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1

MOLECULAR EVENT EXTRACTION FROM LINK GRAMMAR PARSE TREES IN THE BIONLP’09 SHARED TASK

Jörg Hakenberg, Illés Solt, Domonkos Tikk, Võ Há Nguyên, Luis Tari, Quang Long Nguyen, Chitta Baral, Ulf Leser

Journal:

Computational Intelligence

Année:

2011

Langue:

english

Fichier:

PDF, 364 KB

english, 2011

2

[ACM Press the 12th International Conference - Saint Petersburg, Russia (2009.03.24-2009.03.26)] Proceedings of the 12th International Conference on Extending Database Technology Advances in Database Technology - EDBT '09 - High-performance information extraction with AliBaba

Palaga, Peter, Nguyen, Long, Leser, Ulf, Hakenberg, Jörg

Année:

2009

Langue:

english

Fichier:

PDF, 658 KB

english, 2009

3

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Chen, Rong, Shi, Lisong, Hakenberg, Jörg, Naughton, Brian, Sklar, Pamela, Zhang, Jianguo, Zhou, Hanlin, Tian, Lifeng, Prakash, Om, Lemire, Mathieu, Sleiman, Patrick, Cheng, Wei-yi, Chen, Wanting, Shah

Journal:

Nature Biotechnology

Année:

2016

Langue:

english

Fichier:

PDF, 775 KB

english, 2016

4

Incremental Information Extraction Using Relational Databases

Tari, Luis, Phan Huy Tu,, Hakenberg, Jorg, Yi Chen,, Tran Cao Son,, Gonzalez, Graciela, Baral, Chitta

Journal:

IEEE Transactions on Knowledge and Data Engineering

Année:

2012

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2012

5

[ACM Press the 2005 ACM symposium - Santa Fe, New Mexico (2005.03.13-2005.03.17)] Proceedings of the 2005 ACM symposium on Applied computing - SAC '05 - Optimizing syntax patterns for discovering protein-protein interactions

Plake, Conrad, Hakenberg, Jörg, Leser, Ulf

Année:

2005

Langue:

english

Fichier:

PDF, 184 KB

english, 2005

6

Predicting the clinical impact of human mutation with deep neural networks

Sundaram, Laksshman, Gao, Hong, Padigepati, Samskruthi Reddy, McRae, Jeremy F., Li, Yanjun, Kosmicki, Jack A., Fritzilas, Nondas, Hakenberg, Jörg, Dutta, Anindita, Shon, John, Xu, Jinbo, Batzloglou, S

Journal:

Nature Genetics

Année:

2018

Langue:

english

Fichier:

PDF, 1.95 MB

english, 2018

7

[Lecture Notes in Computer Science] Knowledge Discovery in Life Science Literature Volume 3886 || Extracting Named Entities Using Support Vector Machines

Bremer, Eric G., Hakenberg, Jörg, Han, Eui-Hong (Sam), Berrar, Daniel, Dubitzky, Werner

Année:

2006

Langue:

english

Fichier:

PDF, 267 KB

english, 2006

8

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

Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter

Journal:

BMC Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 1011 KB

english, 2009

9

Systematic feature evaluation for gene name recognition

Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer

Journal:

BMC Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 352 KB

english, 2005

10

Finding Kinetic Parameters Using Text Mining

Hakenberg, Jörg, Schmeier, Sebastian, Kowald, Axel, Klipp, Edda, Leser, Ulf

Journal:

Omics A Journal of Integrative Biology

Année:

2004

Langue:

english

Fichier:

PDF, 416 KB

english, 2004

11

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

Jörg Hakenberg, Dmitry Voronov, Võ Hà Nguyên, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral

Journal:

Journal of Biomedical Informatics

Année:

2012

Langue:

english

Fichier:

PDF, 650 KB

english, 2012

12

[Lecture Notes in Computer Science] Knowledge Discovery in Life Science Literature Volume 3886 || GetItFull – A Tool for Downloading and Pre-processing Full-Text Journal Articles

Bremer, Eric G., Hakenberg, Jörg, Han, Eui-Hong (Sam), Berrar, Daniel, Dubitzky, Werner

Année:

2006

Langue:

english

Fichier:

PDF, 207 KB

english, 2006

13

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

Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser…

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 636 KB

english, 2008

14

Salvage Surgical Resection for Isolated Locally Recurrent Inguinal Lymph Node Metastasis of Penile Cancer: International Study Collaboration

Baumgarten, Adam S., Alhammali, Eihab, Hakky, Tariq S., Espiritu, Patrick N., Pow-Sang, Julio M., Sexton, Wade J., Lockhart, Jorge L., Protzel, Chris, Hakenberg, Oliver, Muneer, Asif, Spiess, Philippe

Journal:

The Journal of Urology

Année:

2014

Langue:

english

Fichier:

PDF, 228 KB

english, 2014

15

[IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Philadelphia, PA, USA (2012.10.4-2012.10.7)] 2012 IEEE International Conference on Bioinformatics and Biomedicine - A high-throughput analysis pipeline for large next generation DNA sequencing studies

Albertyn, Zayed, Hakenberg, Jorg, Bian, Hongjin, Niu, Huifeng, Cai, James

Année:

2012

Langue:

english

Fichier:

PDF, 874 KB

english, 2012

16

[IEEE 2010 IEEE 26th International Conference on Data Engineering (ICDE 2010) - Long Beach, CA, USA (2010.03.1-2010.03.6)] 2010 IEEE 26th International Conference on Data Engineering (ICDE 2010) - GenerIE: Information extraction using database queries

Tari, Luis, Phan, Huy Tu, Hakenberg, Jorg, Chen, Yi, Tran, Cao Son, Gonzalez, Graciela, Baral, Chitta

Année:

2010

Langue:

english

Fichier:

PDF, 191 KB

english, 2010

17

Evidence from the ‘PROspective MulticEnTer RadIcal Cystectomy Series 2011 (PROMETRICS 2011)’ Study: How are Preoperative Patient Characteristics Associated with Urinary Diversion Type After Radical Cystectomy for Bladder Cancer?

Schmid, Marianne, Rink, Michael, Traumann, Miriam, Bastian, Patrick J., Bartsch, Georg, Ellinger, Jörg, Grimm, Marc-Oliver, Hadaschik, Boris, Haferkamp, Axel, Hakenberg, Oliver W., Aziz, Atiqullah, Ha

Journal:

Annals of Surgical Oncology

Année:

2015

Langue:

english

Fichier:

PDF, 240 KB

english, 2015

18

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (4 – 8 January 2015)] Biocomputing 2015 - AN INTEGRATIVE PIPELINE FOR MULTI-MODAL DISCOVERY OF DISEASE RELATIONSHIPS

GLICKSBERG, BENJAMIN S., LI, LI, CHENG, WEI-YI, SHAMEER, KHADER, HAKENBERG, JÖRG, CASTELLANOS, RAFAEL, MA, MENG, SHI, LISONG, SHAH, HARDIK, DUDLEY, JOEL T., CHEN, RONG

Langue:

english

Fichier:

PDF, 1.09 MB

english

19

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature

Tikk, Domonkos, Thomas, Philippe, Palaga, Peter, Hakenberg, Jörg, Leser, Ulf, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Année:

2010

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2010

20

[ACM Press the First ACM International Conference - Niagara Falls, New York (2010.08.02-2010.08.04)] Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10 - Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

Ahmed, Syed Toufeeq, Nair, Radhika, Patel, Chintan, Kanwar, Sheela P., Hakenberg, Jörg, Davulcu, Hasan

Année:

2010

Langue:

english

Fichier:

PDF, 218 KB

english, 2010

21

DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts: Fig. 1.

Cheng, Wei-Yi, Hakenberg, Jörg, Li, Shuyu Dan, Chen, Rong

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 199 KB

english, 2015

22

ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

Wang, Jinlian, Liao, Jun, Zhang, Jinglan, Cheng, Wei-Yi, Hakenberg, Jörg, Ma, Meng, Webb, Bryn D., Ramasamudram-chakravarthi, Rajasekar, Karger, Lisa, Mehta, Lakshmi, Kornreich, Ruth, Diaz, George A.,

Journal:

Genome Medicine

Année:

2015

Langue:

english

Fichier:

PDF, 2.80 MB

english, 2015

23

Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts

Hakenberg, Jörg, Cheng, Wei-Yi, Thomas, Philippe, Wang, Ying-Chih, Uzilov, Andrew V., Chen, Rong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2016

24

SETH detects and normalizes genetic variants in text

Thomas, Philippe, Rocktäschel, Tim, Hakenberg, Jörg, Lichtblau, Yvonne, Leser, Ulf

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 130 KB

english, 2016

25

Disease-associated variants in different categories of disease located in distinct regulatory elements

Ma, Meng, Ru, Ying, Chuang, Ling-Shiang, Hsu, Nai-Yun, Shi, Li-Song, Hakenberg, Jörg, Cheng, Wei-Yi, Uzilov, Andrew, Ding, Wei, Glicksberg, Benjamin S, Chen, Rong

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2015

26

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

Glicksberg, Benjamin S., Li, Li, Badgeley, Marcus A., Shameer, Khader, Kosoy, Roman, Beckmann, Noam D., Pho, Nam, Hakenberg, Jörg, Ma, Meng, Ayers, Kristin L., Hoffman, Gabriel E., Dan Li, Shuyu, Scha

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 4.46 MB

english, 2016

27

Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease

Chen, Brenden, Solis-Villa, Constanza, Hakenberg, Jörg, Qiao, Wanqiong, Srinivasan, Ramakrishnan R., Yasuda, Makiko, Balwani, Manisha, Doheny, Dana, Peter, Inga, Chen, Rong, Desnick, Robert J.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 943 KB

english, 2016

28

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (5 – 9 January 2009)] Biocomputing 2009 - QUERYING PARSE TREE DATABASE OF MEDLINE TEXT TO SYNTHESIZE USER-SPECIFIC BIOMOLECULAR NETWORKS

TARI, LUIS, HAKENBERG, JÖRG, GONZALEZ, GRACIELA, BARAL, CHITTA

Langue:

english

Fichier:

PDF, 2.12 MB

english

29

Literature Mining Solutions for Life Science Research

Hakenberg, Jörg, Nenadic, Goran, Rebholz-Schuhmann, Dietrich, Kim, Jin-Dong

Journal:

Advances in Bioinformatics

Année:

2013

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2013

30

Author Correction: Predicting the clinical impact of human mutation with deep neural networks

Sundaram, Laksshman, Gao, Hong, Padigepati, Samskruthi Reddy, McRae, Jeremy F., Li, Yanjun, Kosmicki, Jack A., Fritzilas, Nondas, Hakenberg, Jörg, Dutta, Anindita, Shon, John, Xu, Jinbo, Batzoglou, Se

Journal:

Nature Genetics

Année:

2018

Fichier:

PDF, 482 KB

2018