Welcome to the Yandell Lab located in the Eccles Institute of Human Genetics on the Campus of the University of Utah's Health Sciences Center.
Current Research in the Yandell Lab:
Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics. New areas of inquiry include high-throughput biological image analysis, and exploring the relationships between sequence variation and human disease.
More About Research Interests...
Recent Publications:
Quantitative Measures for the Management and
Comparison of Annotated Genomes
Eilbeck K,
Moore B,
Holt C,
Yandell MD
BMC Bioinformatics 2009, 10:67
Genome-wide Analysis of Human Disease Alleles Reveals
That Their Locations Are Correlated in Paralogous
Proteins.
Yandell MD,
Moore B,
Salas F,
Mungall CJ,
MacBride A,
White C,
Reese MG
PLoS Computational Biology. 2008 4(11).
MAKER: An Easy-to-use Annotation Pipeline Designed for
Emerging Model Organism Genomes.
Cantarel B,
Korf I,
Robb SMC,
Parra G,
Ross E,
Moore B,
Holt C,
Sanchez Alvarado A,
Yandell MD.
Genome Research 2008 18(1) 188-96.
Software:
MAKER (updated 5-13-2009)
MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
MAKER Webserver!!! Coming soon.