Thomas J. Hoffmann, Ph.D.

Picture of me

Assistant Professor
Department of Epidemiology and Biostatistics
University of California, San Francisco
tjhoffm ‡

I am an assistant professor at the University of California - San Francisco in the Department of Epidemiology and Biostatistics. I received my Ph.D. in Biostatistics from Harvard University in 2009. Before that, I received a B.S. from University of Wisconsin-Madison in 2004, triple majoring in Computer Science, Mathematics, and Statistics.

My interest in public health and problems arising from collaborating with individuals doing research in genetics drives my methodological work and research interests. My research is focused on human genetics, developing new methods to efficiently analyze the data that next-generation sequencing is producing, and developing new methods as necessary to get the most information from genome-wide and candidate gene studies. Publications are listed below.

My methodology has been implemented in several R packages, all freely available online, and documented on this website. These include the R packages fbati (methods developed for family-based gene-environment interaction, Gen Epi 2009, Biometrics in press), thgenetics (methods for rare variants, PLoS ONE 2010). I've also shared some computational tools I've developed: batch (a computer cluster aid, JSS in press), and fgui (automate GUI creation, JSS 2010). I've also created the R package pbatR, Bioinformatics 2006, a graphical/command-line R interface to Christoph Lange's PBAT software.


  1. Hoffmann, TJ, and Lange, C. P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R. Bioinformatics, 22(24):3103-3105, Dec 2006. PMID: 17021156.
  2. Hoffmann, TJ, and Laird, NM. fgui: A method for automatically creating graphical user interfaces for command-line R packages. Journal of Statistical Software. 30(2), Apr 2009.
  3. Hoffmann, TJ, Lange, C, Vansteelandt, S, and Laird, NM. Gene-Environment Interaction Test for Dichotomous Traits in Nuclear Families. Genetic Epidemiology. 33(8):691-699.
  4. Hoffmann, TJ, Lange, C, Vansteelandt, S, Raby, BA, DeMeo, DL, Silverman, EK, and Laird, NM. Parsing the effects of individual SNPs in candidate genes with Family Data. Human Heredity 2010; 69:91-103.
  5. Cho, MH, Washko, GR, Hoffmann, TJ, Criner, GJ, Hoffman, EA, Martinez, FJ, Laird, NM, Reilly, JJ, and Silverman, EK. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation. Respiratory Research, 11:30, 2010.
  6. Sebro, R, Hoffmann TJ, Lange C, Rogus J, and Risch N. Testing for nonrandom mating: Evidence from the Framingham Heart Study. Genetic Epidemiology, 34(7):674-679, 2010.
  7. Hoffmann, TJ. Passing in command line arguments and parallel cluster/multicore batching in R with batch.. Journal of Statistical Software, Code Snippets, 39(1), 1-11.
  8. Witte, JS, and Hoffmann, TJ. Polygenic modeling of genome-wide association studies: An application to prostate and breast cancer. Omics, 15(3), 2011.
  9. Hoffmann, TJ, Marini, NJ, and Witte, JS. Comprehensive approach to analyzing rare genetic variants. PLoS ONE, 5(11): e13584, 2010.
  10. Hoffmann, TJ, Vansteelandt, S, Lange, C, Silverman, EK, DeMeo, DL, Laird, NM. Combining disease models to test for gene-environment interaction in nuclear families. Biometrics, in press.
  11. Kompass, KS*, Hoffmann, TJ*, Witte, JS. Parallel biocomputing. SCBM, 6:4 doi:10.1186/1751-0473-6-4, 2011. (*These authors contributed equally to this work.)
  12. Hoffmann, TJ*, Kvale, MN*, Hesselson, SE*, Zhan, YS*, Aquino, C, Cao, Y, Cawley, S, Chung, E, Connel, S, Eshragh, J, Ewing, M, Gollub, J, Henderson, M, Hubbell, E, Kaufman, J, Lau, R, Lu, Y, Ludwig, D, Mathauda, GK, McGuire, W, Mei, G, Miles, S, Purdy, M, Ranatunga, D, Rowell, S, Saddler, M, Shapero, MH, Shen, L, Shenoy, T, Smethurst, D, Walter, L, Wan, E, Wearly, R, Webster, T, Wen, CC, Weng, L, Williams, A, Wong, S, Zau, C, Finn, A, Schaefer, C, Kwok, P, and Risch, N. Next generation genome wide association tool: Design, coverage and throughput of a European-optimized SNP array. Genomics, 98:79-89. (*These authors contributed equally to this work.)
  13. Hoffmann TJ*, Zhan YS*, Kvale MN, Hesselson SE, Gollub J, Iribarren C, Lu Y, Mei G, Purdy MM, Quesenberry C, Rowell S, Shapero MH, Smethurst D, Somkin CP, Van den Eeeden SK, Walter L, Webster T, Whitmer RA, Finn A, Schaefer C, Kwok P, Risch N. Design and coverage of high throughput genotyping arrays optimized for individuals of East-Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics, to appear. (*These authors contributed equally to this work.)

Peer reviewed proceedings

  1. Kazma R*, Hoffmann TJ*, Witte JS. Use of principal components to aggregate rare variants in case/control and family-based association studies in the presence of multiple covariates. BMC Proc, In Press. (*These authors contributed equally to this work.)

Technical Reports

  1. Hoffmann, TJ. Subpixel morphometric analysis of corpus callosum with application to autism. Technical Report. 2005.