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Results: 19

1.

Estimation of glance from EEG for cursor control.

Tan T, Hakenberg JP, Guan C.

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2919-23. doi: 10.1109/EMBC.2013.6610151.

PMID:
24110338
[PubMed - in process]
2.

Literature mining solutions for life science research.

Hakenberg J, Nenadic G, Rebholz-Schuhmann D, Kim JD.

Adv Bioinformatics. 2013;2013:320436. doi: 10.1155/2013/320436. Epub 2013 Jan 8. No abstract available.

PMID:
23365570
[PubMed]
Free PMC Article
3.

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions.

Hakenberg J, Voronov D, Nguyên VH, Liang S, Anwar S, Lumpkin B, Leaman R, Tari L, Baral C.

J Biomed Inform. 2012 Oct;45(5):842-50. doi: 10.1016/j.jbi.2012.04.006. Epub 2012 Apr 30.

PMID:
22564364
[PubMed - indexed for MEDLINE]
Free Article
4.

The GNAT library for local and remote gene mention normalization.

Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, Schroeder M, Gonzalez G, Nenadic G, Bergman CM.

Bioinformatics. 2011 Oct 1;27(19):2769-71. doi: 10.1093/bioinformatics/btr455. Epub 2011 Aug 3.

PMID:
21813477
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.

Tikk D, Thomas P, Palaga P, Hakenberg J, Leser U.

PLoS Comput Biol. 2010 Jul 1;6:e1000837. doi: 10.1371/journal.pcbi.1000837.

PMID:
20617200
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Efficient extraction of protein-protein interactions from full-text articles.

Hakenberg J, Leaman R, Vo NH, Jonnalagadda S, Sullivan R, Miller C, Tari L, Baral C, Gonzalez G.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):481-94. doi: 10.1109/TCBB.2010.51.

PMID:
20498514
[PubMed - indexed for MEDLINE]
7.

Synthesis of pharmacokinetic pathways through knowledge acquisition and automated reasoning.

Tari L, Anwar S, Liang S, Hakenberg J, Baral C.

Pac Symp Biocomput. 2010:465-76.

PMID:
19908398
[PubMed - indexed for MEDLINE]
Free Article
8.

GoGene: gene annotation in the fast lane.

Plake C, Royer L, Winnenburg R, Hakenberg J, Schroeder M.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W300-4. doi: 10.1093/nar/gkp429. Epub 2009 May 22.

PMID:
19465383
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Querying parse tree database of Medline text to synthesize user-specific biomolecular networks.

Tari L, Hakenberg J, Gonzalez G, Baral C.

Pac Symp Biocomput. 2009:87-98.

PMID:
19209697
[PubMed - indexed for MEDLINE]
Free Article
10.

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.

Alexopoulou D, Andreopoulos B, Dietze H, Doms A, Gandon F, Hakenberg J, Khelif K, Schroeder M, Wächter T.

BMC Bioinformatics. 2009 Jan 21;10:28. doi: 10.1186/1471-2105-10-28.

PMID:
19159460
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Introducing meta-services for biomedical information extraction.

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A.

Genome Biol. 2008;9 Suppl 2:S6. doi: 10.1186/gb-2008-9-s2-s6. Epub 2008 Sep 1.

PMID:
18834497
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Overview of BioCreative II gene normalization.

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L.

Genome Biol. 2008;9 Suppl 2:S3. doi: 10.1186/gb-2008-9-s2-s3. Epub 2008 Sep 1.

PMID:
18834494
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Gene mention normalization and interaction extraction with context models and sentence motifs.

Hakenberg J, Plake C, Royer L, Strobelt H, Leser U, Schroeder M.

Genome Biol. 2008;9 Suppl 2:S14. doi: 10.1186/gb-2008-9-s2-s14. Epub 2008 Sep 1.

PMID:
18834492
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Inter-species normalization of gene mentions with GNAT.

Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G.

Bioinformatics. 2008 Aug 15;24(16):i126-132. doi: 10.1093/bioinformatics/btn299.

PMID:
18689813
[PubMed - indexed for MEDLINE]
Free Article
15.

AliBaba: PubMed as a graph.

Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U.

Bioinformatics. 2006 Oct 1;22(19):2444-5. Epub 2006 Jul 26.

PMID:
16870931
[PubMed - indexed for MEDLINE]
Free Article
16.

What makes a gene name? Named entity recognition in the biomedical literature.

Leser U, Hakenberg J.

Brief Bioinform. 2005 Dec;6(4):357-69.

PMID:
16420734
[PubMed - indexed for MEDLINE]
Free Article
17.

Systematic feature evaluation for gene name recognition.

Hakenberg J, Bickel S, Plake C, Brefeld U, Zahn H, Faulstich L, Leser U, Scheffer T.

BMC Bioinformatics. 2005;6 Suppl 1:S9. Epub 2005 May 24.

PMID:
15960843
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Finding kinetic parameters using text mining.

Hakenberg J, Schmeier S, Kowald A, Klipp E, Leser U.

OMICS. 2004 Summer;8(2):131-52.

PMID:
15268772
[PubMed - indexed for MEDLINE]
19.

MAPPP: MHC class I antigenic peptide processing prediction.

Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhütter HG, Kloetzel PM, Kaufmann SH, Mollenkopf HJ.

Appl Bioinformatics. 2003;2(3):155-8.

PMID:
15130801
[PubMed - indexed for MEDLINE]

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