Arif O. Harmanci

GlioVision: A Multi-Modal MRI Framework for Non-Invasive Glioma Molecular Biomarkers Prediction

GlioVision predicts four glioma molecular biomarkers from MRI data using a multi-modal framework, achieving high AUC scores across multiple cohorts.

Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuronal Regeneration.

This study shows that deleting Hdac2 in adult CNS endothelial cells reactivates pro-angiogenic programs, promoting revascularization and neuronal regeneration after stroke.

Enhancing Fairness in Disease Prediction by Optimizing Multiple Domain Adversarial Networks

This paper introduces a Multiple Domain Adversarial Neural Network (MDANN) to improve fairness in disease prediction by reducing biases in brain imaging data for Alzheimer's and Autism populations.

Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability

This study shows that mutant IDH impairs PDGFB's chromatin binding, leading to chromosome instability and accelerated gliomagenesis.

Inferred Developmental Origins of Brain Tumors from Single Cell RNA-Sequencing Data

This study uses scRNA-seq data to identify developmental-like cell states in brain tumors, suggesting potential cells of origin for medulloblastoma, glioma, and diffuse midline glioma.

Local Haplotype Classifiers enable Efficient, Flexible, and Secure Genotype Imputation and Downstream Analyses

The paper introduces a privacy-preserving genotype imputation method using haplotype classifiers, improving accuracy and throughput compared to linear models.

Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma

The paper identifies hybrid cells in human glioma with both neuronal and glial electrophysiological and transcriptomic features using Patch-sequencing and a new computational tool.

FedGMMAT: Federated Generalized Linear Mixed Model Association Tests

FedGMMAT enables privacy-preserving genetic association testing across institutions using federated learning and homomorphic encryption.

Leveraging Single-Cell Sequencing to Classify and Characterize Tumor Subgroups in Bulk RNA-Sequencing Data

This study develops CLIPPR, an algorithm that integrates single-cell and bulk RNA-seq data to improve meningioma classification and resolve benign-malignant confusion.

ProxyTyper: Generation of Proxy Panels for Privacy-aware Outsourcing of Genotype Imputation

ProxyTyper generates proxy panels to protect genetic data privacy during genotype imputation with minimal accuracy loss.

XCVATR: Detection and Characterization of Variant Impact on the Embeddings of Single -Cell and Bulk RNA-Sequencing Samples

XCVATR identifies and characterizes variant impact on embeddings of single-cell and bulk RNA-seq samples by detecting local variant enrichment in embedding space.

Establishing And Maintaining The Blood-Brain Barrier: Epigenetic And Signaling Determinants.

The paper identifies epigenetic and signaling factors that regulate BBB formation and maintenance in CNS endothelial cells.

Evaluation of Vicinity-based Hidden Markov Models for Genotype Imputation

This paper evaluates local hidden Markov models for genotype imputation, showing they can accurately impute common, uncommon, and rare variants.

Privacy-Aware Kinship Inference in Admixed Populations using Projection on Reference Panels

This paper develops a privacy-aware kinship inference method for admixed populations using reference panels and homomorphic encryption to protect genetic data.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

Open Imputation Server provides secure Imputation services with provable genomic privacy

The paper introduces a secure imputation server that provides encrypted genotype imputation with provable privacy, demonstrating its utility through benchmarking and simulated GWAS.

SVAT: Secure Outsourcing of Variant Annotation and Genotype Aggregation

SVAT securely outsources variant annotation and genotype aggregation using homomorphic encryption to protect genetic privacy during analysis and data sharing.

Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation

This paper develops secure genotype imputation methods using homomorphic encryption, showing comparable accuracy and efficiency to non-secure methods while protecting genetic data privacy.

scRegulocity: Detection of local RNA velocity patterns in embeddings of single cell RNA-Seq data

scRegulocity detects local RNA velocity patterns in single-cell RNA-seq embeddings to identify regulatory changes and cell state transitions.

SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

SVFX assigns pathogenicity scores to structural variants in cancer and cardiovascular disease cohorts using machine learning.

Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols

The paper quantifies privacy leakage in functional genomics data and proposes a data-sanitization protocol to reduce it while preserving utility.

An integrative ENCODE resource for cancer genomics

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

Integrative pathway enrichment analysis of multivariate omics data

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data

CaSpER identifies and analyzes CNV events in single-cell and bulk RNA sequencing data, revealing novel sub-clones and therapeutic targets in GBM.

HaploHide: A Data Hiding Framework for Privacy Enhanced Sharing of Personal Genetic Data

HaploHide hides individual haplotypes within population haplotypes to protect privacy during genetic data sharing without changing infrastructure.

EpiSAFARI: Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements

EpiSAFARI detects valleys in epigenetic signals to improve functional element annotations, showing high conservation and enrichment in regulatory regions.

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

The paper analyzes 2500 cancer genomes to assess the molecular functional impact of mutations, finding that some putative passenger variants may influence gene activity and contribute to cancer phenotypes.