Publications

An in silico analysis of microRNAs: mining the miRNAome

Murray BS, Choe SE, Woods M, Ryan TE, Liu W.

Mol Biosyst. 2010 Oct; 6(10):1853-62

PMID: 20539892

http://www.ncbi.nlm.nih.gov/pubmed/20539892

Abstract

Systematic analysis of literature- and experimentally-derived datasets using text mining with ontological enrichment and network modeling revealed global trends in the microRNA (miRNA) interactome.


Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244)

Dry JR, Pavey S, Pratilas CA, Harbron C, Runswick S, Hodgson D, Chresta C, McCormack R, Byrne N, Cockerill M, Graham A, Beran G, Cassidy A, Haggerty C, Brown H, Ellison G, Dering J, Taylor BS, Stark M, Bonazzi V, Ravishankar S, Packer L, Xing F, Solit DB, Finn RS, Rosen N, Hayward NK, French T, Smith PD.

Cancer Res. 2010 Mar 15; 70(6):2264-73

PMID: 20215513

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166660/


Identifying and classifying biomedical perturbations in text

Rodriguez-Esteban R, Roberts PM, Crawford ME.

Nucleic Acids Res. 2009 Feb; 37(3):771-7

PMID: 19074486

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647287/


The CALBC Silver Standard Corpus - Harmonizing multiple semantic annotations in a large biomedical corpus

Rebholz-Schuhmann D, Jimeno Yepes AJ, Van Mulligen EM, Kang N, Kors J, Milward D, Corbett P, Hahn U.

Proc 3rd Int Symp Languages Biology Medicine. 2009 Nov; pp64-72

PMID: N/A

http://lbm2009.biopathway.org/papers/long/The_CALBC_Silver_Standard_Corp...


Mining protein-protein interactions from published literature using Linguamatics I2E

Bandy J, Milward D, McQuay S.

Methods Mol Biol. 2009; 563:3-13

PMID: 19597777

http://link.springer.com/protocol/10.1007%2F978-1-60761-175-2_1

Abstract

Natural language processing (NLP) technology can be used to rapidly extract protein-protein interactions from large collections of published literature. In this chapter we will work through a case study using MEDLINE biomedical abstracts (1) to find how a specific set of 50 genes interact with each other.