Awards and achievements


April 4, 2016

BME Associate Professors Beer and Karchin named top performers at CAGI4

BME associate professors Michael Beer and Rachel Karchin have been recognized as being top performers at the fourth Critical Assessment of Genome Interpretation Challenge (CAGI4). They were invited to participate in the March 2016 CAGI4 Conference on the UCSF Mission Bay campus in San Francisco.

Michael Beer made a strong showing in the “eQTL challenge.” The eQTL challenge was designed as a blind competition to predict the expression of ~6000 human DNA fragments in lymphoblasts. Beer’s approach was noteworthy in that he built his computational model from ENCODE data — rather than training data — thereby rendering Michael’s approach broadly applicable to other human cell types.

Rachel Karchin’s research group has been a leader in the CAGI Personal Genome Project (PGP) challenge for three straight years.  A summary of the core method used in the challenge has been published in PLoS Computational Biology “A probabilistic model to predict clinical phenotypic traits from genome sequencing.”

The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to objectively assess computational methods for predicting phenotypic impacts of genomic variation and to inform future research directions.