Hamid Alinejad‐Rokny

Comparative Analysis of Single-Nucleus and Single-Cell RNA Sequencing in Human Bone Marrow Mononuclear Cells: Methodological Insights and Trade-offs

This study compares single-nucleus and single-cell RNA sequencing in human bone marrow mononuclear cells, identifying method-specific biases and trade-offs.

Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE

scCAFE is a deep learning model that detects multi-scale chromatin architectural features in single-cell Hi-C data, outperforming existing methods and enabling cell-type annotation from 3D genome features.

Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML

This study identifies a synergy between hypomethylating agents and SUMOylation blockade in MDS/AML using CRISPR-Cas9 screening, showing improved therapeutic outcomes in xenograft models.

Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells

The paper identifies cell-type-specific regulatory roles of a heptad of transcription factors in human hematopoietic stem and progenitor cells.

Seeing the forest through the trees: Identifying functional interactions from Hi-C

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

Insight into the origin of 5UTR and source of CpG reduction in SARS-CoV-2 genome

The paper investigates the origin of SARS-CoV-2 genome and the source of its low CpG content, finding evidence of recombination between bat and pangolin coronaviruses and ruling out ZAP as the cause of CpG reduction.

Brain-enriched coding and long non-coding RNA genes are overrepresented in recurrent autism spectrum disorder CNVs

The paper identifies 47 high-confidence ASD-associated CNV regions and shows brain-enriched coding and lncRNA genes are overrepresented in these regions.

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders

The paper identifies 49 novel noncoding RNAs associated with neurodevelopmental disorders by linking enhancer activity to genetic variants and eQTLs.

MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments

MaxHiC improves Hi-C and capture Hi-C analysis by robustly correcting biases and identifying significant chromatin interactions with better biological relevance.

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

CANCERSIGN identifies and classifies mutational signatures in cancer genomes using raw mutation data, enabling clustering and analysis of ICGC datasets to discover novel signatures.