Skip Navigation

Faculty Directory

Andrew Jaffe, PhD

  • Investigator, Lieber Institute for Brain Development
  • Assistant Professor

Departmental Affiliations

Center & Institute Affiliations

Contact Information

855 N. Wolfe Street
Suite 300
Baltimore, Maryland 21205


Lab Webpage:


PhD, Johns Hopkins Bloomberg School of Public Health, 2011
MHS, Johns Hopkins Bloomberg School of Public Health, 2011


I work largely at the intersection of genomics, biostatistics, and computational biology, leveraging large datasets to better understand how genomic signatures associate with human brain development and subsequent dysregulation in mental illness. My research consists of several broad, and often overlapping, domains: 1) developing statistical methodology and corresponding software tools for the spatial analysis of epigenomic and transcriptomic data across the genome, 2) developing and applying computational approaches in genomic data to identify new biological insights in development and aging, and 3) identifying molecular signatures related to causes and consequences of mental disorders in human postmortem brain samples.

Honors and Awards

2013: The James V. Neel Young Investigator Award for Best Platform Presentation, 22nd Annual Conference of the International Genetic Epidemiology Society)

2012: Young Investigator Award, Statistics in Epidemiology Section, American StatisticalAssociation

2011: The Louis I. and Thomas D. Dublin Award for the Advancement of Epidemiology and Biostatistics (Department of Biostatistics and Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health)

  • Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jian Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR. Developmental regulation of human cortex transcription at base resolution. Nat Neurosci. 2015 Jan;18(1):154-61. PMID: 25501035. 

  • Jaffe AE, Murakami P, Lee H, Fallin MD, Leek JT, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int. J. Epidemiol. (2012)  41 (1):200-209. PMID: 22422453

  • Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylation regions. Biostatistics. 2012; 13(1): 166-178. PMID: 21685414. 

  • Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014 Feb 4;15(2):R31 (Epub). PMID: 24495553

  • Multhaup ML*, Seldin M*, Jaffe AE*, Lei X, Kirchner H, Mondal P, Li P, Rodriguez V, Drong A, Hussain M, Lindgren C, McCarthy M, Näslund E, Zierath JR, Wong GW, Feinberg AP. Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab. 2015 Jan 6;21(1):138-49. PMID: 25565211.*These authors contributed equally to this work.