News

Special Issue in Advances of Artificial Intelligence - Call for papers

aai

JSPS Fellowship
From November 2008 to October 2010 I am on a temporary  leave of absence from the University of Ulster to collaborate with Dr. Hiroaki Kitano.


Books (edited)

Fundamentals of Data Mining in Genomics and Proteomics
edited by Werner Dubitzky, Martin Granzow, and Daniel Berrar

2007, Springer, 282 pages,  ISBN-10: 0-387-47508-7
ISBN-13: 978-0-387-47508-0

 A Practical Approach to Microarray Data Analysis
edited by Werner Dubitzky, Martin Granzow, and Daniel Berrar

2002, Kluwer Academic Publishers,
384 pages, ISBN: 1-4020-7260-0		 Knowledge Discovery in Life Science Literature
edited by Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel Berrar, and Werner Dubitzky

2006, 147 pages, Proceedings Series: Lecture Notes in Computer Science
Subseries: Lecture Notes in Bioinformatics, Vol. 3886, ISBN: 978-3-540-32809-4
pdfTOC, Preface, Index TOC, Preface, Index TOC and Preface
Sample chapter Review


Journals, conference proceedings, and book chapters

2009 McGeough C., Berrar D., Middleton D., Gilmore P., Wright G., Mathews C., Bjourson A.J. (2009) Predicting response to anti-TNF-alpha therapy in rheumatoid arthritis patients. Submitted.
Deligianni E., Pattison S., Berrar D., Ternan N.G., Haylock R.W., Moore J.E., Elborn J.S. and Dooley J.S.G. (2009) Isogenic strains of Pseudomonas aeruginosa Cystic Fibrosis isolates exhibit diversity in biofilm phenotype. Submitted.
Berrar D., Sato N., and Schuster A. (2009) Artificial intelligence, quo vadis? To appear in Artificial Intelligence in Neuroscience and Systems Biology: Lessons Learnt, Open Problems, and the Road Ahead. Special issue in Advances in Artificial Intelligence, Hindawi.
2008 Graham J.E., McGilligan V.E., Berrar D., Leccisotti A., Moore J.E., Bron A.J., Moore T.C.B. (2008) Attitudes towards diagnostic tests and therapies for dry eye disease. Ophthalmic Res. In press.
McCann M.J., Gill C.I., Linton T., Berrar D., McGlynn H., Rowland I.R. (2008) Enterolactone restricts the proliferation of the LNCaP human prostate cancer cell line in vitro. Mol. Nutr. Food Res. 52(5):567-80.
2007 Berrar D., Granzow M., and Dubitzky W. (2006) Introduction to genomic and proteomic data analysis. In Dubitzky W., Granzow M., and Berrar D. (eds.), Fundamentals of Data Mining in Genomics and Proteomics, Springer, pp. 1-37.
2006 Natarajan J., Berrar D., Dubitzky W., Hack K., Zhang Y., Van Brocklyn J.R., Bremer E. (2006) Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics 7:373.
Berrar D., Dubitzky W. (2006) Neural plasma. IFIP International Federation for Information Processing, Vol. 217, Artificial intelligence in Theory and Practice (ed. M. Bramer), Boston, Springer, pp. 159-68.
Silva C.G., Ostropytskyy V., Loureiro-Ferreira N., Berrar D., Dubitzky W., Brito R.M.M. (2006) P-found: A protein folding and unfolding simulation data repository. Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp. 101-108.
Berrar D., Bradbury I., Dubitzky W. (2006) Avoiding model selection bias in small-sample genomic data sets. Bioinformatics 22(10):1245-50.
Berrar D., Bradbury I., Dubitzky W. (2006) Corrigendum. Bioinformatics 22(19):2453.
Berrar D., Bradbury I., Dubitzky W. (2006) Instance-based concept learning from multiclass DNA microarray data. BMC Bioinformatics 7:73.
2005 Berrar D., Stahl F., Silva C., Rodrigues J.R., Brito R.M.M., Dubitzky W. (2005) Towards data warehousing and mining of protein unfolding simulation data. J. Clin. Mon. Comp. 19:307-17.
Berrar D., Bradbury I., Sturgeon B., Downes C.S., Dubitzky W. (2005) Survival trees for analyzing clinical outcome in lung adenocarcinomas based on gene expression profiles: Identification of neogenin and diacylglycerol kinase alpha as critical factors. J. Comp. Biol. 12(5):534-44.
Stahl F., Berrar D., Silva C., Rodrigues J.R., Brito R.M.M., Dubitzky W. (2005) Grid warehousing of molecular dynamics protein unfolding data. Proc. 5th IEEE Intl. Symp. Cluster Computing and the Grid (CCGrid'05), Vol.1, pp. 496-503.
Natarajan J., Berrar D., Hack C.J., Dubitzky W. (2005) Knowledge discovery in biology and biotechnology texts: A review of techniques, evaluation strategies, and applications. Crit. Rev. Biotech. 25:1-22.
2004 Berrar D., Sturgeon B., Bradbury I., Downes C.S., Dubitzky W. (2004) Integration of microarray data for a comparative study of classifiers and identification of marker genes. Proc. 4th Intl. Conf. Critical Assessment of Microarray Data Analysis (CAMDA03), Durham, North Carolina, USA, pp. 147-162.
2003 Berrar D., Sturgeon B., Bradbury I., C. Stephen Downes, Dubitzky W. (2003) Microarray data integration and machine learning methods for lung cancer survival prediction. In Oral and Poster Presenters’ Abstracts, 4th Intl. Conf. Critical Assessment of Microarray Data Analysis, (CAMDA03), Durham, North Carolina, USA, pp. 43-54.
Berrar D., Downes C.S., Dubitzky W. (2003) A probabilistic neural network for gene selection and classification of microarray data. Proc. Intl. Conf. Artificial Intelligence (IC-AI'03), June 23-26, Monte Carlo Resort, Las Vegas, USA, pp. 342-349.
O’Donoghue P., Dubitzky W., Lopes P., Berrar D., Lagan K., Hassan D., Bairner A., Darby P. (2003) An evaluation of quantitative and qualitative methods of predicting the 2002 FIFA World Cup. Proc. 5th World Conference on Science and Football, pp. 44-45.
Berrar D., Downes C.S., Dubitzky W. (2003) Multiclass cancer classification using gene expression profiling and probabilistic neural networks. Proc. 8th Pac. Symp. Biocomp., World Scientific, New Jersey/London/Singapore/Hong Kong, pp. 5-16.
2002 Dubitzky W., Granzow M., Downes C.S., Berrar D. (2002) Introduction to Microarray Data Analysis. In: Berrar D., Dubitzky W., M. Granzow (eds.), A Practical Approach to Microarray Data Analysis, Kluwer Academic Publishers, Boston/Dordrecht/London, pp. 1-46.
2001 Dubitzky W., Granzow M., Berrar D. (2001) Comparing symbolic and subsymbolic machine learning approaches to classification of cancer and gene identification. In Lin S. and Johnson K. (eds.), Methods of Microarray Data Analysis, Kluwer Academic Publishers, ISBN: 0792375645, pp. 151-166.
Dubitzky W., Granzow M., Berrar D. (2001) Data mining and machine learning methods for microarray analysis. In Lin S. and Johnson K. (eds.), Methods of Microarray Data Analysis, Kluwer Academic Publishers, ISBN: 0792375645, pp. 5-22.
Dubitzky W., Berrar D., Granzow M., Eils R. (2001) Detecting broad-band and selective correlation patters among gene expression and drug activity data. In Oral and Poster Presenters’ Abstracts, Critical Assessment of Microarray Data Analysis 2001, (CAMDA01), Durham, North Carolina, USA, pp. 17-22.
Berrar D., Dubitzky W., Granzow M., Eils R.: Analysis of gene expression and drug activity data by knowledge-based association mining. In Oral and Poster Presenters’ Abstracts, Critical Assessment of Microarray Data Analysis 2001, (CAMDA01), Durham, North Carolina, USA, pp. 23-28.
Berrar D., Granzow M., Dubitzky W., Stilgenbauer S., Wilgenbus K., Döhner H., Lichter P., Eils R. (2001) New insights in clinical impact of molecular genetic data by knowledge-driven data mining. Proc. 2nd Intl. Conf. Systems Biology, Omnipress, pp. 275-281.
Granzow M., Berrar D., Dubitzky W., Schuster A., Azuaje F., Eils R. (2001) Tumor classification by gene expression profiling: comparison and validation of five clustering methods. SIGBIO Newsletter Special Interest Group on Biomedical Computing of the ACM, ACM Press, 21(1):16-22.
Berrar D., Dubitzky W., Solinas-Toldo S., Bulashevska S., Granzow M., Conrad C., Kalla J., Lichter P., Eils R. (2001) A database system for comparative genomic hybridization analysis. IEEE Engineering in Medicine and Biology 20(4):75-83.