-
1
-
-
31144432293
-
Literature mining for the biologist: From information retrieval to biological discovery
-
10.1038/nrg1768 16418747
-
Jensen LJ Saric J Bork P Literature mining for the biologist: From information retrieval to biological discovery Nat Rev Genet 2006, 7(2):119-129 10.1038/nrg1768 16418747
-
(2006)
Nat Rev Genet
, vol.7
, Issue.2
, pp. 119-129
-
-
Jensen, L.J.1
Saric, J.2
Bork, P.3
-
2
-
-
0038017587
-
Mining microarray expression data by literature profiling
-
RESEARCH0055 134484 12372143 10.1186/gb-2002-3-10-research0055
-
Chaussabel D Sher A Mining microarray expression data by literature profiling Genome Biol 2002, 3:10 RESEARCH0055 134484 12372143 10.1186/ gb-2002-3-10-research0055
-
(2002)
Genome Biol
, vol.3
, pp. 10
-
-
Chaussabel, D.1
Sher, A.2
-
3
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
10.1038/88213 11326270
-
Jenssen TK Laegreid A Komorowski J Hovig E A literature network of human genes for high-throughput analysis of gene expression Nat Genet 2001, 28(1):21-28 10.1038/88213 11326270
-
(2001)
Nat Genet
, vol.28
, Issue.1
, pp. 21-28
-
-
Jenssen, T.K.1
Laegreid, A.2
Komorowski, J.3
Hovig, E.4
-
4
-
-
3042786293
-
A gene network for navigating the literature
-
10.1038/ng0704-664 15226743
-
Hoffmann R Valencia A A gene network for navigating the literature Nat Genet 2004, 36(7):664 10.1038/ng0704-664 15226743
-
(2004)
Nat Genet
, vol.36
, Issue.7
, pp. 664
-
-
Hoffmann, R.1
Valencia, A.2
-
5
-
-
25444530343
-
CoPub Mapper: Mining MEDLINE based on search term co-publication
-
1274248 15760478 10.1186/1471-2105-6-51
-
Alako BT Veldhoven A van Baal S Jelier R Verhoeven S Rullmann T Polman J Jenster G CoPub Mapper: Mining MEDLINE based on search term co-publication BMC Bioinformatics 2005, 6(1):51 1274248 15760478 10.1186/ 1471-2105-6-51
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.1
, pp. 51
-
-
Alako, B.T.1
Veldhoven, A.2
van Baal, S.3
Jelier, R.4
Verhoeven, S.5
Rullmann, T.6
Polman, J.7
Jenster, G.8
-
6
-
-
13244251064
-
MILANO - Custom annotation of microarray results using automatic literature searches
-
547913 15661078 10.1186/1471-2105-6-12
-
Rubinstein R Simon I MILANO - custom annotation of microarray results using automatic literature searches BMC Bioinformatics 2005, 6(1):12 547913 15661078 10.1186/1471-2105-6-12
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.1
, pp. 12
-
-
Rubinstein, R.1
Simon, I.2
-
8
-
-
33748669610
-
Constructing biological networks through combined literature mining and microarray analysis: A LMMA approach
-
10.1093/bioinformatics/btl363
-
Li S Wu L Zhang Z Constructing biological networks through combined literature mining and microarray analysis: A LMMA approach Bioinformatics 2006 22 17 2143-2150 10.1093/bioinformatics/btl363 16820422
-
(2006)
Bioinformatics
, vol.22
, pp. 2143-2150
-
-
Li, S.1
Wu, L.2
Zhang, Z.3
-
9
-
-
34547771661
-
Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
-
1940026 17620146 10.1186/1471-2105-8-243
-
Daraselia N Yuryev A Egorov S Mazo I Ispolatov I Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks BMC Bioinformatics 2007, 8(1):243 1940026 17620146 10.1186/ 1471-2105-8-243
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.1
, pp. 243
-
-
Daraselia, N.1
Yuryev, A.2
Egorov, S.3
Mazo, I.4
Ispolatov, I.5
-
10
-
-
34047269282
-
An application of bioinformatics and text mining to the discovery of novel genes related to bone biology
-
10.1016/j.bone.2006.12.067 17320499
-
Gajendran VK Lin JR Fyhrie DP An application of bioinformatics and text mining to the discovery of novel genes related to bone biology Bone 2007, 40(5):1378-1388 10.1016/j.bone.2006.12.067 17320499
-
(2007)
Bone
, vol.40
, Issue.5
, pp. 1378-1388
-
-
Gajendran, V.K.1
Lin, J.R.2
Fyhrie, D.P.3
-
11
-
-
34347334548
-
GeneCite: A Stand-alone Open Source Tool for High-Throughput Literature and Pathway Mining
-
10.1089/omi.2007.4322 17594234
-
Hammamieh R Chakraborty N Wang Y Laing M Liu Z Mulligan J Jett M GeneCite: A Stand-alone Open Source Tool for High-Throughput Literature and Pathway Mining Omics 2007, 11(2):143-151 10.1089/omi.2007.4322 17594234
-
(2007)
Omics
, vol.11
, Issue.2
, pp. 143-151
-
-
Hammamieh, R.1
Chakraborty, N.2
Wang, Y.3
Laing, M.4
Liu, Z.5
Mulligan, J.6
Jett, M.7
-
12
-
-
34548499877
-
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
-
1964768 17683642 10.1186/1471-2105-8-293
-
Rodriguez-Penagos C Salgado H Martinez-Flores I Collado-Vides J Automatic reconstruction of a bacterial regulatory network using Natural Language Processing BMC Bioinformatics 2007, 8:293 1964768 17683642 10.1186/1471-2105-8-293
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 293
-
-
Rodriguez-Penagos, C.1
Salgado, H.2
Martinez-Flores, I.3
Collado-Vides, J.4
-
13
-
-
38449084004
-
Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations
-
2217664 18047707 10.1186/1471-2105-8-S9-S6
-
Kim H Park H Drake BL Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations BMC Bioinformatics 2007, 8(Suppl 9):S6 2217664 18047707 10.1186/1471-2105-8-S9-S6
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 9
-
-
Kim, H.1
Park, H.2
Drake, B.L.3
-
14
-
-
43749110484
-
Extraction of semantic biomedical relations from text using conditional random fields
-
2386138 18433469 10.1186/1471-2105-9-207
-
Bundschus M Dejori M Stetter M Tresp V Kriegel HP Extraction of semantic biomedical relations from text using conditional random fields BMC Bioinformatics 2008, 9(1):207 2386138 18433469 10.1186/1471-2105-9-207
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 207
-
-
Bundschus, M.1
Dejori, M.2
Stetter, M.3
Tresp, V.4
Kriegel, H.P.5
-
15
-
-
84874653629
-
-
PubMed
-
PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
-
-
-
-
16
-
-
84871717384
-
-
Entrez Gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=gene
-
Entrez Gene
-
-
-
17
-
-
84886763843
-
-
Entrez E-Search http://www.ncbi.nlm.nih.gov/entrez/query/static/ esearch_help.html
-
Entrez E-Search
-
-
-
19
-
-
84886754979
-
-
Unigene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
-
Unigene
-
-
-
20
-
-
0037499970
-
MatchMiner: A tool for batch navigation among gene and gene product identifiers
-
154578 12702208 10.1186/gb-2003-4-4-r27
-
Bussey KJ Kane D Sunshine M Narasimhan S Nishizuka S Reinhold WC Zeeberg B Ajay W Weinstein JN MatchMiner: A tool for batch navigation among gene and gene product identifiers Genome Biol 2003, 4(4):R27 154578 12702208 10.1186/gb-2003-4-4-r27
-
(2003)
Genome Biol
, vol.4
, Issue.4
-
-
Bussey, K.J.1
Kane, D.2
Sunshine, M.3
Narasimhan, S.4
Nishizuka, S.5
Reinhold, W.C.6
Zeeberg, B.7
Ajay, W.8
Weinstein, J.N.9
-
21
-
-
84886757499
-
-
MatchMiner http://discover.nci.nih.gov/matchminer/index.jsp
-
MatchMiner
-
-
-
22
-
-
33748656943
-
Gene and protein nomenclature in public databases
-
1560172 16899134 10.1186/1471-2105-7-372
-
Fundel K Zimmer R Gene and protein nomenclature in public databases BMC Bioinformatics 2006, 7:372 1560172 16899134 10.1186/1471-2105-7-372
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 372
-
-
Fundel, K.1
Zimmer, R.2
-
23
-
-
33644946285
-
Various criteria in the evaluation of biomedical named entity recognition
-
1402329 16504116 10.1186/1471-2105-7-92
-
Tsai RT Wu SH Chou WC Lin YC He D Hsiang J Sung TY Hsu WL Various criteria in the evaluation of biomedical named entity recognition BMC Bioinformatics 2006, 7:92 1402329 16504116 10.1186/1471-2105-7-92
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 92
-
-
Tsai, R.T.1
Wu, S.H.2
Chou, W.C.3
Lin, Y.C.4
He, D.5
Hsiang, J.6
Sung, T.Y.7
Hsu, W.L.8
-
24
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
24541 9843981 10.1073/pnas.95.25.14863
-
Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1998, 95(25):14863-14868 24541 9843981 10.1073/pnas.95.25.14863
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
25
-
-
84886758327
-
-
Elsen Lab http://rana.lbl.gov/EisenSoftware.htm
-
Elsen Lab
-
-
-
26
-
-
70349756285
-
-
WinGraphviz http://wingraphviz.sourceforge.net/wingraphviz/
-
WinGraphviz
-
-
-
27
-
-
3142653088
-
Construction of tree models for pathogenesis of nasopharyngeal carcinoma
-
10.1002/gcc.20036 15188453
-
Huang Z Desper R Schaffer AA Yin Z Li X Yao K Construction of tree models for pathogenesis of nasopharyngeal carcinoma Genes Chromosomes Cancer 2004, 40(4):307-315 10.1002/gcc.20036 15188453
-
(2004)
Genes Chromosomes Cancer
, vol.40
, Issue.4
, pp. 307-315
-
-
Huang, Z.1
Desper, R.2
Schaffer, A.A.3
Yin, Z.4
Li, X.5
Yao, K.6
-
28
-
-
0035259439
-
Tree models for dependent copy number changes in bladder cancer
-
11172603
-
Schaffer AA Simon R Desper R Richter J Sauter G Tree models for dependent copy number changes in bladder cancer Int J Oncol 2001, 18(2):349-354 11172603
-
(2001)
Int J Oncol
, vol.18
, Issue.2
, pp. 349-354
-
-
Schaffer, A.A.1
Simon, R.2
Desper, R.3
Richter, J.4
Sauter, G.5
-
29
-
-
41949132878
-
Differential gene expression profile of keloids: A study with cDNA microarray
-
16546734
-
Hu ZF Gao JH Li W Song YB Li CL [Differential gene expression profile of keloids: A study with cDNA microarray] Nan Fang Yi Ke Da Xue Xue Bao 2006, 26(3):308-312 16546734
-
(2006)
Nan Fang Yi Ke Da Xue Xue Bao
, vol.26
, Issue.3
, pp. 308-312
-
-
Hu, Z.F.1
Gao, J.H.2
Li, W.3
Song, Y.B.4
Li, C.L.5
-
30
-
-
33847361673
-
Cell type-specific effect of hypoxia and platelet-derived growth factor-BB on extracellular matrix turnover and its consequences for lung remodeling
-
10.1074/jbc.M602178200 17099219
-
Karakiulakis G Papakonstantinou E Aletras AJ Tamm M Roth M Cell type-specific effect of hypoxia and platelet-derived growth factor-BB on extracellular matrix turnover and its consequences for lung remodeling J Biol Chem 2007, 282(2):908-915 10.1074/jbc.M602178200 17099219
-
(2007)
J Biol Chem
, vol.282
, Issue.2
, pp. 908-915
-
-
Karakiulakis, G.1
Papakonstantinou, E.2
Aletras, A.J.3
Tamm, M.4
Roth, M.5
-
31
-
-
33751569391
-
Tumor-stromal cell interaction under hypoxia increases the invasiveness of pancreatic cancer cells through the hepatocyte growth factor/c-Met pathway
-
10.1002/ijc.22178 16998831
-
Ide T Kitajima Y Miyoshi A Ohtsuka T Mitsuno M Ohtaka K Koga Y Miyazaki K Tumor-stromal cell interaction under hypoxia increases the invasiveness of pancreatic cancer cells through the hepatocyte growth factor/c-Met pathway Int J Cancer 2006, 119(12):2750-2759 10.1002/ ijc.22178 16998831
-
(2006)
Int J Cancer
, vol.119
, Issue.19
, pp. 2750-2759
-
-
Ide, T.1
Kitajima, Y.2
Miyoshi, A.3
Ohtsuka, T.4
Mitsuno, M.5
Ohtaka, K.6
Koga, Y.7
Miyazaki, K.8
-
32
-
-
84886764016
-
-
Pathguide http://www.pathguide.org/
-
Pathguide
-
-
-
33
-
-
35748962289
-
Tools for visually exploring biological networks
-
10.1093/bioinformatics/btm401 17720984
-
Suderman M Hallett M Tools for visually exploring biological networks Bioinformatics 2007, 23(20):2651-2659 10.1093/bioinformatics/btm401 17720984
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2651-2659
-
-
Suderman, M.1
Hallett, M.2
-
34
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
403769 14597658 10.1101/gr.1239303
-
Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13(11):2498-2504 403769 14597658 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
-
35
-
-
33751435209
-
cPath: Open source software for collecting, storing, and querying biological pathways
-
1660554 17101041 10.1186/1471-2105-7-497
-
Cerami EG Bader GD Gross BE Sander C cPath: Open source software for collecting, storing, and querying biological pathways BMC Bioinformatics 2006, 7:497 1660554 17101041 10.1186/1471-2105-7-497
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 497
-
-
Cerami, E.G.1
Bader, G.D.2
Gross, B.E.3
Sander, C.4
-
36
-
-
38449106018
-
BioCAD: An information fusion platform for bio-network inference and analysis
-
2217660 18047703 10.1186/1471-2105-8-S9-S2
-
Lee D Kim S Kim Y BioCAD: An information fusion platform for bio-network inference and analysis BMC Bioinformatics 2007, 8(Suppl 9):S2 2217660 18047703 10.1186/1471-2105-8-S9-S2
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 9
-
-
Lee, D.1
Kim, S.2
Kim, Y.3
|