A team of computer engineers at City University (CityU) are helping biologists crack a problem of more accurately reading microimages of genes.
Prof Hong Yan and his researchers have developed computer software that reduces the error rate of reading a DNA chip by about half. This means computer images of a DNA chip, or slide, packed with about 10,000 genes can be read in one day instead of about two.

Gene microarrays using Prof Yan’s software (left) and existing software. White circles on the right show missing data

Tests show the software, named GeneIcon, outperforms the currently widely-used program. An application to patent GeneIcon is being made. Analysing genes is important to biologists in identifying the causes of disease and the effects on the body of therapeutic drugs.
In preparation for analysis, a DNA chip is converted to computer images with the use of a laser scanner. Problems in the scanning, said Prof Yan, are similar to optical character reader processing where some characters are omitted or misformed. Someone then has to clean up the computer image manually.
“It’s a time-consuming business but our software considerably reduces the need for manual correction.” Images break down because of noise; dust, scratches, and dirt. Low contrast is also a problem. GeneIcon stills need “polishing,” said Prof Yan. Improvements include a more friendly user interface.
The cross-disciplinary project is in collaboration with biologists at CityU. The next stage of the research is to work with biologists on computer analysis of DNA chip data to study gene functions.
“Existing techniques are still very primitive,” said Prof Yan. “We’re helping the biologists by providing them with tools to do their job. There’s quite a gap between electronic engineering and biology but, by doing this, we are helping to bridge that gap.”

Principal Investigator
Prof Hong Yan: h.yan@cityu.edu.hk