-
1
-
-
0032489015
-
The cell as a collection of protein machines: Preparing the next generation of molecular biologists
-
Alberts B (1998). The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294.
-
(1998)
Cell
, vol.92
, pp. 291-294
-
-
Alberts, B.1
-
2
-
-
79959706804
-
Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling
-
Alexander J et al. (2011). Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal 4, ra42.
-
(2011)
Sci Signal
, vol.4
-
-
Alexander, J.1
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
79954986866
-
A new face and new challenges for online mendelian inheritance in man (omim)
-
Amberger J, Bocchini C, Hamosh A (2011). A new face and new challenges for Online Mendelian Inheritance in Man (OMIM). Hum Mutat 32, 564-567.
-
(2011)
Hum Mutat
, vol.32
, pp. 564-567
-
-
Amberger, J.1
Bocchini, C.2
Hamosh, A.3
-
5
-
-
84864001338
-
Antibodies for profiling the human proteome-The human protein atlas as a resource for cancer research
-
Asplund A, Edqvist PH, Schwenk JM, Ponten F (2012). Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research. Proteomics 12, 2067-2077.
-
(2012)
Proteomics
, vol.12
, pp. 2067-2077
-
-
Asplund, A.1
Edqvist, P.H.2
Schwenk, J.M.3
Ponten, F.4
-
6
-
-
84874271270
-
Ncbi geo: Archive for functional genomics data sets-update
-
Barrett T et al. (2013). NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 41, D991-D995.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Barrett, T.1
-
7
-
-
2442604715
-
The genetic association database
-
Becker KG, Barnes KC, Bright TJ, Wang SA (2004). The genetic association database. Nat Genet 36, 431-432.
-
(2004)
Nat Genet
, vol.36
, pp. 431-432
-
-
Becker, K.G.1
Barnes, K.C.2
Bright, T.J.3
Wang, S.A.4
-
8
-
-
84891797680
-
Genbank
-
Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2014). GenBank. Nucleic Acids Res 42, D32-D37.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Benson, D.A.1
Clark, K.2
Karsch-Mizrachi, I.3
Lipman, D.J.4
Ostell, J.5
Sayers, E.W.6
-
9
-
-
84891762026
-
The chembl bioactivity database: An update
-
Bento AP et al. (2014). The ChEMBL bioactivity database: an update. Nucleic Acids Res 42, D1083-D1090.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Bento, A.P.1
-
11
-
-
84874253819
-
Gene ontology annotations and resources
-
Blake JA (2013). Gene Ontology annotations and resources. Nucleic Acids Res 41, D530-D535.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Blake, J.A.1
-
12
-
-
45549089565
-
The art and design of genetic screens: Rna interference
-
Boutros M, Ahringer J (2008). The art and design of genetic screens: RNA interference. Nat Rev Genet 9, 554-566.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 554-566
-
-
Boutros, M.1
Ahringer, J.2
-
13
-
-
84891779149
-
Decipher: Database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation
-
Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, Swaminathan GJ (2014). DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res 42, D993-D1000.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Bragin, E.1
Chatzimichali, E.A.2
Wright, C.F.3
Hurles, M.E.4
Firth, H.V.5
Bevan, A.P.6
Swaminathan, G.J.7
-
14
-
-
84891785390
-
Cansar: Updated cancer research and drug discovery knowledgebase
-
Bulusu KC, Tym JE, Coker EA, Schierz AC, Al-Lazikani B (2014). canSAR: updated cancer research and drug discovery knowledgebase. Nucleic Acids Res 42, D1040-D1047.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Bulusu, K.C.1
Tym, J.E.2
Coker, E.A.3
Schierz, A.C.4
Al-Lazikani, B.5
-
15
-
-
77956055139
-
Analysis of gene function using dna microarrays
-
Capaldi AP (2010). Analysis of gene function using DNA microarrays. Methods Enzymol 470, 3-17.
-
(2010)
Methods Enzymol
, vol.470
, pp. 3-17
-
-
Capaldi, A.P.1
-
16
-
-
84874947727
-
The biogrid interaction database: 2013 update
-
Chatr-Aryamontri A et al. (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Res 41, D816-D823.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Chatr-Aryamontri, A.1
-
17
-
-
84891753483
-
The reactome pathway knowledgebase
-
Croft D et al. (2014). The Reactome pathway knowledgebase. Nucleic Acids Res 42, D472-D477.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Croft, D.1
-
18
-
-
84876467333
-
The comparative toxicogenomics database: Update 2013
-
Davis AP et al. (2013). The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res 41, D1104-D1114.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Davis, A.P.1
-
20
-
-
77953292595
-
Post-translational modifications in signal integration
-
Deribe YL, Pawson T, Dikic I (2010). Post-translational modifications in signal integration. Nat Struct Mol Biol 17, 666-672.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 666-672
-
-
Deribe, Y.L.1
Pawson, T.2
Dikic, I.3
-
21
-
-
78651320816
-
Phospho.Elm: A database of phosphorylation sites-update 2011
-
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F (2011). Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res 39, D261-D267.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Dinkel, H.1
Chica, C.2
Via, A.3
Gould, C.M.4
Jensen, L.J.5
Gibson, T.J.6
Diella, F.7
-
22
-
-
84891752434
-
The eukaryotic linear motif resource elm: 10 years and counting
-
Dinkel H et al. (2014). The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res 42, D259-D266.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Dinkel, H.1
-
23
-
-
0037096158
-
From cdc2 to cdk1: When did the cell cycle kinase join its cyclin partner?
-
Dorée M, Hunt T (2002). From Cdc2 to Cdk1: when did the cell cycle kinase join its cyclin partner? J Cell Sci 115, 2461-2464.
-
(2002)
J Cell Sci
, vol.115
, pp. 2461-2464
-
-
Dorée, M.1
Hunt, T.2
-
24
-
-
77952778270
-
Prediction of posttranslational modification of proteins from their amino acid sequence
-
Eisenhaber B, Eisenhaber F (2010). Prediction of posttranslational modification of proteins from their amino acid sequence. Methods Mol Biol 609, 365-384.
-
(2010)
Methods Mol Biol
, vol.609
, pp. 365-384
-
-
Eisenhaber, B.1
Eisenhaber, F.2
-
26
-
-
84891782659
-
Pfam: The protein families database
-
Finn RD et al. (2014). Pfam: the protein families database. Nucleic Acids Res 42, D222-D230.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Finn, R.D.1
-
27
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch WM (2000). Homology a personal view on some of the problems. Trends Genet 16, 227-231.
-
(2000)
Trends Genet
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
28
-
-
9144253910
-
Intenz, the integrated relational enzyme database
-
Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R (2004). IntEnz, the integrated relational enzyme database. Nucleic Acids Res 32, D434-D437.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Fleischmann, A.1
Darsow, M.2
Degtyarenko, K.3
Fleischmann, W.4
Boyce, S.5
Axelsen, K.B.6
Bairoch, A.7
Schomburg, D.8
Tipton, K.F.9
Apweiler, R.10
-
29
-
-
84891768365
-
Ensembl 2014
-
Flicek P et al. (2014). Ensembl 2014. Nucleic Acids Res 42, D749-D755.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Flicek, P.1
-
30
-
-
78651330430
-
Cosmic: Mining complete cancer genomes in the catalogue of somatic mutations in cancer
-
Forbes SA et al. (2011). COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39, D945-D950.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Forbes, S.A.1
-
31
-
-
0035458366
-
The art and design of genetic screens: Yeast
-
Forsburg SL (2001). The art and design of genetic screens: yeast. Nat Rev Genet 2, 659-668.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 659-668
-
-
Forsburg, S.L.1
-
32
-
-
84876515907
-
String v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini A 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
-
-
Franceschini, A.1
-
33
-
-
84874083265
-
Nextprot: Organizing protein knowledge in the context of human proteome projects
-
Gaudet P et al. (2013). neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res 12, 293-298.
-
(2013)
J Proteome Res
, vol.12
, pp. 293-298
-
-
Gaudet, P.1
-
34
-
-
0036796467
-
Cdart: Protein homology by domain architecture
-
Geer LY, Domrachev M, Lipman DJ, Bryant SH (2002). CDART: protein homology by domain architecture. Genome Res 12, 1619-1623.
-
(2002)
Genome Res
, vol.12
, pp. 1619-1623
-
-
Geer, L.Y.1
Domrachev, M.2
Lipman, D.J.3
Bryant, S.H.4
-
35
-
-
75549088021
-
The ncbi biosystems database
-
Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH (2010). The NCBI BioSystems database. Nucleic Acids Res 38, D492-D496.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Geer, L.Y.1
Marchler-Bauer, A.2
Geer, R.C.3
Han, L.4
He, J.5
He, S.6
Liu, C.7
Shi, W.8
Bryant, S.H.9
-
36
-
-
78651277460
-
Phosida 2011: The posttranslational modification database
-
Gnad F, Gunawardena J, Mann M (2011). PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res 39, D253-D260.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Gnad, F.1
Gunawardena, J.2
Mann, M.3
-
37
-
-
79955770162
-
Scaffold proteins: Hubs for controlling the flow of cellular information
-
Good MC, Zalatan JG, Lim WA (2011). Scaffold proteins: hubs for controlling the flow of cellular information. Science 332, 680-686.
-
(2011)
Science
, vol.332
, pp. 680-686
-
-
Good, M.C.1
Zalatan, J.G.2
Lim, W.A.3
-
38
-
-
80055109819
-
Consequences of the discontinuation of the international protein index (ipi) database and its substitution by the uniprotkb "complete proteome"sets
-
Griss J, Martin M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaino JA (2011). Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics 11, 4434-4438.
-
(2011)
Proteomics
, vol.11
, pp. 4434-4438
-
-
Griss, J.1
Martin, M.2
O'Donovan, C.3
Apweiler, R.4
Hermjakob, H.5
Vizcaino, J.A.6
-
39
-
-
84891774970
-
Pdbe: Protein data bank in europe
-
Gutmanas A et al. (2014). PDBe: Protein Data Bank in Europe. Nucleic Acids Res 42, D285-D291.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Gutmanas, A.1
-
40
-
-
84894298369
-
A genome-wide resource of cell cycle and cell shape genes of fission yeast
-
Hayles J, Wood V, Jeffery L, Hoe KL, Kim DU, Park HO, Salas-Pino S, Heichinger C, Nurse P (2013). A genome-wide resource of cell cycle and cell shape genes of fission yeast. Open Biol 3, 130053.
-
(2013)
Open Biol
, vol.3
, pp. 130053
-
-
Hayles, J.1
Wood, V.2
Jeffery, L.3
Hoe, K.L.4
Kim, D.U.5
Park, H.O.6
Salas-Pino, S.7
Heichinger, C.8
Nurse, P.9
-
41
-
-
70449664627
-
Methods for interpreting lists of affected genes obtained in a dna microarray experiment
-
Hedegaard J et al. (2009). Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc 3 (Suppl 4), S5.
-
(2009)
BMC Proc
, vol.3
, Issue.SUPPL. 4
-
-
Hedegaard, J.1
-
42
-
-
33746124556
-
Biomolecules in the computer: Jmol to the rescue
-
Herraez A (2006). Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 34, 255-261.
-
(2006)
Biochem Mol Biol Educ
, vol.34
, pp. 255-261
-
-
Herraez, A.1
-
43
-
-
35748950713
-
Exploring the functional landscape of gene expression: Directed search of large microarray compendia
-
Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG (2007). Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 23, 2692-2699.
-
(2007)
Bioinformatics
, vol.23
, pp. 2692-2699
-
-
Hibbs, M.A.1
Hess, D.C.2
Myers, C.L.3
Huttenhower, C.4
Li, K.5
Troyanskaya, O.G.6
-
45
-
-
84857047339
-
Phosphositeplus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
-
Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012). PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 40, D261-270.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Hornbeck, P.V.1
Kornhauser, J.M.2
Tkachev, S.3
Zhang, B.4
Skrzypek, E.5
Murray, B.6
Latham, V.7
Sullivan, M.8
-
46
-
-
0029297969
-
One-gene-one-enzyme: Remembering biochemical genetics
-
Horowitz NH (1995). One-gene-one-enzyme: remembering biochemical genetics. Protein Sci 4, 1017-1019.
-
(1995)
Protein Sci
, vol.4
, pp. 1017-1019
-
-
Horowitz, N.H.1
-
47
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang da W, Sherman BT, Lempicki RA (2009a). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
48
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using david bioinformatics resources
-
Huang da W, Sherman BT, Lempicki RA (2009b). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57.
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
49
-
-
84861793773
-
Gene set enrichment analysis: Performance evaluation and usage guidelines
-
Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C (2012). Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform 13, 281-291.
-
(2012)
Brief Bioinform
, vol.13
, pp. 281-291
-
-
Hung, J.H.1
Yang, T.H.2
Hu, Z.3
Weng, Z.4
DeLisi, C.5
-
50
-
-
75849120634
-
Protein sequence motifs involved in recognition and targeting: A new series
-
Hunt T (1990). Protein sequence motifs involved in recognition and targeting: a new series. Trends Biochem Sci 15, 305.
-
(1990)
Trends Biochem Sci
, vol.15
, pp. 305
-
-
Hunt, T.1
-
51
-
-
84858602406
-
Interpro in 2011: New developments in the family and domain prediction database
-
Hunter S et al. (2012). InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40, D306-D312.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Hunter, S.1
-
52
-
-
79959688563
-
Quickgo: A user tutorial for the web-based gene ontology browser
-
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R (2009). QuickGO: a user tutorial for the web-based Gene Ontology browser. Database (Oxford) 2009, bap010.
-
(2009)
Database (Oxford)
, vol.2009
-
-
Huntley, R.P.1
Binns, D.2
Dimmer, E.3
Barrell, D.4
O'Donovan, C.5
Apweiler, R.6
-
53
-
-
77951819088
-
Systematic analysis of human protein complexes identifies chromosome segregation proteins
-
Hutchins JRA et al. (2010). Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 328, 593-599.
-
(2010)
Science
, vol.328
, pp. 593-599
-
-
Hutchins, J.R.A.1
-
54
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in kegg
-
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014). Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42, D199-D205.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
55
-
-
84891771466
-
The ucsc genome browser database: 2014 update
-
Karolchik D et al. (2014). The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 42, D764-D770.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Karolchik, D.1
-
56
-
-
84891822189
-
Ensembl genomes 2013: Scaling up access to genome-wide data
-
Kersey PJ et al. (2014). Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42, D546-D552.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Kersey, P.J.1
-
57
-
-
3042818018
-
The international protein index: An integrated database for proteomics experiments
-
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R (2004). The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985-1988.
-
(2004)
Proteomics
, vol.4
, pp. 1985-1988
-
-
Kersey, P.J.1
Duarte, J.2
Williams, A.3
Karavidopoulou, Y.4
Birney, E.5
Apweiler, R.6
-
58
-
-
77953255163
-
Analysis of a genome-wide set of gene deletions in the fission yeast schizosaccharomyces pombe
-
Kim DU et al. (2010). Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 28, 617-623.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 617-623
-
-
Kim, D.U.1
-
59
-
-
19344375343
-
The meaning of systems biology
-
Kirschner MW (2005). The meaning of systems biology. Cell 121, 503-504.
-
(2005)
Cell
, vol.121
, pp. 503-504
-
-
Kirschner, M.W.1
-
60
-
-
0025238430
-
The private life of dna polymerase i
-
Kornberg A (1990). The private life of DNA polymerase I. Methods Enzymol 182, 783-788.
-
(1990)
Methods Enzymol
, vol.182
, pp. 783-788
-
-
Kornberg, A.1
-
61
-
-
84891798026
-
Ddbj progress report: A new submission system for leading to a correct annotation
-
Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y (2014). DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res 42, D44-D49.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Kosuge, T.1
Mashima, J.2
Kodama, Y.3
Fujisawa, T.4
Kaminuma, E.5
Ogasawara, O.6
Okubo, K.7
Takagi, T.8
Nakamura, Y.9
-
63
-
-
84891809093
-
Clinvar: Public archive of relationships among sequence variation and human phenotype
-
Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR (2014). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 42, D980-D985.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Landrum, M.J.1
Lee, J.M.2
Riley, G.R.3
Jang, W.4
Rubinstein, W.S.5
Church, D.M.6
Maglott, D.R.7
-
65
-
-
84876527890
-
Dbvar and dgva: Public archives for genomic structural variation
-
Lappalainen I et al. (2013). DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res 41, D936-D941.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Lappalainen, I.1
-
66
-
-
84891767304
-
Drugbank 4.0: Shedding new light on drug metabolism
-
Law V et al. (2014). DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 42, D1091-D1097.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Law, V.1
-
67
-
-
13444273452
-
The tigr gene indices: Clustering and assembling est and known genes and integration with eukaryotic genomes
-
Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J (2005). The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 33, D71-D74.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Lee, Y.1
Tsai, J.2
Sunkara, S.3
Karamycheva, S.4
Pertea, G.5
Sultana, R.6
Antonescu, V.7
Chan, A.8
Cheung, F.9
Quackenbush, J.10
-
68
-
-
84891757330
-
Gene3d: Multi-domain annotations for protein sequence and comparative genome analysis
-
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA (2014). Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. Nucleic Acids Res 42, D240-D245.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Lees, J.G.1
Lee, D.2
Studer, R.A.3
Dawson, N.L.4
Sillitoe, I.5
Das, S.6
Yeats, C.7
Dessailly, B.H.8
Rentzsch, R.9
Orengo, C.A.10
-
69
-
-
84862221167
-
Smart 7: Recent updates to the protein domain annotation resource
-
Letunic I, Doerks T, Bork P (2012). SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40, D302-D305.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Letunic, I.1
Doerks, T.2
Bork, P.3
-
70
-
-
30544453247
-
Bioinformatic "harvester": A search engine for genome-wide human, mouse, and rat protein resources
-
Liebel U, Kindler B, Pepperkok R (2005). Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources. Methods Enzymol 404, 19-26.
-
(2005)
Methods Enzymol
, vol.404
, pp. 19-26
-
-
Liebel, U.1
Kindler, B.2
Pepperkok, R.3
-
71
-
-
0031024171
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 23, 3-25.
-
(1997)
Adv Drug Deliv Rev
, vol.23
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
72
-
-
84877944199
-
Cytoscape app store
-
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR (2013). Cytoscape app store. Bioinformatics 29, 1350-1351.
-
(2013)
Bioinformatics
, vol.29
, pp. 1350-1351
-
-
Lotia, S.1
Montojo, J.2
Dong, Y.3
Bader, G.D.4
Pico, A.R.5
-
73
-
-
84876523828
-
Dbptm 3.0: An informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
-
Lu CT, Huang KY, Su MG, Lee TY, Bretana NA, Chang WC, Chen YJ, Huang HD (2013). dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res 41, D295-D305.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Lu, C.T.1
Huang, K.Y.2
Su, M.G.3
Lee, T.Y.4
Bretana, N.A.5
Chang, W.C.6
Chen, Y.J.7
Huang, H.D.8
-
74
-
-
79954533893
-
Pubmed and beyond: A survey of web tools for searching biomedical literature
-
Lu Z (2011). PubMed and beyond: a survey of Web tools for searching biomedical literature. Database (Oxford) 2011, baq036.
-
(2011)
Database (Oxford)
, vol.2011
-
-
Lu, Z.1
-
75
-
-
79958083843
-
Sciencenet-towards a global search and share engine for all scientific knowledge
-
Lütjohann DS, Shah AH, Christen MP, Richter F, Knese K, Liebel U (2011). "Sciencenet"-towards a global search and share engine for all scientific knowledge. Bioinformatics 27, 1734-1735.
-
(2011)
Bioinformatics
, vol.27
, pp. 1734-1735
-
-
Lütjohann, D.S.1
Shah, A.H.2
Christen, M.P.3
Richter, F.4
Knese, K.5
Liebel, U.6
-
76
-
-
84861664072
-
Mmdb: 3d structures and macromolecular interactions
-
Madej T et al. (2012). MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res 40, D461-D464.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Madej, T.1
-
77
-
-
84875445608
-
Cdd: Conserved domains and protein three-dimensional structure
-
Marchler-Bauer A et al. (2013). CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41, D348-D352.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Marchler-Bauer, A.1
-
78
-
-
84874969184
-
Panther in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
-
Mi H, Muruganujan A, Thomas PD (2013). PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41, D377-D386.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Mi, H.1
Muruganujan, A.2
Thomas, P.D.3
-
79
-
-
84859219888
-
Minimotif miner 3.0: Database expansion and significantly improved reduction of false-positive predictions from consensus sequences
-
Mi T et al. (2012). Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res 40, D252-D260.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Mi, T.1
-
80
-
-
14044254746
-
Textpresso: An ontology-based information retrieval and extraction system for biological literature
-
Müller HM, Kenny EE, Sternberg PW (2004). Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2, e309.
-
(2004)
PLoS Biol
, vol.2
-
-
Müller, H.M.1
Kenny, E.E.2
Sternberg, P.W.3
-
81
-
-
84891804649
-
Database resources of the national center for biotechnology information
-
NCBI Resource Coordinators
-
NCBI Resource Coordinators (2014). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 42, D7-D17.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
-
82
-
-
77950387346
-
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
-
Neumann B et al. (2010). Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721-727.
-
(2010)
Nature
, vol.464
, pp. 721-727
-
-
Neumann, B.1
-
83
-
-
79959212998
-
Landscape of next-generation sequencing technologies
-
Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011). Landscape of next-generation sequencing technologies. Anal Chem 83, 4327-4341.
-
(2011)
Anal Chem
, vol.83
, pp. 4327-4341
-
-
Niedringhaus, T.P.1
Milanova, D.2
Kerby, M.B.3
Snyder, M.P.4
Barron, A.E.5
-
85
-
-
0042622251
-
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
-
Obenauer JC, Cantley LC, Yaffe MB (2003). Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31, 3635-3641.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3635-3641
-
-
Obenauer, J.C.1
Cantley, L.C.2
Yaffe, M.B.3
-
86
-
-
67749125573
-
ANNIE: integrated de novo protein sequence annotation
-
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G (2009). ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res 37, W435-W440.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Ooi, H.S.1
Kwo, C.Y.2
Wildpaner, M.3
Sirota, F.L.4
Eisenhaber, B.5
Maurer-Stroh, S.6
Wong, W.C.7
Schleiffer, A.8
Eisenhaber, F.9
Schneider, G.10
-
87
-
-
84859208501
-
Protein interaction data curation: The international molecular exchange (imex) consortium
-
Orchard S 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
-
88
-
-
84891799734
-
The mintact project-intact as a common curation platform for 11 molecular interaction databases
-
Orchard S et al. (2014). The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42, D358-363.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Orchard, S.1
-
89
-
-
53549115579
-
Research highlight: Determining druggability
-
Owens J (2007). Research highlight: determining druggability. Nat Rev Drug Discov 6, 187.
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 187
-
-
Owens, J.1
-
90
-
-
78751570979
-
Rna sequencing: Advances, challenges and opportunities
-
Ozsolak F, Milos PM (2011). RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12, 87-98.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
91
-
-
84891753169
-
Assembly information services in the european nucleotide archive
-
Pakseresht N et al. (2014). Assembly information services in the European Nucleotide Archive. Nucleic Acids Res 42, D38-D43.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Pakseresht, N.1
-
92
-
-
84891768855
-
Expression atlas update-A database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments
-
Petryszak R et al. (2014). Expression Atlas update-a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments. Nucleic Acids Res 42, D926-D932.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Petryszak, R.1
-
93
-
-
84891767394
-
Refseq: An update on mammalian reference sequences
-
Pruitt KD et al. (2014). RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42, D756-763.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Pruitt, K.D.1
-
94
-
-
77949921369
-
Evaluation of protein phosphorylation site predictors
-
Que S, Wang Y, Chen P, Tang YR, Zhang Z, He H (2010). Evaluation of protein phosphorylation site predictors. Protein Pept Lett 17, 64-69.
-
(2010)
Protein Pept Lett
, vol.17
, pp. 64-69
-
-
Que, S.1
Wang, Y.2
Chen, P.3
Tang, Y.R.4
Zhang, Z.5
He, H.6
-
95
-
-
84891723065
-
Project ranks billions of drug interactions
-
Reardon S (2013). Project ranks billions of drug interactions. Nature 503, 449-450.
-
(2013)
Nature
, vol.503
, pp. 449-450
-
-
Reardon, S.1
-
96
-
-
84876529328
-
The rcsb protein data bank: New resources for research and education
-
Rose PW et al. (2013). The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res 41, D475-D482.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Rose, P.W.1
-
97
-
-
84875945705
-
Encode data in the ucsc genome browser: Year 5 update
-
Rosenbloom KR et al. (2013). ENCODE Data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res 41, D56-D63.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Rosenbloom, K.R.1
-
98
-
-
84876097557
-
Arrayexpress update-trends in database growth and links to data analysis tools
-
Rustici G et al. (2013). ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res 41, D987-D990.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Rustici, G.1
-
99
-
-
84869054051
-
A travel guide to cytoscape plugins
-
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T (2012). A travel guide to Cytoscape plugins. Nat Methods 9, 1069-1076.
-
(2012)
Nat Methods
, vol.9
, pp. 1069-1076
-
-
Saito, R.1
Smoot, M.E.2
Ono, K.3
Ruscheinski, J.4
Wang, P.L.5
Lotia, S.6
Pico, A.R.7
Bader, G.D.8
Ideker, T.9
-
100
-
-
84876522835
-
Brenda in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in brenda
-
Schomburg I et al. (2013). BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res 41, D764-772.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Schomburg, I.1
-
101
-
-
84891766808
-
Treefam v9: A new website, more species and orthology-on-the-fly
-
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (2014). TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic Acids Res 42, D922-D925.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Schreiber, F.1
Patricio, M.2
Muffato, M.3
Pignatelli, M.4
Bateman, A.5
-
102
-
-
84876588470
-
New and continuing developments at prosite
-
Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I (2013). New and continuing developments at PROSITE. Nucleic Acids Res 41, D344-D347.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Sigrist, C.J.1
De Castro, E.2
Cerutti, L.3
Cuche, B.A.4
Hulo, N.5
Bridge, A.6
Bougueleret, L.7
Xenarios, I.8
-
103
-
-
84876578144
-
New functional families (funfams) in cath to improve the mapping of conserved functional sites to 3d structures
-
Sillitoe I et al. (2013). New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41, D490-D498.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Sillitoe, I.1
-
104
-
-
84870461332
-
Intermine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data
-
Smith RN et al. (2012). InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28, 3163-3165.
-
(2012)
Bioinformatics
, vol.28
, pp. 3163-3165
-
-
Smith, R.N.1
-
105
-
-
79551587720
-
Cytoscape 2.8: New features for data integration and network visualization
-
Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432.
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.-L.4
Ideker, T.5
-
106
-
-
15844431376
-
Full-genome rnai profiling of early embryogenesis in caenorhabditis elegans
-
Sönnichsen B et al. (2005). Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462-469.
-
(2005)
Nature
, vol.434
, pp. 462-469
-
-
Sönnichsen, B.1
-
107
-
-
84860615255
-
In-silico human genomics with genecards
-
Stelzer G et al. (2011). In-silico human genomics with GeneCards. Hum Genomics 5, 709-717.
-
(2011)
Hum Genomics
, vol.5
, pp. 709-717
-
-
Stelzer, G.1
-
108
-
-
34347388470
-
Uniref: Comprehensive and non-redundant uniprot reference clusters
-
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH (2007). UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282-1288.
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
109
-
-
84891783174
-
Activities at the universal protein resource (uniprot
-
UniProt Consortium
-
UniProt Consortium (2014). Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42, D191-D198.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
-
110
-
-
80052780634
-
Dasty3, a web framework for das
-
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H (2011). Dasty3, a WEB framework for DAS. Bioinformatics 27, 2616-2617.
-
(2011)
Bioinformatics
, vol.27
, pp. 2616-2617
-
-
Villaveces, J.M.1
Jimenez, R.C.2
Garcia, L.J.3
Salazar, G.A.4
Gel, B.5
Mulder, N.6
Martin, M.7
Garcia, A.8
Hermjakob, H.9
-
111
-
-
84940264082
-
Posttranslational modification of proteins: Expanding nature's inventory, greenwood village, co: Roberts and company. Walther tc, mann m (2010). Mass spectrometry-based proteomics in cell biology
-
Walsh CT (2006). Posttranslational Modification of Proteins: Expanding Nature's Inventory, Greenwood Village, CO: Roberts and Company. Walther TC, Mann M (2010). Mass spectrometry-based proteomics in cell biology. J Cell Biol 190, 491-500.
-
(2006)
J Cell Biol
, vol.190
, pp. 491-500
-
-
Walsh, C.T.1
-
112
-
-
84891805328
-
Pubchem bioassay: 2014 update
-
Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH (2014). PubChem BioAssay: 2014 update. Nucleic Acids Res 42, D1075-D1082.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Wang, Y.1
Suzek, T.2
Zhang, J.3
Wang, J.4
He, S.5
Cheng, T.6
Shoemaker, B.A.7
Gindulyte, A.8
Bryant, S.H.9
-
113
-
-
67849104638
-
Pubchem: A public information system for analyzing bioactivities of small molecules
-
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH (2009). PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37, W623-W633.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wang, Y.1
Xiao, J.2
Suzek, T.O.3
Zhang, J.4
Wang, J.5
Bryant, S.H.6
-
114
-
-
0036730532
-
A user's guide to the human genome
-
Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD (2002). A user's guide to the human genome. Nat Genet 32 (Suppl), 1-79.
-
(2002)
Nat Genet
, vol.32
, Issue.SUPPL.
, pp. 1-79
-
-
Wolfsberg, T.G.1
Wetterstrand, K.A.2
Guyer, M.S.3
Collins, F.S.4
Baxevanis, A.D.5
-
115
-
-
84858305675
-
Pombase: A comprehensive online resource for fission yeast
-
Wood V et al. (2012). PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res 40, D695-D699.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Wood, V.1
-
116
-
-
84876563391
-
Genomics of drug sensitivity in cancer (gdsc): A resource for therapeutic biomarker discovery in cancer cells
-
Yang W et al. (2013). Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res 41, D955-D961.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Yang, W.1
-
117
-
-
77951634725
-
Systems-wide proteomic characterization of combinatorial post-translational modification patterns
-
Young NL, Plazas-Mayorca MD, Garcia BA (2010). Systems-wide proteomic characterization of combinatorial post-translational modification patterns. Expert Rev Proteomics 7, 79-92.
-
(2010)
Expert Rev Proteomics
, vol.7
, pp. 79-92
-
-
Young, N.L.1
Plazas-Mayorca, M.D.2
Garcia, B.A.3
|