-
1
-
-
58149293009
-
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
-
10.1186/1471-2105-9-495, 2613159, 19036135
-
Hestand M, Galen VM, Villerius M, et al. CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. BMC bioinformatics 2008, 9:495. 10.1186/1471-2105-9-495, 2613159, 19036135.
-
(2008)
BMC bioinformatics
, vol.9
, pp. 495
-
-
Hestand, M.1
Galen, V.M.2
Villerius, M.3
-
2
-
-
34547560557
-
OPOSSUM: integrated tools for analysis of regulatory motif over-representation
-
10.1093/nar/gkm427, 1933229, 17576675
-
Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW. oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic acids research 2007, 35:W245. 10.1093/nar/gkm427, 1933229, 17576675.
-
(2007)
Nucleic acids research
, vol.35
-
-
Ho Sui, S.J.1
Fulton, D.L.2
Arenillas, D.J.3
Kwon, A.T.4
Wasserman, W.W.5
-
3
-
-
33644876958
-
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
-
10.1093/nar/gkj143, 1347505, 16381825
-
Matys V, Kel-Margoulis OV, Fricke E, et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. Nucleic acids research 2006, 34:D108. 10.1093/nar/gkj143, 1347505, 16381825.
-
(2006)
Nucleic acids research
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
-
4
-
-
21444443478
-
MatInspector and beyond: promoter analysis based on transcription factor binding sites
-
10.1093/bioinformatics/bti473, 15860560
-
Cartharius K, Frech K, Grote K, et al. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933. 10.1093/bioinformatics/bti473, 15860560.
-
(2005)
Bioinformatics
, vol.21
, pp. 2933
-
-
Cartharius, K.1
Frech, K.2
Grote, K.3
-
5
-
-
38549096565
-
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
-
10.1093/nar/gkn449, 2238834, 18006571
-
Bryne JC, Valen E, Tang MHE, et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic acids research 2008, 36:D102. 10.1093/nar/gkn449, 2238834, 18006571.
-
(2008)
Nucleic acids research
, vol.36
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.H.E.3
-
6
-
-
33646502826
-
The transcriptional regulatory code of eukaryotic cells-insights from genome-wide analysis of chromatin organization and transcription factor binding
-
10.1016/j.ceb.2006.04.002, 16647254
-
Barrera LO, Ren B. The transcriptional regulatory code of eukaryotic cells-insights from genome-wide analysis of chromatin organization and transcription factor binding. Current opinion in cell biology 2006, 18:291-298. 10.1016/j.ceb.2006.04.002, 16647254.
-
(2006)
Current opinion in cell biology
, vol.18
, pp. 291-298
-
-
Barrera, L.O.1
Ren, B.2
-
8
-
-
0005540823
-
Modern information retrieval
-
ACM press New York
-
Baeza-Yates R, Ribeiro-Neto B. Modern information retrieval. 1999, 463. ACM press New York.
-
(1999)
, vol.463
-
-
Baeza-Yates, R.1
Ribeiro-Neto, B.2
-
9
-
-
0022786956
-
Fish oil, Raynaud's syndrome, and undiscovered public knowledge
-
Swanson DR. Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspectives in biology and medicine 1986, 30:7.
-
(1986)
Perspectives in biology and medicine
, vol.30
, pp. 7
-
-
Swanson, D.R.1
-
10
-
-
25444530343
-
CoPub Mapper: mining MEDLINE based on search term co-publication
-
10.1186/1471-2105-6-51, 1274248, 15760478
-
Alako B, Veldhoven A, Baal VS, et al. CoPub Mapper: mining MEDLINE based on search term co-publication. BMC bioinformatics 2005, 6:51. 10.1186/1471-2105-6-51, 1274248, 15760478.
-
(2005)
BMC bioinformatics
, vol.6
, pp. 51
-
-
Alako, B.1
Veldhoven, A.2
Baal, V.S.3
-
11
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen TK, Lægreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nature genetics 2001, 28:21-28.
-
(2001)
Nature genetics
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
Lægreid, A.2
Komorowski, J.3
Hovig, E.4
-
12
-
-
13344278672
-
Content-rich biological network constructed by mining PubMed abstracts
-
10.1186/1471-2105-5-147, 528731, 15473905
-
Chen H, Sharp B. Content-rich biological network constructed by mining PubMed abstracts. BMC bioinformatics 2004, 5:147. 10.1186/1471-2105-5-147, 528731, 15473905.
-
(2004)
BMC bioinformatics
, vol.5
, pp. 147
-
-
Chen, H.1
Sharp, B.2
-
13
-
-
1342330525
-
Knowledge discovery by automated identification and ranking of implicit relationships
-
10.1093/bioinformatics/btg421, 14960466
-
Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 2004, 20:389. 10.1093/bioinformatics/btg421, 14960466.
-
(2004)
Bioinformatics
, vol.20
, pp. 389
-
-
Wren, J.D.1
Bekeredjian, R.2
Stewart, J.A.3
Shohet, R.V.4
Garner, H.R.5
-
14
-
-
34548139028
-
Clustering microarray-derived gene lists through implicit literature relationships
-
10.1093/bioinformatics/btm261, 17537751
-
Burkart MF, Wren JD, Herschkowitz JI, Perou CM, Garner HR. Clustering microarray-derived gene lists through implicit literature relationships. Bioinformatics 2007, 23:1995. 10.1093/bioinformatics/btm261, 17537751.
-
(2007)
Bioinformatics
, vol.23
, pp. 1995
-
-
Burkart, M.F.1
Wren, J.D.2
Herschkowitz, J.I.3
Perou, C.M.4
Garner, H.R.5
-
15
-
-
3242889751
-
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining
-
10.1093/nar/gkh484, 441622, 15215386
-
Pan H, Zuo L, Choudhary V, et al. Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. Nucleic acids research 2004, 32:W230. 10.1093/nar/gkh484, 441622, 15215386.
-
(2004)
Nucleic acids research
, vol.32
-
-
Pan, H.1
Zuo, L.2
Choudhary, V.3
-
16
-
-
33645104154
-
Extraction of regulatory gene/protein networks from Medline
-
10.1093/bioinformatics/bti597, 16046493
-
Šaric J, Jensen LJ, Ouzounova R, Rojas I, Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics 2006, 22:645. 10.1093/bioinformatics/bti597, 16046493.
-
(2006)
Bioinformatics
, vol.22
, pp. 645
-
-
Šaric, J.1
Jensen, L.J.2
Ouzounova, R.3
Rojas, I.4
Bork, P.5
-
17
-
-
34548499877
-
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
-
10.1186/1471-2105-8-293, 1964768, 17683642
-
Rodríguez-Penagos C, Salgado H, Martínez-Flores I, Collado-Vides J. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC bioinformatics 2007, 8:293. 10.1186/1471-2105-8-293, 1964768, 17683642.
-
(2007)
BMC bioinformatics
, vol.8
, pp. 293
-
-
Rodríguez-Penagos, C.1
Salgado, H.2
Martínez-Flores, I.3
Collado-Vides, J.4
-
18
-
-
70349456436
-
Assigning roles to protein mentions: The case of transcription factors
-
10.1016/j.jbi.2009.04.001, 19364541
-
Yang H, Keane J, Bergman CM, Nenadic G. Assigning roles to protein mentions: The case of transcription factors. Journal of biomedical informatics 2009, 42:887-894. 10.1016/j.jbi.2009.04.001, 19364541.
-
(2009)
Journal of biomedical informatics
, vol.42
, pp. 887-894
-
-
Yang, H.1
Keane, J.2
Bergman, C.M.3
Nenadic, G.4
-
19
-
-
12744279636
-
Gene clustering by latent semantic indexing of MEDLINE abstracts
-
10.1093/bioinformatics/bth464, 15308538
-
Homayouni R, Heinrich K, Wei L, Berry MW. Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 2005, 21:104. 10.1093/bioinformatics/bth464, 15308538.
-
(2005)
Bioinformatics
, vol.21
, pp. 104
-
-
Homayouni, R.1
Heinrich, K.2
Wei, L.3
Berry, M.W.4
-
21
-
-
84888274795
-
SMART stoplist
-
SMART stoplist. , ftp://ftp.cs.cornell.edu/pub/smart/english.stop
-
-
-
-
22
-
-
80054096543
-
Understanding search engines: mathematical modeling and text retrieval
-
Berry MW, Browne M. Understanding search engines: mathematical modeling and text retrieval. Soc for Industrial & Applied Math 2005, 8.
-
(2005)
Soc for Industrial & Applied Math
, vol.8
-
-
Berry, M.W.1
Browne, M.2
-
23
-
-
0004161838
-
Numerical recipes in C: the art of scientific computing
-
Cambridge University Press
-
Press WH. Numerical recipes in C: the art of scientific computing. 1992, Cambridge University Press.
-
(1992)
-
-
Press, W.H.1
-
24
-
-
58149182724
-
NCBI GEO: archive for high-throughput functional genomic data
-
10.1093/nar/gkn764, 2686538, 18940857
-
Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic acids research 2009, 37:D885. 10.1093/nar/gkn764, 2686538, 18940857.
-
(2009)
Nucleic acids research
, vol.37
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
-
25
-
-
84870490179
-
National Center for Biotechnology Information
-
National Center for Biotechnology Information. , http://www.ncbi.nlm.nih.gov/
-
-
-
-
26
-
-
3843123219
-
Role of nuclear factor-κB in the antiviral action of interferon and interferon-regulated gene expression
-
10.1074/jbc.M308975200, 15131130
-
Pfeffer LM, Kim JG, Pfeffer SR, et al. Role of nuclear factor-κB in the antiviral action of interferon and interferon-regulated gene expression. Journal of Biological Chemistry 2004, 279:31304. 10.1074/jbc.M308975200, 15131130.
-
(2004)
Journal of Biological Chemistry
, vol.279
, pp. 31304
-
-
Pfeffer, L.M.1
Kim, J.G.2
Pfeffer, S.R.3
-
27
-
-
78049367774
-
Alternatively activated macrophages inhibit T-cell proliferation by Stat6-dependent expression of PD-L2
-
10.1182/blood-2010-02-271981, 20625006
-
Huber S, Hoffmann R, Muskens F, Voehringer D. Alternatively activated macrophages inhibit T-cell proliferation by Stat6-dependent expression of PD-L2. Blood 2010, 116:3311. 10.1182/blood-2010-02-271981, 20625006.
-
(2010)
Blood
, vol.116
, pp. 3311
-
-
Huber, S.1
Hoffmann, R.2
Muskens, F.3
Voehringer, D.4
-
28
-
-
10644233167
-
CHOP induces death by promoting protein synthesis and oxidation in the stressed endoplasmic reticulum
-
10.1101/gad.1250704, 3174266, 21941616
-
Marciniak SJ, Yun CY, Oyadomari S, et al. CHOP induces death by promoting protein synthesis and oxidation in the stressed endoplasmic reticulum. Genes & development 2004, 18:3066. 10.1101/gad.1250704, 3174266, 21941616.
-
(2004)
Genes & development
, vol.18
, pp. 3066
-
-
Marciniak, S.J.1
Yun, C.Y.2
Oyadomari, S.3
-
29
-
-
78049502195
-
The transcription factors signal transducer and activator of transcription 5A (STAT5A) and STAT5B negatively regulate cell proliferation through the activation of cyclin-dependent kinase inhibitor 2b (Cdkn2b) and Cdkn1a expression
-
10.1002/hep.23882, 21038417
-
Yu JH, Zhu BM, Wickre M, et al. The transcription factors signal transducer and activator of transcription 5A (STAT5A) and STAT5B negatively regulate cell proliferation through the activation of cyclin-dependent kinase inhibitor 2b (Cdkn2b) and Cdkn1a expression. Hepatology 2010, 52:1808-1818. 10.1002/hep.23882, 21038417.
-
(2010)
Hepatology
, vol.52
, pp. 1808-1818
-
-
Yu, J.H.1
Zhu, B.M.2
Wickre, M.3
-
30
-
-
71949089376
-
Nuclear Factor IC Links Platelet-Derived Growth Factor and Transforming Growth Factor β1 Signaling to Skin Wound Healing Progression
-
10.1128/MCB.01921-08, 2772573, 19752192
-
Plasari G, Calabrese A, Dusserre Y, et al. Nuclear Factor IC Links Platelet-Derived Growth Factor and Transforming Growth Factor β1 Signaling to Skin Wound Healing Progression. Molecular and cellular biology 2009, 29:6006. 10.1128/MCB.01921-08, 2772573, 19752192.
-
(2009)
Molecular and cellular biology
, vol.29
, pp. 6006
-
-
Plasari, G.1
Calabrese, A.2
Dusserre, Y.3
-
31
-
-
84870267223
-
The generalization of student's problem when several different population variances are involved
-
Welch BL. The generalization of student's problem when several different population variances are involved. Biometrika 1947, 28-35.
-
(1947)
Biometrika
, pp. 28-35
-
-
Welch, B.L.1
-
32
-
-
51349164382
-
Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes
-
10.1089/jir.2007.0136, 3173967, 21941579
-
Wei L, Fan M, Xu L, et al. Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes. Journal of Interferon & Cytokine Research 2008, 28:541-552. 10.1089/jir.2007.0136, 3173967, 21941579.
-
(2008)
Journal of Interferon & Cytokine Research
, vol.28
, pp. 541-552
-
-
Wei, L.1
Fan, M.2
Xu, L.3
-
33
-
-
0018079655
-
Basic principles of ROC analysis
-
10.1016/S0001-2998(78)80014-2, 112681
-
Metz CE. Basic principles of ROC analysis. Seminars in nuclear medicine 1978, 8:283-298. 10.1016/S0001-2998(78)80014-2, 112681.
-
(1978)
Seminars in nuclear medicine
, vol.8
, pp. 283-298
-
-
Metz, C.E.1
-
34
-
-
0020083498
-
A simple generalization of the area under the ROC curve to multiple class classification problems
-
Hanley JA, McNeal BJ. A simple generalization of the area under the ROC curve to multiple class classification problems. Radiology 1982, 143:29-36.
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.A.1
McNeal, B.J.2
-
35
-
-
27744481203
-
Markov model recognition and classification of DNA/protein sequences within large text databases
-
10.1093/bioinformatics/bti657, 16159926
-
Wren JD, Hildebrand WH, Chandrasekaran S, Melcher U. Markov model recognition and classification of DNA/protein sequences within large text databases. Bioinformatics 2005, 21:4046. 10.1093/bioinformatics/bti657, 16159926.
-
(2005)
Bioinformatics
, vol.21
, pp. 4046
-
-
Wren, J.D.1
Hildebrand, W.H.2
Chandrasekaran, S.3
Melcher, U.4
-
36
-
-
4444222696
-
A genome-wide and nonredundant mouse transcription factor database
-
10.1016/j.bbrc.2004.07.179, 15336533
-
Kanamori M, Konno H, Osato N, et al. A genome-wide and nonredundant mouse transcription factor database. Biochemical and biophysical research communications 2004, 322:787-793. 10.1016/j.bbrc.2004.07.179, 15336533.
-
(2004)
Biochemical and biophysical research communications
, vol.322
, pp. 787-793
-
-
Kanamori, M.1
Konno, H.2
Osato, N.3
-
37
-
-
57649133991
-
VENNY. An interactive tool for comparing lists with Venn Diagrams
-
VENNY. An interactive tool for comparing lists with Venn Diagrams. , http://bioinfogp.cnb.csic.es/tools/venny/index.html
-
-
-
|