Galip Gürkan Yardımcı

Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities

The paper investigates how host inflammation reshapes oral microbiome communities by analyzing paired clinical specimens and identifying metabolic shifts associated with inflammatory states.

PU.1 inhibition sensitizes stem-monocytic AML to BCL2 blockade

This study identifies stem-monocytic AML as a distinct subtype resistant to venetoclax and shows that PU.1 inhibition synergizes with BCL2 blockade to enhance therapeutic response.

Mutant ASXL1 Drives Transcriptional Activation and Repression in Human Hematopoiesis

This study functionally characterizes mutant ASXL1 in human hematopoietic stem cells, showing it drives transcriptional activation and repression through interactions with BRD4 and MECOM, with implications for therapy.

Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles

This study profiles hypoxic glioblastoma stem cells using multi-omics to reveal distinct subpopulations with unique epigenetic and CNV profiles.

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

Single-cell DNA methylation analysis tool Amethyst reveals distinct noncanonical methylation patterns in human glial cells

Robust CNV detection using single-cell ATAC-seq

This paper introduces RIDDLER, a single-cell ATAC-seq CNV detection algorithm that outperforms existing methods in cancer cell line models and 10x multimome data.

Multi-center integrated analysis of non-coding CRISPR screens

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

GoPeaks: Histone Modification Peak Calling for CUT&Tag

GoPeaks is a peak calling method for CUT&Tag data that improves sensitivity in detecting H3K27Ac peaks compared to standard algorithms.

High-content single-cell combinatorial indexing

This paper introduces a novel adaptor-switching strategy, s3, that significantly improves usable reads per cell in single-cell genomics assays while maintaining high-throughput capabilities.

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

This study uses topic modeling on scHi-C data to identify cell type-specific chromatin structural patterns and compartment structures.

Dynamic reorganization of nuclear architecture during human cardiogenesis

The paper studies how nuclear architecture changes during human heart development using Hi-C, RNA-seq, and ATAC-seq, revealing dynamic chromosomal organization and gene regulation.

Measuring the reproducibility and quality of Hi-C data

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

Unsupervised embedding of single-cell Hi-C data

This paper applies bulk Hi-C analysis methods to scHi-C data with unsupervised embedding, finding HiCRep with MDS outperforms other methods and is robust to low sequencing depth.

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

GenomeDISCO measures concordance between chromosome conformation capture contact maps by smoothing them with random walks, distinguishing biological replicates from different cell types.

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

HiCRep assesses Hi-C data reproducibility using a stratum-adjusted correlation coefficient, improving accuracy over existing methods.

HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

HiC-Spector provides a matrix library for spectral analysis and reproducibility assessment of Hi-C contact maps, distinguishing biological replicates from pseudo-replicates and different cell types.

Software tools for visualizing Hi-C data

The paper reviews Hi-C visualization tools designed for non-programmers, highlighting their functionalities and visualization capabilities.