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; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis.

More About Research Interests...


Recent Publications:

A probabilistic disease-gene finder for personal genomes
Yandell M Huff CD Hu H Singleton M Moore B Xing J Jorde L Reese MG
Genome Res. 2011 Jul
Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency
Rope AF Wang K Evjenth R Xing J Johnston JJ Swensen JJ Johnson WJ Moore B Huff CD Bird LM Carey JC Opitz JM Stevens CA Jiang T Schank C Fain HD Robison R Dalley B Chin S South ST Pysher TJ Jorde LB Hakonarson H Lillehaug JR Biesecker LG Yandell M Arnesen T Lyon GJ
Am J Hum Genet. 2011 Jul 15;89(1):28-43
Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics
Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M.
Genet Med. 2011 Mar;13(3):210-7.
The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights Into Its Obligate Symbiotic Lifestyle.
Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera E J, Cash E, Cavanaugh A, Denas O, Elhaik E, Fave M-J, Gadau J, Gibson J D, Graur D, Grubbs K J, Hagen D E, Harkins T T, Helmkampf M, Hu H, Johnson B R, Kim J, Marsh S E, Moeller J A, Munoz-Torres M C, Murphy M C, Naughton M C, Nigam S, Overson R, Rajakumar R, Reese J T, Scott J J, Smith C R, Tao S, Tsutsui N D, Viljakainen L, Wissler L, Yandell M D, Zimmer F, Taylor J, Slater S C, Clifton S W, Warren W C, Elsik C G, Smith C D, Weinstock G M, Gerardo N M, Currie C R
PLoS Genet. 2011 Feb 10;7(2)
A Draft Genome of the Red Harvester Ant, Pogonomyrmex barbatus.
Smith C R, Smith C D, Robertson H M, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie C R, Elhaik E, Elsik C G, Fave M-J, Fernandes V, Gibson J D, Graur D, Gronenberg W, Grubbs K J, Hagen D E, Viniegra A S I, Johnson B R, Johnson R M, Khila A, Kim J W, Mathis K A, Munoz-Torres M C, Murphy M C, Mustard J A, Nakamura R, Niehuis O, Nigam S, Overson R P, Placek J E, Rajakumar R, Reese J T, Suen G, Tao S, Torres C W, Tsutsui N D, Viljakainen L, Wolschin F, Gadau J,
Proc Natl Acad Sci U S A. 2011 Jan 31
The Draft Genome of the Globally Widespread and Invasive Argentine ant (Linepithema humile).
Smith C D, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset, V, Currie C R, Elhaik E, Elsik C G, Fave M-J, Fernandes V, Gadau J, Gibson J D, Graur D, Grubbs K J, Hagen D E, Helmkampf M, Holley J-A, Hu H, Viniegra A S I, Johnson B R, Johnson R M, Khila A, Kim J W, Laird J, Mathis K A, Moeller J A, Munoz-Torres M C, Murphy M C, Nakamura R, Nigam S, Overson R P, Placek J E, Rajakumar R, Reese J T, Robertsonl H M, Smith C R, Suarez A V, Suen G, Suhr E L, Tao S, Torres C W, Wilgenburg E van, Viljakainen L, Walden K K O, Wild A L, Yandell M, Yorke J A, Tsutsui N D,
Proc Natl Acad Sci U S A. 2011 Jan 31
Characterization of the Conus bullatus genome and its venom-duct transcriptome.
Hu H, Bandyopadhyay P, Olivera B, Yandell M.
BMC Genomics. 2011; 12: 60
A standard variation file format for human genome sequences.
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth G, Stein L, Flicek P, Yandell M, Eilbeck K.
Genome Biology 2010, 11:R88
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequence.
Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.
BMC Genomics 2010, Jul 7;11(1):420.
Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire.
Levesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR.
Genome Biol. 2010 Jul 13;11(7):R73.

More Publications...

Software:

VAAST

VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology.

MAKER 2 (updated 01-16-2012)

MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic 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 2 is now here!!

More Software...