EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res 2009, 37:D629-D635. 10.1093/nar/gkn853, 2686479, 19004873.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Andres Leon, E.1
Ezkurdia, I.2
García, B.3
Valencia, A.4
Juan, D.5
-
5
-
-
33846680167
-
Identification of conserved protein complexes based on a model of protein network evolution
-
10.1093/bioinformatics/btl295, 17237088
-
Hirsh E, Sharan R. Identification of conserved protein complexes based on a model of protein network evolution. Bioinformatics 2007, 23:e170-e176. 10.1093/bioinformatics/btl295, 17237088.
-
(2007)
Bioinformatics
, vol.23
-
-
Hirsh, E.1
Sharan, R.2
-
6
-
-
34248371273
-
Predicting protein-protein interactions based only on sequences information
-
10.1073/pnas.0607879104, 1838603, 17360525
-
Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 2007, 104:4337-4341. 10.1073/pnas.0607879104, 1838603, 17360525.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4337-4341
-
-
Shen, J.1
Zhang, J.2
Luo, X.3
Zhu, W.4
Yu, K.5
Chen, K.6
Li, Y.7
Jiang, H.8
-
7
-
-
80052059113
-
Sequence-based protein-protein interaction prediction via support vector machine
-
Wang Y, Wang J, Yang Z, Deng N. Sequence-based protein-protein interaction prediction via support vector machine. J Syst Sci & Complexity 2010, 23:1012-1023.
-
(2010)
J Syst Sci & Complexity
, vol.23
, pp. 1012-1023
-
-
Wang, Y.1
Wang, J.2
Yang, Z.3
Deng, N.4
-
8
-
-
3042569597
-
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
-
10.1101/gr.1774904, 419789, 15173116
-
Yu H, Luscombe N, Lu H, Zhu X, Xia Y, Han J, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 2004, 14:1107-1118. 10.1101/gr.1774904, 419789, 15173116.
-
(2004)
Genome Res
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.2
Lu, H.3
Zhu, X.4
Xia, Y.5
Han, J.6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
9
-
-
47149115729
-
Sequence-based prediction of protein-protein interactions by means of codon usage
-
10.1186/gb-2008-9-5-r87, 2441473, 18501006
-
Najafabadi H, Salavati R. Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 2008, 9:R87. 10.1186/gb-2008-9-5-r87, 2441473, 18501006.
-
(2008)
Genome Biol
, vol.9
-
-
Najafabadi, H.1
Salavati, R.2
-
10
-
-
78449281410
-
Predicting protein-protein interactions from protein sequences using meta predictor
-
10.1007/s00726-010-0588-1, 20386937
-
Xia J, Zhao X, Huang D. Predicting protein-protein interactions from protein sequences using meta predictor. Amino Acids 2010, 39:1595-1599. 10.1007/s00726-010-0588-1, 20386937.
-
(2010)
Amino Acids
, vol.39
, pp. 1595-1599
-
-
Xia, J.1
Zhao, X.2
Huang, D.3
-
11
-
-
77958498250
-
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
-
10.1093/bioinformatics/btq510, 3025743, 20817744
-
You Z, Lei Y, Huang D, Zhou X. Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. Bioinformatics 2010, 26:2744-2751. 10.1093/bioinformatics/btq510, 3025743, 20817744.
-
(2010)
Bioinformatics
, vol.26
, pp. 2744-2751
-
-
You, Z.1
Lei, Y.2
Huang, D.3
Zhou, X.4
-
12
-
-
77951667947
-
Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset
-
10.1007/s00726-009-0295-y, 19387790
-
Shi M, Xia J, Li X, Huang D. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids 2010, 38:891-899. 10.1007/s00726-009-0295-y, 19387790.
-
(2010)
Amino Acids
, vol.38
, pp. 891-899
-
-
Shi, M.1
Xia, J.2
Li, X.3
Huang, D.4
-
13
-
-
0038476173
-
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
-
10.1093/nar/gkg306, 153734, 12682375
-
Jansen R, Bussemaker H, Gerstein M. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res 2003, 31:2242-2251. 10.1093/nar/gkg306, 153734, 12682375.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2242-2251
-
-
Jansen, R.1
Bussemaker, H.2
Gerstein, M.3
-
14
-
-
0032508046
-
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
-
10.1038/31159, 9634230
-
Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon S, Eiglmeier K, Gas S, Barry C, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393:537-544. 10.1038/31159, 9634230.
-
(1998)
Nature
, vol.393
, pp. 537-544
-
-
Cole, S.1
Brosch, R.2
Parkhill, J.3
Garnier, T.4
Churcher, C.5
Harris, D.6
Gordon, S.7
Eiglmeier, K.8
Gas, S.9
Barry, C.10
-
15
-
-
13444272070
-
The Biomolecular Interaction Network Database and related tools - 2005 update
-
540005, 15608229
-
Alfarano C, Andrade C, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, et al. The Biomolecular Interaction Network Database and related tools - 2005 update. Nucleic Acids Res 2005, 33:D418-D424. 540005, 15608229.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Alfarano, C.1
Andrade, C.2
Anthony, K.3
Bahroos, N.4
Bajec, M.5
Bantoft, K.6
Betel, D.7
Bobechko, B.8
Boutilier, K.9
Burgess, E.10
-
16
-
-
34250191844
-
Reactome: a knowledge base of biologic pathways and processes
-
10.1186/gb-2007-8-3-r39, 1868929, 17367534
-
Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007, 8:R39. 10.1186/gb-2007-8-3-r39, 1868929, 17367534.
-
(2007)
Genome Biol
, vol.8
-
-
Vastrik, I.1
D'Eustachio, P.2
Schmidt, E.3
Joshi-Tope, G.4
Gopinath, G.5
Croft, D.6
de Bono, B.7
Gillespie, M.8
Jassal, B.9
Lewis, S.10
Matthews, L.11
Wu, G.12
Birney, E.13
Stein, L.14
-
17
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
10.1101/gr.205602, 155252, 11779829
-
Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12:37-46. 10.1101/gr.205602, 155252, 11779829.
-
(2002)
Genome Res
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
18
-
-
29144461552
-
Predicting protein-protein interaction by searching evolutionary tree automorphism space
-
10.1093/bioinformatics/bti1009, 1618802, 15961463
-
Jothi R, Kann M, Przytycka T. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 2005, 21:i241-i250. 10.1093/bioinformatics/bti1009, 1618802, 15961463.
-
(2005)
Bioinformatics
, vol.21
-
-
Jothi, R.1
Kann, M.2
Przytycka, T.3
-
19
-
-
34547834154
-
False positive reduction in protein-protein interaction predictions using gene ontology annotations
-
10.1186/1471-2105-8-262, 1941744, 17645798
-
Mahdavi M, Lin Y. False positive reduction in protein-protein interaction predictions using gene ontology annotations. BMC Bioinformatics 2007, 8:262. 10.1186/1471-2105-8-262, 1941744, 17645798.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 262
-
-
Mahdavi, M.1
Lin, Y.2
-
20
-
-
33644835242
-
Inferring protein interactions from experimental data by association probabilistic method
-
10.1002/prot.20783, 16395667
-
Chen L, Wu L, Wang Y, Zhang X. Inferring protein interactions from experimental data by association probabilistic method. Proteins 2006, 62:833-837. 10.1002/prot.20783, 16395667.
-
(2006)
Proteins
, vol.62
, pp. 833-837
-
-
Chen, L.1
Wu, L.2
Wang, Y.3
Zhang, X.4
-
22
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
10.1038/nrg1272, 14735121
-
Barabasi A, Oltvai Z. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.1
Oltvai, Z.2
-
23
-
-
0034660322
-
Protein function in the post-genomic era
-
10.1038/35015694, 10866208
-
Eisenberg D, Marcotte E, Xenarios I, Yeates T. Protein function in the post-genomic era. Nature 2000, 405:823-826. 10.1038/35015694, 10866208.
-
(2000)
Nature
, vol.405
, pp. 823-826
-
-
Eisenberg, D.1
Marcotte, E.2
Xenarios, I.3
Yeates, T.4
-
24
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
10.1126/science.1087361, 14564010
-
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan N, Chung S, Emili A, Snyder M, Greenblatt J, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302:449-453. 10.1126/science.1087361, 14564010.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.5
Chung, S.6
Emili, A.7
Snyder, M.8
Greenblatt, J.9
Gerstein, M.10
-
25
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
10.1126/science.1099511, 15567862
-
Lee I, Date S, Adai A, Marcotte E. A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558. 10.1126/science.1099511, 15567862.
-
(2004)
Science
, vol.306
, pp. 1555-1558
-
-
Lee, I.1
Date, S.2
Adai, A.3
Marcotte, E.4
-
26
-
-
44349159560
-
Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
-
10.1093/nar/gkn159, 2396404, 18390576
-
Guo Y, Yu L, Wen Z, Li M. Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res 2008, 36:3025-3030. 10.1093/nar/gkn159, 2396404, 18390576.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3025-3030
-
-
Guo, Y.1
Yu, L.2
Wen, Z.3
Li, M.4
-
27
-
-
33846047770
-
IntAct-open source resource for molecular interaction data
-
10.1093/nar/gkl958, 1751531, 17145710
-
Kerrien S, Alam-Faruque Y, Aranda B, et al. IntAct-open source resource for molecular interaction data. Nucleic Acids Res 2007, 35:D561-D565. 10.1093/nar/gkl958, 1751531, 17145710.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kerrien, S.1
Alam-Faruque, Y.2
Aranda, B.3
-
28
-
-
0036088133
-
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
-
10.1093/nar/30.1.303, 99070, 11752321
-
Xenarios I, Salwinski L, Duan X, Higney P, Kim S, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305. 10.1093/nar/30.1.303, 99070, 11752321.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
Salwinski, L.2
Duan, X.3
Higney, P.4
Kim, S.5
Eisenberg, D.6
-
29
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
32
-
-
33846064113
-
NCBI GEO: mining tens of millions of expression profiles-database and tools update
-
10.1093/nar/gkl887, 1669752, 17099226
-
Barrett T, Troup D, Wilhite S, Ledoux P, Rudnev D, Evangelista C, Kim I, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 2007, 35:D760-D765. 10.1093/nar/gkl887, 1669752, 17099226.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Barrett, T.1
Troup, D.2
Wilhite, S.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.7
Soboleva, A.8
Tomashevsky, M.9
Edgar, R.10
-
33
-
-
0033956060
-
The COG database: a tool for genome-scale analysis of protein functions and evolution
-
10.1093/nar/28.1.33, 102395, 10592175
-
Tatusov R, Galperin M, Natale D, Koonin E. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36. 10.1093/nar/28.1.33, 102395, 10592175.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 33-36
-
-
Tatusov, R.1
Galperin, M.2
Natale, D.3
Koonin, E.4
-
34
-
-
0034069495
-
Gene ontology: tool for the unification of biology
-
10.1038/75556, 3037419, 10802651, Gene Ontology Consortium
-
Gene Ontology Consortium Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651, Gene Ontology Consortium.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
-
35
-
-
9144252016
-
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
-
10.1093/nar/gkh021, 308756, 14681408
-
Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, 32:D262-D266. 10.1093/nar/gkh021, 308756, 14681408.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Camon, E.1
Magrane, M.2
Barrell, D.3
Lee, V.4
Dimmer, E.5
Maslen, J.6
Binns, D.7
Harte, N.8
Lopez, R.9
Apweiler, R.10
-
36
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
-
10.1093/bioinformatics/btg153, 12835272
-
Lord P, Stevens R, Brass A, Goble C. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19:1275-1283. 10.1093/bioinformatics/btg153, 12835272.
-
(2003)
Bioinformatics
, vol.19
, pp. 1275-1283
-
-
Lord, P.1
Stevens, R.2
Brass, A.3
Goble, C.4
-
37
-
-
33748335463
-
A new measure for functional similarity of gene products based on Gene Ontology
-
10.1186/1471-2105-7-302, 1559652, 16776819
-
Schlicker A, Domingues F, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302. 10.1186/1471-2105-7-302, 1559652, 16776819.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 302
-
-
Schlicker, A.1
Domingues, F.2
Rahnenfuhrer, J.3
Lengauer, T.4
-
38
-
-
41149141455
-
Predicting gene ontology functions from protein's regional surface structures
-
10.1186/1471-2105-8-475, 2233648, 18070366
-
Liu ZP, Wu LY, Wang Y, Chen L, Zhang XS. Predicting gene ontology functions from protein's regional surface structures. BMC Bioinformatics 2007, 8:475. 10.1186/1471-2105-8-475, 2233648, 18070366.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 475
-
-
Liu, Z.P.1
Wu, L.Y.2
Wang, Y.3
Chen, L.4
Zhang, X.S.5
|