Jörg Hakenberg
Jörg Hakenberg
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Genomic hallmarks and structural variation in metastatic prostate cancer
DA Quigley, HX Dang, SG Zhao, P Lloyd, R Aggarwal, JJ Alumkal, A Foye, ...
Cell 174 (3), 758-769. e9, 2018
Overview of BioCreative II gene normalization
AA Morgan, Z Lu, X Wang, AM Cohen, J Fluck, P Ruch, A Divoli, K Fundel, ...
Genome biology 9, 1-19, 2008
Predicting the clinical impact of human mutation with deep neural networks
L Sundaram, H Gao, SR Padigepati, JF McRae, Y Li, JA Kosmicki, ...
Nature genetics 50 (8), 1161-1170, 2018
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases
R Chen, L Shi, J Hakenberg, B Naughton, P Sklar, J Zhang, H Zhou, ...
Nature biotechnology 34 (5), 531-538, 2016
What makes a gene name? Named entity recognition in the biomedical literature
U Leser, J Hakenberg
Briefings in bioinformatics 6 (4), 357-369, 2005
A comprehensive benchmark of kernel methods to extract protein–protein interactions from literature
D Tikk, P Thomas, P Palaga, J Hakenberg, U Leser
PLoS computational biology 6 (7), e1000837, 2010
AliBaba: PubMed as a graph
C Plake, T Schiemann, M Pankalla, J Hakenberg, U Leser
Bioinformatics 22 (19), 2444-2445, 2006
Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease
B Chen, C Solis‐Villa, J Hakenberg, W Qiao, RR Srinivasan, M Yasuda, ...
Human mutation 37 (11), 1215-1222, 2016
Inter-species normalization of gene mentions with GNAT
J Hakenberg, C Plake, R Leaman, M Schroeder, G Gonzalez
Bioinformatics 24 (16), i126-i132, 2008
MAPPP: MHC class I antigenic peptide processing prediction.
J Hakenberg, AK Nussbaum, H Schild, HG Rammensee, C Kuttler, ...
Applied bioinformatics 2 (3), 155-158, 2003
The GNAT library for local and remote gene mention normalization
J Hakenberg, M Gerner, M Haeussler, I Solt, C Plake, M Schroeder, ...
Bioinformatics 27 (19), 2769-2771, 2011
Introducing meta-services for biomedical information extraction
F Leitner, M Krallinger, C Rodriguez-Penagos, J Hakenberg, C Plake, ...
Genome biology 9, 1-11, 2008
Gene mention normalization and interaction extraction with context models and sentence motifs
J Hakenberg, C Plake, L Royer, H Strobelt, U Leser, M Schroeder
Genome biology 9, 1-16, 2008
Disease-associated variants in different categories of disease located in distinct regulatory elements
M Ma, Y Ru, LS Chuang, NY Hsu, LS Shi, J Hakenberg, WY Cheng, ...
BMC genomics 16, 1-13, 2015
Towards effective sentence simplification for automatic processing of biomedical text
S Jonnalagadda, L Tari, J Hakenberg, C Baral, G Gonzalez
arXiv preprint arXiv:1001.4277, 2010
Efficient extraction of protein-protein interactions from full-text articles
J Hakenberg, R Leaman, NH Vo, S Jonnalagadda, R Sullivan, C Miller, ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics 7 (3), 481-494, 2010
LLL’05 challenge: Genic interaction extraction-identification of language patterns based on alignment and finite state automata
J Hakenberg, C Plake, U Leser, H Kirsch, D Rebholz-Schuhmann
Proceedings of LLL. Bonn, Germany, 38-45, 2005
Finding kinetic parameters using text mining
J Hakenberg, S Schmeier, A Kowald, E Klipp, U Leser
OMICS: A Journal of Integrative Biology 8 (2), 131-152, 2004
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks
BS Glicksberg, L Li, MA Badgeley, K Shameer, R Kosoy, ND Beckmann, ...
Bioinformatics 32 (12), i101-i110, 2016
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
D Alexopoulou, B Andreopoulos, H Dietze, A Doms, F Gandon, ...
BMC bioinformatics 10, 1-15, 2009
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