Andrew E. Jaffe

Andrew E. Jaffe

Assistant Professor
Additional Title: 
Lead Investigator, Lieber Institute for Brain Development
Primary Appointment: 
Department of Mental Health; Johns Hopkins Bloomberg School of Public Health (JHSPH)
Secondary Appointment: 
Departments of Neuroscience, Psychiatry and Behavioral Science, and Human Genetics; Johns Hopkins School of Medicine (JHSOM). Department of Biostatistics; JHSPH

Lieber Institute for Brain Development
855 N. Wolfe St., Ste. 336
Baltimore, MD 21205

Research topic: 

Biological Psychiatry, Computational Biology, Biostatistics

I work at the intersection of biological psychiatry, computational biology, and biostatistics, leveraging large human brain and human pluripotent stem cell datasets to better understand how genomic signatures associate with brain development and subsequent dysregulation in mental illness. My research consists of several broad, and often overlapping, domains: 1) developing and applying computational approaches in genomic data to identify new biological insights in development and aging, 2) identifying molecular signatures related to causes and consequences of mental disorders in human postmortem brain samples and in neurons derived from human iPSCs, and 3) developing statistical methodology and corresponding software tools for the spatial analysis of epigenomic and transcriptomic data and 4) developing approaches to process and normalize genomic data for biological inference.

BCMB students currently in the lab:
Selected Publications: 

1)  Collado-Torres L, Burke EE, Peterson A, Shin JH, Straub RE, Rajpurohit A, Semick SA, Ulrich WS; BrainSeq Consortium, Price AJ, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR+, Jaffe AE+. Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia. Neuron. 2019 May 29. PMID: 31174959

2)  Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE+, Jaffe AE+. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Mol Psychiatry. 2018 Aug 21. PMID: 30131587

3)  Jaffe AE+, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich B, Maher BJ, Deep-Soboslay A, The BrainSeq Consortium, Cross A, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR+. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nat Neurosci. 2018 Aug;21(8):1117-1125. PMID: 30050107

4)  Jaffe AE+, Tao R, Norris A, Kealhofer M, Nellore A, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR. A framework for RNA quality correction in differential expression analysis. Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. PMID: 28634288

5)  Collado-Torres L*, Nellore A*, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE+, Langmead B+, Leek JT+. Reproducible RNA-seq analysis using recount2. Nat Biotechnol. 2017 Apr 11;35(4):319-321. PMID: 28398307

6)  Jaffe AE+, Gao Y, Deep-Soboslay A, Tao R, Hyde TM, Weinberger DR, Kleinman JE. Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex. Nature Neuroscience. 2016 Jan;19(1):40-7. PMID: 26619358.

7)  Jaffe AE+, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR+. Developmental regulation of human cortex transcription and its clinical relevance at base resolution. Nature Neuroscience, 2015 Jan;18(1):154-61. PMID: 25501035.

8)  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. Select preprints:

9)  Jaffe AE*, Hoeppner DJ*, Saito T, Blanpain L, Joy Ukaigwe J, Burke EE, Tao R, Tajinda K, Deep-Soboslay A, Shin JH, Kleinman JE, Weinberger DR, Matsumoto M+, Hyde TM+. Cell type-specific genetic regulation of expression in the granule cell layer of the human dentate gyrus. bioRxiv. 2019. doi: 10.1101/612200

10) Price AJ*, Collado-Torres L*, Ivanov NA, Xia W, Burke EE, Shin JH, Tao R, Ma L, Jia Y, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE+. Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation. bioRxiv. 2018. doi: 10.1101/428391.

11) Han S+, Lin Y, Wang M, Goes FS, Tan K, Zandi P, Hyde T, Weinberger DR, Potash JB, Kleinman JE, Jaffe AE. Integrating brain methylome with GWAS for psychiatric risk gene discovery. bioRxiv. 2018. doi: 10.1101/440206.

12) Phan BDN, Page SC, Campbell MN, Bohlen JF, Thaxton CL, Simon JM, Burke EE, Shin JH, Kennedy AJ, Sweatt JD, Philpot BD, Jaffe AE+, Maher BJ+. Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders. bioRxiv 128124

13) Burke EE*, Chenoweth JG*, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Straub RE, Hoeppner DJ, Chen H-Y, Lescure A, Shibbani K, Hamersky GR, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bürli R, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay RD+, Jaffe AE+. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. bioRxiv. 2018. doi: 10.1101/380758.