-
1
-
-
70350641870
-
Structured correspondence topic models for mining captioned figures in biological literature
-
In, New York: ACM
-
Ahmed, A., E. Xing, W. Cohen, and R. F. Murphy. Structured correspondence topic models for mining captioned figures in biological literature. In Proceedings of the Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. New York: ACM, 2009, 39-48.
-
(2009)
Proceedings of the Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.
, pp. 39-48
-
-
Ahmed, A.1
Xing, E.2
Cohen, W.3
Murphy, R.F.4
-
2
-
-
34047182529
-
PharmGKB: A logical home for knowledge relating genotype to drug response phenotype
-
Altman, R. B. 2007. PharmGKB: A logical home for knowledge relating genotype to drug response phenotype. Nature Genetics 39 (4): 426.
-
(2007)
Nature Genetics
, vol.39
, Issue.4
, pp. 426
-
-
Altman, R.B.1
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S., T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25 (17): 3389-3402.
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
4
-
-
33751111173
-
Text mining and its potential applications in systems biology
-
Ananiadou, S., B. Kell, and J. Tsujii. 2006. Text mining and its potential applications in systems biology. Trends in Biotechnology 24 (12): 571-579.
-
(2006)
Trends in Biotechnology
, vol.24
, Issue.12
, pp. 571-579
-
-
Ananiadou, S.1
Kell, B.2
Tsujii, J.3
-
5
-
-
33344468683
-
Text Mining for Biology and Biomedicine
-
Norwood, MA: Artech House.
-
Ananiadou, S., and J. McNaught. 2006. Text Mining for Biology and Biomedicine. Norwood, MA: Artech House.
-
(2006)
-
-
Ananiadou, S.1
McNaught, J.2
-
6
-
-
84895631691
-
Systematic association of genes to phenotypes by genome and literature mining
-
Ananiadou, S., D. Sullivan, W. Black, G.-A. Levow, J. Gillespie, C. Mao, S. Pyysalo, B. Kolluru, J. Tsujii, and B. Sobrai. 2010. Systematic association of genes to phenotypes by genome and literature mining. PLoS ONE 6 (3): e14780.
-
(2010)
PLoS ONE
, vol.6
, Issue.3
-
-
Ananiadou, S.1
Sullivan, D.2
Black, W.3
Levow, G.-A.4
Gillespie, J.5
Mao, C.6
Pyysalo, S.7
Kolluru, B.8
Tsujii, J.9
Sobrai, B.10
-
7
-
-
0003177228
-
A note on the number of queries needed to identify regular languages
-
Angluin, D. 1981. A note on the number of queries needed to identify regular languages. Information and Control 51: 76-87.
-
(1981)
Information and Control
, vol.51
, pp. 76-87
-
-
Angluin, D.1
-
8
-
-
0000710299
-
Queries and concept learning
-
Angluin, D. 1988. Queries and concept learning. Machine Learning 2: 319-342.
-
(1988)
Machine Learning
, vol.2
, pp. 319-342
-
-
Angluin, D.1
-
9
-
-
75549087047
-
The IntAct molecular interaction database in 2010
-
Database Issue
-
Aranda, B., P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, et al. 2010. The IntAct molecular interaction database in 2010. Nucleic Acids Research 38 (Database Issue): D525-D531.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
Armean, I.4
Bridge, A.5
Derow, C.6
Feuermann, M.7
-
10
-
-
80053393894
-
BioCreative III interactive task: An overview
-
Arighi, C. N., P. M. Roberts, S. Agarwal, S. Bhattacharya, G. Cesareni, A. Chatraryamontri, S. Clematide, P. Gaudet, M. G. Giglio, I. Harrow, E. Huala, M. Krallinger, U. Leser, D. Li, F. Liu, Z. Lu, L. J. Maltais, N. Okazaki, L. Perfetto, F. Rinaldi, R. Sætre, D. Salgado, P. Srinivasan, P. E. Thomas, L. Toldo, L. Hirschman, and C. H. Wu. 2011. BioCreative III interactive task: An overview. BMC Bioinformatics 12 (Suppl. 8): S4.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.SUPPL. 8
-
-
Arighi, C.N.1
Roberts, P.M.2
Agarwal, S.3
Bhattacharya, S.4
Cesareni, G.5
Chatraryamontri, A.6
Clematide, S.7
Gaudet, P.8
Giglio, M.G.9
Harrow, I.10
Huala, E.11
Krallinger, M.12
Leser, U.13
Li, D.14
Liu, F.15
Lu, Z.16
Maltais, L.J.17
Okazaki, N.18
Perfetto, L.19
Rinaldi, F.20
Sætre, R.21
Salgado, D.22
Srinivasan, P.23
Thomas, P.E.24
Toldo, L.25
Hirschman, L.26
Wu, C.H.27
more..
-
11
-
-
0037245913
-
BIND: The biomolecular interaction network database
-
Bader, G., D. Betel, and C. Hogue. 2003. BIND: The biomolecular interaction network database. Nucleic Acids Research 31 (1): 248-250.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 248-250
-
-
Bader, G.1
Betel, D.2
Hogue, C.3
-
12
-
-
33846114132
-
BRENDA, AMENDA and FRENDA: The enzyme information system in 2007
-
Database Issue
-
Barthelmes, J., C. Ebeling, A. Chang, I. Schomburg, and D. Schomburg. 2007. BRENDA, AMENDA and FRENDA: The enzyme information system in 2007. Nucleic Acids Research 35 (Database Issue): D511-D514.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Barthelmes, J.1
Ebeling, C.2
Chang, A.3
Schomburg, I.4
Schomburg, D.5
-
13
-
-
3142665525
-
GOstat: Find statistically overrepresented gene ontologies within a group of genes
-
Beissbarth, T., and T. P. Speed. 2004. GOstat: Find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20 (9): 1464-1465.
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1464-1465
-
-
Beissbarth, T.1
Speed, T.P.2
-
16
-
-
84895699320
-
Biomolecular Interaction Network Database
-
BIND.
-
BIND. Biomolecular Interaction Network Database. http://www.bind.ca, 2011.
-
(2011)
-
-
-
17
-
-
84895600222
-
-
BioCreative Critical Assessment of Information Extraction in Biology.
-
BioCreative Critical Assessment of Information Extraction in Biology. http://www.biocreative.org/, 2011.
-
(2011)
-
-
-
18
-
-
84895624064
-
-
BioGRID.
-
BioGRID. http://thebiogrid.org/, 2011.
-
(2011)
-
-
-
19
-
-
84857112501
-
Scaling up biomedical event extraction to the entire PubMed
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Björne, J., F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski. Scaling up biomedical event extraction to the entire PubMed. In Proceedings of the 2010 Workshop on Biomedical Natural Language Processing. Stroudsburg, PA: Association for Computational Linguistics, 2010.
-
(2010)
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing.
-
-
Björne, J.1
Ginter, F.2
Pyysalo, S.3
Tsujii, J.4
Salakoski, T.5
-
20
-
-
0033292011
-
Automatic extraction of biological information from scientific text: Protein-protein interactions
-
In, Menlo Park, CA: AAAI Press
-
Blaschke, C., M. Andrade, C. Ouzounis, and A. Valencia. Automatic extraction of biological information from scientific text: Protein-protein interactions. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press, 1999, 60-67.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology.
, pp. 60-67
-
-
Blaschke, C.1
Andrade, M.2
Ouzounis, C.3
Valencia, A.4
-
21
-
-
0034868773
-
Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study
-
Blaschke, C., and A. Valencia. 2001. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comparative and Functional Genomics 2: 196-206.
-
(2001)
Comparative and Functional Genomics
, vol.2
, pp. 196-206
-
-
Blaschke, C.1
Valencia, A.2
-
22
-
-
0141607824
-
Latent Dirichlet allocation
-
Blei, D. M., A. Y. Ng, M. I. Jordan, and J. Lafferty. 2003. Latent Dirichlet allocation. Journal of Machine Learning Research 3: 993-1022.
-
(2003)
Journal of Machine Learning Research
, vol.3
, pp. 993-1022
-
-
Blei, D.M.1
Ng, A.Y.2
Jordan, M.I.3
Lafferty, J.4
-
23
-
-
40549096793
-
EpiLoc: A (working) text-based system for predicting protein subcellular location
-
In, Hackensack, NJ: World Scientific
-
Brady, S., and H. Shatkay. EpiLoc: A (working) text-based system for predicting protein subcellular location. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2008, 604-615.
-
(2008)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 604-615
-
-
Brady, S.1
Shatkay, H.2
-
24
-
-
0003802343
-
Classification and Regression Trees
-
Monterey, CA: Wadsworth and Brooks.
-
Breiman, L., J. Friedman, R. Olshen, and C. Stone. 1984. Classification and Regression Trees. Monterey, CA: Wadsworth and Brooks.
-
(1984)
-
-
Breiman, L.1
Friedman, J.2
Olshen, R.3
Stone, C.4
-
25
-
-
38549173606
-
The BioGRID interaction database: 2008 update
-
Breitkreutz, B., C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, et al. 2008. The BioGRID interaction database: 2008 update. Nucleic Acids Research (Database Issue) 36: 637-640.
-
(2008)
Nucleic Acids Research (Database Issue)
, vol.36
, pp. 637-640
-
-
Breitkreutz, B.1
Stark, C.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Livstone, M.6
Oughtred, R.7
-
26
-
-
84895612011
-
-
BRENDA.
-
BRENDA. http://www.brenda-enzymes.org/, 2011.
-
(2011)
-
-
-
27
-
-
84895691386
-
-
BRENDA Tissue Ontology.
-
BRENDA Tissue Ontology. http://www.brenda-enzymes.org/ontology/tissue/tree/update/update_files/BrendaTissueOBO, 2011.
-
(2011)
-
-
-
28
-
-
70449428562
-
SherLoc2: A high-accuracy hybrid method for predicting subcellular localization of proteins
-
Briesemeister, S., T. Blum, S. Brady, Y. P. Lam, O. Kohlbacher, and H. Shatkay. 2009. SherLoc2: A high-accuracy hybrid method for predicting subcellular localization of proteins. Journal of Proteome Research 8 (11): 5363-5366.
-
(2009)
Journal of Proteome Research
, vol.8
, Issue.11
, pp. 5363-5366
-
-
Briesemeister, S.1
Blum, T.2
Brady, S.3
Lam, Y.P.4
Kohlbacher, O.5
Shatkay, H.6
-
29
-
-
84867919822
-
Transformation-based error-driver learning and natural language processing: A case study in part-of-speech tagging
-
Brill, E. 1995. Transformation-based error-driver learning and natural language processing: A case study in part-of-speech tagging. Computational Linguistics 21 (4): 543-565.
-
(1995)
Computational Linguistics
, vol.21
, Issue.4
, pp. 543-565
-
-
Brill, E.1
-
30
-
-
38549117309
-
The HGNC database in 2008: A resource for the human genome
-
Bruford, E., M. Lush, M. Wright, T. Sneddon, S. Povey, and E. Birney. 2008. The HGNC database in 2008: A resource for the human genome. Nucleic Acids Research 36: D445-D448.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Bruford, E.1
Lush, M.2
Wright, M.3
Sneddon, T.4
Povey, S.5
Birney, E.6
-
31
-
-
16244423656
-
Comparative experiments on learning information extractors for proteins and their interactions
-
Bunescu, R., R. Ge, R. Kate, E. Marcotte, R. Mooney, A. Ramani, and Y. Wong. 2005. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 33 (2): 139-155.
-
(2005)
Artificial Intelligence in Medicine
, vol.33
, Issue.2
, pp. 139-155
-
-
Bunescu, R.1
Ge, R.2
Kate, R.3
Marcotte, E.4
Mooney, R.5
Ramani, A.6
Wong, Y.7
-
32
-
-
0031360033
-
Empirical methods in information extraction
-
Cardie, C. 1997. Empirical methods in information extraction. AI Magazine 18 (4): 65-80.
-
(1997)
AI Magazine
, vol.18
, Issue.4
, pp. 65-80
-
-
Cardie, C.1
-
33
-
-
75549083295
-
MINT: A Molecular INTeraction database, 2009 update
-
Ceol, A., A. C. Aryamontri, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli, and G. Cesareni. 2010. MINT: A Molecular INTeraction database, 2009 update. Nucleic Acids Research (Database Issue) 38 (1): 532-539.
-
(2010)
Nucleic Acids Research (Database Issue)
, vol.38
, Issue.1
, pp. 532-539
-
-
Ceol, A.1
Aryamontri, A.C.2
Licata, L.3
Peluso, D.4
Briganti, L.5
Perfetto, L.6
Castagnoli, L.7
Cesareni, G.8
-
34
-
-
33644638865
-
Discovering semantic features in the literature: A foundation for building functional associations
-
Chagoyen, M., P. Carmona-Saez, H. Shatkay, J. M. Caraz, and A. Pascual-Montano. 2006. Discovering semantic features in the literature: A foundation for building functional associations. BMC Bioinformatics 7: 41.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 41
-
-
Chagoyen, M.1
Carmona-Saez, P.2
Shatkay, H.3
Caraz, J.M.4
Pascual-Montano, A.5
-
35
-
-
58149185126
-
BRENDA, AMENDA and FRENDA the enzyme information system: New content and tools in 2009
-
Chang, A., M. Scheer, A. Grote, I. Schomburg, and D. Schomburg. 2009. BRENDA, AMENDA and FRENDA the enzyme information system: New content and tools in 2009. Nucleic Acids Research 37: D588-D592.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Chang, A.1
Scheer, M.2
Grote, A.3
Schomburg, I.4
Schomburg, D.5
-
36
-
-
0035222129
-
Including biological literature improves homology search
-
In, Hackensack, NJ: World Scientific
-
Chang, J. T., S. Raychaudhuri, and R. B. Altman. Including biological literature improves homology search. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2001, 374-383.
-
(2001)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 374-383
-
-
Chang, J.T.1
Raychaudhuri, S.2
Altman, R.B.3
-
37
-
-
33748372941
-
Automatic document classification of biological literature
-
Chen, D., H.-M. Muller, and P. W. Sternberg. 2006. Automatic document classification of biological literature. BMC Bioinformatics 7 (7): 370.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.7
, pp. 370
-
-
Chen, D.1
Muller, H.-M.2
Sternberg, P.W.3
-
39
-
-
33750959071
-
Use of figures in literature mining for biomedical digital libraries
-
In, Piscataway, NJ: IEEE
-
Chen, N., D. Blostein, and H. Shatkay. Use of figures in literature mining for biomedical digital libraries. In Proceedings of the Second IEEE International Conference on Document Image Analysis for Libraries. Piscataway, NJ: IEEE, 2006, 180-197.
-
(2006)
Proceedings of the Second IEEE International Conference on Document Image Analysis for Libraries.
, pp. 180-197
-
-
Chen, N.1
Blostein, D.2
Shatkay, H.3
-
40
-
-
67651243692
-
Processing free-text input to obtain a database of medical information
-
In, New York: ACM
-
Chi, E. C., C. Friedman, N. Sager, and M. S. Lyman. Processing free-text input to obtain a database of medical information. In Proceedings of the Eighth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 1985, 82-90.
-
(1985)
Proceedings of the Eighth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
, pp. 82-90
-
-
Chi, E.C.1
Friedman, C.2
Sager, N.3
Lyman, M.S.4
-
41
-
-
0024878606
-
Designing an introspective, multipurpose, controlled medical vocabulary
-
In
-
Cimino, J., G. Hripcsak, S. Johnson, and P. Clayton. Designing an introspective, multipurpose, controlled medical vocabulary. In Proceedings of the Annual Symposium on Computer Applications in Medical Care, 1989, 513-518.
-
(1989)
Proceedings of the Annual Symposium on Computer Applications in Medical Care
, pp. 513-518
-
-
Cimino, J.1
Hripcsak, G.2
Johnson, S.3
Clayton, P.4
-
42
-
-
77953756788
-
Structured literature image finder: Extracting, information from text and images in biomedical literature
-
In, C. Blaschke, L. Hirschman, H. Shatkay, and A. Valencia, eds., New York: Springer
-
Coelho, L. P., A. Ahmed, A. Arnold, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy. Structured literature image finder: Extracting, information from text and images in biomedical literature. In Lecture Notes in Bioinformatics: Linking Literature, Information, and Knowledge for Biology, C. Blaschke, L. Hirschman, H. Shatkay, and A. Valencia, eds., vol. 6004, 23-32. New York: Springer, 2010.
-
(2010)
Lecture Notes in Bioinformatics: Linking Literature, Information, and Knowledge for Biology
, vol.6004
, pp. 23-32
-
-
Coelho, L.P.1
Ahmed, A.2
Arnold, A.3
Kangas, J.4
Sheikh, A.-S.5
Xing, E.6
Cohen, W.7
Murphy, R.F.8
-
43
-
-
0001345686
-
Context-sensitive learning methods for text categorization
-
Cohen, W. W., and Y. Singer. 1999. Context-sensitive learning methods for text categorization. ACM Transactions on Information Systems 17 (2): 141-173.
-
(1999)
ACM Transactions on Information Systems
, vol.17
, Issue.2
, pp. 141-173
-
-
Cohen, W.W.1
Singer, Y.2
-
44
-
-
0002670150
-
Extracting the names of genes and gene products with a hidden Markov model
-
In, Burlington, MA: Morgan Kaufmann
-
Collier, N., C. Nobata, and J. Tsujii. Extracting the names of genes and gene products with a hidden Markov model. In Proceedings of the Eighteenth International Conference on Computational Linguistics. Burlington, MA: Morgan Kaufmann, 2000, 201-207.
-
(2000)
Proceedings of the Eighteenth International Conference on Computational Linguistics.
, pp. 201-207
-
-
Collier, N.1
Nobata, C.2
Tsujii, J.3
-
45
-
-
84895688585
-
-
CoNLL-2010 Shared Task.
-
CoNLL-2010 Shared Task. http://www.inf.u-szeged.hu/rgai/conll2010st/, 2010.
-
(2010)
-
-
-
47
-
-
0033290514
-
Constructing biological knowledge bases by extracting information from text sources
-
In, Menlo Park, CA: AAAI Press
-
Craven, M., and J. Kumlien. Constructing biological knowledge bases by extracting information from text sources. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press, 1999, 77-86.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology.
, pp. 77-86
-
-
Craven, M.1
Kumlien, J.2
-
48
-
-
80052694841
-
Integration of gene normalization stages and co-reference resolution using a Markov-logic network
-
Dai, H.-J., Y.-C. Chang, R. T.-H. Tsai, and W.-L. Hsu. 2011. Integration of gene normalization stages and co-reference resolution using a Markov-logic network. Bioinformatics 27 (18): 2586-2594.
-
(2011)
Bioinformatics
, vol.27
, Issue.18
, pp. 2586-2594
-
-
Dai, H.-J.1
Chang, Y.-C.2
Tsai, R.T.-H.3
Hsu, W.-L.4
-
49
-
-
84895687100
-
-
Database of Interacting Proteins.
-
Database of Interacting Proteins. http://dip.doe-mbi.ucla.edu/dip/Main.cgi, 2011.
-
(2011)
-
-
-
51
-
-
84989525001
-
Indexing by latent semantic analysis
-
Deerwester, S., S. T. Dumais, G. Furnas, T. Landauer, and R. Harshman. 1990. Indexing by latent semantic analysis. Journal of the Society for Information Science 41 (6): 391-407.
-
(1990)
Journal of the Society for Information Science
, vol.41
, Issue.6
, pp. 391-407
-
-
Deerwester, S.1
Dumais, S.T.2
Furnas, G.3
Landauer, T.4
Harshman, R.5
-
52
-
-
0004234657
-
Probability and Statistics
-
2nd ed. Reading, MA: Addison-Wesley.
-
DeGroot, M. H. 1986. Probability and Statistics. 2nd ed. Reading, MA: Addison-Wesley.
-
(1986)
-
-
DeGroot, M.H.1
-
53
-
-
81355148409
-
Combining Text and Visual Features for Biomedical Information Retrieval. A Report to the Board of Scientific Counselors
-
Bethesda, MD: Lister Hill National Center for Biomedical Communications.
-
Demner-Fushman, D., S. Antani, and M. Simpson. 2010. Combining Text and Visual Features for Biomedical Information Retrieval. A Report to the Board of Scientific Counselors. Bethesda, MD: Lister Hill National Center for Biomedical Communications.
-
(2010)
-
-
Demner-Fushman, D.1
Antani, S.2
Simpson, M.3
-
54
-
-
77953740821
-
Toward computerassisted text curation: Classification is easy (choosing training data can be hard..)
-
In, C. Blaschke, L. Hirschman, H. Shatkay, and A. Valencia, eds., New York: Springer
-
Denroche, R., R. Madupu, S. Yooseph, G. Sutton, and H. Shatkay. Toward computerassisted text curation: Classification is easy (choosing training data can be hard..). In Lecture Notes in Bioinformatics: Linking Literature, Information, and Knowledge for Biology, C. Blaschke, L. Hirschman, H. Shatkay, and A. Valencia, eds., vol. 6004, 33-42. New York: Springer, 2010.
-
(2010)
Lecture Notes in Bioinformatics: Linking Literature, Information, and Knowledge for Biology
, vol.6004
, pp. 33-42
-
-
Denroche, R.1
Madupu, R.2
Yooseph, S.3
Sutton, G.4
Shatkay, H.5
-
55
-
-
0024492974
-
Fish-oil dietary supplementation in patients with Raynaud's phenomenon: A double-blind, controlled, prospective study
-
DiGiacomo, R., J. Kremer, and D. Shah. 1989. Fish-oil dietary supplementation in patients with Raynaud's phenomenon: A double-blind, controlled, prospective study. American Journal of Medicine 86 (2): 158-164.
-
(1989)
American Journal of Medicine
, vol.86
, Issue.2
, pp. 158-164
-
-
DiGiacomo, R.1
Kremer, J.2
Shah, D.3
-
56
-
-
77956324768
-
Full text and figure display improves bioscience literature search
-
Divoli, A., M. Wooldridge, and M. Hearst. 2010. Full text and figure display improves bioscience literature search. PLoS ONE 5 (4): e9619.
-
(2010)
PLoS ONE
, vol.5
, Issue.4
-
-
Divoli, A.1
Wooldridge, M.2
Hearst, M.3
-
57
-
-
24644450611
-
Predicting protein subcellular localization: Past, present, and future
-
Dönnes, P., and A. Höglund. 2004. Predicting protein subcellular localization: Past, present, and future. Genomics, Proteomics & Bioinformatics 2 (4): 209-215.
-
(2004)
Genomics, Proteomics & Bioinformatics
, vol.2
, Issue.4
, pp. 209-215
-
-
Dönnes, P.1
Höglund, A.2
-
58
-
-
84908088795
-
Integrating text mining into the MGI biocuration workflow
-
Database, November
-
Dowell, K., M. McAndrews-Hill, D. Hill, H. Drabkin, and J. Blake. Integrating text mining into the MGI biocuration workflow. Database, November 2009.
-
(2009)
-
-
Dowell, K.1
McAndrews-Hill, M.2
Hill, D.3
Drabkin, H.4
Blake, J.5
-
59
-
-
0037293075
-
Global functional profiling of gene expression
-
Draghici, S., P. Khatri, R. P. Martins, G. C. Ostermeier, and S. A. Krawetz. 2003. Global functional profiling of gene expression. Genomics 81 (2): 98-104.
-
(2003)
Genomics
, vol.81
, Issue.2
, pp. 98-104
-
-
Draghici, S.1
Khatri, P.2
Martins, R.P.3
Ostermeier, G.C.4
Krawetz, S.A.5
-
61
-
-
85031726785
-
Using latent semantic analysis to improve access to textual information
-
In, New York: ACM
-
Dumais, S. T., G. W. Furnas, T. K. Landauer, S. Deerwester, and R. Harshman. Using latent semantic analysis to improve access to textual information. In Proceedings of the ACM CHI 88 Human Factors in Computing Systems Conference. New York: ACM, 1988, 281-285.
-
(1988)
Proceedings of the ACM CHI 88 Human Factors in Computing Systems Conference.
, pp. 281-285
-
-
Dumais, S.T.1
Furnas, G.W.2
Landauer, T.K.3
Deerwester, S.4
Harshman, R.5
-
62
-
-
85105809948
-
Inductive learning algorithms and representations for text categorization
-
In, New York: ACM
-
Dumais, S. T., J. Platt, D. Heckerman, and M. Sahami. Inductive learning algorithms and representations for text categorization. In Proceedings of the 1998 ACM CIKM International Conference on Information and Knowledge Management. New York: ACM, 1998, 148-155.
-
(1998)
Proceedings of the 1998 ACM CIKM International Conference on Information and Knowledge Management.
, pp. 148-155
-
-
Dumais, S.T.1
Platt, J.2
Heckerman, D.3
Sahami, M.4
-
63
-
-
84895680546
-
-
Elsevier Grand Challenge.
-
Elsevier Grand Challenge. http://www.elseviergrandchallenge.com/index.html, 2009.
-
(2009)
-
-
-
64
-
-
84863790360
-
The CoNLL-2010 shared task: Learning to detect hedges and their scope in natural language text
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Farkas, R., V. Vincze, G. Móra, J. Csirik, and G. Szarvas. The CoNLL-2010 shared task: Learning to detect hedges and their scope in natural language text. In Proceedings of the Fourteenth Conference on Computational Natural Language Learning: Shared Task. Stroudsburg, PA: Association for Computational Linguistics, 2010, 1-12.
-
(2010)
Proceedings of the Fourteenth Conference on Computational Natural Language Learning: Shared Task.
, pp. 1-12
-
-
Farkas, R.1
Vincze, V.2
Móra, G.3
Csirik, J.4
Szarvas, G.5
-
65
-
-
0036799765
-
BRCA1 interacts directly with the Fanconi anemia protein FANCA
-
Folias, A., M. Matkovic, D. Bruun, S. Reid, J. Hejna, M. Grompe, A. D'Andrea, and R. Moses. 2002. BRCA1 interacts directly with the Fanconi anemia protein FANCA. Human Molecular Genetics 11 (21): 2591-2597.
-
(2002)
Human Molecular Genetics
, vol.11
, Issue.21
, pp. 2591-2597
-
-
Folias, A.1
Matkovic, M.2
Bruun, D.3
Reid, S.4
Hejna, J.5
Grompe, M.6
D'Andrea, A.7
Moses, R.8
-
67
-
-
0035236048
-
GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles
-
Friedman, C., P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. 2001. GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17 (suppl. 1): S74-S82.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Friedman, C.1
Kra, P.2
Yu, H.3
Krauthammer, M.4
Rzhetsky, A.5
-
68
-
-
0020932292
-
Computer structuring of free-text patient data
-
In
-
Friedman, C., N. Sager, E. C. Chi, E. Marsh, C. Christenson, and M. S. Lyman. Computer structuring of free-text patient data. In Proceedings of the Seventh Annual Symposium on Computer Applications in Medical Care, 1983, 688-691.
-
(1983)
Proceedings of the Seventh Annual Symposium on Computer Applications in Medical Care
, pp. 688-691
-
-
Friedman, C.1
Sager, N.2
Chi, E.C.3
Marsh, E.4
Christenson, C.5
Lyman, M.S.6
-
69
-
-
0031633368
-
Toward information extraction: Identifying protein names from biological papers
-
In, Hackensack, NJ: World Scientific
-
Fukuda, K., T. Tsunoda, A. Tamura, and T. Takagi. Toward information extraction: Identifying protein names from biological papers. In Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 1998, 707-718.
-
(1998)
Pacific Symposium on Biocomputing.
, pp. 707-718
-
-
Fukuda, K.1
Tsunoda, T.2
Tamura, A.3
Takagi, T.4
-
70
-
-
33847294345
-
RelEx - relation extraction using dependency parse trees
-
Fundel, K., R. Küffner, and R. Zimmer. 2007. RelEx - relation extraction using dependency parse trees. Bioinformatics 23 (3): 365-371.
-
(2007)
Bioinformatics
, vol.23
, Issue.3
, pp. 365-371
-
-
Fundel, K.1
Küffner, R.2
Zimmer, R.3
-
71
-
-
85024509216
-
Information retrieval using a singular value decomposition model of latent semantic structure
-
In, New York: ACM
-
Furnas, G. W., S. Deerwester, S. T. Dumais, T. K. Landauer, R. A. Harshman, L. A. Streeter, and K. E. Lochbaum. Information retrieval using a singular value decomposition model of latent semantic structure. In Proceedings of the Eleventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 1988, 465-480.
-
(1988)
Proceedings of the Eleventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
, pp. 465-480
-
-
Furnas, G.W.1
Deerwester, S.2
Dumais, S.T.3
Landauer, T.K.4
Harshman, R.A.5
Streeter, L.A.6
Lochbaum, K.E.7
-
72
-
-
58149185138
-
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009
-
Database Issue
-
Galperin, M. Y., and G. R. Cochrane. 2009. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. Nucleic Acids Research (Database Issue) 37: D1-D4.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Galperin, M.Y.1
Cochrane, G.R.2
-
73
-
-
63049114009
-
Pharmspresso: A text mining tool for extraction of pharmacogenomic concepts and relationships from full text. Selected Proceedings of the First Summit on Translational Bioinformatics 2008
-
Garten, Y., and R. B. Altman. 2009. Pharmspresso: A text mining tool for extraction of pharmacogenomic concepts and relationships from full text. Selected Proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinformatics 10 (suppl. 2): S6.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 2
-
-
Garten, Y.1
Altman, R.B.2
-
74
-
-
84895647374
-
-
Gene Ontology.
-
Gene Ontology. http://www.geneontology.org/, 2011.
-
(2011)
-
-
-
75
-
-
77949431037
-
LINNAEUS: A species name identification system for biomedical literature
-
Gerner, M., G. Nenadic, and C. Bergman. 2010. LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics 11: 85.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 85
-
-
Gerner, M.1
Nenadic, G.2
Bergman, C.3
-
77
-
-
49949150022
-
Language identification in the limit
-
Gold, E. M. 1967. Language identification in the limit. Information and Control 10: 447-474.
-
(1967)
Information and Control
, vol.10
, pp. 447-474
-
-
Gold, E.M.1
-
78
-
-
0001187706
-
Complexity of automaton identification from given data
-
Gold, E. M. 1978. Complexity of automaton identification from given data. Information and Control 37: 302-320.
-
(1978)
Information and Control
, vol.37
, pp. 302-320
-
-
Gold, E.M.1
-
79
-
-
0006019644
-
A probabilistic approach to full-text document clustering
-
Technical Report ITAD-433-MS-98-044, SRI International
-
Goldszmidt, M., and M. Sahami. A probabilistic approach to full-text document clustering. Technical Report ITAD-433-MS-98-044, SRI International, 1998.
-
(1998)
-
-
Goldszmidt, M.1
Sahami, M.2
-
81
-
-
85047691899
-
A comparison of parsing technologies for the biomedical domain
-
Grover, C., A. Lascarides, and M. Lapata. 2005. A comparison of parsing technologies for the biomedical domain. Natural Language Engineering 11 (1): 27-65.
-
(2005)
Natural Language Engineering
, vol.11
, Issue.1
, pp. 27-65
-
-
Grover, C.1
Lascarides, A.2
Lapata, M.3
-
82
-
-
78049479811
-
The text-mining based PubChem bioassay neighboring analysis
-
Han, L., T. O. Suzek, Y. Wang, and S. H. Bryant. 2010. The text-mining based PubChem bioassay neighboring analysis. BMC Bioinformatics 11 (1): 549.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 549
-
-
Han, L.1
Suzek, T.O.2
Wang, Y.3
Bryant, S.H.4
-
83
-
-
0043130572
-
Playing biology's name game: Identifying protein names in scientific text
-
In, Hackensack, NJ: World Scientific
-
Hanisch, D., J. Fluck, H. Mevissen, and R. Zimmer. Playing biology's name game: Identifying protein names in scientific text. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2003, 403-414.
-
(2003)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 403-414
-
-
Hanisch, D.1
Fluck, J.2
Mevissen, H.3
Zimmer, R.4
-
84
-
-
0035224502
-
Disambiguating proteins, genes, and RNA in text: A machine learning approach
-
Hatzivassiloglou, V., P. Duboué, and A. Rzhetsky. 2001. Disambiguating proteins, genes, and RNA in text: A machine learning approach. Bioinformatics 17 (suppl. 1): S97-S106.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Hatzivassiloglou, V.1
Duboué, P.2
Rzhetsky, A.3
-
85
-
-
34548561812
-
Biotext search engine: Beyond abstract search
-
Hearst, M., A. Divoli, H. Guturu, A. Ksikes, P. Nakov, M. Wooldridge, and J. Ye. 2007. Biotext search engine: Beyond abstract search. Bioinformatics 23 (16): 2196-2197.
-
(2007)
Bioinformatics
, vol.23
, Issue.16
, pp. 2196-2197
-
-
Hearst, M.1
Divoli, A.2
Guturu, H.3
Ksikes, A.4
Nakov, P.5
Wooldridge, M.6
Ye, J.7
-
87
-
-
16244404792
-
TREC 2004 genomics track overview
-
In
-
Hersh, W., R. T. Bhupatiraju, L. Ross, P. Johnson, A. M. Cohen, and D. F. Kraemer. TREC 2004 genomics track overview. In Proceedings of the Text REtrieval Conference, 2004.
-
(2004)
Proceedings of the Text REtrieval Conference
-
-
Hersh, W.1
Bhupatiraju, R.T.2
Ross, L.3
Johnson, P.4
Cohen, A.M.5
Kraemer, D.F.6
-
88
-
-
85030313899
-
OHSUMED: An interactive retrieval evaluation and new large test collection for research
-
In, New York: ACM
-
Hersh, W., C. Buckley, T. Leone, and D. Hickam. OHSUMED: An interactive retrieval evaluation and new large test collection for research. In Proceedings of the Seventeenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 1994.
-
(1994)
Proceedings of the Seventeenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
-
-
Hersh, W.1
Buckley, C.2
Leone, T.3
Hickam, D.4
-
89
-
-
33747886119
-
TREC 2005 genomics track overview
-
In
-
Hersh, W., A. M. Cohen, J. Yang, R. T. Bhupatiraju, P. Roberts, and M. Hearst. TREC 2005 genomics track overview. In Proceedings of the Text REtrieval Conference, 2005.
-
(2005)
Proceedings of the Text REtrieval Conference
-
-
Hersh, W.1
Cohen, A.M.2
Yang, J.3
Bhupatiraju, R.T.4
Roberts, P.5
Hearst, M.6
-
90
-
-
33947321307
-
Overview of BioCreative Task 1B: Normalized gene lists
-
Hirschman, L., M. Colosimo, A. Morgan, and A. Yeh. 2005. Overview of BioCreative Task 1B: Normalized gene lists. BMC Bioinformatics 6 (suppl. 1): S11.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
Hirschman, L.1
Colosimo, M.2
Morgan, A.3
Yeh, A.4
-
91
-
-
3943106585
-
Accomplishments and challenges in literature data mining for biology
-
Hirschman, L., J. Park, J. Tsujii, L. Wong, and C. H. Wu. 2002. Accomplishments and challenges in literature data mining for biology. Bioinformatics 18: 1553-1561.
-
(2002)
Bioinformatics
, vol.18
, pp. 1553-1561
-
-
Hirschman, L.1
Park, J.2
Tsujii, J.3
Wong, L.4
Wu, C.H.5
-
92
-
-
33947304181
-
Overview of BioCreative: Critical assessment of information extraction for biology
-
Hirschman, L., A. Yeh, C. Blaschke, and A. Valencia. 2005. Overview of BioCreative: Critical assessment of information extraction for biology. BMC Bioinformatics 6 (suppl. 1): S1.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
Hirschman, L.1
Yeh, A.2
Blaschke, C.3
Valencia, A.4
-
93
-
-
3042786293
-
A gene network for navigating the literature
-
Hoffmann, R., and A. Valencia. 2004. A gene network for navigating the literature. Nature Genetics 36 (7): 664.
-
(2004)
Nature Genetics
, vol.36
, Issue.7
, pp. 664
-
-
Hoffmann, R.1
Valencia, A.2
-
94
-
-
27544448536
-
Implementing the iHOP concept for navigation of biomedical literature
-
Hoffmann, R., and A. Valencia. 2005. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 (suppl. 2): ii252-ii258.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Hoffmann, R.1
Valencia, A.2
-
96
-
-
39049189808
-
Significantly improved prediction of subcellular localization by integrating text and protein sequence data
-
In, Hackensack, NJ: World Scientific
-
Höglund, A., T. Blum, S. Brady, P. Dönnes, J. S. Miguel, M. Rocheford, O. Kohlbacher, and H. Shatkay. Significantly improved prediction of subcellular localization by integrating text and protein sequence data. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2006, 16-27.
-
(2006)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 16-27
-
-
Höglund, A.1
Blum, T.2
Brady, S.3
Dönnes, P.4
Miguel, J.S.5
Rocheford, M.6
Kohlbacher, O.7
Shatkay, H.8
-
97
-
-
33646861792
-
MultiLoc: Prediction of protein subcellular localization using n-terminal targeting sequences, sequence motifs, and amino acid composition
-
Höglund, A., P. Dönnes, T. Blum, H. Adolph, and O. Kohlbacher. 2006. MultiLoc: Prediction of protein subcellular localization using n-terminal targeting sequences, sequence motifs, and amino acid composition. BMC Bioinformatics 22 (10): 1158-1165.
-
(2006)
BMC Bioinformatics
, vol.22
, Issue.10
, pp. 1158-1165
-
-
Höglund, A.1
Dönnes, P.2
Blum, T.3
Adolph, H.4
Kohlbacher, O.5
-
98
-
-
84872892528
-
Retrieving hierarchical text structure from typeset scientific articles - a prerequisite for e-science text mining
-
In
-
Hollingsworth, B., I. Lewin, and D. Tidhar. Retrieving hierarchical text structure from typeset scientific articles - a prerequisite for e-science text mining. In Proceedings of the UK e-Science All Hands Meeting, 2005.
-
(2005)
Proceedings of the UK e-Science All Hands Meeting
-
-
Hollingsworth, B.1
Lewin, I.2
Tidhar, D.3
-
99
-
-
12744279636
-
Gene clustering by latent semantic indexing of MEDLINE abstracts
-
Homayouni, R., K. Heinrich, L. Wei, and M. W. Berry. 2005. Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 21 (1): 104-115.
-
(2005)
Bioinformatics
, vol.21
, Issue.1
, pp. 104-115
-
-
Homayouni, R.1
Heinrich, K.2
Wei, L.3
Berry, M.W.4
-
100
-
-
46249123634
-
Integrating high dimensional bi-directional parsing models for gene mention tagging
-
Hsu, C.-N., Y.-M. Chang, C.-J. Kuo, Y.-S. Lin, H.-S. Huang, and I.-F. Chung. 2008. Integrating high dimensional bi-directional parsing models for gene mention tagging. Bioinformatics 24 (13): i286-i294.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Hsu, C.-N.1
Chang, Y.-M.2
Kuo, C.-J.3
Lin, Y.-S.4
Huang, H.-S.5
Chung, I.-F.6
-
101
-
-
36348961230
-
Identifying fluorescence microscope images in online journal articles using both image and text features
-
In, Piscataway, NJ: IEEE
-
Hua, J., O. Ayasli, W. Cohen, and R. Murphy. Identifying fluorescence microscope images in online journal articles using both image and text features. In Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging. Piscataway, NJ: IEEE, 2007, 1224-1227.
-
(2007)
Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging.
, pp. 1224-1227
-
-
Hua, J.1
Ayasli, O.2
Cohen, W.3
Murphy, R.4
-
102
-
-
41349107398
-
OpenDMAP: An open source, ontology-driven concept analysis engine with applications to capturing knowledge regarding protein transport, protein interactions and celltype- specific gene expression
-
Hunter, L., Z. Lu, J. Firby, and W. Baumgartner, H. Johnson, P. Ogren, and K. B. Cohen. 2008. OpenDMAP: An open source, ontology-driven concept analysis engine with applications to capturing knowledge regarding protein transport, protein interactions and celltype- specific gene expression. BMC Bioinformatics 9: 78.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 78
-
-
Hunter, L.1
Lu, Z.2
Firby, J.3
Baumgartner, W.4
Johnson, H.5
Ogren, P.6
Cohen, K.B.7
-
103
-
-
84895592523
-
-
iHOP.
-
iHOP. http://www.ihop-net.org/, 2010.
-
(2010)
-
-
-
104
-
-
84895684823
-
IntAct Molecular Interaction Database
-
IntAct Molecular Interaction Database. http://www.ebi.ac.uk/intact/, 2010.
-
(2010)
-
-
-
105
-
-
12144290446
-
GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data
-
Iossifov, I., M. Krauthammer, C. Friedman, V. Hatzivassilogou, J. Bader, K. White, and A. Rzhetsky. 2004. GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. Journal of Biomedical Informatics 37 (1): 43-53.
-
(2004)
Journal of Biomedical Informatics
, vol.37
, Issue.1
, pp. 43-53
-
-
Iossifov, I.1
Krauthammer, M.2
Friedman, C.3
Hatzivassilogou, V.4
Bader, J.5
White, K.6
Rzhetsky, A.7
-
106
-
-
0030333390
-
Identification of suspected tuberculosis patients based on natural language processing of chest radiograph reports
-
In
-
Jain, N., C. Knirsch, C. Friedman, and G. Hripcsak. Identification of suspected tuberculosis patients based on natural language processing of chest radiograph reports. In Proceedings of the Annual Symposium of the American Medical Informatics Association, 1996, 542-546.
-
(1996)
Proceedings of the Annual Symposium of the American Medical Informatics Association
, pp. 542-546
-
-
Jain, N.1
Knirsch, C.2
Friedman, C.3
Hripcsak, G.4
-
107
-
-
84895589848
-
-
JCVI CHAR Database.
-
JCVI CHAR Database. http://www.jcvi.org/cms/research/projects/algorithmically-tuned-protein-families-rule-base-and-characterized-proteins/overview/, 2011.
-
(2011)
-
-
-
108
-
-
84876308716
-
Comprehensive Microbial Resource
-
JCVI.
-
JCVI. Comprehensive Microbial Resource. http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi, 2011.
-
(2011)
-
-
-
109
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen, T.-K., A. Laegreid, J. Komorowski, and E. Hovig. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics 28: 21-28.
-
(2001)
Nature Genetics
, vol.28
, pp. 21-28
-
-
Jenssen, T.-K.1
Laegreid, A.2
Komorowski, J.3
Hovig, E.4
-
110
-
-
0008347163
-
Approximate dimension equalization in vector-based information retrieval
-
In, Burlington, MA: Morgan Kaufmann
-
Jiang, F., and M. Littman. Approximate dimension equalization in vector-based information retrieval. In Proceedings of Seventeenth International Conference on Machine Learning. Burlington, MA: Morgan Kaufmann, 2000, 423-430.
-
(2000)
Proceedings of Seventeenth International Conference on Machine Learning.
, pp. 423-430
-
-
Jiang, F.1
Littman, M.2
-
111
-
-
34848845892
-
An empirical study of tokenization strategies for biomedical information retrieval
-
Jiang, J., and C. Zhai. 2007. An empirical study of tokenization strategies for biomedical information retrieval. Information Retrieval 10 (4-5): 341-363.
-
(2007)
Information Retrieval
, vol.10
, Issue.4-5
, pp. 341-363
-
-
Jiang, J.1
Zhai, C.2
-
112
-
-
0002409860
-
A probabilistic analysis of the Rocchio algorithm with TFIDF for text categorization
-
In, Burlington, MA: Morgan Kaufmann
-
Joachims, T. A probabilistic analysis of the Rocchio algorithm with TFIDF for text categorization. In Proceedings of the Fourteenth International Conference on Machine Learning. Burlington, MA: Morgan Kaufmann, 1997, 143-151.
-
(1997)
Proceedings of the Fourteenth International Conference on Machine Learning.
, pp. 143-151
-
-
Joachims, T.1
-
113
-
-
84957069814
-
Text categorization with support vector machines: Learning with many relevant features
-
In, New York: Springer
-
Joachims, T. Text categorization with support vector machines: Learning with many relevant features. In Proceedings of the Tenth European Conference on Machine Learning. New York: Springer, 1998, 137-142.
-
(1998)
Proceedings of the Tenth European Conference on Machine Learning.
, pp. 137-142
-
-
Joachims, T.1
-
114
-
-
34248403477
-
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies
-
In, Hackensack, NJ: World Scientific
-
Johnson, H., K. B. Cohen, W. A. Baumgartner, Z. Lu, M. Bada, T. Kester, H. Kim, and L. Hunter. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2006, 28-39.
-
(2006)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 28-39
-
-
Johnson, H.1
Cohen, K.B.2
Baumgartner, W.A.3
Lu, Z.4
Bada, M.5
Kester, T.6
Kim, H.7
Hunter, L.8
-
115
-
-
0003847769
-
Speech and Language Processing: An Introduction to Natural Language Processing, Speech Recognition, and Computational Linguistics
-
2nd ed. Upper Saddle River, NJ: Prentice Hall.
-
Jurafsky, D., and J. Martin. 2009. Speech and Language Processing: An Introduction to Natural Language Processing, Speech Recognition, and Computational Linguistics. 2nd ed. Upper Saddle River, NJ: Prentice Hall.
-
(2009)
-
-
Jurafsky, D.1
Martin, J.2
-
117
-
-
36348936987
-
Integrating natural language processing with FlyBase curation
-
In, Hackensack, NJ: World Scientific
-
Karamanis, N., I. Lewin, R. Seal, R. Drysdale, and E. J. Briscoe. Integrating natural language processing with FlyBase curation. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2007, 245-256.
-
(2007)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 245-256
-
-
Karamanis, N.1
Lewin, I.2
Seal, R.3
Drysdale, R.4
Briscoe, E.J.5
-
118
-
-
42549103568
-
Natural language processing in aid of FlyBase curators
-
Karamanis, N., R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, and T. Briscoe. 2008. Natural language processing in aid of FlyBase curators. BMC Bioinformatics 9: 193.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 193
-
-
Karamanis, N.1
Seal, R.2
Lewin, I.3
McQuilton, P.4
Vlachos, A.5
Gasperin, C.6
Drysdale, R.7
Briscoe, T.8
-
119
-
-
84895601882
-
-
KDD Cup
-
KDD Cup 2002. http://www.biostat.wisc.edu/~craven/kddcup/.
-
(2002)
-
-
-
120
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools, limitations, and open problems
-
Khatri, P., and S. Draghici. 2005. Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics 21: 3587-3595.
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
121
-
-
85104042765
-
Overview of BioNLP'09 shared task on event extraction
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Kim, J.-D., T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii. Overview of BioNLP'09 shared task on event extraction. In Proceedings of the Workshop on BioNLP: Shared Task. Stroudsburg, PA: Association for Computational Linguistics, 2009.
-
(2009)
Proceedings of the Workshop on BioNLP: Shared Task.
-
-
Kim, J.-D.1
Ohta, T.2
Pyysalo, S.3
Kano, Y.4
Tsujii, J.5
-
122
-
-
84901593338
-
Overview of BioNLP shared task 2011
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Kim, J.-D., S. Pyysalo, T. Ohta, R. Bossy, N. Nguyen, and J. Tsujii. Overview of BioNLP shared task 2011. In Proceedings of the BioNLP Shared Task 2011 Workshop. Stroudsburg, PA: Association for Computational Linguistics, 2011.
-
(2011)
Proceedings of the BioNLP Shared Task 2011 Workshop.
-
-
Kim, J.-D.1
Pyysalo, S.2
Ohta, T.3
Bossy, R.4
Nguyen, N.5
Tsujii, J.6
-
123
-
-
0035755351
-
Integrating genotype and phenotype information: An overview of the PharmGKB project
-
Klein, T., J. Chang, M. Cho, K. Easton, R. Fergerson, M. Hewett, Z. Lin, et al. 2001. Integrating genotype and phenotype information: An overview of the PharmGKB project. Pharmacogenomics Journal 1 (3): 167-170.
-
(2001)
Pharmacogenomics Journal
, vol.1
, Issue.3
, pp. 167-170
-
-
Klein, T.1
Chang, J.2
Cho, M.3
Easton, K.4
Fergerson, R.5
Hewett, M.6
Lin, Z.7
-
124
-
-
46249113462
-
Detection of IUPAC and IUPAC-like chemical names
-
Klinger, R., C. Kolarik, J. Fluck, M. Hofmann-Apitius, and C. Friedrich. 2008. Detection of IUPAC and IUPAC-like chemical names. Bioinformatics 24 (13): i268-i276.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Klinger, R.1
Kolarik, C.2
Fluck, J.3
Hofmann-Apitius, M.4
Friedrich, C.5
-
125
-
-
36348973158
-
A stacked graphical model for associating information from text and images in figures
-
In, Hackensack, NJ: World Scientific
-
Kou, Z., W. Cohen, and R. Murphy. A stacked graphical model for associating information from text and images in figures. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2007, 257-268.
-
(2007)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 257-268
-
-
Kou, Z.1
Cohen, W.2
Murphy, R.3
-
126
-
-
51049088875
-
Overview of the protein-protein interaction annotation extraction task of BioCreative II
-
Krallinger, M., F. Leitner, C. Rodriguez-Penagos, and A. Valencia. 2008. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology 9 (suppl. 2): S4.
-
(2008)
Genome Biology
, vol.9
, Issue.SUPPL. 2
-
-
Krallinger, M.1
Leitner, F.2
Rodriguez-Penagos, C.3
Valencia, A.4
-
127
-
-
51049084462
-
Evaluation of text-mining systems for biology: overview of the Second BioCreativecommunity challenge
-
Krallinger, M., A. Morgan, L. Smith, F. Leitner, L. Tanabe, J. Wilbur, L. Hirschman, and A. Valencia. 2008. Evaluation of text-mining systems for biology: overview of the Second BioCreativecommunity challenge. Genome Biology 9 (suppl. 2): S1.
-
(2008)
Genome Biology
, vol.9
, Issue.SUPPL. 2
-
-
Krallinger, M.1
Morgan, A.2
Smith, L.3
Leitner, F.4
Tanabe, L.5
Wilbur, J.6
Hirschman, L.7
Valencia, A.8
-
128
-
-
84889788225
-
Applications of text mining in molecular biology, from name recognition to protein interaction maps
-
In, F. Azuaje and J. Dopazo, eds., Hoboken, NJ: Wiley.
-
Krallinger, M., and A. Valencia. 2005. Applications of text mining in molecular biology, from name recognition to protein interaction maps. In Data Analysis and Visualization in Genomics and Proteomics, F. Azuaje and J. Dopazo, eds., Hoboken, NJ: Wiley.
-
(2005)
Data Analysis and Visualization in Genomics and Proteomics
-
-
Krallinger, M.1
Valencia, A.2
-
129
-
-
11244311539
-
Of truth and pathways: Chasing bits of information through myriads of articles
-
Krauthammer, M., P. Kra, I. Iossifov, S. Gomez, G. Hripcsak, V. Hatzivassiloglou, C. Friedman, and A. Rzhetsky. 2002. Of truth and pathways: Chasing bits of information through myriads of articles. Bioinformatics 18 (suppl. 1): S249-S257.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Krauthammer, M.1
Kra, P.2
Iossifov, I.3
Gomez, S.4
Hripcsak, G.5
Hatzivassiloglou, V.6
Friedman, C.7
Rzhetsky, A.8
-
130
-
-
27544475950
-
Expert knowledge without the expert: Integrated analysis of gene expression and literature to derive active functional contexts
-
Küffner, R., K. Fundel, and R. Zimmer. 2005. Expert knowledge without the expert: Integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics 21: 259-267.
-
(2005)
Bioinformatics
, vol.21
, pp. 259-267
-
-
Küffner, R.1
Fundel, K.2
Zimmer, R.3
-
131
-
-
0142192295
-
Conditional random fields: Probabilistic models for segmenting and labeling sequence data
-
In, Burlington, MA: Morgan Kaufmann
-
Lafferty, J., A. McCallum, and F. Pereira. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In Proceedings of the Eighteenth International Conference on Machine Learning. Burlington, MA: Morgan Kaufmann, 2001, 282-289.
-
(2001)
Proceedings of the Eighteenth International Conference on Machine Learning.
, pp. 282-289
-
-
Lafferty, J.1
McCallum, A.2
Pereira, F.3
-
133
-
-
77955355179
-
Using annotations from controlled vocabularies to find meaningful associations
-
In
-
Lee, W.-J., L. Raschid, P. Srinivasan, N. Shah, D. Rubin, and N. Noy. Using annotations from controlled vocabularies to find meaningful associations. In Proceedings of the Workshop on Data Integration in the Life Sciences, 2007.
-
(2007)
Proceedings of the Workshop on Data Integration in the Life Sciences
-
-
Lee, W.-J.1
Raschid, L.2
Srinivasan, P.3
Shah, N.4
Rubin, D.5
Noy, N.6
-
134
-
-
0003598542
-
Information extraction using hidden Markov models
-
Master's thesis, Department of Computer Science and Engineering, University of California, San Diego
-
Leek, T. Information extraction using hidden Markov models. Master's thesis, Department of Computer Science and Engineering, University of California, San Diego, 1997.
-
(1997)
-
-
Leek, T.1
-
135
-
-
77955441742
-
An overview of BioCreative II.5
-
Leitner, F., S. A. Mardis, M. Krallinger, G. Cesareni, L. A. Hirschman, and A. Valencia. 2010. An overview of BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics 7 (3): 385-399.
-
(2010)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.7
, Issue.3
, pp. 385-399
-
-
Leitner, F.1
Mardis, S.A.2
Krallinger, M.3
Cesareni, G.4
Hirschman, L.A.5
Valencia, A.6
-
138
-
-
0344080097
-
Guest editorial for the special issue on text categorization
-
Lewis, D. D., and P. J. Hayes. 1994. Guest editorial for the special issue on text categorization. ACM Transactions on Information Systems 12 (3): 231.
-
(1994)
ACM Transactions on Information Systems
, vol.12
, Issue.3
, pp. 231
-
-
Lewis, D.D.1
Hayes, P.J.2
-
140
-
-
0030405371
-
Training algorithms for linear text classifiers
-
In, New York: ACM
-
Lewis, D. D., R. E. Schapire, J. P. Callan, and R. Papka. Training algorithms for linear text classifiers. In Proceedings of the Nineteenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, New York: ACM, 1996, 298-306.
-
(1996)
Proceedings of the Nineteenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval
, pp. 298-306
-
-
Lewis, D.D.1
Schapire, R.E.2
Callan, J.P.3
Papka, R.4
-
141
-
-
84876811202
-
RCV1: A new benchmark collection for text categorization research
-
Lewis, D. D., Y. Yang, T. Rose, and F. Li. 2004. RCV1: A new benchmark collection for text categorization research. Journal of Machine Learning Research 5: 361-397.
-
(2004)
Journal of Machine Learning Research
, vol.5
, pp. 361-397
-
-
Lewis, D.D.1
Yang, Y.2
Rose, T.3
Li, F.4
-
142
-
-
68949148714
-
Incorporating rich background knowledge for gene named entity classification and recognition
-
Li, Y., H. Lin, and Z. Yang. 2009. Incorporating rich background knowledge for gene named entity classification and recognition. BMC Bioinformatics 10: 223.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 223
-
-
Li, Y.1
Lin, H.2
Yang, Z.3
-
143
-
-
29244479649
-
The language of bioscience: Facts, speculations, and statements in between
-
In, Ontologies and Databases
-
Light, M., X. Quiu, and P. Srinivasan. The language of bioscience: Facts, speculations, and statements in between. In Proceedings of the BioLINK Workshop on Linking Biological Literature, Ontologies and Databases, 2004.
-
(2004)
Proceedings of the BioLINK Workshop on Linking Biological Literature
-
-
Light, M.1
Quiu, X.2
Srinivasan, P.3
-
145
-
-
0028230073
-
Understanding and using the Medical Subject Headings (MeSH) vocabulary to perform literature searches
-
Lowe, H. J., and G. O. Barnett. 1994. Understanding and using the Medical Subject Headings (MeSH) vocabulary to perform literature searches. Journal of the American Medical Association 271 (14): 1103-1108.
-
(1994)
Journal of the American Medical Association
, vol.271
, Issue.14
, pp. 1103-1108
-
-
Lowe, H.J.1
Barnett, G.O.2
-
146
-
-
80052774027
-
The gene normalization task in BioCreative III
-
Lu, Z., H.-Y. Kao, C.-H. Wei, M. Huang, J. Liu, C.-J. Kuo, C.-N. Hsu, R. T.-H. Tsai, H.-J. Dai, N. Okazaki, H.-C. Cho, M. Gerner, I. Solt, S. Agarwal, F. Liu, D. Vishnyakova, P. Ruch, M. Romacker, F. Rinaldi, S. Bhattacharya, P. Srinivasan, H. Liu, M. Torii, S. Matos, D. Campos, K. Verspoor, K. M. Livingston, and W. J. Wilbur. 2011. The gene normalization task in BioCreative III. BMC Bioinformatics 12 (suppl. 8): S2.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.SUPPL. 8
-
-
Lu, Z.1
Kao, H.-Y.2
Wei, C.-H.3
Huang, M.4
Liu, J.5
Kuo, C.-J.6
Hsu, C.-N.7
Tsai, R.T.-H.8
Dai, H.-J.9
Okazaki, N.10
Cho, H.-C.11
Gerner, M.12
Solt, I.13
Agarwal, S.14
Liu, F.15
Vishnyakova, D.16
Ruch, P.17
Romacker, M.18
Rinaldi, F.19
Bhattacharya, S.20
Srinivasan, P.21
Liu, H.22
Torii, M.23
Matos, S.24
Campos, D.25
Verspoor, K.26
Livingston, K.M.27
Wilbur, W.J.28
more..
-
147
-
-
34548080780
-
Introduction to Information Retrieval
-
Cambridge, UK: Cambridge University Press.
-
Manning, C., and P. Raghavan. 2008. Introduction to Information Retrieval. Cambridge, UK: Cambridge University Press.
-
(2008)
-
-
Manning, C.1
Raghavan, P.2
-
148
-
-
0003612818
-
Foundations of Statistical Natural Language Processing
-
Cambridge, MA: MIT Press.
-
Manning, C., and H. Schütze. 1999. Foundations of Statistical Natural Language Processing. Cambridge, MA: MIT Press.
-
(1999)
-
-
Manning, C.1
Schütze, H.2
-
149
-
-
0035002541
-
Mining literature for protein-protein interactions
-
Marcotte, E., I. Xenarios, and D. Eisenberg. 2000. Mining literature for protein-protein interactions. Bioinformatics 17: 359-363.
-
(2000)
Bioinformatics
, vol.17
, pp. 359-363
-
-
Marcotte, E.1
Xenarios, I.2
Eisenberg, D.3
-
153
-
-
84863395582
-
Automatic domain adaptation for parsing
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
McClosky, D., E. Charniak, and M. Johnson. Automatic domain adaptation for parsing. In Proceedings of Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics. Stroudsburg, PA: Association for Computational Linguistics, 2010, 28-36.
-
(2010)
Proceedings of Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics.
, pp. 28-36
-
-
McClosky, D.1
Charniak, E.2
Johnson, M.3
-
154
-
-
84859080792
-
Event extraction as dependency parsing
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
McClosky, D., M. Surdeanu, and C. Manning. Event extraction as dependency parsing. In Proceedings of the Forty-Ninth Annual Meeting of the Association for Computational Linguistics: Human Language Technologies. Stroudsburg, PA: Association for Computational Linguistics, 2011.
-
(2011)
Proceedings of the Forty-Ninth Annual Meeting of the Association for Computational Linguistics: Human Language Technologies.
-
-
McClosky, D.1
Surdeanu, M.2
Manning, C.3
-
155
-
-
72449173918
-
Addressing morphological variation in alphabetic languages
-
In, New York: ACM
-
McNamee, P., C. Nicholas, and J. Mayfield. Addressing morphological variation in alphabetic languages. In Proceedings of the Thirty-Second Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 2009, 75-82.
-
(2009)
Proceedings of the Thirty-Second Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
, pp. 75-82
-
-
McNamee, P.1
Nicholas, C.2
Mayfield, J.3
-
156
-
-
46649112949
-
Exploring hedge identification in biomedical literature
-
Medlock, B. 2008. Exploring hedge identification in biomedical literature. Journal of Biomedical Informatics 41 (4): 636-654.
-
(2008)
Journal of Biomedical Informatics
, vol.41
, Issue.4
, pp. 636-654
-
-
Medlock, B.1
-
157
-
-
84895698832
-
-
MeSH: Medical Subject Headings.
-
MeSH: Medical Subject Headings. http://www.nlm.nih.gov/mesh/, 2011.
-
(2011)
-
-
-
158
-
-
0003928465
-
Mouse Genome Informatics
-
MGI.
-
MGI. Mouse Genome Informatics. 2011. http://www.informatics.jax.org/
-
(2011)
-
-
-
159
-
-
84895612290
-
The Molecular Interaction Database
-
MINT.
-
MINT. The Molecular Interaction Database. http://mint.bio.uniroma2.it/mint/, 2011.
-
(2011)
-
-
-
160
-
-
0004255908
-
Machine Learning
-
New York: McGraw-Hill.
-
Mitchell, T. 1997. Machine Learning. New York: McGraw-Hill.
-
(1997)
-
-
Mitchell, T.1
-
161
-
-
0004255908
-
Machine Learning
-
Web revisions towards 2nd edition
-
Mitchell, T. Machine Learning. Web revisions towards 2nd edition, http://www.cs.cmu.edu/People/tom/mlbook/NBayesLogReg.pdf, 2005.
-
(2005)
-
-
Mitchell, T.1
-
162
-
-
71549135535
-
Protein-protein interaction extraction by leveraging multiple kernels and parsers
-
Miwa, M., R. Saetre, Y. Miyao, and J. Tsujii. 2009. Protein-protein interaction extraction by leveraging multiple kernels and parsers. International Journal of Medical Informatics 78 (12): e39-e46.
-
(2009)
International Journal of Medical Informatics
, vol.78
, Issue.12
-
-
Miwa, M.1
Saetre, R.2
Miyao, Y.3
Tsujii, J.4
-
163
-
-
8444240427
-
Gene name identification and normalization using a model organism database
-
Morgan, A., L. Hirschman, M. Colosimo, A. Yeh, and J. Colombe. 2004. Gene name identification and normalization using a model organism database. Journal of Biomedical Informatics 37 (6): 396-410.
-
(2004)
Journal of Biomedical Informatics
, vol.37
, Issue.6
, pp. 396-410
-
-
Morgan, A.1
Hirschman, L.2
Colosimo, M.3
Yeh, A.4
Colombe, J.5
-
164
-
-
41349103793
-
Overview of BioCreative II gene normalization
-
Morgan, A., Z. Lu, X. Wang, A. Cohen, J. Fluck, P. Ruch, A. Divoli, et al. 2008. Overview of BioCreative II gene normalization. Genome Biology 9 (S2): S3.
-
(2008)
Genome Biology
, vol.9
, Issue.S2
-
-
Morgan, A.1
Lu, Z.2
Wang, X.3
Cohen, A.4
Fluck, J.5
Ruch, P.6
Divoli, A.7
-
165
-
-
14044254746
-
Textpresso: An ontology-based information retrieval and extraction system for biological literature
-
Muller, H.-M., E. E. Kenny, and P. W. Sternberg. 2004. Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biology 2 (11): e309.
-
(2004)
PLoS Biology
, vol.2
, Issue.11
-
-
Muller, H.-M.1
Kenny, E.E.2
Sternberg, P.W.3
-
166
-
-
58549107557
-
Textpresso for neuroscience: Searching the full text of thousands of neuroscience research papers
-
Muller, H.-M., A. Rangarajan, T. K. Teal, and P. W. Sternberg. 2008. Textpresso for neuroscience: Searching the full text of thousands of neuroscience research papers. Neuroinformatics 6 (3): 195-204.
-
(2008)
Neuroinformatics
, vol.6
, Issue.3
, pp. 195-204
-
-
Muller, H.-M.1
Rangarajan, A.2
Teal, T.K.3
Sternberg, P.W.4
-
167
-
-
29144506690
-
Extracting and structuring subcellular location information from on-line journal articles: The subcellular location image finder
-
In, Calgary, Alberta, Canada: ACTA Press
-
Murphy, R. F., Z. Kou, J. Hua, M. Joffe, and W. W. Cohen. Extracting and structuring subcellular location information from on-line journal articles: The subcellular location image finder. In Proceedings of the IASTED International Conference on Knowledge Sharing and Collaborative Engineering. Calgary, Alberta, Canada: ACTA Press, 2004.
-
(2004)
Proceedings of the IASTED International Conference on Knowledge Sharing and Collaborative Engineering.
-
-
Murphy, R.F.1
Kou, Z.2
Hua, J.3
Joffe, M.4
Cohen, W.W.5
-
168
-
-
84898757106
-
Searching online journals for fluorescence microscope images depicting protein subcellular location patterns
-
In, Piscataway, NJ: IEEE
-
Murphy, R. F., M. Velliste, J. Yao, and G. Porreca. Searching online journals for fluorescence microscope images depicting protein subcellular location patterns. In Proceedings of the IEEE International Symposium on Bioinformatics and Biomedical Engineering. Piscataway, NJ: IEEE, 2001, 119-128.
-
(2001)
Proceedings of the IEEE International Symposium on Bioinformatics and Biomedical Engineering.
, pp. 119-128
-
-
Murphy, R.F.1
Velliste, M.2
Yao, J.3
Porreca, G.4
-
169
-
-
0344480548
-
Inferring sub-cellular localization through automated lexical analysis
-
Nair, R., and B. Rost. 2002. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics 18 (suppl. 1): S78-S86.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Nair, R.1
Rost, B.2
-
170
-
-
84859507820
-
The gene normalization and interactive systems of the University of Tokyo in the BioCreative III challenge
-
In
-
Naoaki, O., H.-C. Cho, R. Sætre, S. Pyysalo, T. Ohta, and J. Tsujii. The gene normalization and interactive systems of the University of Tokyo in the BioCreative III challenge. In Proceedings of the BioCreative III Workshop, 2010, 125-130.
-
(2010)
Proceedings of the BioCreative III Workshop
, pp. 125-130
-
-
Naoaki, O.1
Cho, H.-C.2
Sætre, R.3
Pyysalo, S.4
Ohta, T.5
Tsujii, J.6
-
171
-
-
84895696630
-
-
Entrez
-
Entrez, http://www.ncbi.nlm.nih.gov/Entrez/, 2011.
-
(2011)
-
-
-
172
-
-
84895627699
-
Taxonomy Database
-
NCBI.
-
NCBI. Taxonomy Database. http://www.ncbi.nlm.nih.gov/Taxonomy/, 2011.
-
(2011)
-
-
-
173
-
-
34250305651
-
Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis
-
Newton, M. A., F. A. Quintana, J. A. Den, S. Sengupta, P. Ahlquist, and C. Chile. 2007. Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Annals of Applied Statistics 1 (1): 85-106.
-
(2007)
Annals of Applied Statistics
, vol.1
, Issue.1
, pp. 85-106
-
-
Newton, M.A.1
Quintana, F.A.2
Den, J.A.3
Sengupta, S.4
Ahlquist, P.5
Chile, C.6
-
174
-
-
59549087165
-
On discriminative vs. generative classifiers: A comparison of logistic regression and naive Bayes
-
In, G. Tesauro, D. Touretzky, and T. Leen, eds., Cambridge, MA: MIT Press.
-
Ng, A., and M. Jordan. 2002. On discriminative vs. generative classifiers: A comparison of logistic regression and naive Bayes. In Advances in Neural Information Processing Systems. vol. 14. G. Tesauro, D. Touretzky, and T. Leen, eds., Cambridge, MA: MIT Press.
-
(2002)
Advances in Neural Information Processing Systems.
, vol.14
-
-
Ng, A.1
Jordan, M.2
-
175
-
-
84866845985
-
Challenges in pronoun resolution system for biomedical text
-
In, Paris: European Language Resources Association
-
Nguyen, N., J.-D. Kim, and J. Tsujii. Challenges in pronoun resolution system for biomedical text. In Proceedings of the Sixth International Conference on Language Resources and Evaluation. Paris: European Language Resources Association, 2008, 26-28.
-
(2008)
Proceedings of the Sixth International Conference on Language Resources and Evaluation.
, pp. 26-28
-
-
Nguyen, N.1
Kim, J.-D.2
Tsujii, J.3
-
176
-
-
2442640613
-
The compositional structure of Gene Ontology terms
-
In, Hackensack, NJ: World Scientific
-
Ogren, P. V., K. B. Cohen, G. K. Acquaah-Mensah, J. Eberlein, and L. Hunter. The compositional structure of Gene Ontology terms. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2004, 214-225.
-
(2004)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 214-225
-
-
Ogren, P.V.1
Cohen, K.B.2
Acquaah-Mensah, G.K.3
Eberlein, J.4
Hunter, L.5
-
177
-
-
67149113481
-
Reflect: Augmented browsing for the life scientist
-
Pafilis, E., S. O'Donoghue, L. J. Jensen, H. Horn, M. Kuhn, N. P. Brown, and R. Schneider. 2009. Reflect: Augmented browsing for the life scientist. Nature Biotechnology 27 (6): 508-510.
-
(2009)
Nature Biotechnology
, vol.27
, Issue.6
, pp. 508-510
-
-
Pafilis, E.1
O'Donoghue, S.2
Jensen, L.J.3
Horn, H.4
Kuhn, M.5
Brown, N.P.6
Schneider, R.7
-
178
-
-
0034297382
-
Latent semantic indexing: A probabilistic analysis
-
Papadimitriou, C. H., P. Raghavan, H. Tamaki, and S. Vempala. 2000. Latent semantic indexing: A probabilistic analysis. Journal of Computer and System Sciences 61 (2): 217-235.
-
(2000)
Journal of Computer and System Sciences
, vol.61
, Issue.2
, pp. 217-235
-
-
Papadimitriou, C.H.1
Raghavan, P.2
Tamaki, H.3
Vempala, S.4
-
179
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson, J. D., L. A. Umayam, T. M. Dickinson, E. K. Hickey, and O. White. 2001. The comprehensive microbial resource. Nucleic Acids Research 29 (1): 123-125.
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.M.3
Hickey, E.K.4
White, O.5
-
181
-
-
83055180631
-
Joint inference for knowledge extraction from the biomedical literature
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Poon, H., and L. Vanderwende. Joint inference for knowledge extraction from the biomedical literature. In Proceedings of Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics. Stroudsburg, PA: Association for Computational Linguistics, 2010, 813-821.
-
(2010)
Proceedings of Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics.
, pp. 813-821
-
-
Poon, H.1
Vanderwende, L.2
-
182
-
-
84948481845
-
An algorithm for suffix stripping
-
Porter, M. F. 1980. An algorithm for suffix stripping. Program 14 (3): 127-130.
-
(1980)
Program
, vol.14
, Issue.3
, pp. 127-130
-
-
Porter, M.F.1
-
183
-
-
84895686730
-
-
Protein Data Bank.
-
Protein Data Bank. http://www.rcsb.org/pdb/, 2011.
-
(2011)
-
-
-
184
-
-
84895599739
-
-
PubChem.
-
PubChem. http://pubchem.ncbi.nlm.nih.gov/, 2011.
-
(2011)
-
-
-
185
-
-
84895673558
-
-
PubGene.
-
PubGene. http://www.pubgene.org/, 2011.
-
(2011)
-
-
-
186
-
-
84895568547
-
-
PubMed.
-
PubMed. http://www.ncbi.nlm.nih.gov/pubmed/, 2011.
-
(2011)
-
-
-
187
-
-
84895618025
-
-
PubMed Central.
-
PubMed Central. http://www.ncbi.nlm.nih.gov/pmc/, 2011.
-
(2011)
-
-
-
188
-
-
39149117418
-
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models
-
Qian, Y., and R. Murphy. 2008. Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinformatics 24: 569-576.
-
(2008)
Bioinformatics
, vol.24
, pp. 569-576
-
-
Qian, Y.1
Murphy, R.2
-
189
-
-
0003500248
-
C4.5: Programs for Machine Learning
-
Burlington, MA: Morgan Kaufmann.
-
Quinlan, J. 1993. C4.5: Programs for Machine Learning. Burlington, MA: Morgan Kaufmann.
-
(1993)
-
-
Quinlan, J.1
-
190
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner, L. R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77 (2): 257-286.
-
(1989)
Proceedings of the IEEE
, vol.77
, Issue.2
, pp. 257-286
-
-
Rabiner, L.R.1
-
192
-
-
25144516911
-
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
-
Ramani, A., R. Bunescu, R. Mooney, and E. Marcotte. 2005. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biology 6: R40.
-
(2005)
Genome Biology
, vol.6
-
-
Ramani, A.1
Bunescu, R.2
Mooney, R.3
Marcotte, E.4
-
194
-
-
84880914660
-
Representing sentence structure in hidden Markov models for information extraction
-
In, Burlington, MA: Morgan Kaufmann
-
Ray, S., and M. Craven. Representing sentence structure in hidden Markov models for information extraction. In Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence. Burlington, MA: Morgan Kaufmann, 2001, 1273-1279.
-
(2001)
Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence.
, pp. 1273-1279
-
-
Ray, S.1
Craven, M.2
-
195
-
-
84895595833
-
-
Reflect.
-
Reflect. http://reflect.ws/, 2011.
-
(2011)
-
-
-
196
-
-
0742324214
-
Rule-based extraction of experimental evidence in the biomedical domain - the KDD Cup (task 1)
-
Regev, Y., M. Finkelstein-Landau, R. Feldman, M. Gorodetsky, X. Zheng, S. Levy, R. Charlab, et al. 2002. Rule-based extraction of experimental evidence in the biomedical domain - the KDD Cup (task 1). SIGKDD Explorations 4 (2): 90-91.
-
(2002)
SIGKDD Explorations
, vol.4
, Issue.2
, pp. 90-91
-
-
Regev, Y.1
Finkelstein-Landau, M.2
Feldman, R.3
Gorodetsky, M.4
Zheng, X.5
Levy, S.6
Charlab, R.7
-
197
-
-
0742324214
-
Rule-based extraction of experimental evidence in the biomedical domain - the KDD Cup 2002 (task 1)
-
December
-
Regev, Y., M. Finkelstein-Landau, R. Feldman, X. Zheng, S. Levy, R. Charlab, C. Lawrence, R. A. Lippert, Q. Zhang, and H. Shatkay. December 2002. Rule-based extraction of experimental evidence in the biomedical domain - the KDD Cup 2002 (task 1). SIGKDD Explorations 4 (2): 90-92.
-
(2002)
SIGKDD Explorations
, vol.4
, Issue.2
, pp. 90-92
-
-
Regev, Y.1
Finkelstein-Landau, M.2
Feldman, R.3
Zheng, X.4
Levy, S.5
Charlab, R.6
Lawrence, C.7
Lippert, R.A.8
Zhang, Q.9
Shatkay, H.10
-
198
-
-
0033642065
-
High-throughput functional annotation of novel gene products using document clustering
-
In, Hackensack, NJ: World Scientific
-
Renner, A., and A. Aszódi. High-throughput functional annotation of novel gene products using document clustering. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2000, 54-65.
-
(2000)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 54-65
-
-
Renner, A.1
Aszódi, A.2
-
199
-
-
84895697662
-
-
Reuters-21578 Test Collections.
-
Reuters-21578 Test Collections. http://www.daviddlewis.com/resources/testcollections/reuters21578, 2011.
-
(2011)
-
-
-
200
-
-
80053284695
-
Fast and robust joint models for biomedical event extraction
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Riedel, S., and A. McCallum. Fast and robust joint models for biomedical event extraction. In Proceedings of the 2011 Conference on Empirical Methods in Natural Language Processing. Stroudsburg, PA: Association for Computational Linguistics, 2011, 1-12.
-
(2011)
Proceedings of the 2011 Conference on Empirical Methods in Natural Language Processing.
, pp. 1-12
-
-
Riedel, S.1
McCallum, A.2
-
201
-
-
0028460389
-
Information extraction as a basis for high-precision text classification
-
Riloff, E., and W. Lehnert. 1994. Information extraction as a basis for high-precision text classification. ACM Transactions on Information Systems 12: 296-333.
-
(1994)
ACM Transactions on Information Systems
, vol.12
, pp. 296-333
-
-
Riloff, E.1
Lehnert, W.2
-
202
-
-
84865989647
-
ODIN: An advanced interface for the curation of biomedical literature
-
Rinaldi, F., S. Clematide, G. Schneider, M. Romacker, and T. Vachon. ODIN: An advanced interface for the curation of biomedical literature. Nature Precedings, http://precedings.nature.com/documents/5169/version/1, 2010.
-
(2010)
Nature Precedings
-
-
Rinaldi, F.1
Clematide, S.2
Schneider, G.3
Romacker, M.4
Vachon, T.5
-
203
-
-
58149218476
-
Tasks, topics and relevance judging for the TREC Genomics track: Five years of experience evaluating biomedical text information retrieval systems
-
Roberts, P. M., A. M. Cohen, and W. R. Hersh. 2009. Tasks, topics and relevance judging for the TREC Genomics track: Five years of experience evaluating biomedical text information retrieval systems. Information Retrieval 12 (1): 81-97.
-
(2009)
Information Retrieval
, vol.12
, Issue.1
, pp. 81-97
-
-
Roberts, P.M.1
Cohen, A.M.2
Hersh, W.R.3
-
204
-
-
0003584577
-
Artificial Intelligence: A Modern Approach
-
Upper Saddle River, NJ: Prentice Hall.
-
Russell, S., and P. Norvig. 2002. Artificial Intelligence: A Modern Approach. Upper Saddle River, NJ: Prentice Hall.
-
(2002)
-
-
Russell, S.1
Norvig, P.2
-
205
-
-
84895688655
-
-
Saccharomyces Genome Database.
-
Saccharomyces Genome Database. http://www.yeastgenome.org/, 2011.
-
(2011)
-
-
-
206
-
-
0003882234
-
Automatic Text Processing
-
Reading, MA: Addison-Wesley.
-
Salton, G. 1989. Automatic Text Processing. Reading, MA: Addison-Wesley.
-
(1989)
-
-
Salton, G.1
-
207
-
-
58149200954
-
Database resources of the National Center for Biotechnology Information
-
Sayers, E., T. Barrett, D. Benson, S. Bryant, K. Canese, V. Chetvernin, D. Church, et al. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 37: D5-D15.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Sayers, E.1
Barrett, T.2
Benson, D.3
Bryant, S.4
Canese, K.5
Chetvernin, V.6
Church, D.7
-
208
-
-
0029206376
-
A comparison of classifiers and document representations for the routing problem
-
In, New York: ACM
-
Schütze, H., D. A. Hull, and J. O. Pedersen. A comparison of classifiers and document representations for the routing problem. In Proceedings of the Eighteenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 1995, 229-237.
-
(1995)
Proceedings of the Eighteenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
, pp. 229-237
-
-
Schütze, H.1
Hull, D.A.2
Pedersen, J.O.3
-
209
-
-
0002442796
-
Machine learning in automated text categorization
-
Sebastiani, F. 2002. Machine learning in automated text categorization. ACM Computing Surveys 34 (1): 1-47.
-
(2002)
ACM Computing Surveys
, vol.34
, Issue.1
, pp. 1-47
-
-
Sebastiani, F.1
-
210
-
-
25144520247
-
ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text
-
Settles, B. 2005. ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text. Bioinformatics 21 (14): 3191-3192.
-
(2005)
Bioinformatics
, vol.21
, Issue.14
, pp. 3191-3192
-
-
Settles, B.1
-
211
-
-
68949137209
-
Active learning literature survey
-
Computer Sciences Technical Report 1648, Department of Computer Sciences, University of Wisconsin-Madison
-
Settles, B. Active learning literature survey. Computer Sciences Technical Report 1648, Department of Computer Sciences, University of Wisconsin-Madison, 2010.
-
(2010)
-
-
Settles, B.1
-
212
-
-
33747874337
-
Integrating image data into biomedical text categorization
-
Shatkay, H., N. Chen, and D. Blostein. 2006. Integrating image data into biomedical text categorization. Bioinformatics 22 (14): e446-e453.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Shatkay, H.1
Chen, N.2
Blostein, D.3
-
213
-
-
0034565168
-
Genes, themes and microarrays: Using information retrieval for large scale gene analysis
-
In, Menlo Park, CA: AAAI Press
-
Shatkay, H., S. Edwards, W. J. Wilbur, and M. Boguski. Genes, themes and microarrays: Using information retrieval for large scale gene analysis. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press, 2000, 317-328.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology.
, pp. 317-328
-
-
Shatkay, H.1
Edwards, S.2
Wilbur, W.J.3
Boguski, M.4
-
214
-
-
0742321913
-
Mining the biomedical literature in the genomic era: An overview
-
Shatkay, H., and R. Feldman. 2003. Mining the biomedical literature in the genomic era: An overview. Journal of Computational Biology 10 (6): 821-855.
-
(2003)
Journal of Computational Biology
, vol.10
, Issue.6
, pp. 821-855
-
-
Shatkay, H.1
Feldman, R.2
-
215
-
-
34447304880
-
SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
-
Shatkay, H., A. Höglund, S. Brady, T. Blum, P. Dönnes, and O. Kohlbacher. 2007. SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 23 (11): 1410-1417.
-
(2007)
Bioinformatics
, vol.23
, Issue.11
, pp. 1410-1417
-
-
Shatkay, H.1
Höglund, A.2
Brady, S.3
Blum, T.4
Dönnes, P.5
Kohlbacher, O.6
-
216
-
-
51749123368
-
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users
-
Shatkay, H., F. Pan, A. Rzhetsky, and W. J. Wilbur. 2008. Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. Bioinformatics 24 (18): 2086-2093.
-
(2008)
Bioinformatics
, vol.24
, Issue.18
, pp. 2086-2093
-
-
Shatkay, H.1
Pan, F.2
Rzhetsky, A.3
Wilbur, W.J.4
-
217
-
-
0033684719
-
Finding themes in MEDLINE documents: Probabilistic similarity search
-
In, Piscataway, NJ: IEEE
-
Shatkay, H., and W. J. Wilbur. Finding themes in MEDLINE documents: Probabilistic similarity search. In Proceedings of the IEEE Conference on Advances in Digital Libraries. Piscataway, NJ: IEEE, 2000, 183-192.
-
(2000)
Proceedings of the IEEE Conference on Advances in Digital Libraries.
, pp. 183-192
-
-
Shatkay, H.1
Wilbur, W.J.2
-
218
-
-
0030735796
-
Performance standards and evaluations in IR test collections: Cluster-based retrieval models
-
Shaw, W. M., R. Burgin, and P. Howell. 1997. Performance standards and evaluations in IR test collections: Cluster-based retrieval models. Information Processing & Management 33 (1): 1-14.
-
(1997)
Information Processing & Management
, vol.33
, Issue.1
, pp. 1-14
-
-
Shaw, W.M.1
Burgin, R.2
Howell, P.3
-
219
-
-
0030783243
-
Performance standards and evaluations in IR test collections: Vector-space and other retrieval models
-
Shaw, W. M., R. Burgin, and P. Howell. 1997. Performance standards and evaluations in IR test collections: Vector-space and other retrieval models. Information Processing & Management 33 (1): 15-36.
-
(1997)
Information Processing & Management
, vol.33
, Issue.1
, pp. 15-36
-
-
Shaw, W.M.1
Burgin, R.2
Howell, P.3
-
220
-
-
8444234386
-
Effective adaptation of hidden Markov model-based named entity recognizer for biomedical domain
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Shen, D., J. Zhang, G. Zhou, J. Su, and C.-L. Tan. Effective adaptation of hidden Markov model-based named entity recognizer for biomedical domain. In Proceedings of the ACL Workshop on Natural Language Processing in Biomedicine. Stroudsburg, PA: Association for Computational Linguistics, 2003.
-
(2003)
Proceedings of the ACL Workshop on Natural Language Processing in Biomedicine.
-
-
Shen, D.1
Zhang, J.2
Zhou, G.3
Su, J.4
Tan, C.-L.5
-
221
-
-
84880805498
-
Hierarchical hidden Markov models for information extraction
-
In, Burlington, MA: Morgan Kaufmann
-
Skounakis, M., M. Craven, and S. Ray. Hierarchical hidden Markov models for information extraction. In Proceedings of the Eighteenth International Joint Conference on Artificial Intelligence. Burlington, MA: Morgan Kaufmann, 2003, 427-433.
-
(2003)
Proceedings of the Eighteenth International Joint Conference on Artificial Intelligence.
, pp. 427-433
-
-
Skounakis, M.1
Craven, M.2
Ray, S.3
-
222
-
-
79960310877
-
The place of literature-based discovery in contemporary scientific practice
-
In, M. Weeber and P. Bruza, eds., New York: Springer
-
Smalheiser, N. R., and V. I. Torvik. 2008. The place of literature-based discovery in contemporary scientific practice. In Literature-Based Discovery. vol. 15. M. Weeber and P. Bruza, eds., New York: Springer, 13-22.
-
(2008)
Literature-Based Discovery.
, vol.15
, pp. 13-22
-
-
Smalheiser, N.R.1
Torvik, V.I.2
-
223
-
-
35948989284
-
The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration
-
Smith, B., M. Ashburner, C. Rosse, J. Bard, W. Bug, W. Ceusters, L. Goldberg, K. Eilbeck, A. Ireland, and C. Mungall, N. Leontis, P. Rocca-Serra, A. Ruttenberg, S.-A. Sansone, R. Scheurmann, N. Shah, P. Whetzel, and S. Lewis. 2007. The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25 (11): 1251-1255.
-
(2007)
Nature Biotechnology
, vol.25
, Issue.11
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
Rosse, C.3
Bard, J.4
Bug, W.5
Ceusters, W.6
Goldberg, L.7
Eilbeck, K.8
Ireland, A.9
Mungall, C.10
Leontis, N.11
Rocca-Serra, P.12
Ruttenberg, A.13
Sansone, S.-A.14
Scheurmann, R.15
Shah, N.16
Whetzel, P.17
Lewis, S.18
-
224
-
-
5044241106
-
MedPost: A part-of-speech tagger for biomedical text
-
Smith, L., T. Rindflesch, and W. J. Wilbur. 2004. MedPost: A part-of-speech tagger for biomedical text. Bioinformatics 20 (14): 2320-2321.
-
(2004)
Bioinformatics
, vol.20
, Issue.14
, pp. 2320-2321
-
-
Smith, L.1
Rindflesch, T.2
Wilbur, W.J.3
-
225
-
-
51049088874
-
Overview of BioCreative II gene mention recognition
-
Smith, L., L. Tanabe, R. Ando, C. Kuo, I. Chung, C. Hsu, Y. Lin, et al. 2008. Overview of BioCreative II gene mention recognition. Genome Biology 9 (suppl. 2): S2.
-
(2008)
Genome Biology
, vol.9
, Issue.SUPPL. 2
-
-
Smith, L.1
Tanabe, L.2
Ando, R.3
Kuo, C.4
Chung, I.5
Hsu, C.6
Lin, Y.7
-
228
-
-
6344276917
-
Mining MEDLINE for implicit links between dietary substances and diseases
-
Srinivasan, P., and B. Libbus. 2004. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 20 (suppl. 1): i290-i296.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Srinivasan, P.1
Libbus, B.2
-
229
-
-
0033655017
-
Bibliometrics: Information retrieval and visualization from co-occurrences of gene names in MEDLINE abstracts
-
In, Hackensack, NJ: World Scientific
-
Stapley, B. J., and G. Benoit. Bibliometrics: Information retrieval and visualization from co-occurrences of gene names in MEDLINE abstracts. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2000, 526-537.
-
(2000)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 526-537
-
-
Stapley, B.J.1
Benoit, G.2
-
230
-
-
0036358850
-
Predicting the subcellular location of proteins from text using support vector machines
-
In, Hackensack, NJ: World Scientific
-
Stapley, B. J., L. A. Kelley, and M. J. E. Sternberg. Predicting the subcellular location of proteins from text using support vector machines. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack, NJ: World Scientific, 2002, 374-385.
-
(2002)
Proceedings of the Pacific Symposium on Biocomputing.
, pp. 374-385
-
-
Stapley, B.J.1
Kelley, L.A.2
Sternberg, M.J.E.3
-
231
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Database Issue
-
Stark, C., B. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Research 34 (Database Issue): 535-539.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 535-539
-
-
Stark, C.1
Breitkreutz, B.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
232
-
-
84895667410
-
-
STITCH.
-
STITCH. http://stitch.embl.de/, 2011.
-
(2011)
-
-
-
233
-
-
33750032384
-
An introduction to conditional random fields for relational learning
-
In, L. Getoor and B. Taskar, eds., Cambridge, MA: MIT Press.
-
Sutton, C., and A. McCallum. 2006. An introduction to conditional random fields for relational learning. In Introduction to Statistical Relational Learning, L. Getoor and B. Taskar, eds., Cambridge, MA: MIT Press.
-
(2006)
Introduction to Statistical Relational Learning
-
-
Sutton, C.1
McCallum, A.2
-
234
-
-
0022786956
-
Fish-oil, Raynaud's syndrome and undiscovered public knowledge
-
Swanson, D. R. 1986. Fish-oil, Raynaud's syndrome and undiscovered public knowledge. Perspectives in Biology and Medicine 30 (1): 7-18.
-
(1986)
Perspectives in Biology and Medicine
, vol.30
, Issue.1
, pp. 7-18
-
-
Swanson, D.R.1
-
235
-
-
0000786889
-
Undiscovered public knowledge
-
Swanson, D. R. 1986. Undiscovered public knowledge. Library Quarterly 56 (2): 103-118.
-
(1986)
Library Quarterly
, vol.56
, Issue.2
, pp. 103-118
-
-
Swanson, D.R.1
-
236
-
-
0024031265
-
Migraine and magnesium: Eleven neglected connections
-
Swanson, D. R. 1988. Migraine and magnesium: Eleven neglected connections. Perspectives in Biology and Medicine 31 (4): 526-557.
-
(1988)
Perspectives in Biology and Medicine
, vol.31
, Issue.4
, pp. 526-557
-
-
Swanson, D.R.1
-
237
-
-
0025323307
-
Somatomedin C and Arginine: Implicit connections between mutually isolated literatures
-
Swanson, D. R. 1990. Somatomedin C and Arginine: Implicit connections between mutually isolated literatures. Perspectives in Biology and Medicine 33 (2): 157-186.
-
(1990)
Perspectives in Biology and Medicine
, vol.33
, Issue.2
, pp. 157-186
-
-
Swanson, D.R.1
-
238
-
-
0031125707
-
An interactive system for finding complementary literatures: A stimulus to scientific discovery
-
Swanson, D. R., and N. R. Smalheiser. 1997. An interactive system for finding complementary literatures: A stimulus to scientific discovery. Artificial Intelligence 91: 183-203.
-
(1997)
Artificial Intelligence
, vol.91
, pp. 183-203
-
-
Swanson, D.R.1
Smalheiser, N.R.2
-
239
-
-
0033467661
-
Implicit text linkage between MEDLINE records: Using Arrowsmith as an aid to scientific discovery
-
Swanson, D. R., and N. R. Smalheiser. 1999. Implicit text linkage between MEDLINE records: Using Arrowsmith as an aid to scientific discovery. Library Trends 48 (1): 48-59.
-
(1999)
Library Trends
, vol.48
, Issue.1
, pp. 48-59
-
-
Swanson, D.R.1
Smalheiser, N.R.2
-
241
-
-
84895600652
-
The Arabidopsis Information Resource
-
TAIR.
-
TAIR. The Arabidopsis Information Resource. http://www.arabidopsis.org/, 2011.
-
(2011)
-
-
-
242
-
-
40749162318
-
Syntax annotation for the GENIA corpus
-
In, R. Dale, K.-F. Wong, J. Su, and O. Y. Kwong, eds., New York: Springer
-
Tateisi, Y., A. Yakushiji, T. Ohta, and J. Tsujii. 2005. Syntax annotation for the GENIA corpus. In Natural Language Processing - IJCNLP 2005, R. Dale, K.-F. Wong, J. Su, and O. Y. Kwong, eds., New York: Springer, 222-227.
-
(2005)
Natural Language Processing - IJCNLP 2005
, pp. 222-227
-
-
Tateisi, Y.1
Yakushiji, A.2
Ohta, T.3
Tsujii, J.4
-
243
-
-
84895620949
-
-
Text REtrieval Conference (TREC).
-
Text REtrieval Conference (TREC). http://trec.nist.gov, 2011.
-
(2011)
-
-
-
244
-
-
84895712039
-
-
Textpresso.
-
Textpresso. http://www.textpresso.org/, 2011.
-
(2011)
-
-
-
245
-
-
0036081052
-
The FlyBase database of the Drosophila genome projects and community literature
-
The FlyBase Consortium.
-
The FlyBase Consortium. 2002. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Research 30 (1): 106-108.
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.1
, pp. 106-108
-
-
-
246
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
The Gene Ontology Consortium.
-
The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the unification of biology. Nature Genetics 25: 25-29.
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
-
247
-
-
75849158230
-
The Gene Ontology in 2010: Extensions and refinements
-
The Gene Ontology Consortium., Database Issue
-
The Gene Ontology Consortium. 2010. The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Research 38 (Database Issue): D 331-D335.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
-
248
-
-
58149191270
-
The universal protein resource (UniProt)
-
The UniProt Consortium., Database Issue
-
The UniProt Consortium. 2009. The universal protein resource (UniProt). Nucleic Acids Research 37(Database Issue): D169-D174.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
-
249
-
-
23544443798
-
Automating the Production of Bibliographic Records for MEDLINE
-
Technical Report. Bethesda, MD: National Library of Medicine.
-
Thoma, G. 2001. Automating the Production of Bibliographic Records for MEDLINE. Technical Report. Bethesda, MD: National Library of Medicine.
-
(2001)
-
-
Thoma, G.1
-
250
-
-
84874106680
-
Geneview gene-centric ranking of biomedical text
-
In
-
Thomas, P. E., J. Starlinger, C. Jacob, I. Solt, J. Hakenberg, and U. Leser. Geneview gene-centric ranking of biomedical text. In Proceedings of the BioCreative III Workshop, 2010, 137-142.
-
(2010)
Proceedings of the BioCreative III Workshop
, pp. 137-142
-
-
Thomas, P.E.1
Starlinger, J.2
Jacob, C.3
Solt, I.4
Hakenberg, J.5
Leser, U.6
-
251
-
-
84895691426
-
-
LingPipe.
-
LingPipe. http://alias-i.com/lingpipe/.
-
-
-
-
252
-
-
84983470508
-
Feature-rich part-of-speech tagging with a cyclic dependency network
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Toutanova, K., D. Klein, C. Manning, and Y. Singer. Feature-rich part-of-speech tagging with a cyclic dependency network. In Proceedings of the 2003 Human Language Technology Conference of the North American Chapter of the Association for Computational Linguistics. Stroudsburg, PA: Association for Computational Linguistics, 2003, 252-259.
-
(2003)
Proceedings of the 2003 Human Language Technology Conference of the North American Chapter of the Association for Computational Linguistics.
, pp. 252-259
-
-
Toutanova, K.1
Klein, D.2
Manning, C.3
Singer, Y.4
-
253
-
-
84895702455
-
Genomics Track
-
TREC.
-
TREC. Genomics Track. http://ir.ohsu.edu/genomics, 2008.
-
(2008)
-
-
-
254
-
-
33646502601
-
Developing a robust part-of-speech tagger for biomedical text
-
In, P. Bozanis and E. Houstis, eds., New York: Springer
-
Tsuruoka, Y., Y. Tateishi, J.-D. Kim, T. Ohta, J. McNaught, S. Ananiadou, and J. Tsujii. 2005. Developing a robust part-of-speech tagger for biomedical text. In Advances in Informatics. vol. 3746. P. Bozanis and E. Houstis, eds., New York: Springer, 382-392.
-
(2005)
Advances in Informatics.
, vol.3746
, pp. 382-392
-
-
Tsuruoka, Y.1
Tateishi, Y.2
Kim, J.-D.3
Ohta, T.4
McNaught, J.5
Ananiadou, S.6
Tsujii, J.7
-
255
-
-
33846111969
-
The Rat Genome Database, update 2007 - easing the path from disease to data and back again
-
and the RGD Team., Database Issue
-
Twigger, S., M. Shimoyama, S. Bromberg, A. Kwitek, and H. Jacob, and the RGD Team. 2007. The Rat Genome Database, update 2007 - easing the path from disease to data and back again. Nucleic Acids Research 35 (Database Issue): D658-D662.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Twigger, S.1
Shimoyama, M.2
Bromberg, S.3
Kwitek, A.4
Jacob, H.5
-
256
-
-
84895580391
-
-
Unified Medical Language System.
-
Unified Medical Language System. http://www.nlm.nih.gov/research/umls/, 2011.
-
(2011)
-
-
-
257
-
-
84895611775
-
-
UniProt.
-
UniProt. http://www.uniprot.org/, 2011.
-
(2011)
-
-
-
258
-
-
70350455266
-
Semiautomated curation of protein subcellular localization: A text mining-based approach to gene ontology (GO) cellular component curation
-
Van Auken, K., J. Jaffery, J. Chan, H.-M. Muller, and P. W. Sternberg. 2009. Semiautomated curation of protein subcellular localization: A text mining-based approach to gene ontology (GO) cellular component curation. BMC Bioinformatics 10: 228.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 228
-
-
Van Auken, K.1
Jaffery, J.2
Chan, J.3
Muller, H.-M.4
Sternberg, P.W.5
-
259
-
-
0017500411
-
A theoretical basis for the use of co-occurrence data in information retrieval
-
van Rijsbergen, C. J. 1977. A theoretical basis for the use of co-occurrence data in information retrieval. Journal of Documentation 33 (2): 106-119.
-
(1977)
Journal of Documentation
, vol.33
, Issue.2
, pp. 106-119
-
-
van Rijsbergen, C.J.1
-
260
-
-
0004217877
-
Information Retrieval
-
London: Butterworth.
-
van Rijsbergen, C. J. 1979. Information Retrieval. London: Butterworth.
-
(1979)
-
-
van Rijsbergen, C.J.1
-
261
-
-
0003450542
-
The Nature of Statistical Learning Theory
-
New York: Springer.
-
Vapnik, V. 1995. The Nature of Statistical Learning Theory. New York: Springer.
-
(1995)
-
-
Vapnik, V.1
-
262
-
-
79960748455
-
Detecting speculative language using syntactic dependencies and logistic regression
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Vlachos, A., and M. Craven. Detecting speculative language using syntactic dependencies and logistic regression. In Proceedings of the Fourteenth Conference on Computational Natural Language Learning. Stroudsburg, PA: Association for Computational Linguistics, 2010, 18-25.
-
(2010)
Proceedings of the Fourteenth Conference on Computational Natural Language Learning.
, pp. 18-25
-
-
Vlachos, A.1
Craven, M.2
-
263
-
-
84862273238
-
Search-based structured prediction applied to biomedical event extraction
-
In, Stroudsburg, PA: Association for Computational Linguistics
-
Vlachos, A., and M. Craven. Search-based structured prediction applied to biomedical event extraction. In Proceedings of the Fifteenth Conference on Computational Natural Language Learning. Stroudsburg, PA: Association for Computational Linguistics, 2011, 49-57.
-
(2011)
Proceedings of the Fifteenth Conference on Computational Natural Language Learning.
, pp. 49-57
-
-
Vlachos, A.1
Craven, M.2
-
264
-
-
0035337361
-
Using concepts in literature-based discovery: Simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries
-
Weeber, M., H. Klein, L. T. de Jong-van den Berg, and R. Vos. 2001. Using concepts in literature-based discovery: Simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries. Journal of the American Society for Information Science 52 (7): 548-557.
-
(2001)
Journal of the American Society for Information Science
, vol.52
, Issue.7
, pp. 548-557
-
-
Weeber, M.1
Klein, H.2
de Jong-van den Berg, L.T.3
Vos, R.4
-
265
-
-
0000545303
-
An information measure of retrieval performance
-
Wilbur, W. J. 1992. An information measure of retrieval performance. Information Systems 17 (4): 283-298.
-
(1992)
Information Systems
, vol.17
, Issue.4
, pp. 283-298
-
-
Wilbur, W.J.1
-
266
-
-
0029989103
-
An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology text
-
Wilbur, W. J., and Y. Yang. 1996. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology text. Computers in Biology and Medicine 26 (3): 209-222.
-
(1996)
Computers in Biology and Medicine
, vol.26
, Issue.3
, pp. 209-222
-
-
Wilbur, W.J.1
Yang, Y.2
-
267
-
-
0003756969
-
Managing Gigabytes, Compressing and Indexing Documents and Images
-
2nd ed. Burlington, MA: Morgan Kaufmann.
-
Witten, I. H., A. Moffat, and T. C. Bell. 1999. Managing Gigabytes, Compressing and Indexing Documents and Images. 2nd ed. Burlington, MA: Morgan Kaufmann.
-
(1999)
-
-
Witten, I.H.1
Moffat, A.2
Bell, T.C.3
-
268
-
-
84895567825
-
-
WormBase.
-
WormBase. http://www.wormbase.org/, 2011.
-
(2011)
-
-
-
269
-
-
1342330525
-
Knowledge discovery by automated identification and ranking of implicit relationships
-
Wren, J. D., R. Bekeredjian, J. A. Stewart, R. V. Shohet, and H. R. Garner. 2004. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20 (3): 389398.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 389398
-
-
Wren, J.D.1
Bekeredjian, R.2
Stewart, J.A.3
Shohet, R.V.4
Garner, H.R.5
-
270
-
-
0033971642
-
DIP: The database of interacting proteins
-
Xenarios, I., D. Rice, L. Salwinski, M. Baron, E. Marcotte, and D. Eisenberg. 2000. DIP: The database of interacting proteins. Nucleic Acids Research 28: 289-291.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.2
Salwinski, L.3
Baron, M.4
Marcotte, E.5
Eisenberg, D.6
-
272
-
-
50549096372
-
Yale image finder (YIF): A new search engine for retrieving biomedical images
-
Xu, S., J. McCusker, and M. Krauthammer. 2008. Yale image finder (YIF): A new search engine for retrieving biomedical images. Bioinformatics 24 (17): 1968-1970.
-
(2008)
Bioinformatics
, vol.24
, Issue.17
, pp. 1968-1970
-
-
Xu, S.1
McCusker, J.2
Krauthammer, M.3
-
273
-
-
37149035254
-
Tagging sentence boundaries in biomedical literature
-
In, A. Gelbukh, ed., New York: Springer
-
Xuan, W., S. Watson, and F. Meng. 2007. Tagging sentence boundaries in biomedical literature. In Computational Linguistics and Intelligent Text Processing. vol. 4394. A. Gelbukh, ed., New York: Springer, 186-195.
-
(2007)
Computational Linguistics and Intelligent Text Processing.
, vol.4394
, pp. 186-195
-
-
Xuan, W.1
Watson, S.2
Meng, F.3
-
274
-
-
27144441097
-
An evaluation of statistical approaches to text categorization
-
Yang, Y. 1999. An evaluation of statistical approaches to text categorization. Information Retrieval 1 (1-2): 69-90.
-
(1999)
Information Retrieval
, vol.1
, Issue.1-2
, pp. 69-90
-
-
Yang, Y.1
-
276
-
-
0028461554
-
An example-based mapping method for text categorization and retrieval
-
Yang, Y., and C. G. Chute. 1994. An example-based mapping method for text categorization and retrieval. ACM Transactions on Information Systems 12 (3): 252-277.
-
(1994)
ACM Transactions on Information Systems
, vol.12
, Issue.3
, pp. 252-277
-
-
Yang, Y.1
Chute, C.G.2
-
278
-
-
0742306576
-
Background and overview for KDD Cup 2002 task 1: Information extraction from biomedical articles
-
Yeh, A., L. Hirschman, and A. Morgan. 2002. Background and overview for KDD Cup 2002 task 1: Information extraction from biomedical articles. SIGKDD Explorations 4 (2): 87-89.
-
(2002)
SIGKDD Explorations
, vol.4
, Issue.2
, pp. 87-89
-
-
Yeh, A.1
Hirschman, L.2
Morgan, A.3
-
279
-
-
33947359082
-
BioCreative Task 1a: Gene mention finding evaluation
-
May
-
Yeh, A., A. Morgan, M. Colosimo, and L. Hirschman. (May 2005). BioCreative Task 1a: Gene mention finding evaluation. BMC Bioinformatics 6 (suppl. 1): S2.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
Yeh, A.1
Morgan, A.2
Colosimo, M.3
Hirschman, L.4
-
280
-
-
33747886579
-
Accessing bioscience images from abstract sentences
-
Yu, H., and M. Lee. 2006. Accessing bioscience images from abstract sentences. Bioinformatics 22 (14): e547-e556.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Yu, H.1
Lee, M.2
-
281
-
-
78049274221
-
Automatic figure ranking and user interfacing for intelligent figure search
-
Yu, H., F. Liu, and B. Ramesh. 2010. Automatic figure ranking and user interfacing for intelligent figure search. PLoS ONE 5 (10): e12983.
-
(2010)
PLoS ONE
, vol.5
, Issue.10
-
-
Yu, H.1
Liu, F.2
Ramesh, B.3
-
282
-
-
0037138406
-
MINT: A Molecular INTeraction database
-
Zanzoni, A., L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, and G. Cesareni. 2002. MINT: A Molecular INTeraction database. FEBS Letters 513 (1): 135-140.
-
(2002)
FEBS Letters
, vol.513
, Issue.1
, pp. 135-140
-
-
Zanzoni, A.1
Montecchi-Palazzi, L.2
Quondam, M.3
Ausiello, G.4
Helmer-Citterich, M.5
Cesareni, G.6
-
283
-
-
77951252234
-
Introduction to Semi-Supervised Learning
-
San Rafael, CA: Morgan and Claypool.
-
Zhu, X., and A. B. Goldberg. 2009. Introduction to Semi-Supervised Learning. San Rafael, CA: Morgan and Claypool.
-
(2009)
-
-
Zhu, X.1
Goldberg, A.B.2
-
284
-
-
36348990139
-
Frontiers of biomedical text mining: Current progress
-
Zweigenbaum, P., D. Demner-Fushman, H. Yu, and K. B. Cohen. 2007. Frontiers of biomedical text mining: Current progress. Briefings in Bioinformatics 8: 358-375.
-
(2007)
Briefings in Bioinformatics
, vol.8
, pp. 358-375
-
-
Zweigenbaum, P.1
Demner-Fushman, D.2
Yu, H.3
Cohen, K.B.4
|