Alaaddin Bulak Arpat

Integrating knowledge, omics and AI to develop patient-specific virtual avatars

The paper develops a method to create personalized regulatory networks for cancer patients using PDX models, integrating gene expression data and genetic algorithms with GCNs to predict treatment outcomes.

Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms

Seq2scFv annotates and characterizes scFv sequences from long-read sequencing data to improve antibody discovery.

Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms

The paper investigates diurnal regulation of IRE-containing mRNAs via IRP1 and IRP2 in mouse liver, showing that feeding rhythms drive rhythmicity even without a functional circadian clock.

Translational contributions to tissue-specificity in rhythmic and constitutive gene expression.

The paper investigates how translation efficiency contributes to tissue-specific rhythmic and constitutive gene expression in kidney and liver, revealing translational control mechanisms and compensation effects.