-
1
-
-
84941092929
-
The Rat Genome Database 2015: Genomic, phenotypic and environmental variations and disease
-
Database issue
-
Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H (2015) The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res 43(Database issue):D743–D750. https://doi.org/10.1093/nar/gku1026
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D743-D750
-
-
Shimoyama, M.1
de Pons, J.2
Hayman, G.T.3
Laulederkind, S.J.4
Liu, W.5
Nigam, R.6
Petri, V.7
Smith, J.R.8
Tutaj, M.9
Wang, S.J.10
Worthey, E.11
Dwinell, M.12
Jacob, H.13
-
2
-
-
84927942575
-
The pathway ontology - updates and applications
-
Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ (2014) The pathway ontology - updates and applications. J Biomed Semantics 5(1):7. https://doi. org/10.1186/2041-1480-5-7
-
(2014)
J Biomed Semantics
, vol.5
, Issue.1
, pp. 7
-
-
Petri, V.1
Jayaraman, P.2
Tutaj, M.3
Hayman, G.T.4
Smith, J.R.5
de Pons, J.6
Laulederkind, S.J.7
Lowry, T.F.8
Nigam, R.9
Wang, S.J.10
Shimoyama, M.11
Dwinell, M.R.12
Munzenmaier, D.H.13
Worthey, E.A.14
Jacob, H.J.15
-
3
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi. org/10.1101/gr.1239303
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
4
-
-
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 FS, Cesareni G, Chatr-Aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stumpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 9(4):345–350. https://doi. org/10.1038/nmeth.1931
-
(2012)
Nat Methods
, vol.9
, Issue.4
, 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
Chatr-Aryamontri, A.11
Chautard, E.12
Chen, C.13
Dumousseau, M.14
Goll, J.15
Hancock, R.E.16
Hannick, L.I.17
Jurisica, I.18
Khadake, J.19
Lynn, D.J.20
Mahadevan, U.21
Perfetto, L.22
Raghunath, A.23
Ricard-Blum, S.24
Roechert, B.25
Salwinski, L.26
Stumpflen, V.27
Tyers, M.28
Uetz, P.29
Xenarios, I.30
Hermjakob, H.31
more..
-
5
-
-
84891799734
-
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases
-
Database issue
-
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363. https://doi. org/10.1093/nar/gkt1115
-
(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
Duesbury, M.11
Dumousseau, M.12
Galeota, E.13
Hinz, U.14
Iannuccelli, M.15
Jagannathan, S.16
Jimenez, R.17
Khadake, J.18
Lagreid, A.19
Licata, L.20
Lovering, R.C.21
Meldal, B.22
Melidoni, A.N.23
Milagros, M.24
Peluso, D.25
Perfetto, L.26
Porras, P.27
Raghunath, A.28
Ricard-Blum, S.29
Roechert, B.30
Stutz, A.31
Tognolli, M.32
van Roey, K.33
Cesareni, G.34
Hermjakob, H.35
more..
-
6
-
-
79953172202
-
Setting up the JBrowse genome browser
-
Skinner ME, Holmes IH (2010) Setting up the JBrowse genome browser. Curr Protoc Bioinformatics 32:9.13.1–9.13.13. https://doi.org/10.1002/0471250953.bi0913s32
-
(2010)
Curr Protoc Bioinformatics
, vol.32
, pp. 1-9
-
-
Skinner, M.E.1
Holmes, I.H.2
-
7
-
-
84875582766
-
Visualizing next-generation sequencing data with JBrowse
-
Westesson O, Skinner M, Holmes I (2013) Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 14(2):172– 177. https://doi.org/10.1093/bib/bbr078
-
(2013)
Brief Bioinform
, vol.14
, Issue.2
, pp. 172-177
-
-
Westesson, O.1
Skinner, M.2
Holmes, I.3
-
8
-
-
84963620866
-
JBrowse: A dynamic web platform for genome visualization and analysis
-
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17:66. https://doi.org/10.1186/s13059-016-0924-1
-
(2016)
Genome Biol
, vol.17
, pp. 66
-
-
Buels, R.1
Yao, E.2
Diesh, C.M.3
Hayes, R.D.4
Munoz-Torres, M.5
Helt, G.6
Goodstein, D.M.7
Elsik, C.G.8
Lewis, S.E.9
Stein, L.10
Holmes, I.H.11
-
9
-
-
85016136235
-
The BioGRID interaction database: 2017 update
-
Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O’Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res 45(D1):D369– d379. https://doi.org/10.1093/nar/gkw1102
-
(2017)
Nucleic Acids Res
, vol.45
, Issue.D1
, 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
Stark, C.11
Breitkreutz, B.J.12
Dolinski, K.13
Tyers, M.14
-
10
-
-
77955034237
-
Online tools for understanding rat physiology
-
Dwinell MR (2010) Online tools for understanding rat physiology. Brief Bioinform 11(4):431–439. https://doi.org/10.1093/bib/bbp069
-
(2010)
Brief Bioinform
, vol.11
, Issue.4
, pp. 431-439
-
-
Dwinell, M.R.1
-
11
-
-
73349108077
-
National BioResource Project-Rat and related activities
-
Serikawa T, Mashimo T, Takizawa A, Okajima R, Maedomari N, Kumafuji K, Tagami F, Neoda Y, Otsuki M, Nakanishi S, Yamasaki K, Voigt B, Kuramoto T (2009) National BioResource Project-Rat and related activities. Exp Anim 58(4):333–341
-
(2009)
Exp Anim
, vol.58
, Issue.4
, pp. 333-341
-
-
Serikawa, T.1
Mashimo, T.2
Takizawa, A.3
Okajima, R.4
Maedomari, N.5
Kumafuji, K.6
Tagami, F.7
Neoda, Y.8
Otsuki, M.9
Nakanishi, S.10
Yamasaki, K.11
Voigt, B.12
Kuramoto, T.13
-
12
-
-
84928822697
-
Genomic landscape of rat strain and substrain variation
-
Hermsen R, de Ligt J, Spee W, Blokzijl F, Schafer S, Adami E, Boymans S, Flink S, van Boxtel R, van der Weide RH, Aitman T, Hubner N, Simonis M, Tabakoff B, Guryev V, Cuppen E (2015) Genomic landscape of rat strain and substrain variation. BMC Genomics 16:357. https://doi.org/10.1186/s12864-015-1594-1
-
(2015)
BMC Genomics
, vol.16
, pp. 357
-
-
Hermsen, R.1
de Ligt, J.2
Spee, W.3
Blokzijl, F.4
Schafer, S.5
Adami, E.6
Boymans, S.7
Flink, S.8
van Boxtel, R.9
van der Weide, R.H.10
Aitman, T.11
Hubner, N.12
Simonis, M.13
Tabakoff, B.14
Guryev, V.15
Cuppen, E.16
-
13
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29. https://doi.org/10.1038/75556
-
(2000)
Nat Genet
, vol.25
, Issue.1
, 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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
14
-
-
26844450908
-
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
-
Smith CL, Goldsmith CA, Eppig JT (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6(1):R7. https://doi.org/10.1186/gb-2004-6-1-r7
-
(2005)
Genome Biol
, vol.6
, Issue.1
, pp. R7
-
-
Smith, C.L.1
Goldsmith, C.A.2
Eppig, J.T.3
-
15
-
-
84862262998
-
Ontology searching and browsing at the Rat Genome Database
-
Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Dwinell MR, Jacob HJ (2012) Ontology searching and browsing at the Rat Genome Database. Database (Oxford) 2012:bas016. https://doi. org/10.1093/database/bas016
-
(2012)
Database (Oxford) 2012:Bas016
-
-
Laulederkind, S.J.1
Tutaj, M.2
Shimoyama, M.3
Hayman, G.T.4
Lowry, T.F.5
Nigam, R.6
Petri, V.7
Smith, J.R.8
Wang, S.J.9
de Pons, J.10
Dwinell, M.R.11
Jacob, H.J.12
|