-
1
-
-
33748372941
-
Automatic document classification of biological literature
-
D. Chen, H.M. Müller, and P.W. Sternberg, "Automatic Document Classification of Biological Literature," BMC Bioinformatics, vol.7, p. 370, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 370
-
-
Chen, D.1
Müller, H.M.2
Sternberg, P.W.3
-
2
-
-
33947258447
-
ProMiner: Rule-based protein and gene entity recognition
-
D. Hanisch, K. Fundel, H.T. Mevissen, R. Zimmer, and J. Fluck, "ProMiner: Rule-Based Protein and Gene Entity Recognition," BMC Bioinformatics, vol.6, pp. S14-S22, 2005.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Hanisch, D.1
Fundel, K.2
Mevissen, H.T.3
Zimmer, R.4
Fluck, J.5
-
3
-
-
8444226721
-
Biomedical named entity recognition using two-phase model based on SVMs
-
K.J. Lee, Y.S. Hwang, S. Kim, and H.C. Rim, "Biomedical Named Entity Recognition Using Two-Phase Model Based on SVMs," J. Biomedical Informatics, vol.37, pp. 436-447, 2004.
-
(2004)
J. Biomedical Informatics
, vol.37
, pp. 436-447
-
-
Lee, K.J.1
Hwang, Y.S.2
Kim, S.3
Rim, H.C.4
-
5
-
-
12144290446
-
GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data
-
Feb.
-
A. Rzhetsky, I. Iossifov, T. Koike, M. Krauthammer, P. Kra, M. Morris, H. Yu, P.A. Duboué,W.Weng, W.J. Wilbur, V. Hatzivassiloglou, and C. Friedman, "GeneWays: A System for Extracting, Analyzing, Visualizing, and Integrating Molecular Pathway Data," J. Biomedical Informatics, vol.37, pp. 43-53, Feb. 2004.
-
(2004)
J. Biomedical Informatics
, vol.37
, pp. 43-53
-
-
Rzhetsky, A.1
Iossifov, I.2
Koike, T.3
Krauthammer, M.4
Kra, P.5
Morris, M.6
Yu, H.7
Duboué, P.A.8
Weng, W.9
Wilbur, W.J.10
Hatzivassiloglou, V.11
Friedman, C.12
-
6
-
-
6344229209
-
Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in alzheimer's disease
-
Oct.
-
M. Krauthammer, C.A. Kaufmann, T.C. Gilliam, and A. Rzhetsky, "Molecular Triangulation: Bridging Linkage and Molecular-Network Information for Identifying Candidate Genes in Alzheimer's Disease," Proc. Nat'l Academy of Sciences USA, vol.101, pp. 15148- 15153, Oct. 2004.
-
(2004)
Proc. Nat'l Academy of Sciences USA
, vol.101
, pp. 15148-15153
-
-
Krauthammer, M.1
Kaufmann, C.A.2
Gilliam, T.C.3
Rzhetsky, A.4
-
7
-
-
0033655017
-
Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in medline abstracts
-
B.J. Stapley and G. Benoit, "Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts," Proc. Pacific Symp. Biocomputing, pp. 529-540, 2000.
-
(2000)
Proc. Pacific Symp. Biocomputing
, pp. 529-540
-
-
Stapley, B.J.1
Benoit, G.2
-
8
-
-
70349571707
-
Mining protein-protein interactions from published literature using linguamatics i2e
-
(Clifton, NJ)
-
J. Bandy, D. Milward, and S. McQuay, "Mining Protein-Protein Interactions from Published Literature Using Linguamatics I2E," Methods in Molecular Biology (Clifton, NJ), vol.563, pp. 3-13, 2009.
-
(2009)
Methods in Molecular Biology
, vol.563
, pp. 3-13
-
-
Bandy, J.1
Milward, D.2
McQuay, S.3
-
9
-
-
0002284942
-
Identifying the interaction between genes and gene products based on frequently seen verbs in medline abstracts
-
T. Sekimizu, H. Park, and J. Tsujii, "Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts," Proc. Workshop Genome Informatics, vol.9, pp. 62-71, 1998.
-
(1998)
Proc. Workshop Genome Informatics
, vol.9
, pp. 62-71
-
-
Sekimizu, T.1
Park, H.2
Tsujii, J.3
-
10
-
-
84872980656
-
Intex: A syntactic role driven protein-protein interaction extractor for bio-medical text
-
S.T. Ahmed, D. Chidambaram, H. Davulcu, and C. Baral, "Intex: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text," Proc. ISMB BioLINK Special Interest Group on Text Data Mining and the ACL Workshop Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, pp. 54-61, 2005.
-
(2005)
Proc. ISMB BioLINK Special Interest Group on Text Data Mining and the ACL Workshop Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
, pp. 54-61
-
-
Ahmed, S.T.1
Chidambaram, D.2
Davulcu, H.3
Baral, C.4
-
11
-
-
0347724100
-
GIS: A biomedical text-mining system for gene information discovery
-
Jan.
-
J. Chiang, H. Yu, and H. Hsu, "GIS: A Biomedical Text-Mining System for Gene Information Discovery," Bioinformatics, vol.20, pp. 120-121, Jan. 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 120-121
-
-
Chiang, J.1
Yu, H.2
Hsu, H.3
-
12
-
-
38049067148
-
Protein-protein interaction extraction: A supervised learning approach
-
J. Xiao, J. Su, G.D. Zhou, and C.L. Tan, "Protein-Protein Interaction Extraction: A Supervised Learning Approach," Proc. Symp. Semantic Mining in Biomedicine, pp. 51-59, 2005.
-
(2005)
Proc. Symp. Semantic Mining in Biomedicine
, pp. 51-59
-
-
Xiao, J.1
Su, J.2
Zhou, G.D.3
Tan, C.L.4
-
13
-
-
33947304181
-
Overview of BioCreAtIvE: Critical assessment of information extraction for biology
-
L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia, "Overview of BioCreAtIvE: Critical Assessment of Information Extraction for Biology," BMC Bioinformatics, vol.6, suppl 1, pp. S1-S10, 2005.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
Hirschman, L.1
Yeh, A.2
Blaschke, C.3
Valencia, A.4
-
14
-
-
51049088875
-
Overview of the protein-protein interaction annotation extraction task of biocreative II
-
M. Krallinger, F. Leitner, C. Rodriguez-Penagos, and A. Valencia, "Overview of the Protein-Protein Interaction Annotation Extraction Task of Biocreative II," Genome Biology, vol.9, suppl 2, pp. S4- S22, 2008.
-
(2008)
Genome Biology
, vol.9
, Issue.SUPPL. 2
-
-
Krallinger, M.1
Leitner, F.2
Rodriguez-Penagos, C.3
Valencia, A.4
-
15
-
-
75249101080
-
Evaluation of linguistic features useful in extraction of interactions from pubmed; Application to annotating known, high-throughput and predicted interactions in i2d
-
Jan.
-
Y. Niu, D. Otasek, and I. Jurisica, "Evaluation of Linguistic Features Useful in Extraction of Interactions from PubMed; Application to Annotating Known, High-Throughput and Predicted Interactions in I2D," Bioinformatics, vol.26, pp. 111-119, Jan. 2010.
-
(2010)
Bioinformatics
, vol.26
, pp. 111-119
-
-
Niu, Y.1
Otasek, D.2
Jurisica, I.3
-
17
-
-
0742321913
-
Mining the biomedical literature in the genomic era: An overview
-
H. Shatkay and R. Feldman, "Mining the Biomedical Literature in the Genomic Era: An Overview," J. Computational Biology, vol.10, pp. 821-855, 2003.
-
(2003)
J. Computational Biology
, vol.10
, pp. 821-855
-
-
Shatkay, H.1
Feldman, R.2
-
18
-
-
0033292011
-
Automatic extraction of biological information from scientific text: Protein-protein interactions
-
C. Blaschke, M.A. Andrade, C. Ouzounis, and A. Valencia, "Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions," Proc. Int'l Conf. Intelligent Systems for Molecular Biology, pp. 60-67, 1999.
-
(1999)
Proc. Int'l Conf. Intelligent Systems for Molecular Biology
, pp. 60-67
-
-
Blaschke, C.1
Andrade, M.A.2
Ouzounis, C.3
Valencia, A.4
-
20
-
-
9144244232
-
MODBASE, a database of annotated comparative protein structure models, and associated resources
-
U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, and A. Sali, "MODBASE, a Database of Annotated Comparative Protein Structure Models, and Associated Resources," Nucleic Acids Research, vol.32, pp. D217-D222, 2004.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Pieper, U.1
Eswar, N.2
Braberg, H.3
Madhusudhan, M.S.4
Davis, F.P.5
Stuart, A.C.6
Mirkovic, N.7
Rossi, A.8
Marti-Renom, M.A.9
Fiser, A.10
Webb, B.11
Greenblatt, D.12
Huang, C.C.13
Ferrin, T.E.14
Sali, A.15
-
21
-
-
0033657262
-
Automatic extraction of protein interactions from scientific abstracts
-
J. Thomas, D. Milward, C. Ouzounis, S. Pulman, and M. Carroll, "Automatic Extraction of Protein Interactions from Scientific Abstracts," Proc. Pacific Symp. Biocomputing, pp. 541-552, 2000.
-
(2000)
Proc. Pacific Symp. Biocomputing
, pp. 541-552
-
-
Thomas, J.1
Milward, D.2
Ouzounis, C.3
Pulman, S.4
Carroll, M.5
-
22
-
-
0035236048
-
GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles
-
(Oxford, England)
-
C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky, "GENIES: A Natural-Language Processing System for the Extraction of Molecular Pathways from Journal Articles," Bioinformatics (Oxford, England), vol.17, pp. 74-82, 2001.
-
(2001)
Bioinformatics
, vol.17
, pp. 74-82
-
-
Friedman, C.1
Kra, P.2
Yu, H.3
Krauthammer, M.4
Rzhetsky, A.5
-
23
-
-
1842559914
-
Extracting human protein interactions from MEDLINE using a full-sentence parser
-
Mar.
-
N. Daraselia, A. Yuryev, S. Egorov, S. Novichkova, A. Nikitin, and I. Mazo, "Extracting Human Protein Interactions from MEDLINE Using a Full-Sentence Parser," Bioinformatics, vol.20, pp. 604-611, Mar. 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 604-611
-
-
Daraselia, N.1
Yuryev, A.2
Egorov, S.3
Novichkova, S.4
Nikitin, A.5
Mazo, I.6
-
24
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
D.R. Rhodes, S.A. Tomlins, S. Varambally, V. Mahavisno, T. Barrette, S. Kalyana-Sundaram, D. Ghosh, A. Pandey, and A.M. Chinnaiyan, "Probabilistic Model of the Human Protein-Protein Interaction Network," Nature Biotechnology, vol.23, pp. 951-959, 2005.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 951-959
-
-
Rhodes, D.R.1
Tomlins, S.A.2
Varambally, S.3
Mahavisno, V.4
Barrette, T.5
Kalyana-Sundaram, S.6
Ghosh, D.7
Pandey, A.8
Chinnaiyan, A.M.9
-
25
-
-
1842765629
-
Prediction of protein-protein interaction sites using support vector machines
-
Feb.
-
A. Koike and T. Takagi, "Prediction of Protein-Protein Interaction Sites Using Support Vector Machines," Protein Eng., Design and Selection, vol.17, pp. 165-173, Feb. 2004.
-
(2004)
Protein Eng., Design and Selection
, vol.17
, pp. 165-173
-
-
Koike, A.1
Takagi, T.2
-
26
-
-
33947305118
-
Identifying gene and protein mentions in text using conditional random fields
-
R. McDonald and F. Pereira, "Identifying Gene and Protein Mentions in Text Using Conditional Random Fields," BMC Bioinformatics, vol.6, suppl 1, pp. S6-S12, 2005.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
McDonald, R.1
Pereira, F.2
-
27
-
-
33645106979
-
Automatic term list generation for entity tagging
-
T. Sandler, A.I. Schein, and L.H. Ungar, "Automatic Term List Generation for Entity Tagging," Bioinformatics, vol.22, pp. 651-657, 2006.
-
(2006)
Bioinformatics
, vol.22
, pp. 651-657
-
-
Sandler, T.1
Schein, A.I.2
Ungar, L.H.3
-
28
-
-
41349103793
-
Overview of BioCreative II gene normalization
-
A. Morgan, Z. Lu, X. Wang, A. Cohen, J. Fluck, P. Ruch, A. Divoli, K. Fundel, R. Leaman, J. Hakenberg, C. Sun, H. Liu, R. Torres, M. Krauthammer, W. Lau, H. Liu, C. Hsu, M. Schuemie, K.B. Cohen, and L. Hirschman, "Overview of BioCreative II Gene Normalization," Genome Biology, vol.9, pp. S3-S21, 2008.
-
(2008)
Genome Biology
, vol.9
-
-
Morgan, A.1
Lu, Z.2
Wang, X.3
Cohen, A.4
Fluck, J.5
Ruch, P.6
Divoli, A.7
Fundel, K.8
Leaman, R.9
Hakenberg, J.10
Sun, C.11
Liu, H.12
Torres, R.13
Krauthammer, M.14
Lau, W.15
Liu, H.16
Hsu, C.17
Schuemie, M.18
Cohen, K.B.19
Hirschman, L.20
more..
-
29
-
-
51049088874
-
Overview of BioCreative II gene mention recognition
-
L. Smith, L. Tanabe, R. Ando, C. Kuo, I. Chung, C. Hsu, Y. Lin, R. Klinger, C. Friedrich, K. Ganchev, M. Torii, H. Liu, B. Haddow, C. Struble, R. Povinelli, A. Vlachos, W. Baumgartner, L. Hunter, B. Carpenter, R. Tsai, H. Dai, F. Liu, Y. Chen, C. Sun, S. Katrenko, P. Adriaans, C. Blaschke, R. Torres, M. Neves, P. Nakov, A. Divoli, M. Mana-Lopez, J. Mata, and W.J. Wilbur, "Overview of BioCreative II Gene Mention Recognition," Genome Biology, vol.9, pp. S2-S20, 2008.
-
(2008)
Genome Biology
, vol.9
-
-
Smith, L.1
Tanabe, L.2
Ando, R.3
Kuo, C.4
Chung, I.5
Hsu, C.6
Lin, Y.7
Klinger, R.8
Friedrich, C.9
Ganchev, K.10
Torii, M.11
Liu, H.12
Haddow, B.13
Struble, C.14
Povinelli, R.15
Vlachos, A.16
Baumgartner, W.17
Hunter, L.18
Carpenter, B.19
Tsai, R.20
Dai, H.21
Liu, F.22
Chen, Y.23
Sun, C.24
Katrenko, S.25
Adriaans, P.26
Blaschke, C.27
Torres, R.28
Neves, M.29
Nakov, P.30
Divoli, A.31
Mana-Lopez, M.32
Mata, J.33
Wilbur, W.J.34
more..
-
30
-
-
84874285402
-
{BioLexicon}: {A} lexical resource for the biology domain
-
Y. Sasaki, S. Montemagni, P. Pezik, D. Schuhman, J. Mcnaught, and S. Ananiadou, "{BioLexicon}: {A} Lexical Resource for the Biology Domain," Proc. Third Int'l Symp. Semantic Mining in Biomedicine (SMBM '08), pp. 109-116, 2008.
-
(2008)
Proc. Third Int'l Symp. Semantic Mining in Biomedicine (SMBM '08)
, pp. 109-116
-
-
Sasaki, Y.1
Montemagni, S.2
Pezik, P.3
Schuhman, D.4
McNaught, J.5
Ananiadou, S.6
-
31
-
-
0036579940
-
Mapping abbreviations to full forms in biomedical articles
-
May
-
H. Yu, G. Hripcsak, and C. Friedman, "Mapping Abbreviations to Full Forms in Biomedical Articles," J. Am. Medical Informatics Assoc., vol.9, pp. 262-272, May 2002.
-
(2002)
J. Am. Medical Informatics Assoc.
, vol.9
, pp. 262-272
-
-
Yu, H.1
Hripcsak, G.2
Friedman, C.3
-
32
-
-
1242349373
-
Extracting synonymous gene and protein terms from biological literature
-
(Oxford, England)
-
H. Yu and E. Agichtein, "Extracting Synonymous Gene and Protein Terms from Biological Literature," Bioinformatics (Oxford, England), vol.19, suppl 1, pp. i340-i349, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Yu, H.1
Agichtein, E.2
-
33
-
-
84976825385
-
Algorithms for the longest common subsequence problem
-
D.S. Hirschberg, "Algorithms for the Longest Common Subsequence Problem," J. ACM, vol.24, pp. 664-675, 1977.
-
(1977)
J. ACM
, vol.24
, pp. 664-675
-
-
Hirschberg, D.S.1
-
34
-
-
0012866045
-
The state of record linkage and current research problems
-
Statistical Research Division, United States Census Bureau
-
W.E. Winkler, "The State of Record Linkage and Current Research Problems," Technical Report RR99-04, Statistical Research Division, United States Census Bureau, 1999.
-
(1999)
Technical Report RR99-04
-
-
Winkler, W.E.1
-
35
-
-
0037138406
-
MINT: A molecular INTeraction database
-
Feb.
-
A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, and G. Cesareni, "MINT: a Molecular INTeraction Database," FEBS Letters, vol.513, pp. 135-140, Feb. 2002.
-
(2002)
FEBS Letters
, vol.513
, pp. 135-140
-
-
Zanzoni, A.1
Montecchi-Palazzi, L.2
Quondam, M.3
Ausiello, G.4
Helmer-Citterich, M.5
Cesareni, G.6
-
36
-
-
33749588452
-
A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations
-
H. Yu, W. Kim, V. Hatzivassiloglou, and J. Wilbur, "A Large Scale, Corpus-Based Approach for Automatically Disambiguating Biomedical Abbreviations," ACM Trans. Information Systems, vol.24, pp. 380-404, 2006.
-
(2006)
ACM Trans. Information Systems
, vol.24
, pp. 380-404
-
-
Yu, H.1
Kim, W.2
Hatzivassiloglou, V.3
Wilbur, J.4
-
37
-
-
33847616032
-
Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles
-
H. Yu, W. Kim, V. Hatzivassiloglou, and W.J. Wilbur, "Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations and Acronyms in Full-Text Biomedical Journal Articles," J. Biomedical Informatics, vol.40, pp. 150-159, 2007.
-
(2007)
J. Biomedical Informatics
, vol.40
, pp. 150-159
-
-
Yu, H.1
Kim, W.2
Hatzivassiloglou, V.3
Wilbur, W.J.4
-
38
-
-
4944229711
-
GENIA corpus- semantically annotated corpus for bio-textmining
-
J. Kim, T. Ohta, Y. Tateisi, and J. Tsujii, "GENIA Corpus- Semantically Annotated Corpus for Bio-Textmining," Bioinformatics, vol.19, suppl 1, pp. i180-i182, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Kim, J.1
Ohta, T.2
Tateisi, Y.3
Tsujii, J.4
-
39
-
-
25144520247
-
ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text
-
July
-
B. Settles, "ABNER: An Open Source Tool for Automatically Tagging Genes, Proteins and Other Entity Names in Text," Bioinformatics, vol.21, pp. 3191-3192, July 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 3191-3192
-
-
Settles, B.1
-
40
-
-
0742324214
-
Rule-based extraction of experimental evidence in the biomedical domain: The KDD Cup 2002 (Task 1)
-
Y. Regev, M. Finkelstein-Landau, R. Feldman, M. Gorodetsky, X. Zheng, S. Levy, R. Charlab, C. Lawrence, R.A. Lippert, Q. Zhang, and H. Shatkay, "Rule-Based Extraction of Experimental Evidence in the Biomedical Domain: The KDD Cup 2002 (Task 1)," ACM SIGKDD Exploration Newsletter, vol.4, pp. 90-92, 2002.
-
(2002)
ACM SIGKDD Exploration Newsletter
, vol.4
, pp. 90-92
-
-
Regev, Y.1
Finkelstein-Landau, M.2
Feldman, R.3
Gorodetsky, M.4
Zheng, X.5
Levy, S.6
Charlab, R.7
Lawrence, C.8
Lippert, R.A.9
Zhang, Q.10
Shatkay, H.11
-
41
-
-
33747886579
-
Accessing bioscience images from abstract sentences
-
H. Yu and M. Lee, "Accessing Bioscience Images from Abstract Sentences," Bioinformatics, vol.22, pp. e547-e556, 2006.
-
(2006)
Bioinformatics
, vol.22
-
-
Yu, H.1
Lee, M.2
|