Ira M. Hall, Ph.D.

Associate Professor
Internal Medicine
Associate Director
The Genome Institute

Molecular Genetics and Genomics Program
Human and Statistical Genetics Program
Computational and Systems Biology Program

  • 314-286-2026

  • 8501



  • genetics; genomics; bioinformatics; genome sequencing; single cell sequencing; cancer evolution; clinical genomics; genome technology; data science

  • We use high-throughput methods to study the causes and consequences of genome variation in mammals

Research Abstract:

My laboratory conducts research in the realms of genetics, genomics and bioinformatics. We are currently focused on using high-throughput methods to study the causes and consequences of genome variation in mammals. Active projects involve topics such as genome structural variation, genetic mosaicism, single cell genomics, cancer evolution, personal genome sequencing, and the development of new bioinformatic tools. As members of The Genome Institute, we also participate in large-scale sequencing projects aimed at defining the genetic causes of human disease, and in efforts to develop and implement genome-based clinical assays.

Selected Publications:

Layer RL, Chiang C, Quinlan AR*, Hall IM*. LUMPY: A probabilistic framework for structural variant discovery. Genome Biology, 15, R84 (2014). PMCID: PMC4197822

McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina, S, Lasken RS, Vermeesch J, Hall IM*, Gage FH*. Mosaic Copy Number Variation in Human Neurons. Science, 342, 632-7 (2013). PMCID: PMC3975283.

Malhotra AM, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR*, Hall IM*. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Research, 23,762-76 (2013). PMCID: PMC3638133

Faust G, Hall IM*. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics, 28, 2416-24 (2012). PMCID: PMC3463118.

Quinlan AR, Hall IM*. Characterizing complex structural variation in germline and somatic genomes. Trends in Genetics, 1, 43-53 (2012). PMCID: PMC3249479.

Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM*. Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell, 9, 366-73 (2011). PMCID: PMC3975295.

Quinlan AR, Clark RA, Sokolova S, Leibowitz M, Zhang Y, Hurles ME, Mell JC, Hall IM*. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Research, 20, 623-35 (2010). PMCID: PMC2860164.

Quinlan AR*, Hall IM*. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-2 (2010). PMCID: PMC2832824.

Egan C, Sridhar S, Wigler M, Hall IM*. Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics, 39, 1384-89 (2007) .

Last Updated: 12/18/2014 9:55:01 AM

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