My bioinformatics research examines the interface between gene regulation and neuroscience. Recently, this has been assisted through developing two R/Bioconductor packages:

1. scDotPlot: Cluster a Single-cell RNA-seq Dot Plot

2. gg4way: 4way Plots of Differential Expression

Most of my postdoctoral research was related to developingDMRichR andCpG_Me, which enable the analysis of low-pass whole genome bisulfite sequencing.The following publications demonstrate their potential:

1. Multi-omic Brain and Behavioral Correlates of Cell-free Fetal DNA Methylation in Macaque Maternal Obesity Models.Nature Communications, 2022.doi:10.1038/s41467-022-33162-7

2. Placenta and Fetal Brain Share a Neurodevelopmental Disorder DNA Methylation Profile in a Mouse Model of Prenatal PCB Exposure.Cell Reports, 2022.doi:10.1016/j.celrep.2022.110442

3. Placental Methylome Reveals a 22q13.33 Brain Regulatory Gene Locus Associated with Autism.Genome Biology, 2022.doi:10.1186/s13059-022-02613-1

4. Cord Blood DNA Methylome in Newborns Later Diagnosed with Autism Spectrum Disorder Reflects Early Dysregulation of Neurodevelopmental and X-linked Genes.Genome Medicine, 2020.doi:10.1186/s13073-020-00785-8

5. Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles.Human Molecular Genetics, 2020.doi:10.1093/hmg/ddaa218

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1. scDotPlotscDotPlotPublic

   Repository for the scDotPlot Bioconductor package

   R 7 1

2. gg4waygg4wayPublic

   Repository for the gg4way Bioconductor package

   R

3. DMRichRDMRichRPublic

   A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosin…

   R 42 23

4. CpG_MeCpG_MePublic

   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)

   Shell 23 12

5. RNA-seqRNA-seqPublic

   RNA-seq alignment and analysis pipeline

   R 6 4

6. FASTQ_MeFASTQ_MePublic

   An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me

   Shell 2