Hall Lab

The Hall Laboratory conducts biological research in the realms of genetics, genomics, and bioinformatics.

The Hall Laboratory conducts biological research in the realms of genetics, genomics and bioinformatics. Broadly speaking, we use a combination of high-throughput experimental and computational methods to study the causes and consequences of genome variation in mammals. Recent projects involve diverse topics including human and statistical genetics, bioinformatics tools development, genome structural variation, genetic mosaicism, tumor evolution, and single cell genomics. Most of our ongoing work is focused on 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.

For job opportunities in the Hall lab, please see Careers.


  • LUMPY: A probabilistic framework for structural variant discovery. Developer: Ryan Layer (pubmed) (download)
  • SpeedSeq: A pipeline for ultra-fast variant detection and clinical genome interpretation. Developer: Colby Chiang (download)(pubmed)
  • SAMBLASTER: Fast duplicate marking and structural variant read extraction. Developer: Gregory Faust (pubmed) (download)
  • BEDTools: A flexible suite of utilities for comparing genomic features. Developer: Aaron Quinlan (pubmed)(download
  • YAHA: Fast and flexible long read alignment. Developer: Gregory Faust (pubmed)(download)
  • HYDRA: Detection of structural variant breakpoints from paired-end data. Developer: Aaron Quinlan (pubmed)(download)
  • SVTools: Tools for processing and analyzing structural variants. Developers: Dave Larson, Colby Chiang, Ryan Layer. (download)
  • SVScore: An impact prediction tool for structural variation. Developer: Liron Ganel. Pubmed: (pubmed)(download)

Selected Publications

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

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†. The impact of structural variation on human gene expression. Nature Genetics, 49, 692-699 (2017)

Ganel L, Abel HJ, FinMetSeq Consortium, Hall IM†. SVScore: an impact prediction tool for structural variation. Bioinformatics, 33, 1083-1085 (2017).

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, 49, 692-699 (2017).

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).