-
1
-
-
55449107518
-
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models
-
Xie, L. and Bourne, P.E. (2005) Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput. Biol., 1, e31.
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
Xie, L.1
Bourne, P.E.2
-
2
-
-
78650034777
-
Towards a knowledge-based human protein atlas
-
Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. et al. (2010) Towards a Knowledge-Based human protein atlas. Nat. Biotechnol., 28, 1248-1250.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1248-1250
-
-
Uhlen, M.1
Oksvold, P.2
Fagerberg, L.3
Lundberg, E.4
Jonasson, K.5
Forsberg, M.6
Zwahlen, M.7
Kampf, C.8
Wester, K.9
Hober, S.10
-
3
-
-
85016153986
-
UniProt: The universal protein knowledgebase
-
UniProt Consortium, T (2018) UniProt: the universal protein knowledgebase. Nucleic Acids Res., 45, D158-D169.
-
(2018)
Nucleic Acids Res.
, vol.45
, pp. D158-D169
-
-
-
4
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
-
Ban, N., Nissen, P., Hansen, J., Moore, P.B. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289, 905-920.
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
5
-
-
85044077887
-
Structure of the nuclear exosome captured on a maturing preribosome
-
Schuller, J.M., Falk, S., Fromm, L., Hurt, E. and Conti, E. (2018) Structure of the nuclear exosome captured on a maturing preribosome. Science, 360, 219-222.
-
(2018)
Science
, vol.360
, pp. 219-222
-
-
Schuller, J.M.1
Falk, S.2
Fromm, L.3
Hurt, E.4
Conti, E.5
-
6
-
-
84930715900
-
Structure, dynamics, assembly, and evolution of protein complexes
-
Marsh, J.A. and Teichmann, S.A. (2015) Structure, dynamics, assembly, and evolution of protein complexes. Annu. Rev. Biochem., 84, 551-575.
-
(2015)
Annu. Rev. Biochem.
, vol.84
, pp. 551-575
-
-
Marsh, J.A.1
Teichmann, S.A.2
-
7
-
-
85044529942
-
Systematic evaluation of molecular networks for discovery of disease genes
-
Huang, J.K., Carlin, D.E., Yu, M.K., Zhang, W., Kreisberg, J.F., Tamayo, P. and Ideker, T. (2018) Systematic evaluation of molecular networks for discovery of disease genes. Cell Syst., 6, 484-495.
-
(2018)
Cell Syst.
, vol.6
, pp. 484-495
-
-
Huang, J.K.1
Carlin, D.E.2
Yu, M.K.3
Zhang, W.4
Kreisberg, J.F.5
Tamayo, P.6
Ideker, T.7
-
8
-
-
85010868689
-
Genome-scale networks link neurodegenerative disease genes to alpha-Synuclein through specific molecular pathways
-
Khurana, V., Peng, J., Chung, C.Y., Auluck, P.K., Fanning, S., Tardiff, D.F., Bartels, T., Koeva, M., Eichhorn, S.W., Benyamini, H. et al. (2017) Genome-scale networks link neurodegenerative disease genes to alpha-Synuclein through specific molecular pathways. Cell Syst., 4, 157-170.
-
(2017)
Cell Syst.
, vol.4
, pp. 157-170
-
-
Khurana, V.1
Peng, J.2
Chung, C.Y.3
Auluck, P.K.4
Fanning, S.5
Tardiff, D.F.6
Bartels, T.7
Koeva, M.8
Eichhorn, S.W.9
Benyamini, H.10
-
9
-
-
84974588949
-
Complex network-based approaches to biomarker discovery
-
Hayashida, M. and Akutsu, T. (2016) Complex network-based approaches to biomarker discovery. Biomark. Med., 10, 621-632.
-
(2016)
Biomark. Med.
, vol.10
, pp. 621-632
-
-
Hayashida, M.1
Akutsu, T.2
-
10
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D. and Ideker, T. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
11
-
-
85026408588
-
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
-
Liu, X., Chang, X., Liu, R., Yu, X., Chen, L. and Aihara, K. (2017) Quantifying critical states of complex diseases using single-sample dynamic network biomarkers. PLoS Comput. Biol., 13, e1005633.
-
(2017)
PLoS Comput. Biol.
, vol.13
-
-
Liu, X.1
Chang, X.2
Liu, R.3
Yu, X.4
Chen, L.5
Aihara, K.6
-
12
-
-
85049892369
-
Mapping of protein-protein interactions: Web-based resources for revealing interactomes
-
Gemovic, B., Sumonja, N., Davidovic, R., Perovic, V. and Veljkovic, N. (2018) Mapping of Protein-Protein interactions:Web-Based resources for revealing interactomes. Curr. Med. Chem., doi:10.2174/0929867325666180214113704.
-
(2018)
Curr. Med. Chem.
-
-
Gemovic, B.1
Sumonja, N.2
Davidovic, R.3
Perovic, V.4
Veljkovic, N.5
-
13
-
-
84903701114
-
Protein-protein interactions and prediction: A comprehensive overview
-
Sowmya, G. and Ranganathan, S. (2014) Protein-protein interactions and prediction: a comprehensive overview. Protein Pept. Lett., 21, 779-789.
-
(2014)
Protein Pept. Lett.
, vol.21
, pp. 779-789
-
-
Sowmya, G.1
Ranganathan, S.2
-
14
-
-
85021320754
-
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
-
Drew, K., Lee, C., Huizar, R.L., Tu, F., Borgeson, B., McWhite, C.D., Ma, Y., Wallingford, J.B. and Marcotte, E.M. (2017) Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol. Syst. Biol., 13, 932.
-
(2017)
Mol. Syst. Biol.
, vol.13
, pp. 932
-
-
Drew, K.1
Lee, C.2
Huizar, R.L.3
Tu, F.4
Borgeson, B.5
McWhite, C.D.6
Ma, Y.7
Wallingford, J.B.8
Marcotte, E.M.9
-
15
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. D449-D451
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
16
-
-
84891799734
-
The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
-
Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., Campbell, N.H., Chavali, G., Chen, C., del-Toro, N. et al. (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D358-D363
-
-
Orchard, S.1
Ammari, M.2
Aranda, B.3
Breuza, L.4
Briganti, L.5
Broackes-Carter, F.6
Campbell, N.H.7
Chavali, G.8
Chen, C.9
Del-Toro, N.10
-
17
-
-
85016136235
-
The BioGRID interaction database: 2017 update
-
Chatr-Aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N.K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A. et al. (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res., 45, D369-D379.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D369-D379
-
-
Chatr-Aryamontri, A.1
Oughtred, R.2
Boucher, L.3
Rust, J.4
Chang, C.5
Kolas, N.K.6
O'Donnell, L.7
Oster, S.8
Theesfeld, C.9
Sellam, A.10
-
18
-
-
85018308823
-
HPIDB 2.0: A curated database for host-pathogen interactions
-
Ammari, M.G., Gresham, C.R., McCarthy, F.M. and Nanduri, B. (2016) HPIDB 2.0: a curated database for host-pathogen interactions. Database (Oxford), 2016, baw103.
-
(2016)
Database (Oxford)
, vol.2016
, pp. baw103
-
-
Ammari, M.G.1
Gresham, C.R.2
McCarthy, F.M.3
Nanduri, B.4
-
19
-
-
84859208501
-
Protein interaction data curation: The International Molecular Exchange (IMEx) consortium
-
Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkman, F.S., Cesareni, G. et al. (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods, 9, 345-350.
-
(2012)
Nat. Methods
, vol.9
, pp. 345-350
-
-
Orchard, S.1
Kerrien, S.2
Abbani, S.3
Aranda, B.4
Bhate, J.5
Bidwell, S.6
Bridge, A.7
Briganti, L.8
Brinkman, F.S.9
Cesareni, G.10
-
20
-
-
84875216538
-
PrePPI: A structure-informed database of protein-protein interactions
-
Zhang, Q.C., Petrey, D., Garzon, J.I., Deng, L. and Honig, B. (2013) PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res., 41, D828-D833.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D828-D833
-
-
Zhang, Q.C.1
Petrey, D.2
Garzon, J.I.3
Deng, L.4
Honig, B.5
-
21
-
-
58149178567
-
PIPs: Human protein-protein interaction prediction database
-
McDowall, M.D., Scott, M.S. and Barton, G.J. (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res., 37, D651-D656.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D651-D656
-
-
McDowall, M.D.1
Scott, M.S.2
Barton, G.J.3
-
22
-
-
85050857032
-
GeneMANIA update 2018
-
Franz, M., Rodriguez, H., Lopes, C., Zuberi, K., Montojo, J., Bader, G.D. and Morris, Q. (2018) GeneMANIA update 2018. Nucleic Acids Res., 46, W60-W64.
-
(2018)
Nucleic Acids Res.
, vol.46
, pp. W60-W64
-
-
Franz, M.1
Rodriguez, H.2
Lopes, C.3
Zuberi, K.4
Montojo, J.5
Bader, G.D.6
Morris, Q.7
-
23
-
-
85040903052
-
FunCoup 4: New species, data, and visualization
-
Ogris, C., Guala, D. and Sonnhammer, E.L.L. (2018) FunCoup 4: new species, data, and visualization. Nucleic Acids Res., 46, D601-D607.
-
(2018)
Nucleic Acids Res.
, vol.46
, pp. D601-D607
-
-
Ogris, C.1
Guala, D.2
Sonnhammer, E.L.L.3
-
24
-
-
84976905746
-
Integrated interactions database: Tissue-specific view of the human and model organism interactomes
-
Kotlyar, M., Pastrello, C., Sheahan, N. and Jurisica, I. (2016) Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Res., 44, D536-D541.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D536-D541
-
-
Kotlyar, M.1
Pastrello, C.2
Sheahan, N.3
Jurisica, I.4
-
25
-
-
84988589217
-
Analyzing and interpreting genome data at the network level with ConsensusPathDB
-
Herwig, R., Hardt, C., Lienhard, M. and Kamburov, A. (2016) Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat. Protoc., 11, 1889-1907.
-
(2016)
Nat. Protoc.
, vol.11
, pp. 1889-1907
-
-
Herwig, R.1
Hardt, C.2
Lienhard, M.3
Kamburov, A.4
-
26
-
-
84979849735
-
IMP 2.0: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
-
Wong, A.K., Krishnan, A., Yao, V., Tadych, A. and Troyanskaya, O.G. (2015) IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res., 43, W128-D133.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W128-D133
-
-
Wong, A.K.1
Krishnan, A.2
Yao, V.3
Tadych, A.4
Troyanskaya, O.G.5
-
27
-
-
79959898376
-
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
-
Lee, I., Blom, U.M., Wang, P.I., Shim, J.E. and Marcotte, E.M. (2011) Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res., 21, 1109-1121.
-
(2011)
Genome Res.
, vol.21
, pp. 1109-1121
-
-
Lee, I.1
Blom, U.M.2
Wang, P.I.3
Shim, J.E.4
Marcotte, E.M.5
-
28
-
-
0034666108
-
STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
-
Snel, B., Lehmann, G., Bork, P. and Huynen, M.A. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res., 28, 3442-3444.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3442-3444
-
-
Snel, B.1
Lehmann, G.2
Bork, P.3
Huynen, M.A.4
-
29
-
-
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
-
30
-
-
84941051170
-
STRING v10: Protein-protein interaction networks, integrated over the tree of life
-
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D447-D452
-
-
Szklarczyk, D.1
Franceschini, A.2
Wyder, S.3
Forslund, K.4
Heller, D.5
Huerta-Cepas, J.6
Simonovic, M.7
Roth, A.8
Santos, A.9
Tsafou, K.P.10
-
31
-
-
85021857514
-
The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible
-
Szklarczyk, D., Morris, J.H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N.T., Roth, A., Bork, P. et al. (2017) The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res., 45, D362-D368.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D362-D368
-
-
Szklarczyk, D.1
Morris, J.H.2
Cook, H.3
Kuhn, M.4
Wyder, S.5
Simonovic, M.6
Santos, A.7
Doncheva, N.T.8
Roth, A.9
Bork, P.10
-
32
-
-
84976905626
-
EggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
-
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M. et al. (2016) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res., 44, D286-D293.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D286-D293
-
-
Huerta-Cepas, J.1
Szklarczyk, D.2
Forslund, K.3
Cook, H.4
Heller, D.5
Walter, M.C.6
Rattei, T.7
Mende, D.R.8
Sunagawa, S.9
Kuhn, M.10
-
33
-
-
84976897983
-
STITCH 5: Augmenting protein-chemical interaction networks with tissue and affinity data
-
Szklarczyk, D., Santos, A., von Mering, C., Jensen, L.J., Bork, P. and Kuhn, M. (2016) STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res., 44, D380-D384.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D380-D384
-
-
Szklarczyk, D.1
Santos, A.2
Von Mering, C.3
Jensen, L.J.4
Bork, P.5
Kuhn, M.6
-
34
-
-
84941749221
-
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines
-
Wang, M., Herrmann, C.J., Simonovic, M., Szklarczyk, D. and von Mering, C. (2015) Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15, 3163-3168.
-
(2015)
Proteomics
, vol.15
, pp. 3163-3168
-
-
Wang, M.1
Herrmann, C.J.2
Simonovic, M.3
Szklarczyk, D.4
Von Mering, C.5
-
35
-
-
85047932882
-
TISSUES 2.0: An integrative web resource on mammalian tissue expression
-
Palasca, O., Santos, A., Stolte, C., Gorodkin, J. and Jensen, L.J. (2018) TISSUES 2.0: an integrative web resource on mammalian tissue expression. Database (Oxford), 2018, bay003.
-
(2018)
Database (Oxford)
, vol.2018
, pp. bay003
-
-
Palasca, O.1
Santos, A.2
Stolte, C.3
Gorodkin, J.4
Jensen, L.J.5
-
36
-
-
85053831193
-
Viruses. STRING: A virus-host protein-protein interaction database
-
Cook, V.H., Doncheva, N.T., Szklarczyk, D., von Mering, C. and Jensen, L.J. (2018) Viruses. STRING: A virus-host protein-protein interaction database. Viruses, 10, 519.
-
(2018)
Viruses
, vol.10
, pp. 519
-
-
Cook, V.H.1
Doncheva, N.T.2
Szklarczyk, D.3
Von Mering, C.4
Jensen, L.J.5
-
37
-
-
85011116474
-
Identifying ELIXIR core data resources [version 2; Referees: 2 approved]
-
Durinx, C., McEntyre, J., Appel, R., Apweiler, R., Barlow, M., Blomberg, N., Cook, C., Gasteiger, E., Kim, J.H., Lopez, R. et al. (2016) Identifying ELIXIR core data resources [version 2; referees: 2 approved]. F1000Res, 5, 2422.
-
(2016)
F1000Res
, vol.5
, pp. 2422
-
-
Durinx, C.1
McEntyre, J.2
Appel, R.3
Apweiler, R.4
Barlow, M.5
Blomberg, N.6
Cook, C.7
Gasteiger, E.8
Kim, J.H.9
Lopez, R.10
-
38
-
-
0035753236
-
Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
-
Enright, A.J. and Ouzounis, C.A. (2001) Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol., 2, RESEARCH0034.
-
(2001)
Genome Biol.
, vol.2
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
39
-
-
0037197886
-
The identification of functional modules from the genomic association of genes
-
Snel, B., Bork, P. and Huynen, M.A. (2002) The identification of functional modules from the genomic association of genes. PNAS, 99, 5890-5895.
-
(2002)
PNAS
, vol.99
, pp. 5890-5895
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
40
-
-
84902461237
-
Functional association networks as priors for gene regulatory network inference
-
Studham, M.E., Tjarnberg, A., Nordling, T.E., Nelander, S. and Sonnhammer, E.L. (2014) Functional association networks as priors for gene regulatory network inference. Bioinformatics, 30, i130-i138.
-
(2014)
Bioinformatics
, vol.30
, pp. i130-i138
-
-
Studham, M.E.1
Tjarnberg, A.2
Nordling, T.E.3
Nelander, S.4
Sonnhammer, E.L.5
-
41
-
-
85016149190
-
KEGG: New perspectives on genomes, pathways, diseases and drugs
-
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. and Morishima, K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 45, D353-D361.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D353-D361
-
-
Kanehisa, M.1
Furumichi, M.2
Tanabe, M.3
Sato, Y.4
Morishima, K.5
-
42
-
-
0034614678
-
Protein interaction mapping in C. Elegans using proteins involved in vulval development
-
Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N. and Vidal, M. (2000) Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 287, 116-122.
-
(2000)
Science
, vol.287
, pp. 116-122
-
-
Walhout, A.J.1
Sordella, R.2
Lu, X.3
Hartley, J.L.4
Temple, G.F.5
Brasch, M.A.6
Thierry-Mieg, N.7
Vidal, M.8
-
43
-
-
3042569597
-
Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs
-
Yu, H., Luscombe, N.M., Lu, H.X., Zhu, X., Xia, Y., Han, J.D., Bertin, N., Chung, S., Vidal, M. and Gerstein, M. (2004) Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res., 14, 1107-1118.
-
(2004)
Genome Res.
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.3
Zhu, X.4
Xia, Y.5
Han, J.D.6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
44
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen, M., Snel, B., Lathe, W. 3rd and Bork, P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe, W.3
Bork, P.4
-
45
-
-
38949138554
-
Computational prediction of protein-protein interactions
-
Skrabanek, L., Saini, H.K., Bader, G.D. and Enright, A.J. (2008) Computational prediction of protein-protein interactions. Mol. Biotechnol., 38, 1-17.
-
(2008)
Mol. Biotechnol.
, vol.38
, pp. 1-17
-
-
Skrabanek, L.1
Saini, H.K.2
Bader, G.D.3
Enright, A.J.4
-
46
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets-update
-
Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
Evangelista, C.4
Kim, I.F.5
Tomashevsky, M.6
Marshall, K.A.7
Phillippy, K.H.8
Sherman, P.M.9
Holko, M.10
-
47
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
Langfelder, P. and Horvath, S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
48
-
-
85045272055
-
Massive mining of publicly available RNA-seq data from human and mouse
-
Lachmann, A., Torre, D., Keenan, A.B., Jagodnik, K.M., Lee, H.J., Wang, L., Silverstein, M.C. and Ma'ayan, A. (2018) Massive mining of publicly available RNA-seq data from human and mouse. Nat. Commun., 9, 1366.
-
(2018)
Nat. Commun.
, vol.9
, pp. 1366
-
-
Lachmann, A.1
Torre, D.2
Keenan, A.B.3
Jagodnik, K.M.4
Lee, H.J.5
Wang, L.6
Silverstein, M.C.7
Ma'Ayan, A.8
-
49
-
-
84954148057
-
TreeClust: An R package for Tree-Based clustering dissimilarities
-
Buttrey, S.L. and Whitaker, L.R. (2015) treeClust: an R package for Tree-Based clustering dissimilarities. TheR Journal, 7, 227-236.
-
(2015)
TheR Journal
, vol.7
, pp. 227-236
-
-
Buttrey, S.L.1
Whitaker, L.R.2
-
50
-
-
84976870113
-
The reactome pathway knowledgebase
-
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S. et al. (2016) The reactome pathway Knowledgebase. Nucleic Acids Res., 44, D481-D487.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D481-D487
-
-
Fabregat, A.1
Sidiropoulos, K.2
Garapati, P.3
Gillespie, M.4
Hausmann, K.5
Haw, R.6
Jassal, B.7
Jupe, S.8
Korninger, F.9
McKay, S.10
-
51
-
-
84976877782
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C.A., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 44, D471-D480.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D471-D480
-
-
Caspi, R.1
Billington, R.2
Ferrer, L.3
Foerster, H.4
Fulcher, C.A.5
Keseler, I.M.6
Kothari, A.7
Krummenacker, M.8
Latendresse, M.9
Mueller, L.A.10
-
52
-
-
85016166168
-
Expansion of the Gene Ontology knowledgebase and resources
-
The Gene Ontology, C. (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res., 45, D331-D338.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D331-D338
-
-
-
53
-
-
84946081339
-
OMIM.org: Online mendelian inheritance in man (OMIM(R)), an online catalog of human genes and genetic disorders
-
Amberger, J.S., Bocchini, C.A., Schiettecatte, F., Scott, A.F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D789-D798
-
-
Amberger, J.S.1
Bocchini, C.A.2
Schiettecatte, F.3
Scott, A.F.4
Hamosh, A.5
-
54
-
-
84953214104
-
Pathway analysis: State of the art
-
Garcia-Campos, M.A., Espinal-Enriquez, J. and Hernandez-Lemus, E. (2015) Pathway analysis: state of the art. Front. Physiol., 6, 383.
-
(2015)
Front. Physiol.
, vol.6
, pp. 383
-
-
Garcia-Campos, M.A.1
Espinal-Enriquez, J.2
Hernandez-Lemus, E.3
-
55
-
-
84896716464
-
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity
-
Tarca, A.L., Bhatti, G. and Romero, R. (2013) A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PLoS One, 8, e79217.
-
(2013)
PLoS One
, vol.8
-
-
Tarca, A.L.1
Bhatti, G.2
Romero, R.3
-
56
-
-
85031009603
-
A strategy for evaluating pathway analysis methods
-
Yu, C., Woo, H.J., Yu, X., Oyama, T., Wallqvist, A. and Reifman, J. (2017) A strategy for evaluating pathway analysis methods. BMC Bioinformatics, 18, 453.
-
(2017)
BMC Bioinformatics
, vol.18
, pp. 453
-
-
Yu, C.1
Woo, H.J.2
Yu, X.3
Oyama, T.4
Wallqvist, A.5
Reifman, J.6
-
57
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benyamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benyamini, Y.1
Hochberg, Y.2
-
58
-
-
84885993905
-
Going the distance for protein function prediction: A new distance metric for protein interaction networks
-
Cao, M., Zhang, H., Park, J., Daniels, N.M., Crovella, M.E., Cowen, L.J. and Hescott, B. (2013) Going the distance for protein function prediction: a new distance metric for protein interaction networks. PLoS One, 8, e76339.
-
(2013)
PLoS One
, vol.8
-
-
Cao, M.1
Zhang, H.2
Park, J.3
Daniels, N.M.4
Crovella, M.E.5
Cowen, L.J.6
Hescott, B.7
-
59
-
-
84902463639
-
New directions for diffusion-based network prediction of protein function: Incorporating pathways with confidence
-
Cao, M., Pietras, C.M., Feng, X., Doroschak, K.J., Schaffner, T., Park, J., Zhang, H., Cowen, L.J. and Hescott, B.J. (2014) New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. Bioinformatics, 30, i219-i227.
-
(2014)
Bioinformatics
, vol.30
, pp. i219-i227
-
-
Cao, M.1
Pietras, C.M.2
Feng, X.3
Doroschak, K.J.4
Schaffner, T.5
Park, J.6
Zhang, H.7
Cowen, L.J.8
Hescott, B.J.9
-
60
-
-
84892719927
-
HPC-CLUST: Distributed hierarchical clustering for large sets of nucleotide sequences
-
Matias Rodrigues, J.F. and von Mering, C. (2014) HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30, 287-288.
-
(2014)
Bioinformatics
, vol.30
, pp. 287-288
-
-
Matias Rodrigues, J.F.1
Von Mering, C.2
-
62
-
-
49649103221
-
The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis
-
Riker, A.I., Enkemann, S.A., Fodstad, O., Liu, S., Ren, S., Morris, C., Xi, Y., Howell, P., Metge, B., Samant, R.S. et al. (2008) The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med. Genomics, 1, 13.
-
(2008)
BMC Med. Genomics
, vol.1
, pp. 13
-
-
Riker, A.I.1
Enkemann, S.A.2
Fodstad, O.3
Liu, S.4
Ren, S.5
Morris, C.6
Xi, Y.7
Howell, P.8
Metge, B.9
Samant, R.S.10
|