Publications

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.
Genome Res. 2013 Mar 20.

GEM: crystal-clear DNA alignment
Faust GG, Hall IM.
Nat Methods. 2012 Dec 7;9(12):1159-60. doi: 10.1038/nmeth.2256.

Binary Interval Search: a scalable algorithm for counting interval intersections
Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR.
Bioinformatics (2013) 29 (1): 1-7.

YAHA: fast and flexible long-read alignment with optimal breakpoint detection
Faust GG and Hall IM
Bioinformatics (2012) 28(19): 2417-2424. Epub 2012 Jul 24. doi:10.1093/bioinformatics.

Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells.
Mell JC, Hall IM, Redfield RJ.
Nucleic Acids Res. 2012 Sep 1;40(17):8536-49. Epub 2012 Jun 29.

Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.
Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME.
Nat Genet. 2012 Mar 4;44(4):390-7, S1. doi: 10.1038/ng.2202

Detection and interpretation of genomic structural variation in mammals.
Hall IM, Quinlan AR.
Methods Mol Biol. 2012;838:225-48.

Characterizing complex structural variation in germline and somatic genomes.
Quinlan AR, Hall IM.
Trends Genet. 2012 Jan;28(1):43-53. Epub 2011 Nov 15.

Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming.
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM.
Cell Stem Cell. 2011 Oct 4;9(4):366-73. doi: 10.1016/j.stem.2011.07.018.

Transformation of natural genetic variation into Haemophilus influenzae genomes.
Mell JC, Shumilina S, Hall IM, Redfield RJ.
PLoS Pathog. 2011 Jul;7(7):e1002151. Epub 2011 Jul 28.

DNA structural variants as genetic risk factors for the long QT syndrome.
Rich SS, Hall IM.
J Am Coll Cardiol. 2011 Jan 4;57(1):48-50. No abstract available.

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.
Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.
Genome Res. 2010 May;20(5):623-35. Epub 2010 Mar 22.

BEDTools: a flexible suite of utilities for comparing genomic features.
Quinlan AR, Hall IM.
Bioinformatics. 2010 Mar 15;26(6):841-2. Epub 2010 Jan 28.

Recurrent DNA copy number variation in the laboratory mouse.
Egan CM, Sridhar S, Wigler M, Hall IM.
Nat Genet. 2007 Nov;39(11):1384-9. Epub 2007 Oct 28.

Identification of alterations in DNA copy number in host stromal cells during tumor progression.
Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D.
Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19848-53. Epub 2006 Dec 13.

Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens.
Lakshmi B, Hall IM, Egan C, Alexander J, Leotta A, Healy J, Zender L, Spector MS, Xue W, Lowe SW, Wigler M, Lucito R.
Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11234-9. Epub 2006 Jul 14.

RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast.
Hall IM, Noma K, Grewal SI.
Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):193-8. Epub 2002 Dec 30.

Establishment and maintenance of a heterochromatin domain.
Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI.
Science. 2002 Sep 27;297(5590):2232-7. Epub 2002 Sep 5.

Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi.
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA.
Science. 2002 Sep 13;297(5588):1833-7. Epub 2002 Aug 22.