Robert Fulton
Research Accomplishments & Interests
As the group leader of finishing at The Genome Institute, my focus is the improvement of DNA sequence. The high-throughput sequencing pipeline is able to produce amazing quantities of sequence data through a highly automated production pipeline, but unfortunately due to the complex nature of DNA sequencing, the resulting product across all regions of genomes is not well represented in all cases. The process of resolving ambiguities, closing gaps, and improving quality of these initial assemblies is my focus. With budgets being tight, and production throughput being so robust and diverse, speed, flexibility, and efficiency of methods are critical. Improvement work can be performed on whole genomes consisting of billions of base pairs to clone based activities as small as thousands of base pairs. Efforts for improvement of these procedures span many aspects of the sequencing pipeline, including sequencing chemistry and assembly algorithm improvements, as well as automated assembly manipulation and reaction selection programs. These improvements have come through close interaction between many groups at The Genome Institute including technical development, production and informatics, as well as outside collaborations with many different groups. These higher throughput mechanisms have been developed in support of manual improvements on some genomes, which require strict quality standards, while also being applied to genomes as a mechanism of high throughput improvement where minimal manual efforts are called for. In either case, the sequence improvement pipeline provides downstream users with a more complete, higher quality product, enabling them to glean as much useful information out of the sequence data as possible.
Selected Publications
Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee…
De novo gene disruptions in children on the autistic spectrum.
Neuron. 2012 Apr 26;74(2):285-99. PubMed | View Abstract
Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan…
Clonal Architecture of Secondary Acute Myeloid Leukemia.
N Engl J Med. 2012 Mar 14. [Epub ahead of print] PubMed | View Abstract
Cheung NK, Zhang J, Lu C, Parker M, Bahrami A, Tickoo SK, Heguy A, Pappo…
Association of age at diagnosis and genetic mutations in patients with neuroblastoma.
JAMA. 2012 Mar 14;307(10):1062-71. PubMed | View Abstract
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding…
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.
Nature. 2012 Feb 22. doi: 10.1038/nature10843. [Epub ahead of print] PubMed | View Abstract
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young…
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] PubMed | View Abstract
Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen…
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
Nature. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725. PubMed | View Abstract
Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu…
A novel retinoblastoma therapy from genomic and epigenetic analyses.
Nature. 2012 Jan 11. doi: 10.1038/nature10733. [Epub ahead of print] PubMed | View Abstract
Graubert T, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, Krysiak K, Harris…
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Nature Genetics. 2011 Dec 11. [Advanced online publication] PubMed | View Abstract
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst…
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. PubMed | View Abstract
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge…
The functional spectrum of low-frequency coding variation.
Genome Biol. 2011 Sep 14;12(9):R84. [Epub ahead of print] PubMed | View Abstract
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs…
Demographic history and rare allele sharing among human populations.
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-11988. Epub 2011 Jul 5. PubMed | View Abstract
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala…
Modernizing reference genome assemblies.
PLoS Biol. 2011 Jul;9(7):e1001091. Epub 2011 Jul 5. PubMed | View Abstract
The Cancer Genome Atlas Research Network
Integrated genomic analyses of ovarian carcinoma
Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. PubMed | View Abstract
The 1000 Genomes Project, Conrad DF, Keebler JE, Depristo MA, Lindsay SJ, Zhang Y, Casals…
Variation in genome-wide mutation rates within and between human families.
Nat Genet. 2011 Jun 12;43(7):712-714. doi: 10.1038/ng.862. PubMed | View Abstract
Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LC, Kiang AS, Campbell M, Weinstock…
A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement.
Eur J Hum Genet. 2011 Jun 8. doi: 10.1038/ejhg.2011.86. [Epub ahead of print] PubMed | View Abstract
