Ira M. Hall, Ph.D.,  McDonnell Genome Institute

Dr. Hall joined the McDonnell Genome Institute (MGI) in 2014. He is an Associate Director of MGI and an Associate Professor in the Department of Medicine.

Dr. Hall is an expert in genetics, genomics and bioinformatics. His current research focuses on developing computational methods to analyze and interpret large-scale genomic datasets, and on using high-throughput DNA sequencing techniques to study genome variation and human disease. Much of his ongoing work involves the application of human genome sequencing and integrative data science approaches to identify the genetic origins of medically relevant human traits. Dr. Hall is co-leader of the NHGRI-funded MGI Center for Common Disease Genomics, which is conducting population-scale genome sequencing studies to identify genetic factors that confer risk or protection for various complex human diseases in the broader cardiovascular, autoimmune and neuropsychiatric disease areas.

Dr. Hall's research career has spanned diverse fields and topics. He received a B.A. in Integrative Biology from the University of California at Berkeley (1998) and a Ph.D. in Genetics from the Watson School of Biological Sciences at Cold Spring Harbor Laboratory (2003). His thesis work established the first direct link between RNA interference and chromatin-based epigenetic inheritance. As a CSHL Fellow (2003-2007), Dr. Hall's lab used microarray technologies and mouse strain genealogies to conduct the first systematic study of DNA copy number variation hotspots. As a faculty member at the University of Virginia (2007-2014) and Washington University School of Medicine (2014-), Dr. Hall’s work has sought to understand the causes and consequences of genome variation in mammals, with an increasing focus on methods development and human genetics. His group has developed novel bioinformatics methods including software for genome structural variation detection and interpretation (hydra, lumpy, svtools), DNA sequence alignment (yaha), data integration (bedtools), and ultra-fast clinical human genome interpretation (speedseq). In various prior studies, Dr. Hall's lab has used genome sequencing technologies to study human disorders, tumor evolution, bacterial recombination, mouse strain variation, genome stability in induced pluripotent stem cells, and single-neuron somatic mosaicism in the human brain.

Dr. Hall's work has been featured in Science Magazine's Breakthrough of the Year (2003 & 2007), the NIMH Director's "Ten Best of 2013" and The Scientist (2013), and he has received several prestigious awards including the AAAS Newcomb Cleveland Prize (2003), the Burroughs Wellcome Fund Career Award (2006), the NIH Director's New Innovator Award (2009), and the March of Dimes Basil O'Connor Research Award (2010). He has also served as an Associate Editor at Genome Research (2009-2014) and is an Associate Editor at Genes, Genomes and Genetics (G3).

Selected Publications

(*co-first authors, †corresponding author(s))

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†. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron, 89,1223-36 (2016).

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM†. SpeedSeq: Ultra-fast personal genome analysis and interpretation. Nature Methods, Epub ahead of print, Aug. 10 (2015).

Malhotra AM*, Wang Y*, Waters J, Chen K, Bernstam F, Hall IM†, Navin N†. Ploidy-Seq: Inferring Mutational Chronology by Deep-Sequencing Polyploid Tumor Subpopulations. Genome Medicine, 7, Epub (2015).

Lindberg MR, Hall IM†, Quinlan AR†. Population-based structural variation discovery with Hydra-Multi. Bioinformatics, 31, 1286-9 (2015).

Layer RL, Chiang C, Quinlan AR†, Hall IM†. LUMPY: A probabilistic framework for structural variant discovery. Genome Biology. 15:R84, DOI: 10.1186/gb-2014-15-6-r84 (2014).

Faust G, Hall IM†. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics, 30, 2505-3 (2014).

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).

Malhotra A, 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, 762-67 (2013).

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

Malhotra A, Shibata Y, Hall IM, Dutta A†. Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17 and LPIN2 genes. Cancer Biology and Therapy, 14, (2013).

Faust G, Hall IM†. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics, 28, 2417-24 (2012).

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

Faust GG and Hall IM†. GEM: crystal clear DNA alignment. Nature Methods, 9, 1159-61 (2012).

Mell JC, Hall IM, Redfield RJ†. Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells. Nucleic Acids Research, 1, 8536-49 (2012).

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†. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nature Genetics, 44, 390-7 (2012).

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 (2011).

Mell JC, Sokolova S, Hall IM, Redfield, RJ†. Transformation of Natural Genetic Variation into Haemophilus influenzae Genomes. PLOS Pathogens, 7 (2011).

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, 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).

Quinlan AR†, Hall IM†. BEDTools: a flexible suite of utilities for comparing genomic features in BED format. Bioinformatics, 26, 841-2 (2010).

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

Pelham RJ, Rodgers L, Hall IM, Lucito R, Nguyen KCQ, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D†. Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proceedings of the National Academy of Sciences, 103, 19848-53 (2006).

Lakshmi B, Hall IM, Egan C, Alexander J, Leotta A, Healy J, Zender L, Spector MS, Xue W, Lowe SW, Wigler M, Lucito R†. Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variation in normal and tumor specimens. Proceedings of the National Academy of Sciences, 103, 11234-11239 (2006).

Hall IM, Noma K, Grewal SI†. RNAi machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proceedings of the National Academy of Sciences, 100, 193-198 (2003).

Hall IM*, Shankaranarayana GD*, Noma K*, Ayoub N, Cohen A, Grewal SI†. Establishment and maintenance of a heterochromatin domain. Science, 297, 2232-2237 (2002).

Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI†, Martienssen RA†. Regulation of heterochromatic silencing and histone H3 Lysine-9 methylation by RNAi. Science, 297, 1833-1837 (2002).


title citation publication date
Co-expression networks reveal the tissue-specific regulation of transcription and splicing Genome Res. 2017 Oct 11. doi: 10.1101/gr.216721.116. [Epub ahead of print] 1970-08-22
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 Oct 11. doi: 10.1101/gr.216754.116. 1970-08-22
The impact of rare variation on gene expression across tissues Nature. 2017 Oct 11;550(7675):239-243. doi: 10.1038/nature24267. 1970-08-22
Genetic effects on gene expression across human tissues Nature. 2017 Oct 11;550(7675):204-213. doi: 10.1038/nature24277. 1970-08-22
Landscape of X chromosome inactivation across human tissues. Nature. 2017 Oct 11;550(7675):244-248. doi: 10.1038/nature24265. 1970-08-22
Dynamic landscape and regulation of RNA editing in mammals Nature. 2017 Oct 11;550(7675):249-254. doi: 10.1038/nature24041. 1970-08-22
The impact of structural variation on human gene expression Nat Genet. 2017 May;49(5):692-699. doi: 10.1038/ng.3834. Epub 2017 Apr 3 2017-04-03
SVScore: an impact prediction tool for structural variation Bioinformatics. 2016 Dec 28. pii: btw789. doi: 10.1093/bioinformatics/btw789. [Epub ahead of print] 1970-08-22
The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron. 2016 Mar 16;89(6):1223-36. doi: 10.1016/j.neuron.2016.02.004. Epub 2016 Mar 3. 2016-03-16
A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. 2015-10-01
SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods. 2015 Aug 10. doi: 10.1038/nmeth.3505. [Epub ahead of print] 2015-08-10
Population-based structural variation discovery with Hydra-Multi. Bioinformatics. 2014 Dec 2. pii: btu771. [Epub ahead of print] 2014-12-02
Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genome Med. 2015 Jan 28;7(1):6. doi: 10.1186/s13073-015-0127-5. eCollection 2015. 2015-01-28