-
1
-
-
0033542408
-
It's sink or swim as a tidal wave of data approaches
-
Reichhardt, T. (1999) It's sink or swim as a tidal wave of data approaches. Nature, 399, 517-520.
-
(1999)
Nature
, vol.399
, pp. 517-520
-
-
Reichhardt, T.1
-
2
-
-
84938709678
-
Big data: Astronomical or genomical?
-
Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S., Robinson, G. E et al. (2015). Big Data: Astronomical or Genomical? PLoS Biol., 13, e1002195.
-
(2015)
PLoS Biol.
, vol.13
, pp. e1002195
-
-
Stephens, Z.D.1
Lee, S.Y.2
Faghri, F.3
Campbell, R.H.4
Zhai, C.5
Efron, M.J.6
Iyer, R.7
Schatz, M.C.8
Sinha, S.9
Robinson, G.E.10
-
3
-
-
84946069451
-
UniProt: A hub for protein information
-
The UniProt Consortium. (2014) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D204-D212
-
-
The UniProt Consortium1
-
4
-
-
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
-
5
-
-
84904815625
-
SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information
-
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L. et al. (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res., 42, W252-W258.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W252-W258
-
-
Biasini, M.1
Bienert, S.2
Waterhouse, A.3
Arnold, K.4
Studer, G.5
Schmidt, T.6
Kiefer, F.7
Cassarino, T.G.8
Bertoni, M.9
Bordoli, L.10
-
6
-
-
58149193233
-
The SWISS-MODEL Repository and associated resources
-
Kiefer, F., Arnold, K., Künzli, M., Bordoli, L. and Schwede, T. (2009) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res., 37, D387-D392.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D387-D392
-
-
Kiefer, F.1
Arnold, K.2
Künzli, M.3
Bordoli, L.4
Schwede, T.5
-
7
-
-
84864434718
-
ExPASy: SIB bioinformatics resource portal
-
Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E. et al. (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res., 40, W597-W603.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W597-W603
-
-
Artimo, P.1
Jonnalagedda, M.2
Arnold, K.3
Baratin, D.4
Csardi, G.5
De Castro, E.6
Duvaud, S.7
Flegel, V.8
Fortier, A.9
Gasteiger, E.10
-
8
-
-
84904799126
-
Fifteen years SIB Swiss Institute of Bioinformatics: Life science databases, tools and support
-
Stockinger, H., Altenhoff, A. M., Arnold, K., Bairoch, A., Bastian, F., Bergmann, S., Bougueleret, L., Bucher, P., Delorenzi, M., Lane, L. et al. (2014) Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res., 42, W436-W441.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W436-W441
-
-
Stockinger, H.1
Altenhoff, A.M.2
Arnold, K.3
Bairoch, A.4
Bastian, F.5
Bergmann, S.6
Bougueleret, L.7
Bucher, P.8
Delorenzi, M.9
Lane, L.10
-
9
-
-
84946073050
-
Content discovery and retrieval services at the European Nucleotide Archive
-
Silvester, N., Alako, B., Amid, C., Cerdeño-Tárraga, A., Cleland, I., Gibson, R., Goodgame, N., Ten Hoopen, P., Kay, S., Leinonen, R. et al. (2015) Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res., 43, D23-D29.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D23-D29
-
-
Silvester, N.1
Alako, B.2
Amid, C.3
Cerdeño-Tárraga, A.4
Cleland, I.5
Gibson, R.6
Goodgame, N.7
Ten Hoopen, P.8
Kay, S.9
Leinonen, R.10
-
10
-
-
84862198590
-
The Sequence Read Archive: Explosive growth of sequencing data
-
Kodama, Y., Shumway, M. and Leinonen, R. (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D54-D56
-
-
Kodama, Y.1
Shumway, M.2
Leinonen, R.3
-
11
-
-
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
-
12
-
-
84874762979
-
The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
-
Vizcaino, J. A., Côté, R. G, Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J. et al. (2014) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069.
-
(2014)
Nucleic Acids Res
, vol.41
, pp. D1063-D1069
-
-
Vizcaino, J.A.1
Côté, R.G.2
Csordas, A.3
Dianes, J.A.4
Fabregat, A.5
Foster, J.M.6
Griss, J.7
Alpi, E.8
Birim, M.9
Contell, J.10
-
13
-
-
84860856503
-
PASSEL: The PeptideAtlas SRM experiment library
-
Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z., Campbell, D. S., Mendoza, L., Kusebauch, U., Brusniak, M. Y., Hüttenhain, R., Schiess, R. et al. (2012) PASSEL: the PeptideAtlas SRM experiment library. Proteomics. 12, 1170-1175.
-
(2012)
Proteomics
, vol.12
, pp. 1170-1175
-
-
Farrah, T.1
Deutsch, E.W.2
Kreisberg, R.3
Sun, Z.4
Campbell, D.S.5
Mendoza, L.6
Kusebauch, U.7
Brusniak, M.Y.8
Hüttenhain, R.9
Schiess, R.10
-
14
-
-
84906540969
-
Expert curation in UniProtKB: A case study on dealing with conflicting and erroneous data
-
Poux, S., Magrane, M., Arighi, C. N., Bridge, A., O'Donovan, C. and Laiho, K. (2014) Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford), bau016.
-
(2014)
Database (Oxford)
, pp. bau016
-
-
Poux, S.1
Magrane, M.2
Arighi, C.N.3
Bridge, A.4
O'Donovan, C.5
Laiho, K.6
-
15
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
Schnoes, A. M., Brown, S. D., Dodevski, I. and Babbitt, P. C. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000605
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
16
-
-
51349115095
-
Big data: The future of biocuration
-
Howe, D., Costanzo, M., Fey, P., Gojobori, T., Hannick, L., Hide, W., Hill, D. P., Kania, R., Schaeffer, M., St Pierre, S. et al. (2008) Big data: the future of biocuration. Nature, 455, 47-50.
-
(2008)
Nature
, vol.455
, pp. 47-50
-
-
Howe, D.1
Costanzo, M.2
Fey, P.3
Gojobori, T.4
Hannick, L.5
Hide, W.6
Hill, D.P.7
Kania, R.8
Schaeffer, M.9
St Pierre, S.10
-
17
-
-
84862266214
-
Biocurators and biocuration: Surveying the 21st century challenges
-
Burge, S., Attwood, T. K., Bateman, A., Berardini, T. Z., Cherry, M., O'Donovan, C., Xenarios, L. and Gaudet, P. (2012) Biocurators and biocuration: surveying the 21st century challenges. Database (Oxford), bar059.
-
(2012)
Database (Oxford)
, pp. bar059
-
-
Burge, S.1
Attwood, T.K.2
Bateman, A.3
Berardini, T.Z.4
Cherry, M.5
O'Donovan, C.6
Xenarios, L.7
Gaudet, P.8
-
18
-
-
84904406947
-
Genetic variations and diseases in UniProtKB/Swiss-Prot: The ins and outs of expert manual curation
-
Famiglietti, M. L., Estreicher, A., Gos, A., Bolleman, J., Géhant, S., Breuza, L., Bridge, A., Poux, S., Redaschi, N., Bougueleret, L. et al. (2014) Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. Hum. Mutat., 35, 927-935.
-
(2014)
Hum. Mutat.
, vol.35
, pp. 927-935
-
-
Famiglietti, M.L.1
Estreicher, A.2
Gos, A.3
Bolleman, J.4
Géhant, S.5
Breuza, L.6
Bridge, A.7
Poux, S.8
Redaschi, N.9
Bougueleret, L.10
-
19
-
-
84946735654
-
Gene Ontology Consortium: Going forward
-
Gene Ontology Consortium. (2014) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D1049-D1056
-
-
Gene Ontology Consortium1
-
20
-
-
84941097826
-
Updates in Rhea-a manually curated resource of biochemical reactions
-
Morgat, A., Axelsen, K. B., Lombardot, T., Alcántara, R., Aimo, L., Zerara, M., Niknejad, A., Belda, E., Hyka-Nouspikel, N., Coudert, E. et al. (2015) Updates in Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Res., 43, D459-D464.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D459-D464
-
-
Morgat, A.1
Axelsen, K.B.2
Lombardot, T.3
Alcántara, R.4
Aimo, L.5
Zerara, M.6
Niknejad, A.7
Belda, E.8
Hyka-Nouspikel, N.9
Coudert, E.10
-
21
-
-
84876560358
-
The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013
-
Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M. et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res., 41, D456-D463.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D456-D463
-
-
Hastings, J.1
De Matos, P.2
Dekker, A.3
Ennis, M.4
Harsha, B.5
Kale, N.6
Muthukrishnan, V.7
Owen, G.8
Turner, S.9
Williams, M.10
-
22
-
-
84976865354
-
MetaNetX/MNXref - Reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
-
Moretti, S., Martin, O., Van Du Tran, T., Bridge, A., Morgat, A. and Pagni, M. (2016) MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res., doi:10.1093/nar/gkv1117.
-
(2016)
Nucleic Acids Res.
-
-
Moretti, S.1
Martin, O.2
Van Du Tran, T.3
Bridge, A.4
Morgat, A.5
Pagni, M.6
-
23
-
-
84940741482
-
The SwissLipids knowledgebase for lipid biology
-
Aimo, L., Liechti, R., Hyka-Nouspikel, N., Niknejad, A., Gleizes, A., Götz, L., Kuznetsov, D., David, F. P. A., van der Goot, F. G., Riezman, H. et al. (2015) The SwissLipids knowledgebase for lipid biology. Bioinformatics, 31, 2860-2866.
-
(2015)
Bioinformatics
, vol.31
, pp. 2860-2866
-
-
Aimo, L.1
Liechti, R.2
Hyka-Nouspikel, N.3
Niknejad, A.4
Gleizes, A.5
Götz, L.6
Kuznetsov, D.7
David, F.P.A.8
Van Der Goot, F.G.9
Riezman, H.10
-
24
-
-
84897873840
-
Protter: Interactive protein feature visualization and integration with experimental proteomic data
-
Omasits, U., Ahrens, CH, Müller, S. and Wollscheid, B. (2014) Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 30, 884-886.
-
(2014)
Bioinformatics
, vol.30
, pp. 884-886
-
-
Omasits, U.1
Ahrens, C.H.2
Müller, S.3
Wollscheid, B.4
-
25
-
-
84876588470
-
New and continuing developments at PROSITE
-
Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., Bougueleret, L. and Xenarios, I. (2013) New and continuing developments at PROSITE. Nucleic Acids Res., 41, D344-D347.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D344-D347
-
-
Sigrist, C.J.A.1
De Castro, E.2
Cerutti, L.3
Cuche, B.A.4
Hulo, N.5
Bridge, A.6
Bougueleret, L.7
Xenarios, I.8
-
26
-
-
84946030378
-
HAMAP in 2015: Updates to the protein family classification and annotation system
-
Pedruzzi, I., Rivoire, C., Auchincloss, A. H., Coudert, E., Keller, G., de Castro, E., Baratin, D., Cuche, B. A., Bougueleret, L., Poux, S. et al. (2014) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res., 43, D1064-D1070.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D1064-D1070
-
-
Pedruzzi, I.1
Rivoire, C.2
Auchincloss, A.H.3
Coudert, E.4
Keller, G.5
De Castro, E.6
Baratin, D.7
Cuche, B.A.8
Bougueleret, L.9
Poux, S.10
-
27
-
-
84941060754
-
The neXtProt knowledgebase on human proteins: Current status
-
Gaudet, P., Michel, P.-A., Zahn-Zabal, M., Cusin, I., Duek, P. D., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Teixeira, D. et al. (2015) The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res., 43, D764-D770.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D764-D770
-
-
Gaudet, P.1
Michel, P.-A.2
Zahn-Zabal, M.3
Cusin, I.4
Duek, P.D.5
Evalet, O.6
Gateau, A.7
Gleizes, A.8
Pereira, M.9
Teixeira, D.10
-
28
-
-
84941057782
-
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification
-
Omenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Nesvizhskii, A. I. and Deutsch, E. W. (2015) Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J. Proteome Res., 14, 3452-3460.
-
(2015)
J. Proteome Res.
, vol.14
, pp. 3452-3460
-
-
Omenn, G.S.1
Lane, L.2
Lundberg, E.K.3
Beavis, R.C.4
Nesvizhskii, A.I.5
Deutsch, E.W.6
-
29
-
-
84885895986
-
Managing the data deluge: Data-driven GO category assignment improves while complexity of functional annotation increases
-
Gobeill, J., Pasche, E., Vishnyakova, D. and Ruch, P. (2013) Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database (Oxford)., bat041.
-
(2013)
Database (Oxford).
, pp. bat041
-
-
Gobeill, J.1
Pasche, E.2
Vishnyakova, D.3
Ruch, P.4
-
30
-
-
84925547058
-
Closing the loop: From paper to protein annotation using supervised Gene Ontology classification
-
Gobeill, J., Pasche, E., Vishnyakova, D. and Ruch, P. (2014) Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database (Oxford), bau088.
-
(2014)
Database (Oxford)
, pp. bau088
-
-
Gobeill, J.1
Pasche, E.2
Vishnyakova, D.3
Ruch, P.4
-
31
-
-
84891757311
-
EggNOG v4.0: Nested orthology inference across 3686 organisms
-
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M. et al. (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res., 42, D231-D239.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D231-D239
-
-
Powell, S.1
Forslund, K.2
Szklarczyk, D.3
Trachana, K.4
Roth, A.5
Huerta-Cepas, J.6
Gabaldón, T.7
Rattei, T.8
Creevey, C.9
Kuhn, M.10
-
32
-
-
33749137280
-
UniPep-a database for human N-linked glycosites: A resource for biomarker discovery
-
Zhang, H., Loriaux, P., Eng, J., Campbell, D., Keller, A., Moss, P., Bonneau, R., Zhang, N., Zhou, Y., Wollscheid, B. et al. (2006) UniPep-a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol., 7, R73.
-
(2006)
Genome Biol.
, vol.7
, pp. R73
-
-
Zhang, H.1
Loriaux, P.2
Eng, J.3
Campbell, D.4
Keller, A.5
Moss, P.6
Bonneau, R.7
Zhang, N.8
Zhou, Y.9
Wollscheid, B.10
-
33
-
-
33646160614
-
GLYCOSCIENCES.de: An Internet portal to support glycomics and glycobiology research
-
Lütteke, T., Bohne-Lang, A., Loss, A., Goetz, T., Frank, M. and von der Lieth, C. W. (2006) GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology, 16, 71R-81R.
-
(2006)
Glycobiology
, vol.16
, pp. 71R-81R
-
-
Lütteke, T.1
Bohne-Lang, A.2
Loss, A.3
Goetz, T.4
Frank, M.5
Von Der Lieth, C.W.6
-
34
-
-
0037250530
-
GlycoSuiteDB: A curated relational database of glycoprotein glycan structures and their biological sources.2003 update
-
Copper, C. A., Joshi, H. J., Harrison, M. J., Wilkins, M. R. and Packer, N. H. (2003) GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources.2003 update. Nucleic Acids Res., 31, 511-513.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 511-513
-
-
Copper, C.A.1
Joshi, H.J.2
Harrison, M.J.3
Wilkins, M.R.4
Packer, N.H.5
-
35
-
-
84891782475
-
UniCarbKB: Building a knowledge platform for glycoproteomics
-
Campbell, M. P., Peterson, R., Mariethoz, J., Gasteiger, E., Akune, Y., Aoki-Kinoshita, K. F., Lisacek, F. and Packer, N. H. (2014) UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res., 42, D215-D221.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D215-D221
-
-
Campbell, M.P.1
Peterson, R.2
Mariethoz, J.3
Gasteiger, E.4
Akune, Y.5
Aoki-Kinoshita, K.F.6
Lisacek, F.7
Packer, N.H.8
-
36
-
-
84979554509
-
SugarBindDB, a resource of glycan-mediated host-pathogen interactions
-
Mariethoz, J., Khatib, K., Alocci, D., Campbell, M. P., Karlsson, N., Packer, N., Mullen, E. and Lisacek, F. (2016) SugarBindDB, a resource of glycan-mediated host-pathogen interactions. Nucleic Acids Res., doi:10.1093/nar/gkv1247.
-
(2016)
Nucleic Acids Res.
-
-
Mariethoz, J.1
Khatib, K.2
Alocci, D.3
Campbell, M.P.4
Karlsson, N.5
Packer, N.6
Mullen, E.7
Lisacek, F.8
-
37
-
-
84876580265
-
SwissRegulon, a database of genome-wide annotations of regulatory sites: Recent updates
-
Pachkov, M., Balwierz, P. J., Arnold, P., Ozonov, E. and van Nimwegen, E. (2013) SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res., 41, D214-D220.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D214-D220
-
-
Pachkov, M.1
Balwierz, P.J.2
Arnold, P.3
Ozonov, E.4
Van Nimwegen, E.5
-
38
-
-
68849123047
-
Methods for analyzing deep sequencing expression data: Constructing the human and mouse promoterome with deepCAGE data
-
Balwierz, P. J., Carninci, P., Daub, C. O., Kawai, J., Hayashizaki, Y., Van Belle, W., Beisel, C. and van Nimwegen, E. (2009) Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol. 10, R79.
-
(2009)
Genome Biol
, vol.10
, pp. R79
-
-
Balwierz, P.J.1
Carninci, P.2
Daub, C.O.3
Kawai, J.4
Hayashizaki, Y.5
Van Belle, W.6
Beisel, C.7
Van Nimwegen, E.8
-
39
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science. 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
40
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
FANTOM Consortium. (2014) A promoter-level mammalian expression atlas. Nature. 507, 462-470.
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
FANTOM Consortium1
-
41
-
-
84857180279
-
MotEvo: Integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
-
Arnold, P., Erb, I., Pachkov, M., Molina, N. and van Nimwegen, E. (2012) MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics. 28, 487-494.
-
(2012)
Bioinformatics
, vol.28
, pp. 487-494
-
-
Arnold, P.1
Erb, I.2
Pachkov, M.3
Molina, N.4
Van Nimwegen, E.5
-
42
-
-
84943176628
-
The eukaryotic promoter database: Expansion of EPDnew and new promoter analysis tools
-
Dreos, R., Ambrosini, G., Périer, R. C. and Bucher, P. (2015) The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. Nucleic Acids Res., 43, D92-D96.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D92-D96
-
-
Dreos, R.1
Ambrosini, G.2
Périer, R.C.3
Bucher, P.4
-
43
-
-
84862099805
-
ArrayMap: A reference resource for genomic copy number imbalances in human malignancies
-
Cai, H., Kumar, N. and Baudis, M. (2012) arrayMap: a reference resource for genomic copy number imbalances in human malignancies. PLoS One, 7, e36944.
-
(2012)
PLoS One
, vol.7
, pp. e36944
-
-
Cai, H.1
Kumar, N.2
Baudis, M.3
-
44
-
-
76649139789
-
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation
-
Tsou, C.-C., Tsai, C.-F., Tsui, Y.-H., Sudhir, P.-R., Wang, Y.-T., Chen, Y.-J., Chen, J.-Y., Sung, T.-Y. and Hsu, W.-L. (2010) IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol. Cell. Proteomics, 9, 131-144.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 131-144
-
-
Tsou, C.-C.1
Tsai, C.-F.2
Tsui, Y.-H.3
Sudhir, P.-R.4
Wang, Y.-T.5
Chen, Y.-J.6
Chen, J.-Y.7
Sung, T.-Y.8
Hsu, W.-L.9
-
45
-
-
0037246058
-
ArrayExpress-a public repository for microarray gene expression data at the EBI
-
Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G. et al. (2003) ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68-71.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 68-71
-
-
Brazma, A.1
Parkinson, H.2
Sarkans, U.3
Shojatalab, M.4
Vilo, J.5
Abeygunawardena, N.6
Holloway, E.7
Kapushesky, M.8
Kemmeren, P.9
Lara, G.G.10
-
46
-
-
84891751110
-
Progenetix: 12 years of oncogenomic data curation
-
Cai, H., Kumar, N., Ai, N., Gupta, S., Rath, P. and Baudis, M. (2014) Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res., 42, D1055-D1062.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1055-D1062
-
-
Cai, H.1
Kumar, N.2
Ai, N.3
Gupta, S.4
Rath, P.5
Baudis, M.6
-
47
-
-
48249136251
-
Bgee: Integrating and comparing heterogeneous transcriptome data among species
-
Bairoch, A, Cohen-Boulakia, S and Froidevaux, C eds
-
Bastian, F., Parmentier, G., Roux, J., Moretti, S., Laudet, V. and Robinson-Rechavi, M. (2008) Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. In: Bairoch, A, Cohen-Boulakia, S and Froidevaux, C (eds). Data Integr. Life Sci. Vol. 5109, pp. 124-131.
-
(2008)
Data Integr. Life Sci
, vol.5109
, pp. 124-131
-
-
Bastian, F.1
Parmentier, G.2
Roux, J.3
Moretti, S.4
Laudet, V.5
Robinson-Rechavi, M.6
-
48
-
-
84909599499
-
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
-
Haendel, M. A., Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. A., Bradford, Y., Comte, A., Dahdul, W. M., Dececchi, T. A., Druzinsky, R. E. et al. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semantics, 5, 21.
-
(2014)
J. Biomed. Semantics
, vol.5
, pp. 21
-
-
Haendel, M.A.1
Balhoff, J.P.2
Bastian, F.B.3
Blackburn, D.C.4
Blake, J.A.5
Bradford, Y.6
Comte, A.7
Dahdul, W.M.8
Dececchi, T.A.9
Druzinsky, R.E.10
-
49
-
-
84900819430
-
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
-
Rosikiewicz, M. and Robinson-Rechavi, M. (2014) IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics, 30, 1392-1399.
-
(2014)
Bioinformatics
, vol.30
, pp. 1392-1399
-
-
Rosikiewicz, M.1
Robinson-Rechavi, M.2
-
50
-
-
84879356063
-
Uncovering hidden duplicated content in public transcriptomics data
-
Rosikiewicz, M., Comte, A., Niknejad, A., Robinson-Rechavi, M. and Bastian, F. B. (2013) Uncovering hidden duplicated content in public transcriptomics data. Database (Oxford), bat010.
-
(2013)
Database (Oxford)
, pp. bat010
-
-
Rosikiewicz, M.1
Comte, A.2
Niknejad, A.3
Robinson-Rechavi, M.4
Bastian, F.B.5
-
51
-
-
84943194552
-
The Confidence Information Ontology: A step towards a standard for asserting confidence in annotations
-
Bastian, F. B., Chibucos, M. C., Gaudet, P., Giglio, M., Holliday, G. L., Huang, H., Lewis, S. E., Niknejad, A., Orchard, S., Poux, S. et al. (2015) The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford)., bav043.
-
(2015)
Database (Oxford).
, pp. bav043
-
-
Bastian, F.B.1
Chibucos, M.C.2
Gaudet, P.3
Giglio, M.4
Holliday, G.L.5
Huang, H.6
Lewis, S.E.7
Niknejad, A.8
Orchard, S.9
Poux, S.10
-
52
-
-
61449229355
-
Protein structure homology modeling using SWISS-MODEL workspace
-
Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J. and Schwede, T. (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protoc., 4, 1-13.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 1-13
-
-
Bordoli, L.1
Kiefer, F.2
Arnold, K.3
Benkert, P.4
Battey, J.5
Schwede, T.6
-
53
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
54
-
-
69249212321
-
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
-
Guex, N., Peitsch, M. C. and Schwede, T. (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis, 30, S162-S173.
-
(2009)
Electrophoresis
, vol.30
, pp. S162-S173
-
-
Guex, N.1
Peitsch, M.C.2
Schwede, T.3
-
55
-
-
0034096904
-
Protein structure computing in the genomic era
-
Schwede, T., Diemand, A., Guex, N. and Peitsch, MC (2000) Protein structure computing in the genomic era. Res. Microbiol., 151, 107-112.
-
(2000)
Res. Microbiol.
, vol.151
, pp. 107-112
-
-
Schwede, T.1
Diemand, A.2
Guex, N.3
Peitsch, M.C.4
-
56
-
-
84883481556
-
The Protein Model Portal-a comprehensive resource for protein structure and model information
-
Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L. and Schwede, T. (2013) The Protein Model Portal-a comprehensive resource for protein structure and model information. Database (Oxford), bat031.
-
(2013)
Database (Oxford)
, pp. bat031
-
-
Haas, J.1
Roth, S.2
Arnold, K.3
Kiefer, F.4
Schmidt, T.5
Bordoli, L.6
Schwede, T.7
-
57
-
-
80054042695
-
The Structural Biology Knowledgebase: A portal to protein structures, sequences, functions, and methods
-
Gabanyi, M. J., Adams, P. D., Arnold, K., Bordoli, L., Carter, L. G., Flippen-Andersen, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W. A. et al. (2011) The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J. Struct. Funct. Genomics, 12, 45-54.
-
(2011)
J. Struct. Funct. Genomics
, vol.12
, pp. 45-54
-
-
Gabanyi, M.J.1
Adams, P.D.2
Arnold, K.3
Bordoli, L.4
Carter, L.G.5
Flippen-Andersen, J.6
Gifford, L.7
Haas, J.8
Kouranov, A.9
McLaughlin, W.A.10
-
58
-
-
84929576044
-
The Protein Data Bank archive as an open data resource
-
Berman, H. M., Kleywegt, G. J., Nakamura, H. and Markley, J. L. (2014) The Protein Data Bank archive as an open data resource. J. Comput. Aided. Mol. Des., 28, 1009-1014.
-
(2014)
J. Comput. Aided. Mol. Des.
, vol.28
, pp. 1009-1014
-
-
Berman, H.M.1
Kleywegt, G.J.2
Nakamura, H.3
Markley, J.L.4
-
59
-
-
59849107733
-
Outcome of a workshop on applications of protein models in biomedical research
-
Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H. M., Jones, D., Brenner, S. E., Burley, S. K., Das, R., Dokholyan, N. V. et al. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure, 17, 151-159.
-
(2009)
Structure
, vol.17
, pp. 151-159
-
-
Schwede, T.1
Sali, A.2
Honig, B.3
Levitt, M.4
Berman, H.M.5
Jones, D.6
Brenner, S.E.7
Burley, S.K.8
Das, R.9
Dokholyan, N.V.10
-
60
-
-
74249088516
-
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
-
Benkert, P., Tosatto, S. C. and Schwede, T. (2009) Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins, 77, 173-180.
-
(2009)
Proteins
, vol.77
, pp. 173-180
-
-
Benkert, P.1
Tosatto, S.C.2
Schwede, T.3
-
61
-
-
84907026703
-
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)
-
Studer, G., Biasini, M. and Schwede, T. (2014) Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics, 30, i505-i511
-
(2014)
Bioinformatics
, vol.30
, pp. i505-i511
-
-
Studer, G.1
Biasini, M.2
Schwede, T.3
-
62
-
-
84876588234
-
SwissSidechain: A molecular and structural database of non-natural sidechains
-
Gfeller, D., Michielin, O. and Zoete, V. (2013) SwissSidechain: a molecular and structural database of non-natural sidechains. Nucleic Acids Res., 41, D327-D332.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D327-D332
-
-
Gfeller, D.1
Michielin, O.2
Zoete, V.3
-
63
-
-
84861818648
-
Expanding molecular modeling and design tools to non-natural sidechains
-
Gfeller, D., Michielin, O. and Zoete, V. (2012) Expanding molecular modeling and design tools to non-natural sidechains. J. Comput. Chem., 33, 1525-1535.
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1525-1535
-
-
Gfeller, D.1
Michielin, O.2
Zoete, V.3
-
64
-
-
84875459673
-
SwissBioisostere: A database of molecular replacements for ligand design
-
Wirth, M., Zoete, V., Michielin, O. and Sauer, W. H. B. (2013) SwissBioisostere: a database of molecular replacements for ligand design. Nucleic Acids Res., 41, D1137-D1143.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1137-D1143
-
-
Wirth, M.1
Zoete, V.2
Michielin, O.3
Sauer, W.H.B.4
-
65
-
-
84919622603
-
ILOGP: A simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach
-
Daina, A., Michielin, O. and Zoete, V. (2014) iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. J. Chem. Inf. Model., 54, 3284-3301.
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 3284-3301
-
-
Daina, A.1
Michielin, O.2
Zoete, V.3
-
66
-
-
84904793576
-
SwissTargetPrediction: A web server for target prediction of bioactive small molecules
-
Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O. and Zoete, V. (2014) SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res., 42, W32-W38.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W32-W38
-
-
Gfeller, D.1
Grosdidier, A.2
Wirth, M.3
Daina, A.4
Michielin, O.5
Zoete, V.6
-
67
-
-
84890023718
-
Shaping the interaction landscape of bioactive molecules
-
Gfeller, D., Michielin, O. and Zoete, V. (2013) Shaping the interaction landscape of bioactive molecules. Bioinformatics, 29, 3073-3079.
-
(2013)
Bioinformatics
, vol.29
, pp. 3073-3079
-
-
Gfeller, D.1
Michielin, O.2
Zoete, V.3
-
68
-
-
84939488957
-
Protein homology reveals new targets for bioactive small molecules
-
Gfeller, D. and Zoete, V. (2015) Protein homology reveals new targets for bioactive small molecules. Bioinformatics, 31, 2721-2727.
-
(2015)
Bioinformatics
, vol.31
, pp. 2721-2727
-
-
Gfeller, D.1
Zoete, V.2
-
69
-
-
84946068839
-
The OMA orthology database in 2015: Function predictions, better plant support, synteny view and other improvements
-
Altenhoff, A. M., Škunca, N., Glover, N., Train, C.-M., Sueki, A., Piližota, I., Gori, K., Tomiczek, B., Müller, S., Redestig, H. et al. (2015) The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res., 43, D240-D249.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D240-D249
-
-
Altenhoff, A.M.1
Škunca, N.2
Glover, N.3
Train, C.-M.4
Sueki, A.5
Piližota, I.6
Gori, K.7
Tomiczek, B.8
Müller, S.9
Redestig, H.10
-
70
-
-
84876566349
-
OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs
-
Waterhouse, R. M., Tegenfeldt, F., Li, J., Zdobnov, E. M. and Kriventseva, E. V (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res., 41, D358-D365.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D358-D365
-
-
Waterhouse, R.M.1
Tegenfeldt, F.2
Li, J.3
Zdobnov, E.M.4
Kriventseva, E.V.5
-
71
-
-
84858602406
-
InterPro in 2011: New developments in the family and domain prediction database
-
Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, 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
, pp. D306-D312
-
-
Hunter, S.1
Jones, P.2
Mitchell, A.3
Apweiler, R.4
Attwood, T.K.5
Bateman, A.6
Bernard, T.7
Binns, D.8
Bork, P.9
Burge, S.10
-
72
-
-
84946081339
-
OMIM.org: Online Mendelian Inheritance in Man (OMIMR ®), 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 (OMIMR ®), 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
-
73
-
-
84940907209
-
BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
-
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. and Zdobnov, E. M. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212.
-
(2015)
Bioinformatics
, vol.31
, pp. 3210-3212
-
-
Simão, F.A.1
Waterhouse, R.M.2
Ioannidis, P.3
Kriventseva, E.V.4
Zdobnov, E.M.5
-
74
-
-
84880039886
-
A robust second-generation genome-wide test for fetal aneuploidy based on shotgun sequencing cell-free DNA in maternal blood
-
Guex, N., Iseli, C., Syngelaki, A., Deluen, C., Pescia, G., Nicolaides, K. H., Xenarios, I. and Conrad, B. (2013) A robust second-generation genome-wide test for fetal aneuploidy based on shotgun sequencing cell-free DNA in maternal blood. Prenat. Diagn., 33, 707-710.
-
(2013)
Prenat. Diagn.
, vol.33
, pp. 707-710
-
-
Guex, N.1
Iseli, C.2
Syngelaki, A.3
Deluen, C.4
Pescia, G.5
Nicolaides, K.H.6
Xenarios, I.7
Conrad, B.8
|