Ben Laufer

Ben Laufer

Principal Scientist

Genentech

Biography

Ben Laufer is a researcher with a focus on gene expression and neuroscience. He is a Principal Scientist in the Neuroinformatics Group in the Department of OMNI Bioinformatics at Genentech. He is also the editor for EpiGenie. Outside of the science world he enjoys hiking, swimming, and photography.

Interests
  • Bioinformatics
  • Gene Regulation
  • Neuroscience
Education
  • Postdoctoral Fellowship, 2021

    University of California Davis, USA

  • PhD in Cellular & Molecular Biology, 2016

    Western University, Canada

  • BSc (Hons) in Genetics, 2010

    Western University, Canada

Research

Click on each project to learn more.
Placental Footprints of Neurodevelopment
Cell-free fetal DNA and placenta contain a subset of differentially methylated regions that reflect brain DNA methylation profiles.
Genetic Impacts on the Epigenome
Over-expression of DNMT3L and RUNX1 contributes to regional DNA hypermethylation and DNA hypomethylation in Down syndrome brain and blood, respectively.
Environmental Impacts on the Epigenome
DNA hypermethylation of the clustered protocadherins is a conserved signature in adult brains from a mouse model of prenatal alcohol exposure and in buccal swabs from human children with fetal alcohol spectrum disorders (FASD).

Recent Publications

(2023). TMEM106B reduction does not rescue GRN deficiency in iPSC-derived human microglia and mouse models. iScience.

PDF Cite DOI

(2023). Lipid nanoparticle delivery limits antisense oligonucleotide activity and cellular distribution in the brain after intracerebroventricular injection. Molecular Therapy — Nucleic Acids.

PDF Cite DOI

(2023). Cross-species transcriptomic atlas of dorsal root ganglia reveals species-specific programs for sensory function. Nature Communications.

PDF Cite DOI

(2022). Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nature Communications.

PDF Cite Project DOI

(2022). Disease-associated oligodendrocyte responses across neurodegenerative diseases. Cell Reports.

PDF Cite DOI

Programs

gg4way
4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way R/Bioconductor package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.
DMRichR
DMRichR is an R package and executable for the preprocessing, statistical analysis, and visualization of differentially methylated regions (DMRs) and global methylation levels from CpG count matrices (Bismark cytosine reports).
CpG_Me
CpG_Me is a whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports).

Science Communication

EpiGenie
EpiGenie was founded in 2007 as the first dedicated Epigenetics news source. I joined in 2013. Initially, my role was that of a technical writer. My role then matured to be editorial, where I select and edit headlines.

Videos

What is Epigenetics?

       

OHSU and Swift Low-pass WGBS Webinar

Contact