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Links and References

Programs used in GenoMesh:

The R Project for Statistical Computing: http://www.r-project.org/

Similar web-based programs:

1. PubGene: http://www.pubgene.org/.
2. PubMatrix: http://pubmatrix.grc.nia.nih.gov/.
3. Gene2Mesh: http://gene2mesh.ncibi.org/.
4. BioSearch-2D: http://biosearch2d.ncibi.org/.

Relevant text ming references:

1. Becker KG, Hosack DA, Dennis G Jr, Lempicki RA, Bright TJ, Cheadle C, Engel J. 2003. PubMatrix: a tool for multiplex literature mining. BMC bioinformatics 4:61 [PubMed: 14667255]
2. Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A. 2006. Discovering semantic features in the literature: a foundation for building functional associations. BMC bioinformatics 7:41 [PubMed: 16438716]
3. Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, Altherr MR, Brettin TS. 2004. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiological genomics 18:51-62 [PubMed: 15069167]
4. Funk ME, Reid CA. 1983. Indexing consistency in MEDLINE. Bulletin of the Medical Library Association 71:176-183 [PubMed: 6344946]
5. Homayouni R, Heinrich K, Wei L, Berry MW. 2005. Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics (Oxford, England) 21:104-115 [PubMed: 15308538]
6. Jenssen TK, Laegreid A, Komorowski J, Hovig E. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nature genetics 28:21-28 [PubMed: 11326270]
7. Küffner R, Fundel K, Zimmer R. 2005. Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics (Oxford, England) 21 Suppl 2:ii259-267 [PubMed: 16204115]
8. Lewis J, Ossowski S, Hicks J, Errami M, Garner HR. 2006. Text similarity: an alternative way to search MEDLINE. Bioinformatics (Oxford, England) 22:2298-2304 [PubMed: 16926219]
9. Maguitman AG, Rechtsteiner A, Verspoor K, Strauss CE, Rocha LM. 2006. Large-scale testing of bibliome informatics using Pfam protein families. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 76-87 [PubMed: 17094229]
10. Raychaudhuri S, Schütze H, Altman RB. 2002. Using text analysis to identify functionally coherent gene groups. Genome research 12:1582-1590 [PubMed: 12368251]
11. Rechtsteiner, A., Luinstra, J., Rocha, L.M., Strauss, C.E. Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology. Joint BioLINK and Bio-Ontologies Meeting 2006 (ISMB Special Interest Group). PDF.
12. Ruch P. 2006. Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics (Oxford, England) 22:658-664 [PubMed: 16287934]
13. Shatkay H, Edwards S, Wilbur WJ, Boguski M. 2000. Genes, themes and microarrays: using information retrieval for large-scale gene analysis. Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 8:317-328 [PubMed: 10977093]
14. Srinivasan P. 2001. MeSHmap: a text mining tool for MEDLINE. Proceedings / AMIA ... Annual Symposium. AMIA Symposium 642-646 [PubMed: 11825264]
15. Verspoor K, Cohn J, Joslyn C, Mniszewski S, Rechtsteiner A, Rocha LM, Simas T. 2005. Protein annotation as term categorization in the gene ontology using word proximity networks. BMC bioinformatics 6 Suppl 1:S20 [PubMed: 15960833]
16. Masys DR, Welsh JB, Lynn Fink J, Gribskov M, Klacansky I, Corbeil J. 2001. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics (Oxford, England) 17:319-326 [PubMed: 11301300]