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Items: 1 to 50 of 62

1.

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.

Regier AA, Farjoun Y, Larson DE, Krasheninina O, Kang HM, Howrigan DP, Chen BJ, Kher M, Banks E, Ames DC, English AC, Li H, Xing J, Zhang Y, Matise T, Abecasis GR, Salerno W, Zody MC, Neale BM, Hall IM.

Nat Commun. 2018 Oct 2;9(1):4038. doi: 10.1038/s41467-018-06159-4.

2.

Drumming-associated anthrax incidents: exposures to low levels of indoor environmental contamination.

Bennett E, Hall IM, Pottage T, Silman NJ, Bennett AM.

Epidemiol Infect. 2018 Sep;146(12):1519-1525. doi: 10.1017/S0950268818001085. Epub 2018 Jul 4.

3.

Modelling the global spread of diseases: A review of current practice and capability.

Walters CE, Meslé MMI, Hall IM.

Epidemics. 2018 May 18. pii: S1755-4365(17)30113-5. doi: 10.1016/j.epidem.2018.05.007. [Epub ahead of print] Review.

4.

Identification of Drivers of Aneuploidy in Breast Tumors.

Pfister K, Pipka JL, Chiang C, Liu Y, Clark RA, Keller R, Skoglund P, Guertin MJ, Hall IM, Stukenberg PT.

Cell Rep. 2018 May 29;23(9):2758-2769. doi: 10.1016/j.celrep.2018.04.102.

5.

The impact of rare variation on gene expression across tissues.

Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB.

Nature. 2017 Oct 11;550(7675):239-243. doi: 10.1038/nature24267.

6.

The impact of structural variation on human gene expression.

Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L; GTEx Consortium, Montgomery SB, Battle A, Conrad DF, Hall IM.

Nat Genet. 2017 May;49(5):692-699. doi: 10.1038/ng.3834. Epub 2017 Apr 3.

7.

SVScore: an impact prediction tool for structural variation.

Ganel L, Abel HJ; FinMetSeq Consortium, Hall IM.

Bioinformatics. 2017 Apr 1;33(7):1083-1085. doi: 10.1093/bioinformatics/btw789.

8.

The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning.

Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, Boland MJ, Martin G, Chubukov P, Tsunemoto RK, Torkamani A, Kupriyanov S, Hall IM, Baldwin KK.

Neuron. 2016 Mar 16;89(6):1223-1236. doi: 10.1016/j.neuron.2016.02.004. Epub 2016 Mar 3.

9.

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.

10.
11.

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.

Malhotra A, Wang Y, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin NE.

Genome Med. 2015 Jan 28;7(1):6. doi: 10.1186/s13073-015-0127-5. eCollection 2015.

12.

Population-based structural variation discovery with Hydra-Multi.

Lindberg MR, Hall IM, Quinlan AR.

Bioinformatics. 2015 Apr 15;31(8):1286-9. doi: 10.1093/bioinformatics/btu771. Epub 2014 Dec 2.

13.

Strategies for controlling non-transmissible infection outbreaks using a large human movement data set.

Hancock PA, Rehman Y, Hall IM, Edeghere O, Danon L, House TA, Keeling MJ.

PLoS Comput Biol. 2014 Sep 11;10(9):e1003809. doi: 10.1371/journal.pcbi.1003809. eCollection 2014 Sep.

14.

LUMPY: a probabilistic framework for structural variant discovery.

Layer RM, Chiang C, Quinlan AR, Hall IM.

Genome Biol. 2014 Jun 26;15(6):R84. doi: 10.1186/gb-2014-15-6-r84.

15.

SAMBLASTER: fast duplicate marking and structural variant read extraction.

Faust GG, Hall IM.

Bioinformatics. 2014 Sep 1;30(17):2503-5. doi: 10.1093/bioinformatics/btu314. Epub 2014 May 7.

16.

A dose and time response Markov model for the in-host dynamics of infection with intracellular bacteria following inhalation: with application to Francisella tularensis.

Wood RM, Egan JR, Hall IM.

J R Soc Interface. 2014 Jun 6;11(95):20140119. doi: 10.1098/rsif.2014.0119. Print 2014 Jun 6.

17.

Mosaic copy number variation in human neurons.

McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH.

Science. 2013 Nov 1;342(6158):632-7. doi: 10.1126/science.1243472.

18.

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes.

Malhotra A, Shibata Y, Hall IM, Dutta A.

Cancer Biol Ther. 2013 Sep;14(9):840-52. doi: 10.4161/cbt.25329. Epub 2013 Jul 26.

19.

An analysis of influenza outbreaks in institutions and enclosed societies.

Finnie TJ, Copley VR, Hall IM, Leach S.

Epidemiol Infect. 2014 Jan;142(1):107-13. doi: 10.1017/S0950268813000733. Epub 2013 Apr 10.

20.

A case-association cluster detection and visualisation tool with an application to Legionnaires' disease.

Sansom P, Copley VR, Naik FC, Leach S, Hall IM.

Stat Med. 2013 Sep 10;32(20):3522-38. doi: 10.1002/sim.5765. Epub 2013 Mar 11.

21.

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 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14.

22.

The application of geographic information systems and spatial data during Legionnaires disease outbreak responses.

Bull M, Hall IM, Leach S, Robesyn E.

Euro Surveill. 2012 Dec 6;17(49). pii: 20331. Review.

23.

GEM: crystal-clear DNA alignment.

Faust GG, Hall IM.

Nat Methods. 2012 Dec;9(12):1159-61. doi: 10.1038/nmeth.2256. No abstract available.

PMID:
23223169
24.

Binary Interval Search: a scalable algorithm for counting interval intersections.

Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR.

Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4.

25.

YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

Faust GG, Hall IM.

Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul 24.

26.

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.

27.

Transmission dynamics of methicillin-resistant Staphylococcus aureus in a medical intensive care unit.

Hall IM, Barrass I, Leach S, Pittet D, Hugonnet S.

J R Soc Interface. 2012 Oct 7;9(75):2639-52. doi: 10.1098/rsif.2012.0134. Epub 2012 May 9.

28.

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.

29.

Behaviour and control of influenza in institutions and small societies.

Finnie TJ, Hall IM, Leach S.

J R Soc Med. 2012 Feb;105(2):66-73. doi: 10.1258/jrsm.2012.110249. Review.

30.

Detection and interpretation of genomic structural variation in mammals.

Hall IM, Quinlan AR.

Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11. Review.

PMID:
22228015
31.

Characterizing complex structural variation in germline and somatic genomes.

Quinlan AR, Hall IM.

Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Epub 2011 Nov 15. Review.

32.

Modeling inhalational tularemia: deliberate release and public health response.

Egan JR, Hall IM, Leach S.

Biosecur Bioterror. 2011 Dec;9(4):331-43. doi: 10.1089/bsp.2011.0004. Epub 2011 Nov 1.

33.

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.

34.

Evidence for two independent associations with type 1 diabetes at the 12q13 locus.

Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P.

Genes Immun. 2012 Jan;13(1):66-70. doi: 10.1038/gene.2011.56. Epub 2011 Aug 18.

35.

Transformation of natural genetic variation into Haemophilus influenzae genomes.

Mell JC, Shumilina S, Hall IM, Redfield RJ.

PLoS Pathog. 2011 Jul;7(7):e1002151. doi: 10.1371/journal.ppat.1002151. Epub 2011 Jul 28.

36.

An individual-based simulation of pneumonic plague transmission following an outbreak and the significance of intervention compliance.

Williams AD, Hall IM, Rubin GJ, Amlôt R, Leach S.

Epidemics. 2011 Jun;3(2):95-102. doi: 10.1016/j.epidem.2011.03.001. Epub 2011 Mar 17.

37.

Re-assessment of mitigation strategies for deliberate releases of anthrax using a real-time outbreak characterization tool.

Egan JR, Legrand J, Hall IM, Cauchemez S, Ferguson NM, Leach S.

Epidemics. 2010 Dec;2(4):189-94. doi: 10.1016/j.epidem.2010.06.001. Epub 2010 Jun 10.

38.

Modeling Legionnaires' disease outbreaks: estimating the timing of an aerosolized release using symptom-onset dates.

Egan JR, Hall IM, Lemon DJ, Leach S.

Epidemiology. 2011 Mar;22(2):188-98. doi: 10.1097/EDE.0b013e31820937c6.

PMID:
21242803
39.

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. doi: 10.1016/j.jacc.2010.07.040. No abstract available.

40.

Data processing of absorption spectra from photoionized plasma experiments at Z.

Hall IM, Durmaz T, Mancini RC, Bailey JE, Rochau GA.

Rev Sci Instrum. 2010 Oct;81(10):10E324. doi: 10.1063/1.3479007.

PMID:
21034022
41.

Stamping out fires! Controlling smallpox with targeted mass vaccination.

Egan JR, Hall IM, Leach S.

Med Decis Making. 2011 Jan-Feb;31(1):69-78. doi: 10.1177/0272989X10369003. Epub 2010 May 18.

PMID:
20484093
42.

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. doi: 10.1101/gr.102970.109. Epub 2010 Mar 22.

43.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

44.

Estimating the location and spatial extent of a covert anthrax release.

Legrand J, Egan JR, Hall IM, Cauchemez S, Leach S, Ferguson NM.

PLoS Comput Biol. 2009 Jan;5(1):e1000356. doi: 10.1371/journal.pcbi.1000356. Epub 2009 Apr 10.

45.

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.

PMID:
17965714
46.

Comparison of smallpox outbreak control strategies using a spatial metapopulation model.

Hall IM, Egan JR, Barrass I, Gani R, Leach S.

Epidemiol Infect. 2007 Oct;135(7):1133-44. Epub 2007 Jan 12.

47.

Real-time epidemic forecasting for pandemic influenza.

Hall IM, Gani R, Hughes HE, Leach S.

Epidemiol Infect. 2007 Apr;135(3):372-85. Epub 2006 Aug 24.

48.

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.

49.

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.

50.

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.

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