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Items: 1 to 20 of 28


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

Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, Balwani M, Doheny D, Peter I, Chen R, Desnick RJ.

Hum Mutat. 2016 Nov;37(11):1215-1222. doi: 10.1002/humu.23067.


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

Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT.

Bioinformatics. 2016 Jun 15;32(12):i101-i110. doi: 10.1093/bioinformatics/btw282.


SETH detects and normalizes genetic variants in text.

Thomas P, Rocktäschel T, Hakenberg J, Lichtblau Y, Leser U.

Bioinformatics. 2016 Sep 15;32(18):2883-5. doi: 10.1093/bioinformatics/btw234. Epub 2016 Jun 2.


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

Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH.

Nat Biotechnol. 2016 May;34(5):531-8. doi: 10.1038/nbt.3514. Epub 2016 Apr 11.


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

Hakenberg J, Cheng WY, Thomas P, Wang YC, Uzilov AV, Chen R.

BMC Bioinformatics. 2016 Jan 8;17:24. doi: 10.1186/s12859-015-0865-9.


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

Cheng WY, Hakenberg J, Li SD, Chen R.

Bioinformatics. 2016 Jan 1;32(1):151-3. doi: 10.1093/bioinformatics/btv511. Epub 2015 Sep 12.


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

Wang J, Liao J, Zhang J, Cheng WY, Hakenberg J, Ma M, Webb BD, Ramasamudram-Chakravarthi R, Karger L, Mehta L, Kornreich R, Diaz GA, Li S, Edelmann L, Chen R.

Genome Med. 2015 Jul 29;7:77. doi: 10.1186/s13073-015-0207-6.


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

Ma M, Ru Y, Chuang LS, Hsu NY, Shi LS, Hakenberg J, Cheng WY, Uzilov A, Ding W, Glicksberg BS, Chen R.

BMC Genomics. 2015;16 Suppl 8:S3. doi: 10.1186/1471-2164-16-S8-S3. Epub 2015 Jun 18.


An integrative pipeline for multi-modal discovery of disease relationships.

Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R.

Pac Symp Biocomput. 2015:407-18.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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