Martin's Corner

About me

Publications

Projects:

ENCODE Genome Annotation Assessment Project (EGASP)

I have been an advisor and editor for the first human GASP (see the Drosophila GASP experiment below), an experiment for an objective assessment of the state-of-the-art in genome annotation in genomic DNA within in ENCODE regions in the human genome. This has been a project by the GENCODE group within the ENCODE project Results were published as the first ever Supplement of Genome Biology Vol. 7 Suppl 1 (available at Amazon.com ) and presented at the EGASP'05 analysis workshop ,which was held at the Wellcome Trust Conference Center at the Sangre Institute in Hinxton, UK, on May 6-7 2005. The project was also reviewed in the scientific press at
• Nature Volume 435, p. 134 (12 May 2005) "Competition boosts bid to find human genes" by Alison Abbott. (PDF)
• Nature Methods "EGASP: collaboration through competition to find human genes", commentary by Guigo & Reese, Nature Methods Vol. 2 No. 8, p. 575 - 577 (2005). (PDF)
• PLoS Biology within a general review article prices in science "Prices for Ingenuity" by Bill O'Neill. (PDF)
• The Scientist within a summary review article about genome annotation "Why You Should Be Annotating" by Jeffrey M. Perkel. (PDF)

Drosophila Genome Annotation

Contributing my program Genie for gene finding I have participated in the Drosophila jamboree to annotate the entire Drosophila melanogaster sequence. The results where published in Science (Medline: Abstract).

Genome Annotation Assessment Project (GASP 1)

I have co-organized an experiment for an objective assessment of the state-of-the-art in genome annotation in genomic DNA using the 2.9 Mbases of the Adh region in Drosophila. Results were published in Genome Research, Vol. 10(4):483-501 and presented at the Tutorial #3 at the ISMB '99 conference in Heidelberg, August 6, 1999. The project was widely reviewed in the press at
• Science, May 5, 2000: 773. (Article)
• Financial Times, April 27, 2000.
• Nature Volume 400 Number 6746, p. 699 (19 August 1999) "Annotation competition spurs Drosophila sequencing efforts" by Alison Abbott. (PDF)

Gene Finding

In collaboration with the UCSC Computational Biology group (David Haussler) and Neomorphic, Inc. (David Kulp) we have developed a gene finding program called Genie for predicting genes in genomic DNA. The program is based on a generalized hidden Markov model, which was pioneered by us in 1996 (Medline: Kulp, Reese et al.).



Promoter Recognition

NNPP2.2, the WWW interface for my Neural Network Promoter Prediction Tool.

Splice Site Recognition

NNSPLICE0.9, the WWW interface for my Neural Network Splice Site Prediction Tool.
A Slide Presentation (PDF-Format) given at RECOMB '97 is available.

Gene Data Sets for Gene Finding

Cleaned representative Human and Drosophila melanogaster fene databases extracted from GenBank are available. These datasets were created for training and testing purposes of gene finding algorithms. Ftp Site