Radoje Drmanac

Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity

This paper introduces ccMPRA, a method that combines Capture-C and MPRA to study promoter interactions and regulatory activity, identifying enhancers and silencers.

Assembly and analysis of the genome of Notholithocarpus densiflorus

The paper assembles the genome of Notholithocarpus densiflorus and identifies genetic variation across 11 individuals with varying susceptibility to sudden oak death.

Comparison of long read methods for sequencing and assembly of a plant genome

This study compares three long-read sequencing technologies for de novo assembly of the Macadamia jansenii genome, evaluating contiguity, accuracy, completeness, cost, and DNA requirements.

CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase

The paper introduces a new sequencing chemistry (CoolMPS) that improves signal intensity and eliminates scar interference in massively parallel sequencing.

Advanced Whole Genome Sequencing Using an Entirely PCR-free Massively Parallel Sequencing Workflow

This paper demonstrates that PCR-free whole genome sequencing using the DNBSEQ platform and machine learning variant calling significantly reduces InDel errors and improves variant calling performance.

Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

This paper introduces a new mate-pair sequencing method called CP-AL that improves DNA-circularization efficiency and reduces contamination, enabling accurate detection of genomic variants.

Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly

This paper introduces stLFR, a low-cost method for long DNA sequencing that enables accurate variant calling, haplotyping, and de novo assembly.

Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

The paper evaluates index mis-assignment rates on DNB-based sequencing platforms and finds they are exceptionally low, suggesting reliable multiplex sequencing.

3’ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3’OH Ends in DNA or RNA

The paper introduces a novel ligation method called 3BL that allows non-complementary DNA to be ligated to 3' ends of DNA or RNA, improving NGS library construction by reducing adapter dimer issues and increasing yield.

Advanced whole genome sequencing and analysis of fetal genomes from amniotic fluid

This study demonstrates the feasibility of whole genome sequencing of fetal genomes from amniotic fluid, revealing additional genetic and clinical information beyond chromosomal abnormalities.

Significant abundance of cis configurations of mutations in diploid human genomes

The paper analyzes mutation phase in diploid human genomes and finds that protein-altering mutations are significantly more common in cis than trans configurations across diverse populations.