-
1
-
-
27744523967
-
The next generation of literature analysis: Integration of genomic analysis into text mining
-
Scherf M, Epple A, Werner T. The next generation of literature analysis: integration of genomic analysis into text mining. Brief Bioinform 2005;6:287-97.
-
(2005)
Brief Bioinform
, vol.6
, pp. 287-297
-
-
Scherf, M.1
Epple, A.2
Werner, T.3
-
2
-
-
0036678776
-
Tagging gene and protein names in biomedical text
-
Tanabe L, Wilbur WJ. Tagging gene and protein names in biomedical text. Bioinformatics 2002;18:1124-32.
-
(2002)
Bioinformatics
, vol.18
, pp. 1124-1132
-
-
Tanabe, L.1
Wilbur, W.J.2
-
3
-
-
3943087720
-
Analyzing cellular biochemistry in terms of molecular networks
-
Xia Y, Yu H, Jansen R, et al. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 2004;73:1051-87.
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 1051-1087
-
-
Xia, Y.1
Yu, H.2
Jansen, R.3
-
4
-
-
17244380380
-
A survey of current work in biomedical text mining
-
Cohen AM, Hersh WR. A survey of current work in biomedical text mining. Brief Bioinform 2005;6:57-71.
-
(2005)
Brief Bioinform
, vol.6
, pp. 57-71
-
-
Cohen, A.M.1
Hersh, W.R.2
-
5
-
-
33645841072
-
Status of textmining techniques applied to biomedical text
-
Erhardt RA, Schneider R, Blaschke C. Status of textmining techniques applied to biomedical text. Drug Discov Today 2006;11:315-25.
-
(2006)
Drug Discov Today
, vol.11
, pp. 315-325
-
-
Erhardt, R.A.1
Schneider, R.2
Blaschke, C.3
-
6
-
-
0038290170
-
Systems biology
-
Henry CM. Systems biology. Chem Eng News 2003;81:45-55.
-
(2003)
Chem Eng News
, vol.81
, pp. 45-55
-
-
Henry, C.M.1
-
8
-
-
33646362551
-
Systematic identification of human mitochondrial disease genes through integrative genomics
-
Epub 2 April 2006
-
Calvo S, Jain M, Xie X, et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 2006; Epub 2 April 2006.
-
(2006)
Nat Genet
-
-
Calvo, S.1
Jain, M.2
Xie, X.3
-
9
-
-
28444498336
-
A data integration methodology for systems biology: Experimental verification
-
Epub 21 November 2005
-
Hwang D, Smith JJ, Leslie DM, et al. A data integration methodology for systems biology: Experimental verification. Proc Natl Acad Sci USA 2005; Epub 21 November 2005.
-
(2005)
Proc Natl Acad Sci USA
-
-
Hwang, D.1
Smith, J.J.2
Leslie, D.M.3
-
10
-
-
22144461265
-
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
-
Epub 28 January 2005
-
Choe SE, Boutros M, Michelson AM, et al. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005; Epub 28 January 2005.
-
(2005)
Genome Biol
-
-
Choe, S.E.1
Boutros, M.2
Michelson, A.M.3
-
11
-
-
4644306020
-
Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction
-
Jansen R, Gerstein M. Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol 2004;7:535-45.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 535-545
-
-
Jansen, R.1
Gerstein, M.2
-
12
-
-
14844329372
-
Ranking the whole MEDLINE database according to a large training set using text indexing
-
Suomela BP, Andrade MA. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinform 2005;6:75.
-
(2005)
BMC Bioinform
, vol.6
, pp. 75
-
-
Suomela, B.P.1
Andrade, M.A.2
-
13
-
-
33644861218
-
BioContrasts: Extracting and exploiting protein-protein contrastive relations from biomedical literature
-
Epub 20 December 2005
-
Kim JJ, Zhang Z, Park JC, et al. BioContrasts: Extracting and exploiting protein-protein contrastive relations from biomedical literature. Bioinformatics 2006; Epub 20 December 2005.
-
(2006)
Bioinformatics
-
-
Kim, J.J.1
Zhang, Z.2
Park, J.C.3
-
14
-
-
33748864015
-
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease
-
Masseroli M, Kilicoglu H, Lang FM, et al. Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinformatics 2006;7:291.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 291
-
-
Masseroli, M.1
Kilicoglu, H.2
Lang, F.M.3
-
15
-
-
33845436494
-
Survey of Ontologies in Bioinformatics
-
In: Baclawski K, Niu T, (eds). MIT Press
-
Survey of Ontologies in Bioinformatics. In: Baclawski K, Niu T, (eds). Ontologies for Bioinformatics. MIT Press, 2005.
-
(2005)
Ontologies for Bioinformatics
-
-
-
16
-
-
33344468105
-
Lexical, Terminological, and Ontological Resources for Biological Text Mining
-
In: Ananiadou S, McNaught J, (eds). Boston: Artech House
-
Bodenreider O. Lexical, Terminological, and Ontological Resources for Biological Text Mining. In: Ananiadou S, McNaught J, (eds). Text Mining for Biology and Biomedicine. Boston: Artech House, 2006.
-
(2006)
Text Mining for Biology and Biomedicine
-
-
Bodenreider, O.1
-
17
-
-
6344276917
-
Mining MEDLINE for implicit links between dietary substances and diseases
-
Srinivasan P, Libbus B. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 2004;4:I290-6.
-
(2004)
Bioinformatics
, vol.4
-
-
Srinivasan, P.1
Libbus, B.2
-
18
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen TK, Laegreid A, Komorowski J, et al. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001;28:21-8.
-
(2001)
Nat Genet
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
Laegreid, A.2
Komorowski, J.3
-
19
-
-
26444609693
-
Searching the MEDLINE literature database through PubMed: A short guide
-
Epub 19 August 2005
-
Motschall E, Falck-Ytter Y. Searching the MEDLINE literature database through PubMed: A short guide. Onkologie 2005; Epub 19 August 2005.
-
(2005)
Onkologie
-
-
Motschall, E.1
Falck-Ytter, Y.2
-
20
-
-
33645757566
-
Searching the literature using medical subject headings versus text word with PubMed
-
Chang AA, Heskett KM, Davidson TM. Searching the literature using medical subject headings versus text word with PubMed. Laryngoscope 2006;116:336-40.
-
(2006)
Laryngoscope
, vol.116
, pp. 336-340
-
-
Chang, A.A.1
Heskett, K.M.2
Davidson, T.M.3
-
21
-
-
84860501618
-
A procedure for assessing GO annotation consistency
-
Dolan ME, Ni L, Camon E, et al. A procedure for assessing GO annotation consistency. Bioinformatics 2005;21:I136-43.
-
(2005)
Bioinformatics
, vol.21
-
-
Dolan, M.E.1
Ni, L.2
Camon, E.3
-
22
-
-
33644875286
-
The Gene Ontology (GO) project in 2006
-
The Gene Ontology (GO) project in 2006. Nucleic Acids Res 2006;34:D322-6.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
-
23
-
-
0034069495
-
Gene ontology: Tool for the unification of biology The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
24
-
-
0345863927
-
The Unified Medical Language System (UMLS): Integrating biomedical terminology
-
Bodenreider O. The Unified Medical Language System (UMLS): Integrating biomedical terminology. Nucleic Acids Res 2004;32:D267-70.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bodenreider, O.1
-
26
-
-
13444256580
-
Gene name ambiguity of eukaryotic nomenclatures
-
Epub 27 August 2004
-
Chen L, Liu H, Friedman C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 2005; Epub 27 August 2004.
-
(2005)
Bioinformatics
-
-
Chen, L.1
Liu, H.2
Friedman, C.3
-
27
-
-
33745090479
-
The success (or not) of HUGO nomenclature
-
Tamames J, Valencia A. The success (or not) of HUGO nomenclature. Genome Biol 2006;7:402.
-
(2006)
Genome Biol
, vol.7
, pp. 402
-
-
Tamames, J.1
Valencia, A.2
-
28
-
-
25444514478
-
Building a protein name dictionary from full text: A machine learning term extraction approach
-
Shi L, Campagne F. Building a protein name dictionary from full text: A machine learning term extraction approach. BMC Bioinform 2005;6:88.
-
(2005)
BMC Bioinform
, vol.6
, pp. 88
-
-
Shi, L.1
Campagne, F.2
-
29
-
-
1342330525
-
Knowledge discovery by automated identification and ranking of implicit relationships
-
Wren JD, Bekeredjian R, Stewart JA, et al. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 2004;20:389-98.
-
(2004)
Bioinformatics
, vol.20
, pp. 389-398
-
-
Wren, J.D.1
Bekeredjian, R.2
Stewart, J.A.3
-
30
-
-
33344465511
-
Biomedical language processing: What's beyond PubMed?
-
Hunter L, Cohen KB. Biomedical language processing: What's beyond PubMed? Mol Cell 2006;21:589-94.
-
(2006)
Mol Cell
, vol.21
, pp. 589-594
-
-
Hunter, L.1
Cohen, K.B.2
-
31
-
-
33845442570
-
Evaluation of BioCreAtIvE assessment of task 2
-
Epub 24 May 2005
-
Blaschke C, Leon EA, Krallinger M, et al. Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinform 2005; Epub 24 May 2005.
-
(2005)
BMC Bioinform
-
-
Blaschke, C.1
Leon, E.A.2
Krallinger, M.3
-
32
-
-
33644873213
-
The Universal Protein Resource (UniProt): An expanding universe of protein information
-
Wu CH, Apweiler R, Bairoch A, et al. The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res 2006;34:D187-91.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wu, C.H.1
Apweiler, R.2
Bairoch, A.3
-
33
-
-
33644876253
-
Database resources of the National Center for Biotechnology Information
-
Wheeler DL, Barrett T, Benson DA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2006;34:D173-80.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
-
34
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi TK, Zhong J, Mathivanan S, et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006;38:285-93.
-
(2006)
Nat Genet
, vol.38
, pp. 285-293
-
-
Gandhi, T.K.1
Zhong, J.2
Mathivanan, S.3
-
35
-
-
27144530248
-
Towards a proteomescale map of the human protein-protein interaction network
-
Epub 28 September 2005
-
Rual JF, Venkatesan K, Hao T, et al. Towards a proteomescale map of the human protein-protein interaction network. Nature 2005; Epub 28 September 2005.
-
(2005)
Nature
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
-
36
-
-
33645499146
-
Disentangling information flow in the Ras-cAMP signaling network
-
Epub 13 March 2006
-
Carter GW, Rupp S, Fink GR, et al. Disentangling information flow in the Ras-cAMP signaling network. Genome Res 2006; Epub 13 March 2006.
-
(2006)
Genome Res
-
-
Carter, G.W.1
Rupp, S.2
Fink, G.R.3
-
37
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
Forster J, Famili I, Fu P, et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003;13:244-53.
-
(2003)
Genome Res
, vol.13
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
-
38
-
-
10744231500
-
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network
-
Tewari M, Hu PJ, Ahn JS, et al. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 2004;13:469-82.
-
(2004)
Mol Cell
, vol.13
, pp. 469-482
-
-
Tewari, M.1
Hu, P.J.2
Ahn, J.S.3
-
39
-
-
33646036758
-
The response of human epithelial cells to TNF involves an inducible autocrine cascade
-
Janes KA, Gaudet S, Albeck JG, et al. The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 2006;124:1225-39.
-
(2006)
Cell
, vol.124
, pp. 1225-1239
-
-
Janes, K.A.1
Gaudet, S.2
Albeck, J.G.3
-
40
-
-
23844494458
-
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
-
Gunsalus KC, Ge H, Schetter AJ, et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 2005;436:861-5.
-
(2005)
Nature
, vol.436
, pp. 861-865
-
-
Gunsalus, K.C.1
Ge, H.2
Schetter, A.J.3
-
41
-
-
2942549190
-
PreBIND and Textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine
-
Epub 27 March 2003
-
Donaldson I, Martin J, de Bruijn B, et al. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics 2003; Epub 27 March 2003.
-
(2003)
BMC Bioinformatics
-
-
Donaldson, I.1
Martin, J.2
de Bruijn, B.3
-
42
-
-
19644392942
-
Cognitive psychology: Rare items often missed in visual searches
-
Wolfe JM, Horowitz TS, Kenner NM. Cognitive psychology: Rare items often missed in visual searches. Nature 2005;435:439-40.
-
(2005)
Nature
, vol.435
, pp. 439-440
-
-
Wolfe, J.M.1
Horowitz, T.S.2
Kenner, N.M.3
-
43
-
-
3342901682
-
Finding kinetic parameters using text mining
-
Hakenberg J, Schmeier S, Kowald A, et al. Finding kinetic parameters using text mining. Omics 2004;8:131-52.
-
(2004)
Omics
, vol.8
, pp. 131-152
-
-
Hakenberg, J.1
Schmeier, S.2
Kowald, A.3
-
45
-
-
33646547951
-
Systems biology approaches identify ATF3 as a negative regulator of Tolllike receptor 4
-
Gilchrist M, Thorsson V, Li B, et al. Systems biology approaches identify ATF3 as a negative regulator of Tolllike receptor 4. Nature 2006;441:173-8.
-
(2006)
Nature
, vol.441
, pp. 173-178
-
-
Gilchrist, M.1
Thorsson, V.2
Li, B.3
-
46
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Epub 22 January 2006
-
Gavin AC, Aloy P, Grandi P, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006; Epub 22 January 2006.
-
(2006)
Nature
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
-
47
-
-
20144388686
-
Ontology-based interactive information extraction from scientific abstracts
-
Milward D, Bjreland M, Hayes W, et al. Ontology-based interactive information extraction from scientific abstracts. Comp Funct Genom 2005;6:67-71.
-
(2005)
Comp Funct Genom
, vol.6
, pp. 67-71
-
-
Milward, D.1
Bjreland, M.2
Hayes, W.3
-
48
-
-
32444441664
-
Mining chemical structural information from the drug literature
-
Banville DL. Mining chemical structural information from the drug literature. Drug DiscovToday 2006;11:35-42.
-
(2006)
Drug DiscovToday
, vol.11
, pp. 35-42
-
-
Banville, D.L.1
-
49
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Epub 11 September 2003
-
Tatusov RL, Fedorova ND, Jackson JD, et al. The COG database: An updated version includes eukaryotes. BMC Bioinform 2003; Epub 11 September 2003.
-
(2003)
BMC Bioinform
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
-
50
-
-
13444266370
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:D514-7.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
-
51
-
-
33644877896
-
The Mouse Functional Genome Database (MfunGD): Functional annotation of proteins in the light of their cellular context
-
Ruepp A, Doudieu ON, van den Oever J, et al. The Mouse Functional Genome Database (MfunGD): Functional annotation of proteins in the light of their cellular context. Nucleic Acids Res 2006;34:D568-71.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ruepp, A.1
Doudieu, O.N.2
van den Oever, J.3
-
52
-
-
33646748283
-
A systems approach to mapping DNA damage response pathways
-
Workman CT, Mak HC, McCuine S, et al. A systems approach to mapping DNA damage response pathways. Science 2006;312:1054-9.
-
(2006)
Science
, vol.312
, pp. 1054-1059
-
-
Workman, C.T.1
Mak, H.C.2
McCuine, S.3
-
53
-
-
27144517984
-
Interlinked fast and slow positive feedback loops drive reliable cell decisions
-
Brandman O, Ferrell JE, Jr, Li R, et al. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 2005;310:496-8.
-
(2005)
Science
, vol.310
, pp. 496-498
-
-
Brandman, O.1
Ferrell Jr., J.E.2
Li, R.3
-
54
-
-
26944476331
-
Regulated cell-to-cell variation in a cell-fate decision system
-
Epub 18 September 2005
-
Colman-Lerner A, Gordon A, Serra E, et al. Regulated cell-to-cell variation in a cell-fate decision system. Nature 2005; Epub 18 September 2005.
-
(2005)
Nature
-
-
Colman-Lerner, A.1
Gordon, A.2
Serra, E.3
-
55
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
Epub 27 Febuary 2005
-
Xie X, Lu J, Kulbokas EJ, et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005; Epub 27 Febuary 2005.
-
(2005)
Nature
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
-
56
-
-
33646679140
-
Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays
-
Stiffler MA, Grantcharova VP, Sevecka M, et al. Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays. J Am Chem Soc 2006;128:5913-22.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 5913-5922
-
-
Stiffler, M.A.1
Grantcharova, V.P.2
Sevecka, M.3
-
57
-
-
27644496624
-
A compendium of signals and responses triggered by prodeath and prosurvival cytokines
-
Epub 18 July 2005
-
Gaudet S, Janes KA, Albeck JG, et al. A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics 2005; Epub 18 July 2005.
-
(2005)
Mol Cell Proteomics
-
-
Gaudet, S.1
Janes, K.A.2
Albeck, J.G.3
-
58
-
-
31444432847
-
The influence of the signal dynamics of activated form of IKK on NF-kappaB and anti-apoptotic gene expressions: A systems biology approach
-
Epub 9 January 2006
-
Park SG, Lee T, Kang HY, et al. The influence of the signal dynamics of activated form of IKK on NF-kappaB and anti-apoptotic gene expressions: a systems biology approach. FEBS Lett 2006; Epub 9 January 2006.
-
(2006)
FEBS Lett
-
-
Park, S.G.1
Lee, T.2
Kang, H.Y.3
-
59
-
-
33645784376
-
An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
-
Estrada B, Choe SE, Gisselbrecht SS, et al. An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes. PLoS Genet 2006;2:e16.
-
(2006)
PLoS Genet
, vol.2
-
-
Estrada, B.1
Choe, S.E.2
Gisselbrecht, S.S.3
-
60
-
-
12144289400
-
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway
-
Epub 25 January 2004
-
Bouwmeester T, Bauch A, Ruffner H, et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 2004; Epub 25 January 2004.
-
(2004)
Nat Cell Biol
-
-
Bouwmeester, T.1
Bauch, A.2
Ruffner, H.3
-
61
-
-
0036923370
-
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping
-
Begley TJ, Rosenbach AS, Ideker T, et al. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res 2002;1:103-12.
-
(2002)
Mol Cancer Res
, vol.1
, pp. 103-112
-
-
Begley, T.J.1
Rosenbach, A.S.2
Ideker, T.3
|