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Achievements

Achievement: StarstruckAchievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

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ben-laufer/README.md

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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 developing DMRichR and CpG_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. scDotPlot scDotPlot Public

    Repository for the scDotPlot Bioconductor package

    R 1

  2. gg4way gg4way Public

    Repository for the gg4way Bioconductor package

    R

  3. DMRichR DMRichR Public

    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 39 23

  4. CpG_Me CpG_Me Public

    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 20 11

  5. RNA-seq RNA-seq Public

    RNA-seq alignment and analysis pipeline

    R 6 4

  6. FASTQ_Me FASTQ_Me Public

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

    Shell 2