Aaron R. Quinlan
Assistant Professor of Public Health Science and
  Biochemistry & Molecular Genetics
Ph.D., Boston College
Computational Genomics and Genome Variation

Laboratory
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The research in our laboratory is focused on developing and applying computational methods that improve our understanding of genome biology and the impact of genetic variation on phenotype. Modern experimental methods allow us to examine entire genomes with exquisite detail. Perhaps not surprisingly, staggering complexity is revealed as we look more closely at genome structure and the landscape of genetic variation. The throughput of modern genomic technologies necessitates efficient approaches for manipulating and comparing large genomic datasets and for characterizing the genetic variation therein. Our laboratory develops new algorithms and data mining techniques so that we and others may apply them to investigations of the impact of genetic variation on human disease, evolution, and somatic differentiation.

We are applying our methods towards 1) understanding the landscape and mechanisms of inherited and somatic differences if chromosome structure, 2) the impact of ionizing radiation on genome stability, 3) the origins of brain and ovarian cancers, 4) the genetics of Type 1 diabetes, and 5) predicting the functional consequence of genetic variation.


Selected References

Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP; NHLBI Exome SequencingProject, Quinlan AR, Nickerson DA, Eichler EE. (2012) "Copy number variation detection and genotyping from exome sequence data." Genome Res. 22:1525-32. Epub 2012 May 14. [PubMed]

Quinlan AR, Hall IM. (2012) "Characterizing complex structural variation in germline and somatic genomes." Trends Genet. 28:43-53. Epub 2011 Nov 15. [PubMed]

Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, HallIM. (2011) "Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming." Cell Stem Cell. Oct 9:366-73. doi: 10.1016/j.stem.2011.07.018. [PubMed]

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, HallIM. (2010) "Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome." Genome Res. 20:623-35. Epub 2010 Mar 22. [PubMed]

Quinlan AR, Hall IM. (2010) "BEDTools: a flexible suite of utilities for comparing genomic features." Bioinformatics. Mar 26:841-2. Epub 2010 Jan 28. [PubMed]

1000 Genomes Project Consortium. (2010) "A map of human genome variation from population-scale sequencing." Nature. Oct 467(7319):1061-73. [PubMed]

Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF,Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC,Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM. (2008) "Rapid whole-genome mutational profiling using next-generation sequencing technologies." Genome Res. 18(10):1638-42. Epub 2008 Sep 4. [PubMed]

Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P,Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, StewartDA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER. (2008) "Whole-genome sequencing and variant discovery in C. elegans." Nat Methods. 5:183-8. Epub 2008 Jan 20. [PubMed]