Ian F. Korf

Female cortical cellular mosaicism underlies shared MeCP2 and PCB impacted gene pathways

The paper investigates how PCB exposure interacts with MeCP2 mutations in female mice, identifying shared gene pathways and transcriptional impacts in the cortex.

Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact.

The paper analyzes citation practices for biological resources over 10 years, showing improved findability and adherence to NIH rigor criteria after adopting RRID citations.

Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip

Rocketchip improves rigor and reproducibility in ChIP-seq, CUT&RUN, and CUT&Tag data analysis by enabling comparison and swapping of analysis components.

Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression

The paper identifies sex-specific transcriptomic changes in a mouse model of Rett syndrome, showing more differentially expressed genes in females and non-cell-autonomous effects.

Placental-brain axis in females detected within broadly impacted metabolic gene networks protects against prenatal PCB exposure

The paper investigates sex-specific transcriptional responses to prenatal PCB exposure in mouse brain and placenta, finding female protective effects mediated by metabolic gene networks.

SpecDB: A Relational Database for Archiving Biomolecular NMR Spectra Data

The paper introduces SpecDB, a relational database for archiving NMR FID data and metadata, to support machine learning in biomolecular NMR analysis.

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

The paper identifies and compares chromatin accessibility in cattle, pig, and mouse tissues using ATAC-seq, finding species-specific regulatory elements and conservation patterns.

Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles

The paper uses low-pass whole genome bisulfite sequencing on neonatal dried blood spots to identify DNA methylation differences in Down syndrome, highlighting RUNX1 hypermethylation and its association with congenital heart disease.

Laocoön: a tool for high-throughput automated cell counting

Laocoön is a Python tool for automated cell counting in images, providing cell cycle proportions and is available on GitHub and PyPi.

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes

The paper evaluates how sequencing parameters affect gene detection in human fecal metagenomes using DIAMOND, finding that read length, e-value thresholds, and custom databases improve detection accuracy.

SAMSA2: A standalone metatranscriptome analysis pipeline

SAMSA2 is a metatranscriptome analysis pipeline designed for supercomputing clusters, offering faster and more flexible analysis of large RNA-seq datasets.