University of Pittsburgh

The Koldamova/ Lefterov Lab

 

Bioinformatics

Data Processing
Subread
STAR
Homer
samtools
Picard
mirPro
SCENIC
Cell Ranger
R
WGCNA
edgeR
DEseq2
yacca
Seurat
GOExpress
External sources
DAVID
IPA
GSEA
Cytoscape
String

Publically Available Datasets
  • Castranio EL, Wolfe CM, Nam KN, Letronne F, Fitz NF, Lefterov I, Koldamova R
    ABCA1 haplodeficiency affects the brain transcriptome following traumatic brain injury in mice expressing human APOE isoforms.
    Acta Neuropathologica Communications 2018 Jul 26; 6(1):69.
    DOI:10.1186/s40478-018-0569-2 PMID:6062955 GEO:GSE109152
  • Nam KN, Wolfe CM, Fitz NF, Letronne F, Castranio EL, Mounier A, Schug J, Lefterov I, Koldamova R
    Integrated approach reveals diet, APOE genotype and sex affect immune response in APP mice.
    Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 2018 Jan; 1864(1):152-161.
    DOI:10.1016/j.bbadis.2017.10.018 PMID:5714325 GEO:GSE109152
  • Castranio EL, Mounier A, Wolfe CM, Nam KN, Fitz NF, Letronne F, Schug J, Koldamova R, Lefterov I
    Gene co-expression networks identify Trem2 and Tyrobp as major hubs in human APOE expressing mice following traumatic brain injury.
    Neurobiology of Disease 2017 Sep; 105:1-14.
    DOI:10.1016/j.nbd.2017.05.006 PMID:5530876 GEO:GSE102014
  • Lefterov I, Schug J, Mounier A, Nam KN, Fitz NF, Koldamova R.
    RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment.
    Neurobiology of Disease 2015 Oct 15; 82:132-40.
    DOI:10.1016/j.nbd.2015.05.019 PMID:4640940 GEO:GSE77569